This notebook creates the BED file S_pombe.filtered.bed provided in
genome length: 5.5Mb It also shows the ability of sequana_coverage tool to handle multi-chromosome input data sets
WARNING: To create the input BED file, you will need an account on synapse to get the FastQ files.
You can skip the steps that build the BED file and download it directly from github:
wget //github.com/sequana/resources/raw/master/coverage/S_pombe.filtered.bed.bz2
bunzip2 S_Pombe.filtered.bedand jump to the Sequana_coverage analysis (using the library) section directly.
Otherwise, we first download 2 FastQ files from Synapse, its reference genome and its genbank annotation. Then, we use BWA to map reads into a BAM file. The BAM file itself is converted to a BED, which is going to be one input file to our analysis. Finally, we use the coverage tool from Sequana project (i) with the standalone (sequana_coverage) and (ii) the Python library to analyse the BED file.
Versions used:
In [15]:
%pylab inline
matplotlib.rcParams['figure.figsize'] = [10,7]
Populating the interactive namespace from numpy and matplotlib
In [2]:
import synapseclient
l = synapseclient.login()
l.get("syn10641621", downloadLocation=".", ifcollision="overwrite.local")
l.get("syn10641896", downloadLocation=".", ifcollision="overwrite.local")
Welcome, Thomas Cokelaer!
Out[2]:
File(modifiedBy='375805', uri='/repo/v1/entity/syn10641896', path='/home/cokelaer/Work/github/sequana_resources/coverage/fungus/M14-19_J29_01_TAAGGCGA-TATCCTCT_L002_R2_001.fastq.gz', concreteType='org.sagebionetworks.repo.model.FileEntity', createdBy='375805', versionLabel='1', accessControlList='/repo/v1/entity/syn10641896/acl', name='M14-19_J29_01_TAAGGCGA-TATCCTCT_L002_R2_001.fastq.gz', versions='/repo/v1/entity/syn10641896/version', etag='9358c658-54ab-41d9-b93f-49e8b7b20888', cacheDir='/home/cokelaer/Work/github/sequana_resources/coverage/fungus', entityType='org.sagebionetworks.repo.model.FileEntity', files=['M14-19_J29_01_TAAGGCGA-TATCCTCT_L002_R2_001.fastq.gz'], annotations='/repo/v1/entity/syn10641896/annotations', id='syn10641896', versionNumber=1, versionUrl='/repo/v1/entity/syn10641896/version/1', dataFileHandleId='17867278', modifiedOn='2017-09-07T20:10:34.962Z', synapseStore=True, _file_handle={'contentSize': 814044782, 'fileName': 'M14-19_J29_01_TAAGGCGA-TATCCTCT_L002_R2_001.fastq.gz', 'contentMd5': '42957c3a1d80c033b3732b866b9a5b33', 'key': '375805/79e49536-46fa-4963-935c-7e3300e821cb/M14-19_J29_01_TAAGGCGA-TATCCTCT_L002_R2_001.fastq.gz', 'contentType': 'binary/octet-stream', 'concreteType': 'org.sagebionetworks.repo.model.file.S3FileHandle', 'etag': '4cf817a3-4081-4c79-b3fa-081a0f1488a9', 'storageLocationId': 1, 'bucketName': 'proddata.sagebase.org', 'createdOn': '2017-09-07T20:10:34.000Z', 'id': '17867278', 'createdBy': '375805', 'externalURL': None}, createdOn='2017-09-07T20:10:34.962Z', parentId='syn10638358')
In [3]:
!sequana_coverage --download-reference CU329670
!sequana_coverage --download-reference CU329671
!sequana_coverage --download-reference CU329672
!sequana_coverage --download-reference X54421
INFO [sequana]: Downloading reference CU329670 from ENA
INFO [sequana]: Downloading reference CU329671 from ENA
INFO [sequana]: Downloading reference CU329672 from ENA
INFO [sequana]: Downloading reference X54421 from ENA
In [4]:
!sequana_coverage --download-genbank CU329670
!sequana_coverage --download-genbank CU329671
!sequana_coverage --download-genbank CU329672
!sequana_coverage --download-genbank X54421
INFO [sequana]: Downloading genbank CU329670 from ENA
INFO [sequana]: Downloading genbank CU329671 from ENA
INFO [sequana]: Downloading genbank CU329672 from ENA
INFO [sequana]: Downloading genbank X54421 from ENA
In [5]:
!cat CU*gbk X*gbk > S_pombe.gbk
!cat CU*.fa X*.fa> S_pombe.fa
The Reference must be altered to rename the header so that they agree with the genbank
In [12]:
files = ['CU329670.fa', "CU329671.fa", "CU329672.fa", "X54421.fa"]
with open("S_pombe.fa", "w") as fout:
for filename in files:
with open(filename, "r") as fin :
for line in fin.readlines():
if line.startswith(">"):
start, end = line.split(None, 1)
accession = start[1:].rsplit("|", 1)[1]
line = ">" + accession + " " + end
fout.write(line)
In [8]:
# The mapping to obtain the sorted BAM file (uses BWA behing the scene)
!time sequana_mapping \
--file1 M14-19_J29_01_TAAGGCGA-TATCCTCT_L002_R1_001.fastq.gz \
--file2 M14-19_J29_01_TAAGGCGA-TATCCTCT_L002_R2_001.fastq.gz \
--reference S_pombe.fa --thread 4
Theoretical Depth of Coverage : 321.5617193567531
[bwa_index] Pack FASTA... 0.09 sec
[bwa_index] Construct BWT for the packed sequence...
[bwa_index] 8.10 seconds elapse.
[bwa_index] Update BWT... 0.07 sec
[bwa_index] Pack forward-only FASTA... 0.06 sec
[bwa_index] Construct SA from BWT and Occ... 3.22 sec
[main] Version: 0.7.17-r1188
[main] CMD: bwa index S_pombe.fa
[main] Real time: 12.113 sec; CPU: 11.547 sec
[M::bwa_idx_load_from_disk] read 0 ALT contigs
[M::process] read 400000 sequences (40000000 bp)...
[M::process] read 400000 sequences (40000000 bp)...
[M::mem_pestat] # candidate unique pairs for (FF, FR, RF, RR): (152, 179061, 18, 137)
[M::mem_pestat] analyzing insert size distribution for orientation FF...
[M::mem_pestat] (25, 50, 75) percentile: (90, 140, 226)
[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 498)
[M::mem_pestat] mean and std.dev: (160.36, 94.83)
[M::mem_pestat] low and high boundaries for proper pairs: (1, 634)
[M::mem_pestat] analyzing insert size distribution for orientation FR...
[M::mem_pestat] (25, 50, 75) percentile: (151, 216, 306)
[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 616)
[M::mem_pestat] mean and std.dev: (235.51, 113.48)
[M::mem_pestat] low and high boundaries for proper pairs: (1, 771)
[M::mem_pestat] analyzing insert size distribution for orientation RF...
[M::mem_pestat] (25, 50, 75) percentile: (46, 187, 1691)
[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 4981)
[M::mem_pestat] mean and std.dev: (543.25, 842.80)
[M::mem_pestat] low and high boundaries for proper pairs: (1, 6626)
[M::mem_pestat] analyzing insert size distribution for orientation RR...
[M::mem_pestat] (25, 50, 75) percentile: (96, 145, 230)
[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 498)
[M::mem_pestat] mean and std.dev: (167.94, 99.86)
[M::mem_pestat] low and high boundaries for proper pairs: (1, 632)
[M::mem_pestat] skip orientation FF
[M::mem_pestat] skip orientation RF
[M::mem_pestat] skip orientation RR
[M::mem_process_seqs] Processed 400000 reads in 30.488 CPU sec, 7.399 real sec
[M::mem_pestat] # candidate unique pairs for (FF, FR, RF, RR): (120, 179120, 16, 118)
[M::mem_pestat] analyzing insert size distribution for orientation FF...
[M::mem_pestat] (25, 50, 75) percentile: (84, 144, 235)
[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 537)
[M::mem_pestat] mean and std.dev: (164.07, 105.56)
[M::mem_pestat] low and high boundaries for proper pairs: (1, 688)
[M::mem_pestat] analyzing insert size distribution for orientation FR...
[M::mem_pestat] (25, 50, 75) percentile: (150, 216, 305)
[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 615)
[M::mem_pestat] mean and std.dev: (235.29, 113.39)
[M::mem_pestat] low and high boundaries for proper pairs: (1, 770)
[M::mem_pestat] analyzing insert size distribution for orientation RF...
[M::mem_pestat] (25, 50, 75) percentile: (353, 1677, 3177)
[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 8825)
[M::mem_pestat] mean and std.dev: (2147.00, 2225.25)
[M::mem_pestat] low and high boundaries for proper pairs: (1, 11649)
[M::mem_pestat] analyzing insert size distribution for orientation RR...
[M::mem_pestat] (25, 50, 75) percentile: (75, 136, 247)
[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 591)
[M::mem_pestat] mean and std.dev: (166.00, 112.81)
[M::mem_pestat] low and high boundaries for proper pairs: (1, 763)
[M::mem_pestat] skip orientation FF
[M::mem_pestat] skip orientation RF
[M::mem_pestat] skip orientation RR
[M::mem_process_seqs] Processed 400000 reads in 31.868 CPU sec, 8.170 real sec
[M::process] read 400000 sequences (40000000 bp)...
[M::mem_pestat] # candidate unique pairs for (FF, FR, RF, RR): (166, 178906, 7, 120)
[M::mem_pestat] analyzing insert size distribution for orientation FF...
[M::mem_pestat] (25, 50, 75) percentile: (102, 159, 241)
[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 519)
[M::mem_pestat] mean and std.dev: (173.33, 101.31)
[M::mem_pestat] low and high boundaries for proper pairs: (1, 658)
[M::mem_pestat] analyzing insert size distribution for orientation FR...
[M::mem_pestat] (25, 50, 75) percentile: (151, 216, 306)
[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 616)
[M::mem_pestat] mean and std.dev: (235.54, 113.20)
[M::mem_pestat] low and high boundaries for proper pairs: (1, 771)
[M::mem_pestat] skip orientation RF as there are not enough pairs
[M::mem_pestat] analyzing insert size distribution for orientation RR...
[M::mem_pestat] (25, 50, 75) percentile: (105, 173, 237)
[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 501)
[M::mem_pestat] mean and std.dev: (181.09, 102.47)
[M::mem_pestat] low and high boundaries for proper pairs: (1, 633)
[M::mem_pestat] skip orientation FF
[M::mem_pestat] skip orientation RR
[M::mem_process_seqs] Processed 400000 reads in 30.243 CPU sec, 7.752 real sec
[M::process] read 400000 sequences (40000000 bp)...
[M::mem_pestat] # candidate unique pairs for (FF, FR, RF, RR): (154, 178894, 18, 123)
[M::mem_pestat] analyzing insert size distribution for orientation FF...
[M::mem_pestat] (25, 50, 75) percentile: (83, 136, 230)
[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 524)
[M::mem_pestat] mean and std.dev: (158.23, 99.87)
[M::mem_pestat] low and high boundaries for proper pairs: (1, 671)
[M::mem_pestat] analyzing insert size distribution for orientation FR...
[M::mem_pestat] (25, 50, 75) percentile: (150, 215, 304)
[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 612)
[M::mem_pestat] mean and std.dev: (234.10, 112.79)
[M::mem_pestat] low and high boundaries for proper pairs: (1, 766)
[M::mem_pestat] analyzing insert size distribution for orientation RF...
[M::mem_pestat] (25, 50, 75) percentile: (120, 240, 2094)
[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 6042)
[M::mem_pestat] mean and std.dev: (843.29, 1153.46)
[M::mem_pestat] low and high boundaries for proper pairs: (1, 8016)
[M::mem_pestat] analyzing insert size distribution for orientation RR...
[M::mem_pestat] (25, 50, 75) percentile: (104, 162, 233)
[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 491)
[M::mem_pestat] mean and std.dev: (167.52, 91.27)
[M::mem_pestat] low and high boundaries for proper pairs: (1, 620)
[M::mem_pestat] skip orientation FF
[M::mem_pestat] skip orientation RF
[M::mem_pestat] skip orientation RR
[M::mem_process_seqs] Processed 400000 reads in 30.984 CPU sec, 7.920 real sec
[M::process] read 400000 sequences (40000000 bp)...
[M::mem_pestat] # candidate unique pairs for (FF, FR, RF, RR): (158, 179005, 10, 139)
[M::mem_pestat] analyzing insert size distribution for orientation FF...
[M::mem_pestat] (25, 50, 75) percentile: (87, 136, 204)
[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 438)
[M::mem_pestat] mean and std.dev: (145.19, 83.58)
[M::mem_pestat] low and high boundaries for proper pairs: (1, 555)
[M::mem_pestat] analyzing insert size distribution for orientation FR...
[M::mem_pestat] (25, 50, 75) percentile: (149, 214, 303)
[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 611)
[M::mem_pestat] mean and std.dev: (233.16, 112.20)
[M::mem_pestat] low and high boundaries for proper pairs: (1, 765)
[M::mem_pestat] analyzing insert size distribution for orientation RF...
[M::mem_pestat] (25, 50, 75) percentile: (211, 886, 5612)
[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 16414)
[M::mem_pestat] mean and std.dev: (2543.10, 2977.92)
[M::mem_pestat] low and high boundaries for proper pairs: (1, 21815)
[M::mem_pestat] analyzing insert size distribution for orientation RR...
[M::mem_pestat] (25, 50, 75) percentile: (86, 141, 220)
[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 488)
[M::mem_pestat] mean and std.dev: (155.16, 84.40)
[M::mem_pestat] low and high boundaries for proper pairs: (1, 622)
[M::mem_pestat] skip orientation FF
[M::mem_pestat] skip orientation RF
[M::mem_pestat] skip orientation RR
[M::mem_process_seqs] Processed 400000 reads in 36.245 CPU sec, 9.350 real sec
[M::process] read 400000 sequences (40000000 bp)...
[M::mem_pestat] # candidate unique pairs for (FF, FR, RF, RR): (142, 178941, 15, 141)
[M::mem_pestat] analyzing insert size distribution for orientation FF...
[M::mem_pestat] (25, 50, 75) percentile: (99, 158, 285)
[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 657)
[M::mem_pestat] mean and std.dev: (189.31, 126.22)
[M::mem_pestat] low and high boundaries for proper pairs: (1, 843)
[M::mem_pestat] analyzing insert size distribution for orientation FR...
[M::mem_pestat] (25, 50, 75) percentile: (149, 213, 301)
[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 605)
[M::mem_pestat] mean and std.dev: (232.08, 111.07)
[M::mem_pestat] low and high boundaries for proper pairs: (1, 757)
[M::mem_pestat] analyzing insert size distribution for orientation RF...
[M::mem_pestat] (25, 50, 75) percentile: (100, 158, 315)
[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 745)
[M::mem_pestat] mean and std.dev: (168.08, 100.68)
[M::mem_pestat] low and high boundaries for proper pairs: (1, 960)
[M::mem_pestat] analyzing insert size distribution for orientation RR...
[M::mem_pestat] (25, 50, 75) percentile: (99, 171, 261)
[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 585)
[M::mem_pestat] mean and std.dev: (177.13, 99.70)
[M::mem_pestat] low and high boundaries for proper pairs: (1, 747)
[M::mem_pestat] skip orientation FF
[M::mem_pestat] skip orientation RF
[M::mem_pestat] skip orientation RR
[M::mem_process_seqs] Processed 400000 reads in 34.786 CPU sec, 8.929 real sec
[M::process] read 400000 sequences (40000000 bp)...
[M::mem_pestat] # candidate unique pairs for (FF, FR, RF, RR): (144, 179092, 9, 112)
[M::mem_pestat] analyzing insert size distribution for orientation FF...
[M::mem_pestat] (25, 50, 75) percentile: (100, 177, 254)
[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 562)
[M::mem_pestat] mean and std.dev: (180.32, 106.20)
[M::mem_pestat] low and high boundaries for proper pairs: (1, 716)
[M::mem_pestat] analyzing insert size distribution for orientation FR...
[M::mem_pestat] (25, 50, 75) percentile: (147, 211, 298)
[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 600)
[M::mem_pestat] mean and std.dev: (229.79, 110.00)
[M::mem_pestat] low and high boundaries for proper pairs: (1, 751)
[M::mem_pestat] skip orientation RF as there are not enough pairs
[M::mem_pestat] analyzing insert size distribution for orientation RR...
[M::mem_pestat] (25, 50, 75) percentile: (92, 142, 214)
[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 458)
[M::mem_pestat] mean and std.dev: (149.69, 77.13)
[M::mem_pestat] low and high boundaries for proper pairs: (1, 580)
[M::mem_pestat] skip orientation FF
[M::mem_pestat] skip orientation RR
[M::mem_process_seqs] Processed 400000 reads in 31.193 CPU sec, 8.030 real sec
[M::process] read 400000 sequences (40000000 bp)...
[M::mem_pestat] # candidate unique pairs for (FF, FR, RF, RR): (142, 178995, 15, 110)
[M::mem_pestat] analyzing insert size distribution for orientation FF...
[M::mem_pestat] (25, 50, 75) percentile: (78, 122, 212)
[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 480)
[M::mem_pestat] mean and std.dev: (146.32, 95.41)
[M::mem_pestat] low and high boundaries for proper pairs: (1, 614)
[M::mem_pestat] analyzing insert size distribution for orientation FR...
[M::mem_pestat] (25, 50, 75) percentile: (147, 211, 297)
[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 597)
[M::mem_pestat] mean and std.dev: (229.25, 109.74)
[M::mem_pestat] low and high boundaries for proper pairs: (1, 747)
[M::mem_pestat] analyzing insert size distribution for orientation RF...
[M::mem_pestat] (25, 50, 75) percentile: (170, 252, 2497)
[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 7151)
[M::mem_pestat] mean and std.dev: (893.40, 1091.46)
[M::mem_pestat] low and high boundaries for proper pairs: (1, 9478)
[M::mem_pestat] analyzing insert size distribution for orientation RR...
[M::mem_pestat] (25, 50, 75) percentile: (81, 148, 236)
[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 546)
[M::mem_pestat] mean and std.dev: (165.68, 102.26)
[M::mem_pestat] low and high boundaries for proper pairs: (1, 701)
[M::mem_pestat] skip orientation FF
[M::mem_pestat] skip orientation RF
[M::mem_pestat] skip orientation RR
[M::mem_process_seqs] Processed 400000 reads in 33.293 CPU sec, 8.545 real sec
[M::process] read 400000 sequences (40000000 bp)...
[M::mem_pestat] # candidate unique pairs for (FF, FR, RF, RR): (143, 178880, 9, 153)
[M::mem_pestat] analyzing insert size distribution for orientation FF...
[M::mem_pestat] (25, 50, 75) percentile: (106, 154, 253)
[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 547)
[M::mem_pestat] mean and std.dev: (171.91, 95.86)
[M::mem_pestat] low and high boundaries for proper pairs: (1, 694)
[M::mem_pestat] analyzing insert size distribution for orientation FR...
[M::mem_pestat] (25, 50, 75) percentile: (148, 211, 298)
[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 598)
[M::mem_pestat] mean and std.dev: (229.77, 109.84)
[M::mem_pestat] low and high boundaries for proper pairs: (1, 748)
[M::mem_pestat] skip orientation RF as there are not enough pairs
[M::mem_pestat] analyzing insert size distribution for orientation RR...
[M::mem_pestat] (25, 50, 75) percentile: (89, 140, 231)
[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 515)
[M::mem_pestat] mean and std.dev: (157.80, 92.03)
[M::mem_pestat] low and high boundaries for proper pairs: (1, 657)
[M::mem_pestat] skip orientation FF
[M::mem_pestat] skip orientation RR
[M::mem_process_seqs] Processed 400000 reads in 31.400 CPU sec, 8.100 real sec
[M::process] read 400000 sequences (40000000 bp)...
[M::mem_pestat] # candidate unique pairs for (FF, FR, RF, RR): (156, 179248, 13, 140)
[M::mem_pestat] analyzing insert size distribution for orientation FF...
[M::mem_pestat] (25, 50, 75) percentile: (75, 129, 202)
[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 456)
[M::mem_pestat] mean and std.dev: (144.25, 92.07)
[M::mem_pestat] low and high boundaries for proper pairs: (1, 583)
[M::mem_pestat] analyzing insert size distribution for orientation FR...
[M::mem_pestat] (25, 50, 75) percentile: (147, 210, 296)
[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 594)
[M::mem_pestat] mean and std.dev: (228.21, 109.07)
[M::mem_pestat] low and high boundaries for proper pairs: (1, 743)
[M::mem_pestat] analyzing insert size distribution for orientation RF...
[M::mem_pestat] (25, 50, 75) percentile: (242, 362, 1908)
[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 5240)
[M::mem_pestat] mean and std.dev: (829.83, 856.97)
[M::mem_pestat] low and high boundaries for proper pairs: (1, 6906)
[M::mem_pestat] analyzing insert size distribution for orientation RR...
[M::mem_pestat] (25, 50, 75) percentile: (87, 148, 232)
[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 522)
[M::mem_pestat] mean and std.dev: (168.72, 103.80)
[M::mem_pestat] low and high boundaries for proper pairs: (1, 667)
[M::mem_pestat] skip orientation FF
[M::mem_pestat] skip orientation RF
[M::mem_pestat] skip orientation RR
[M::mem_process_seqs] Processed 400000 reads in 30.974 CPU sec, 7.961 real sec
[M::process] read 400000 sequences (40000000 bp)...
[M::mem_pestat] # candidate unique pairs for (FF, FR, RF, RR): (160, 179361, 11, 145)
[M::mem_pestat] analyzing insert size distribution for orientation FF...
[M::mem_pestat] (25, 50, 75) percentile: (91, 148, 198)
[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 412)
[M::mem_pestat] mean and std.dev: (152.85, 80.97)
[M::mem_pestat] low and high boundaries for proper pairs: (1, 519)
[M::mem_pestat] analyzing insert size distribution for orientation FR...
[M::mem_pestat] (25, 50, 75) percentile: (146, 209, 294)
[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 590)
[M::mem_pestat] mean and std.dev: (226.99, 107.61)
[M::mem_pestat] low and high boundaries for proper pairs: (1, 738)
[M::mem_pestat] analyzing insert size distribution for orientation RF...
[M::mem_pestat] (25, 50, 75) percentile: (280, 706, 4010)
[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 11470)
[M::mem_pestat] mean and std.dev: (2123.18, 2773.10)
[M::mem_pestat] low and high boundaries for proper pairs: (1, 15200)
[M::mem_pestat] analyzing insert size distribution for orientation RR...
[M::mem_pestat] (25, 50, 75) percentile: (87, 141, 253)
[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 585)
[M::mem_pestat] mean and std.dev: (165.09, 100.44)
[M::mem_pestat] low and high boundaries for proper pairs: (1, 751)
[M::mem_pestat] skip orientation FF
[M::mem_pestat] skip orientation RF
[M::mem_pestat] skip orientation RR
[M::mem_process_seqs] Processed 400000 reads in 30.398 CPU sec, 7.783 real sec
[M::process] read 400000 sequences (40000000 bp)...
[M::mem_pestat] # candidate unique pairs for (FF, FR, RF, RR): (141, 178897, 12, 120)
[M::mem_pestat] analyzing insert size distribution for orientation FF...
[M::mem_pestat] (25, 50, 75) percentile: (87, 146, 245)
[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 561)
[M::mem_pestat] mean and std.dev: (167.24, 100.37)
[M::mem_pestat] low and high boundaries for proper pairs: (1, 719)
[M::mem_pestat] analyzing insert size distribution for orientation FR...
[M::mem_pestat] (25, 50, 75) percentile: (150, 215, 303)
[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 609)
[M::mem_pestat] mean and std.dev: (233.80, 111.66)
[M::mem_pestat] low and high boundaries for proper pairs: (1, 762)
[M::mem_pestat] analyzing insert size distribution for orientation RF...
[M::mem_pestat] (25, 50, 75) percentile: (216, 448, 4855)
[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 14133)
[M::mem_pestat] mean and std.dev: (1757.92, 2082.06)
[M::mem_pestat] low and high boundaries for proper pairs: (1, 18772)
[M::mem_pestat] analyzing insert size distribution for orientation RR...
[M::mem_pestat] (25, 50, 75) percentile: (110, 165, 237)
[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 491)
[M::mem_pestat] mean and std.dev: (175.84, 88.47)
[M::mem_pestat] low and high boundaries for proper pairs: (1, 618)
[M::mem_pestat] skip orientation FF
[M::mem_pestat] skip orientation RF
[M::mem_pestat] skip orientation RR
[M::mem_process_seqs] Processed 400000 reads in 30.359 CPU sec, 7.780 real sec
[M::process] read 400000 sequences (40000000 bp)...
[M::mem_pestat] # candidate unique pairs for (FF, FR, RF, RR): (129, 178940, 15, 132)
[M::mem_pestat] analyzing insert size distribution for orientation FF...
[M::mem_pestat] (25, 50, 75) percentile: (106, 165, 239)
[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 505)
[M::mem_pestat] mean and std.dev: (176.91, 95.67)
[M::mem_pestat] low and high boundaries for proper pairs: (1, 638)
[M::mem_pestat] analyzing insert size distribution for orientation FR...
[M::mem_pestat] (25, 50, 75) percentile: (151, 216, 305)
[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 613)
[M::mem_pestat] mean and std.dev: (235.05, 113.21)
[M::mem_pestat] low and high boundaries for proper pairs: (1, 767)
[M::mem_pestat] analyzing insert size distribution for orientation RF...
[M::mem_pestat] (25, 50, 75) percentile: (113, 233, 1963)
[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 5663)
[M::mem_pestat] mean and std.dev: (1000.73, 1272.19)
[M::mem_pestat] low and high boundaries for proper pairs: (1, 7513)
[M::mem_pestat] analyzing insert size distribution for orientation RR...
[M::mem_pestat] (25, 50, 75) percentile: (85, 156, 233)
[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 529)
[M::mem_pestat] mean and std.dev: (161.96, 96.30)
[M::mem_pestat] low and high boundaries for proper pairs: (1, 677)
[M::mem_pestat] skip orientation FF
[M::mem_pestat] skip orientation RF
[M::mem_pestat] skip orientation RR
[M::mem_process_seqs] Processed 400000 reads in 33.135 CPU sec, 8.558 real sec
[M::process] read 400000 sequences (40000000 bp)...
[M::mem_pestat] # candidate unique pairs for (FF, FR, RF, RR): (161, 178979, 10, 145)
[M::mem_pestat] analyzing insert size distribution for orientation FF...
[M::mem_pestat] (25, 50, 75) percentile: (95, 137, 232)
[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 506)
[M::mem_pestat] mean and std.dev: (163.73, 97.66)
[M::mem_pestat] low and high boundaries for proper pairs: (1, 643)
[M::mem_pestat] analyzing insert size distribution for orientation FR...
[M::mem_pestat] (25, 50, 75) percentile: (151, 217, 306)
[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 616)
[M::mem_pestat] mean and std.dev: (235.66, 113.13)
[M::mem_pestat] low and high boundaries for proper pairs: (1, 771)
[M::mem_pestat] analyzing insert size distribution for orientation RF...
[M::mem_pestat] (25, 50, 75) percentile: (59, 276, 2464)
[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 7274)
[M::mem_pestat] mean and std.dev: (1131.22, 2016.55)
[M::mem_pestat] low and high boundaries for proper pairs: (1, 9679)
[M::mem_pestat] analyzing insert size distribution for orientation RR...
[M::mem_pestat] (25, 50, 75) percentile: (91, 144, 226)
[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 496)
[M::mem_pestat] mean and std.dev: (156.71, 91.57)
[M::mem_pestat] low and high boundaries for proper pairs: (1, 631)
[M::mem_pestat] skip orientation FF
[M::mem_pestat] skip orientation RF
[M::mem_pestat] skip orientation RR
[M::mem_process_seqs] Processed 400000 reads in 27.965 CPU sec, 7.158 real sec
[M::process] read 400000 sequences (40000000 bp)...
[M::mem_pestat] # candidate unique pairs for (FF, FR, RF, RR): (148, 178981, 17, 135)
[M::mem_pestat] analyzing insert size distribution for orientation FF...
[M::mem_pestat] (25, 50, 75) percentile: (100, 158, 223)
[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 469)
[M::mem_pestat] mean and std.dev: (165.31, 92.18)
[M::mem_pestat] low and high boundaries for proper pairs: (1, 592)
[M::mem_pestat] analyzing insert size distribution for orientation FR...
[M::mem_pestat] (25, 50, 75) percentile: (150, 216, 306)
[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 618)
[M::mem_pestat] mean and std.dev: (235.46, 113.84)
[M::mem_pestat] low and high boundaries for proper pairs: (1, 774)
[M::mem_pestat] analyzing insert size distribution for orientation RF...
[M::mem_pestat] (25, 50, 75) percentile: (98, 222, 1538)
[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 4418)
[M::mem_pestat] mean and std.dev: (579.25, 760.97)
[M::mem_pestat] low and high boundaries for proper pairs: (1, 5858)
[M::mem_pestat] analyzing insert size distribution for orientation RR...
[M::mem_pestat] (25, 50, 75) percentile: (104, 142, 212)
[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 428)
[M::mem_pestat] mean and std.dev: (164.40, 88.31)
[M::mem_pestat] low and high boundaries for proper pairs: (1, 536)
[M::mem_pestat] skip orientation FF
[M::mem_pestat] skip orientation RF
[M::mem_pestat] skip orientation RR
[M::mem_process_seqs] Processed 400000 reads in 26.617 CPU sec, 6.799 real sec
[M::process] read 400000 sequences (40000000 bp)...
[M::mem_pestat] # candidate unique pairs for (FF, FR, RF, RR): (166, 178824, 16, 145)
[M::mem_pestat] analyzing insert size distribution for orientation FF...
[M::mem_pestat] (25, 50, 75) percentile: (90, 151, 227)
[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 501)
[M::mem_pestat] mean and std.dev: (157.86, 88.02)
[M::mem_pestat] low and high boundaries for proper pairs: (1, 638)
[M::mem_pestat] analyzing insert size distribution for orientation FR...
[M::mem_pestat] (25, 50, 75) percentile: (150, 215, 303)
[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 609)
[M::mem_pestat] mean and std.dev: (233.72, 111.92)
[M::mem_pestat] low and high boundaries for proper pairs: (1, 762)
[M::mem_pestat] analyzing insert size distribution for orientation RF...
[M::mem_pestat] (25, 50, 75) percentile: (99, 255, 689)
[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 1869)
[M::mem_pestat] mean and std.dev: (292.43, 244.97)
[M::mem_pestat] low and high boundaries for proper pairs: (1, 2459)
[M::mem_pestat] analyzing insert size distribution for orientation RR...
[M::mem_pestat] (25, 50, 75) percentile: (86, 144, 207)
[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 449)
[M::mem_pestat] mean and std.dev: (155.48, 88.00)
[M::mem_pestat] low and high boundaries for proper pairs: (1, 570)
[M::mem_pestat] skip orientation FF
[M::mem_pestat] skip orientation RF
[M::mem_pestat] skip orientation RR
[M::mem_process_seqs] Processed 400000 reads in 27.321 CPU sec, 7.017 real sec
[M::process] read 400000 sequences (40000000 bp)...
[M::mem_pestat] # candidate unique pairs for (FF, FR, RF, RR): (146, 179067, 14, 117)
[M::mem_pestat] analyzing insert size distribution for orientation FF...
[M::mem_pestat] (25, 50, 75) percentile: (93, 143, 220)
[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 474)
[M::mem_pestat] mean and std.dev: (163.01, 96.85)
[M::mem_pestat] low and high boundaries for proper pairs: (1, 601)
[M::mem_pestat] analyzing insert size distribution for orientation FR...
[M::mem_pestat] (25, 50, 75) percentile: (150, 214, 303)
[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 609)
[M::mem_pestat] mean and std.dev: (233.26, 111.83)
[M::mem_pestat] low and high boundaries for proper pairs: (1, 762)
[M::mem_pestat] analyzing insert size distribution for orientation RF...
[M::mem_pestat] (25, 50, 75) percentile: (90, 191, 284)
[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 672)
[M::mem_pestat] mean and std.dev: (144.55, 85.68)
[M::mem_pestat] low and high boundaries for proper pairs: (1, 866)
[M::mem_pestat] analyzing insert size distribution for orientation RR...
[M::mem_pestat] (25, 50, 75) percentile: (100, 147, 223)
[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 469)
[M::mem_pestat] mean and std.dev: (162.01, 90.86)
[M::mem_pestat] low and high boundaries for proper pairs: (1, 592)
[M::mem_pestat] skip orientation FF
[M::mem_pestat] skip orientation RF
[M::mem_pestat] skip orientation RR
[M::mem_process_seqs] Processed 400000 reads in 31.016 CPU sec, 8.166 real sec
[M::process] read 400000 sequences (40000000 bp)...
[M::mem_pestat] # candidate unique pairs for (FF, FR, RF, RR): (167, 179069, 27, 133)
[M::mem_pestat] analyzing insert size distribution for orientation FF...
[M::mem_pestat] (25, 50, 75) percentile: (87, 135, 247)
[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 567)
[M::mem_pestat] mean and std.dev: (169.06, 113.88)
[M::mem_pestat] low and high boundaries for proper pairs: (1, 727)
[M::mem_pestat] analyzing insert size distribution for orientation FR...
[M::mem_pestat] (25, 50, 75) percentile: (149, 213, 301)
[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 605)
[M::mem_pestat] mean and std.dev: (231.96, 111.26)
[M::mem_pestat] low and high boundaries for proper pairs: (1, 757)
[M::mem_pestat] analyzing insert size distribution for orientation RF...
[M::mem_pestat] (25, 50, 75) percentile: (101, 267, 1290)
[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 3668)
[M::mem_pestat] mean and std.dev: (536.08, 704.20)
[M::mem_pestat] low and high boundaries for proper pairs: (1, 4857)
[M::mem_pestat] analyzing insert size distribution for orientation RR...
[M::mem_pestat] (25, 50, 75) percentile: (85, 141, 204)
[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 442)
[M::mem_pestat] mean and std.dev: (140.88, 78.83)
[M::mem_pestat] low and high boundaries for proper pairs: (1, 561)
[M::mem_pestat] skip orientation FF
[M::mem_pestat] skip orientation RF
[M::mem_pestat] skip orientation RR
[M::mem_process_seqs] Processed 400000 reads in 33.927 CPU sec, 8.838 real sec
[M::process] read 400000 sequences (40000000 bp)...
[M::mem_pestat] # candidate unique pairs for (FF, FR, RF, RR): (144, 179206, 10, 125)
[M::mem_pestat] analyzing insert size distribution for orientation FF...
[M::mem_pestat] (25, 50, 75) percentile: (97, 153, 267)
[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 607)
[M::mem_pestat] mean and std.dev: (186.70, 119.64)
[M::mem_pestat] low and high boundaries for proper pairs: (1, 777)
[M::mem_pestat] analyzing insert size distribution for orientation FR...
[M::mem_pestat] (25, 50, 75) percentile: (149, 212, 299)
[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 599)
[M::mem_pestat] mean and std.dev: (230.62, 109.86)
[M::mem_pestat] low and high boundaries for proper pairs: (1, 749)
[M::mem_pestat] analyzing insert size distribution for orientation RF...
[M::mem_pestat] (25, 50, 75) percentile: (129, 191, 663)
[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 1731)
[M::mem_pestat] mean and std.dev: (219.75, 173.10)
[M::mem_pestat] low and high boundaries for proper pairs: (1, 2265)
[M::mem_pestat] analyzing insert size distribution for orientation RR...
[M::mem_pestat] (25, 50, 75) percentile: (99, 139, 211)
[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 435)
[M::mem_pestat] mean and std.dev: (162.64, 89.53)
[M::mem_pestat] low and high boundaries for proper pairs: (1, 547)
[M::mem_pestat] skip orientation FF
[M::mem_pestat] skip orientation RF
[M::mem_pestat] skip orientation RR
[M::mem_process_seqs] Processed 400000 reads in 35.604 CPU sec, 9.594 real sec
[M::process] read 400000 sequences (40000000 bp)...
[M::mem_pestat] # candidate unique pairs for (FF, FR, RF, RR): (133, 179038, 16, 120)
[M::mem_pestat] analyzing insert size distribution for orientation FF...
[M::mem_pestat] (25, 50, 75) percentile: (94, 149, 245)
[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 547)
[M::mem_pestat] mean and std.dev: (180.59, 110.72)
[M::mem_pestat] low and high boundaries for proper pairs: (1, 698)
[M::mem_pestat] analyzing insert size distribution for orientation FR...
[M::mem_pestat] (25, 50, 75) percentile: (148, 213, 300)
[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 604)
[M::mem_pestat] mean and std.dev: (231.35, 110.82)
[M::mem_pestat] low and high boundaries for proper pairs: (1, 756)
[M::mem_pestat] analyzing insert size distribution for orientation RF...
[M::mem_pestat] (25, 50, 75) percentile: (68, 362, 2454)
[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 7226)
[M::mem_pestat] mean and std.dev: (729.00, 1399.41)
[M::mem_pestat] low and high boundaries for proper pairs: (1, 9612)
[M::mem_pestat] analyzing insert size distribution for orientation RR...
[M::mem_pestat] (25, 50, 75) percentile: (94, 142, 212)
[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 448)
[M::mem_pestat] mean and std.dev: (157.81, 92.04)
[M::mem_pestat] low and high boundaries for proper pairs: (1, 566)
[M::mem_pestat] skip orientation FF
[M::mem_pestat] skip orientation RF
[M::mem_pestat] skip orientation RR
[M::mem_process_seqs] Processed 400000 reads in 32.940 CPU sec, 8.520 real sec
[M::process] read 400000 sequences (40000000 bp)...
[M::mem_pestat] # candidate unique pairs for (FF, FR, RF, RR): (140, 179002, 18, 145)
[M::mem_pestat] analyzing insert size distribution for orientation FF...
[M::mem_pestat] (25, 50, 75) percentile: (105, 154, 221)
[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 453)
[M::mem_pestat] mean and std.dev: (165.87, 89.92)
[M::mem_pestat] low and high boundaries for proper pairs: (1, 569)
[M::mem_pestat] analyzing insert size distribution for orientation FR...
[M::mem_pestat] (25, 50, 75) percentile: (148, 211, 296)
[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 592)
[M::mem_pestat] mean and std.dev: (228.90, 108.79)
[M::mem_pestat] low and high boundaries for proper pairs: (1, 740)
[M::mem_pestat] analyzing insert size distribution for orientation RF...
[M::mem_pestat] (25, 50, 75) percentile: (92, 714, 2507)
[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 7337)
[M::mem_pestat] mean and std.dev: (1691.53, 2317.14)
[M::mem_pestat] low and high boundaries for proper pairs: (1, 10960)
[M::mem_pestat] analyzing insert size distribution for orientation RR...
[M::mem_pestat] (25, 50, 75) percentile: (98, 142, 212)
[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 440)
[M::mem_pestat] mean and std.dev: (153.60, 85.11)
[M::mem_pestat] low and high boundaries for proper pairs: (1, 554)
[M::mem_pestat] skip orientation FF
[M::mem_pestat] skip orientation RF
[M::mem_pestat] skip orientation RR
[M::mem_process_seqs] Processed 400000 reads in 35.737 CPU sec, 9.205 real sec
[M::process] read 400000 sequences (40000000 bp)...
[M::mem_pestat] # candidate unique pairs for (FF, FR, RF, RR): (127, 179676, 14, 127)
[M::mem_pestat] analyzing insert size distribution for orientation FF...
[M::mem_pestat] (25, 50, 75) percentile: (96, 155, 251)
[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 561)
[M::mem_pestat] mean and std.dev: (176.52, 107.31)
[M::mem_pestat] low and high boundaries for proper pairs: (1, 716)
[M::mem_pestat] analyzing insert size distribution for orientation FR...
[M::mem_pestat] (25, 50, 75) percentile: (147, 210, 295)
[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 591)
[M::mem_pestat] mean and std.dev: (228.20, 108.57)
[M::mem_pestat] low and high boundaries for proper pairs: (1, 739)
[M::mem_pestat] analyzing insert size distribution for orientation RF...
[M::mem_pestat] (25, 50, 75) percentile: (68, 234, 2499)
[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 7361)
[M::mem_pestat] mean and std.dev: (893.21, 1188.79)
[M::mem_pestat] low and high boundaries for proper pairs: (1, 9792)
[M::mem_pestat] analyzing insert size distribution for orientation RR...
[M::mem_pestat] (25, 50, 75) percentile: (99, 141, 211)
[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 435)
[M::mem_pestat] mean and std.dev: (157.29, 80.58)
[M::mem_pestat] low and high boundaries for proper pairs: (1, 547)
[M::mem_pestat] skip orientation FF
[M::mem_pestat] skip orientation RF
[M::mem_pestat] skip orientation RR
[M::mem_process_seqs] Processed 400000 reads in 29.688 CPU sec, 7.611 real sec
[M::process] read 400000 sequences (40000000 bp)...
[M::mem_pestat] # candidate unique pairs for (FF, FR, RF, RR): (153, 179012, 17, 113)
[M::mem_pestat] analyzing insert size distribution for orientation FF...
[M::mem_pestat] (25, 50, 75) percentile: (97, 154, 264)
[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 598)
[M::mem_pestat] mean and std.dev: (173.73, 104.58)
[M::mem_pestat] low and high boundaries for proper pairs: (1, 765)
[M::mem_pestat] analyzing insert size distribution for orientation FR...
[M::mem_pestat] (25, 50, 75) percentile: (150, 216, 304)
[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 612)
[M::mem_pestat] mean and std.dev: (234.33, 111.89)
[M::mem_pestat] low and high boundaries for proper pairs: (1, 766)
[M::mem_pestat] analyzing insert size distribution for orientation RF...
[M::mem_pestat] (25, 50, 75) percentile: (108, 350, 2497)
[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 7275)
[M::mem_pestat] mean and std.dev: (823.81, 962.22)
[M::mem_pestat] low and high boundaries for proper pairs: (1, 9664)
[M::mem_pestat] analyzing insert size distribution for orientation RR...
[M::mem_pestat] (25, 50, 75) percentile: (88, 160, 249)
[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 571)
[M::mem_pestat] mean and std.dev: (173.15, 104.17)
[M::mem_pestat] low and high boundaries for proper pairs: (1, 732)
[M::mem_pestat] skip orientation FF
[M::mem_pestat] skip orientation RF
[M::mem_pestat] skip orientation RR
[M::mem_process_seqs] Processed 400000 reads in 31.775 CPU sec, 8.257 real sec
[M::process] read 400000 sequences (40000000 bp)...
[M::mem_pestat] # candidate unique pairs for (FF, FR, RF, RR): (152, 178860, 12, 115)
[M::mem_pestat] analyzing insert size distribution for orientation FF...
[M::mem_pestat] (25, 50, 75) percentile: (94, 171, 250)
[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 562)
[M::mem_pestat] mean and std.dev: (180.46, 109.78)
[M::mem_pestat] low and high boundaries for proper pairs: (1, 718)
[M::mem_pestat] analyzing insert size distribution for orientation FR...
[M::mem_pestat] (25, 50, 75) percentile: (152, 219, 309)
[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 623)
[M::mem_pestat] mean and std.dev: (237.88, 114.48)
[M::mem_pestat] low and high boundaries for proper pairs: (1, 780)
[M::mem_pestat] analyzing insert size distribution for orientation RF...
[M::mem_pestat] (25, 50, 75) percentile: (106, 141, 1547)
[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 4429)
[M::mem_pestat] mean and std.dev: (486.45, 749.05)
[M::mem_pestat] low and high boundaries for proper pairs: (1, 5870)
[M::mem_pestat] analyzing insert size distribution for orientation RR...
[M::mem_pestat] (25, 50, 75) percentile: (117, 169, 252)
[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 522)
[M::mem_pestat] mean and std.dev: (181.69, 95.34)
[M::mem_pestat] low and high boundaries for proper pairs: (1, 657)
[M::mem_pestat] skip orientation FF
[M::mem_pestat] skip orientation RF
[M::mem_pestat] skip orientation RR
[M::mem_process_seqs] Processed 400000 reads in 31.651 CPU sec, 8.204 real sec
[M::process] read 400000 sequences (40000000 bp)...
[M::mem_pestat] # candidate unique pairs for (FF, FR, RF, RR): (140, 178609, 19, 128)
[M::mem_pestat] analyzing insert size distribution for orientation FF...
[M::mem_pestat] (25, 50, 75) percentile: (85, 138, 240)
[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 550)
[M::mem_pestat] mean and std.dev: (164.89, 104.14)
[M::mem_pestat] low and high boundaries for proper pairs: (1, 705)
[M::mem_pestat] analyzing insert size distribution for orientation FR...
[M::mem_pestat] (25, 50, 75) percentile: (152, 217, 307)
[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 617)
[M::mem_pestat] mean and std.dev: (236.86, 113.92)
[M::mem_pestat] low and high boundaries for proper pairs: (1, 772)
[M::mem_pestat] analyzing insert size distribution for orientation RF...
[M::mem_pestat] (25, 50, 75) percentile: (72, 429, 1891)
[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 5529)
[M::mem_pestat] mean and std.dev: (984.74, 1203.35)
[M::mem_pestat] low and high boundaries for proper pairs: (1, 7348)
[M::mem_pestat] analyzing insert size distribution for orientation RR...
[M::mem_pestat] (25, 50, 75) percentile: (90, 142, 229)
[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 507)
[M::mem_pestat] mean and std.dev: (159.97, 91.46)
[M::mem_pestat] low and high boundaries for proper pairs: (1, 646)
[M::mem_pestat] skip orientation FF
[M::mem_pestat] skip orientation RF
[M::mem_pestat] skip orientation RR
[M::mem_process_seqs] Processed 400000 reads in 29.486 CPU sec, 7.533 real sec
[M::process] read 400000 sequences (40000000 bp)...
[M::mem_pestat] # candidate unique pairs for (FF, FR, RF, RR): (133, 178455, 18, 129)
[M::mem_pestat] analyzing insert size distribution for orientation FF...
[M::mem_pestat] (25, 50, 75) percentile: (97, 154, 221)
[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 469)
[M::mem_pestat] mean and std.dev: (160.25, 90.04)
[M::mem_pestat] low and high boundaries for proper pairs: (1, 593)
[M::mem_pestat] analyzing insert size distribution for orientation FR...
[M::mem_pestat] (25, 50, 75) percentile: (152, 218, 308)
[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 620)
[M::mem_pestat] mean and std.dev: (236.90, 114.02)
[M::mem_pestat] low and high boundaries for proper pairs: (1, 776)
[M::mem_pestat] analyzing insert size distribution for orientation RF...
[M::mem_pestat] (25, 50, 75) percentile: (86, 341, 569)
[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 1535)
[M::mem_pestat] mean and std.dev: (330.00, 364.87)
[M::mem_pestat] low and high boundaries for proper pairs: (1, 2018)
[M::mem_pestat] analyzing insert size distribution for orientation RR...
[M::mem_pestat] (25, 50, 75) percentile: (98, 155, 223)
[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 473)
[M::mem_pestat] mean and std.dev: (161.59, 82.85)
[M::mem_pestat] low and high boundaries for proper pairs: (1, 598)
[M::mem_pestat] skip orientation FF
[M::mem_pestat] skip orientation RF
[M::mem_pestat] skip orientation RR
[M::mem_process_seqs] Processed 400000 reads in 31.286 CPU sec, 7.991 real sec
[M::process] read 400000 sequences (40000000 bp)...
[M::mem_pestat] # candidate unique pairs for (FF, FR, RF, RR): (147, 178931, 19, 146)
[M::mem_pestat] analyzing insert size distribution for orientation FF...
[M::mem_pestat] (25, 50, 75) percentile: (102, 174, 273)
[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 615)
[M::mem_pestat] mean and std.dev: (192.13, 122.56)
[M::mem_pestat] low and high boundaries for proper pairs: (1, 786)
[M::mem_pestat] analyzing insert size distribution for orientation FR...
[M::mem_pestat] (25, 50, 75) percentile: (151, 217, 306)
[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 616)
[M::mem_pestat] mean and std.dev: (235.60, 113.33)
[M::mem_pestat] low and high boundaries for proper pairs: (1, 771)
[M::mem_pestat] analyzing insert size distribution for orientation RF...
[M::mem_pestat] (25, 50, 75) percentile: (147, 267, 1336)
[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 3714)
[M::mem_pestat] mean and std.dev: (732.61, 959.49)
[M::mem_pestat] low and high boundaries for proper pairs: (1, 4903)
[M::mem_pestat] analyzing insert size distribution for orientation RR...
[M::mem_pestat] (25, 50, 75) percentile: (91, 144, 213)
[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 457)
[M::mem_pestat] mean and std.dev: (154.83, 87.14)
[M::mem_pestat] low and high boundaries for proper pairs: (1, 579)
[M::mem_pestat] skip orientation FF
[M::mem_pestat] skip orientation RF
[M::mem_pestat] skip orientation RR
[M::mem_process_seqs] Processed 400000 reads in 31.412 CPU sec, 8.040 real sec
[M::process] read 400000 sequences (40000000 bp)...
[M::mem_pestat] # candidate unique pairs for (FF, FR, RF, RR): (161, 178707, 14, 137)
[M::mem_pestat] analyzing insert size distribution for orientation FF...
[M::mem_pestat] (25, 50, 75) percentile: (100, 165, 254)
[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 562)
[M::mem_pestat] mean and std.dev: (179.76, 102.96)
[M::mem_pestat] low and high boundaries for proper pairs: (1, 716)
[M::mem_pestat] analyzing insert size distribution for orientation FR...
[M::mem_pestat] (25, 50, 75) percentile: (150, 215, 304)
[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 612)
[M::mem_pestat] mean and std.dev: (234.24, 112.48)
[M::mem_pestat] low and high boundaries for proper pairs: (1, 766)
[M::mem_pestat] analyzing insert size distribution for orientation RF...
[M::mem_pestat] (25, 50, 75) percentile: (126, 248, 853)
[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 2307)
[M::mem_pestat] mean and std.dev: (394.08, 456.24)
[M::mem_pestat] low and high boundaries for proper pairs: (1, 3034)
[M::mem_pestat] analyzing insert size distribution for orientation RR...
[M::mem_pestat] (25, 50, 75) percentile: (84, 150, 231)
[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 525)
[M::mem_pestat] mean and std.dev: (166.19, 103.03)
[M::mem_pestat] low and high boundaries for proper pairs: (1, 672)
[M::mem_pestat] skip orientation FF
[M::mem_pestat] skip orientation RF
[M::mem_pestat] skip orientation RR
[M::mem_process_seqs] Processed 400000 reads in 29.967 CPU sec, 7.676 real sec
[M::process] read 400000 sequences (40000000 bp)...
[M::mem_pestat] # candidate unique pairs for (FF, FR, RF, RR): (160, 179311, 8, 117)
[M::mem_pestat] analyzing insert size distribution for orientation FF...
[M::mem_pestat] (25, 50, 75) percentile: (93, 154, 252)
[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 570)
[M::mem_pestat] mean and std.dev: (176.34, 110.04)
[M::mem_pestat] low and high boundaries for proper pairs: (1, 729)
[M::mem_pestat] analyzing insert size distribution for orientation FR...
[M::mem_pestat] (25, 50, 75) percentile: (149, 214, 303)
[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 611)
[M::mem_pestat] mean and std.dev: (233.16, 112.22)
[M::mem_pestat] low and high boundaries for proper pairs: (1, 765)
[M::mem_pestat] skip orientation RF as there are not enough pairs
[M::mem_pestat] analyzing insert size distribution for orientation RR...
[M::mem_pestat] (25, 50, 75) percentile: (84, 131, 233)
[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 531)
[M::mem_pestat] mean and std.dev: (161.23, 103.36)
[M::mem_pestat] low and high boundaries for proper pairs: (1, 680)
[M::mem_pestat] skip orientation FF
[M::mem_pestat] skip orientation RR
[M::mem_process_seqs] Processed 400000 reads in 29.302 CPU sec, 7.514 real sec
[M::process] read 400000 sequences (40000000 bp)...
[M::mem_pestat] # candidate unique pairs for (FF, FR, RF, RR): (140, 178995, 8, 113)
[M::mem_pestat] analyzing insert size distribution for orientation FF...
[M::mem_pestat] (25, 50, 75) percentile: (97, 149, 219)
[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 463)
[M::mem_pestat] mean and std.dev: (162.89, 93.08)
[M::mem_pestat] low and high boundaries for proper pairs: (1, 585)
[M::mem_pestat] analyzing insert size distribution for orientation FR...
[M::mem_pestat] (25, 50, 75) percentile: (149, 213, 301)
[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 605)
[M::mem_pestat] mean and std.dev: (232.06, 111.17)
[M::mem_pestat] low and high boundaries for proper pairs: (1, 757)
[M::mem_pestat] skip orientation RF as there are not enough pairs
[M::mem_pestat] analyzing insert size distribution for orientation RR...
[M::mem_pestat] (25, 50, 75) percentile: (102, 148, 226)
[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 474)
[M::mem_pestat] mean and std.dev: (161.11, 87.45)
[M::mem_pestat] low and high boundaries for proper pairs: (1, 598)
[M::mem_pestat] skip orientation FF
[M::mem_pestat] skip orientation RR
[M::mem_process_seqs] Processed 400000 reads in 27.671 CPU sec, 7.075 real sec
[M::process] read 400000 sequences (40000000 bp)...
[M::mem_pestat] # candidate unique pairs for (FF, FR, RF, RR): (167, 179002, 19, 112)
[M::mem_pestat] analyzing insert size distribution for orientation FF...
[M::mem_pestat] (25, 50, 75) percentile: (90, 141, 213)
[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 459)
[M::mem_pestat] mean and std.dev: (154.68, 88.86)
[M::mem_pestat] low and high boundaries for proper pairs: (1, 582)
[M::mem_pestat] analyzing insert size distribution for orientation FR...
[M::mem_pestat] (25, 50, 75) percentile: (149, 213, 300)
[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 602)
[M::mem_pestat] mean and std.dev: (231.28, 110.46)
[M::mem_pestat] low and high boundaries for proper pairs: (1, 753)
[M::mem_pestat] analyzing insert size distribution for orientation RF...
[M::mem_pestat] (25, 50, 75) percentile: (99, 176, 449)
[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 1149)
[M::mem_pestat] mean and std.dev: (191.00, 145.20)
[M::mem_pestat] low and high boundaries for proper pairs: (1, 1499)
[M::mem_pestat] analyzing insert size distribution for orientation RR...
[M::mem_pestat] (25, 50, 75) percentile: (74, 131, 236)
[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 560)
[M::mem_pestat] mean and std.dev: (151.63, 107.38)
[M::mem_pestat] low and high boundaries for proper pairs: (1, 722)
[M::mem_pestat] skip orientation FF
[M::mem_pestat] skip orientation RF
[M::mem_pestat] skip orientation RR
[M::mem_process_seqs] Processed 400000 reads in 28.422 CPU sec, 7.217 real sec
[M::process] read 400000 sequences (40000000 bp)...
[M::mem_pestat] # candidate unique pairs for (FF, FR, RF, RR): (144, 178964, 11, 125)
[M::mem_pestat] analyzing insert size distribution for orientation FF...
[M::mem_pestat] (25, 50, 75) percentile: (97, 163, 256)
[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 574)
[M::mem_pestat] mean and std.dev: (177.25, 105.09)
[M::mem_pestat] low and high boundaries for proper pairs: (1, 733)
[M::mem_pestat] analyzing insert size distribution for orientation FR...
[M::mem_pestat] (25, 50, 75) percentile: (148, 211, 298)
[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 598)
[M::mem_pestat] mean and std.dev: (230.08, 109.93)
[M::mem_pestat] low and high boundaries for proper pairs: (1, 748)
[M::mem_pestat] analyzing insert size distribution for orientation RF...
[M::mem_pestat] (25, 50, 75) percentile: (105, 231, 2497)
[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 7281)
[M::mem_pestat] mean and std.dev: (826.00, 1368.73)
[M::mem_pestat] low and high boundaries for proper pairs: (1, 9673)
[M::mem_pestat] analyzing insert size distribution for orientation RR...
[M::mem_pestat] (25, 50, 75) percentile: (97, 152, 242)
[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 532)
[M::mem_pestat] mean and std.dev: (167.57, 105.41)
[M::mem_pestat] low and high boundaries for proper pairs: (1, 677)
[M::mem_pestat] skip orientation FF
[M::mem_pestat] skip orientation RF
[M::mem_pestat] skip orientation RR
[M::mem_process_seqs] Processed 400000 reads in 31.558 CPU sec, 8.015 real sec
[M::process] read 400000 sequences (40000000 bp)...
[M::mem_pestat] # candidate unique pairs for (FF, FR, RF, RR): (156, 179319, 12, 123)
[M::mem_pestat] analyzing insert size distribution for orientation FF...
[M::mem_pestat] (25, 50, 75) percentile: (87, 131, 203)
[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 435)
[M::mem_pestat] mean and std.dev: (143.16, 76.95)
[M::mem_pestat] low and high boundaries for proper pairs: (1, 551)
[M::mem_pestat] analyzing insert size distribution for orientation FR...
[M::mem_pestat] (25, 50, 75) percentile: (147, 210, 295)
[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 591)
[M::mem_pestat] mean and std.dev: (228.15, 108.49)
[M::mem_pestat] low and high boundaries for proper pairs: (1, 739)
[M::mem_pestat] analyzing insert size distribution for orientation RF...
[M::mem_pestat] (25, 50, 75) percentile: (122, 242, 4251)
[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 12509)
[M::mem_pestat] mean and std.dev: (1379.08, 1961.01)
[M::mem_pestat] low and high boundaries for proper pairs: (1, 16638)
[M::mem_pestat] analyzing insert size distribution for orientation RR...
[M::mem_pestat] (25, 50, 75) percentile: (89, 131, 211)
[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 455)
[M::mem_pestat] mean and std.dev: (154.65, 93.62)
[M::mem_pestat] low and high boundaries for proper pairs: (1, 577)
[M::mem_pestat] skip orientation FF
[M::mem_pestat] skip orientation RF
[M::mem_pestat] skip orientation RR
[M::mem_process_seqs] Processed 400000 reads in 29.726 CPU sec, 7.569 real sec
[M::process] read 400000 sequences (40000000 bp)...
[M::mem_pestat] # candidate unique pairs for (FF, FR, RF, RR): (150, 178926, 11, 126)
[M::mem_pestat] analyzing insert size distribution for orientation FF...
[M::mem_pestat] (25, 50, 75) percentile: (76, 135, 218)
[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 502)
[M::mem_pestat] mean and std.dev: (150.08, 88.68)
[M::mem_pestat] low and high boundaries for proper pairs: (1, 644)
[M::mem_pestat] analyzing insert size distribution for orientation FR...
[M::mem_pestat] (25, 50, 75) percentile: (148, 212, 299)
[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 601)
[M::mem_pestat] mean and std.dev: (230.62, 109.87)
[M::mem_pestat] low and high boundaries for proper pairs: (1, 752)
[M::mem_pestat] analyzing insert size distribution for orientation RF...
[M::mem_pestat] (25, 50, 75) percentile: (284, 1840, 5854)
[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 16994)
[M::mem_pestat] mean and std.dev: (2575.45, 2588.72)
[M::mem_pestat] low and high boundaries for proper pairs: (1, 22564)
[M::mem_pestat] analyzing insert size distribution for orientation RR...
[M::mem_pestat] (25, 50, 75) percentile: (98, 145, 209)
[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 431)
[M::mem_pestat] mean and std.dev: (161.58, 89.71)
[M::mem_pestat] low and high boundaries for proper pairs: (1, 542)
[M::mem_pestat] skip orientation FF
[M::mem_pestat] skip orientation RF
[M::mem_pestat] skip orientation RR
[M::mem_process_seqs] Processed 400000 reads in 32.664 CPU sec, 8.337 real sec
[M::process] read 400000 sequences (40000000 bp)...
[M::mem_pestat] # candidate unique pairs for (FF, FR, RF, RR): (156, 178594, 15, 120)
[M::mem_pestat] analyzing insert size distribution for orientation FF...
[M::mem_pestat] (25, 50, 75) percentile: (89, 157, 239)
[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 539)
[M::mem_pestat] mean and std.dev: (167.42, 99.72)
[M::mem_pestat] low and high boundaries for proper pairs: (1, 689)
[M::mem_pestat] analyzing insert size distribution for orientation FR...
[M::mem_pestat] (25, 50, 75) percentile: (152, 219, 309)
[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 623)
[M::mem_pestat] mean and std.dev: (238.14, 114.68)
[M::mem_pestat] low and high boundaries for proper pairs: (1, 780)
[M::mem_pestat] analyzing insert size distribution for orientation RF...
[M::mem_pestat] (25, 50, 75) percentile: (56, 494, 1621)
[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 4751)
[M::mem_pestat] mean and std.dev: (681.29, 875.03)
[M::mem_pestat] low and high boundaries for proper pairs: (1, 6316)
[M::mem_pestat] analyzing insert size distribution for orientation RR...
[M::mem_pestat] (25, 50, 75) percentile: (105, 162, 250)
[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 540)
[M::mem_pestat] mean and std.dev: (176.94, 98.17)
[M::mem_pestat] low and high boundaries for proper pairs: (1, 685)
[M::mem_pestat] skip orientation FF
[M::mem_pestat] skip orientation RF
[M::mem_pestat] skip orientation RR
[M::mem_process_seqs] Processed 400000 reads in 27.473 CPU sec, 6.977 real sec
[M::process] read 400000 sequences (40000000 bp)...
[M::mem_pestat] # candidate unique pairs for (FF, FR, RF, RR): (133, 178883, 11, 108)
[M::mem_pestat] analyzing insert size distribution for orientation FF...
[M::mem_pestat] (25, 50, 75) percentile: (102, 155, 247)
[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 537)
[M::mem_pestat] mean and std.dev: (169.88, 100.82)
[M::mem_pestat] low and high boundaries for proper pairs: (1, 682)
[M::mem_pestat] analyzing insert size distribution for orientation FR...
[M::mem_pestat] (25, 50, 75) percentile: (152, 218, 308)
[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 620)
[M::mem_pestat] mean and std.dev: (237.05, 114.14)
[M::mem_pestat] low and high boundaries for proper pairs: (1, 776)
[M::mem_pestat] analyzing insert size distribution for orientation RF...
[M::mem_pestat] (25, 50, 75) percentile: (190, 242, 1538)
[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 4234)
[M::mem_pestat] mean and std.dev: (462.78, 564.07)
[M::mem_pestat] low and high boundaries for proper pairs: (1, 5582)
[M::mem_pestat] analyzing insert size distribution for orientation RR...
[M::mem_pestat] (25, 50, 75) percentile: (106, 146, 225)
[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 463)
[M::mem_pestat] mean and std.dev: (164.34, 92.91)
[M::mem_pestat] low and high boundaries for proper pairs: (1, 582)
[M::mem_pestat] skip orientation FF
[M::mem_pestat] skip orientation RF
[M::mem_pestat] skip orientation RR
[M::mem_process_seqs] Processed 400000 reads in 28.043 CPU sec, 7.132 real sec
[M::process] read 400000 sequences (40000000 bp)...
[M::mem_pestat] # candidate unique pairs for (FF, FR, RF, RR): (140, 178950, 14, 128)
[M::mem_pestat] analyzing insert size distribution for orientation FF...
[M::mem_pestat] (25, 50, 75) percentile: (84, 148, 222)
[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 498)
[M::mem_pestat] mean and std.dev: (162.85, 101.63)
[M::mem_pestat] low and high boundaries for proper pairs: (1, 636)
[M::mem_pestat] analyzing insert size distribution for orientation FR...
[M::mem_pestat] (25, 50, 75) percentile: (152, 218, 308)
[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 620)
[M::mem_pestat] mean and std.dev: (237.36, 114.13)
[M::mem_pestat] low and high boundaries for proper pairs: (1, 776)
[M::mem_pestat] analyzing insert size distribution for orientation RF...
[M::mem_pestat] (25, 50, 75) percentile: (66, 289, 2507)
[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 7389)
[M::mem_pestat] mean and std.dev: (1092.38, 1792.75)
[M::mem_pestat] low and high boundaries for proper pairs: (1, 9830)
[M::mem_pestat] analyzing insert size distribution for orientation RR...
[M::mem_pestat] (25, 50, 75) percentile: (88, 146, 234)
[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 526)
[M::mem_pestat] mean and std.dev: (164.84, 96.82)
[M::mem_pestat] low and high boundaries for proper pairs: (1, 672)
[M::mem_pestat] skip orientation FF
[M::mem_pestat] skip orientation RF
[M::mem_pestat] skip orientation RR
[M::mem_process_seqs] Processed 400000 reads in 30.549 CPU sec, 7.765 real sec
[M::process] read 400000 sequences (40000000 bp)...
[M::mem_pestat] # candidate unique pairs for (FF, FR, RF, RR): (150, 178975, 10, 102)
[M::mem_pestat] analyzing insert size distribution for orientation FF...
[M::mem_pestat] (25, 50, 75) percentile: (110, 163, 245)
[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 515)
[M::mem_pestat] mean and std.dev: (175.51, 92.36)
[M::mem_pestat] low and high boundaries for proper pairs: (1, 650)
[M::mem_pestat] analyzing insert size distribution for orientation FR...
[M::mem_pestat] (25, 50, 75) percentile: (152, 217, 307)
[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 617)
[M::mem_pestat] mean and std.dev: (236.42, 113.56)
[M::mem_pestat] low and high boundaries for proper pairs: (1, 772)
[M::mem_pestat] analyzing insert size distribution for orientation RF...
[M::mem_pestat] (25, 50, 75) percentile: (185, 343, 674)
[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 1652)
[M::mem_pestat] mean and std.dev: (455.00, 422.81)
[M::mem_pestat] low and high boundaries for proper pairs: (1, 2146)
[M::mem_pestat] analyzing insert size distribution for orientation RR...
[M::mem_pestat] (25, 50, 75) percentile: (86, 126, 222)
[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 494)
[M::mem_pestat] mean and std.dev: (153.94, 96.05)
[M::mem_pestat] low and high boundaries for proper pairs: (1, 630)
[M::mem_pestat] skip orientation FF
[M::mem_pestat] skip orientation RF
[M::mem_pestat] skip orientation RR
[M::mem_process_seqs] Processed 400000 reads in 29.211 CPU sec, 7.416 real sec
[M::process] read 400000 sequences (40000000 bp)...
[M::mem_pestat] # candidate unique pairs for (FF, FR, RF, RR): (135, 179308, 11, 108)
[M::mem_pestat] analyzing insert size distribution for orientation FF...
[M::mem_pestat] (25, 50, 75) percentile: (92, 147, 238)
[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 530)
[M::mem_pestat] mean and std.dev: (166.69, 106.45)
[M::mem_pestat] low and high boundaries for proper pairs: (1, 676)
[M::mem_pestat] analyzing insert size distribution for orientation FR...
[M::mem_pestat] (25, 50, 75) percentile: (150, 216, 305)
[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 615)
[M::mem_pestat] mean and std.dev: (234.72, 112.96)
[M::mem_pestat] low and high boundaries for proper pairs: (1, 770)
[M::mem_pestat] analyzing insert size distribution for orientation RF...
[M::mem_pestat] (25, 50, 75) percentile: (116, 125, 1675)
[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 4793)
[M::mem_pestat] mean and std.dev: (688.40, 856.39)
[M::mem_pestat] low and high boundaries for proper pairs: (1, 6352)
[M::mem_pestat] analyzing insert size distribution for orientation RR...
[M::mem_pestat] (25, 50, 75) percentile: (95, 136, 211)
[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 443)
[M::mem_pestat] mean and std.dev: (152.09, 85.44)
[M::mem_pestat] low and high boundaries for proper pairs: (1, 559)
[M::mem_pestat] skip orientation FF
[M::mem_pestat] skip orientation RF
[M::mem_pestat] skip orientation RR
[M::mem_process_seqs] Processed 400000 reads in 29.662 CPU sec, 7.528 real sec
[M::process] read 400000 sequences (40000000 bp)...
[M::mem_pestat] # candidate unique pairs for (FF, FR, RF, RR): (174, 178790, 11, 117)
[M::mem_pestat] analyzing insert size distribution for orientation FF...
[M::mem_pestat] (25, 50, 75) percentile: (97, 155, 233)
[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 505)
[M::mem_pestat] mean and std.dev: (168.63, 89.70)
[M::mem_pestat] low and high boundaries for proper pairs: (1, 641)
[M::mem_pestat] analyzing insert size distribution for orientation FR...
[M::mem_pestat] (25, 50, 75) percentile: (150, 215, 304)
[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 612)
[M::mem_pestat] mean and std.dev: (233.93, 112.61)
[M::mem_pestat] low and high boundaries for proper pairs: (1, 766)
[M::mem_pestat] analyzing insert size distribution for orientation RF...
[M::mem_pestat] (25, 50, 75) percentile: (200, 242, 2438)
[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 6914)
[M::mem_pestat] mean and std.dev: (1136.82, 1652.26)
[M::mem_pestat] low and high boundaries for proper pairs: (1, 9152)
[M::mem_pestat] analyzing insert size distribution for orientation RR...
[M::mem_pestat] (25, 50, 75) percentile: (99, 138, 233)
[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 501)
[M::mem_pestat] mean and std.dev: (169.12, 106.79)
[M::mem_pestat] low and high boundaries for proper pairs: (1, 635)
[M::mem_pestat] skip orientation FF
[M::mem_pestat] skip orientation RF
[M::mem_pestat] skip orientation RR
[M::mem_process_seqs] Processed 400000 reads in 29.035 CPU sec, 7.346 real sec
[M::process] read 400000 sequences (40000000 bp)...
[M::mem_pestat] # candidate unique pairs for (FF, FR, RF, RR): (133, 179188, 17, 118)
[M::mem_pestat] analyzing insert size distribution for orientation FF...
[M::mem_pestat] (25, 50, 75) percentile: (84, 144, 248)
[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 576)
[M::mem_pestat] mean and std.dev: (172.45, 112.87)
[M::mem_pestat] low and high boundaries for proper pairs: (1, 740)
[M::mem_pestat] analyzing insert size distribution for orientation FR...
[M::mem_pestat] (25, 50, 75) percentile: (150, 214, 302)
[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 606)
[M::mem_pestat] mean and std.dev: (233.09, 111.31)
[M::mem_pestat] low and high boundaries for proper pairs: (1, 758)
[M::mem_pestat] analyzing insert size distribution for orientation RF...
[M::mem_pestat] (25, 50, 75) percentile: (64, 180, 2499)
[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 7369)
[M::mem_pestat] mean and std.dev: (1108.82, 1642.20)
[M::mem_pestat] low and high boundaries for proper pairs: (1, 9804)
[M::mem_pestat] analyzing insert size distribution for orientation RR...
[M::mem_pestat] (25, 50, 75) percentile: (90, 165, 270)
[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 630)
[M::mem_pestat] mean and std.dev: (185.79, 122.01)
[M::mem_pestat] low and high boundaries for proper pairs: (1, 810)
[M::mem_pestat] skip orientation FF
[M::mem_pestat] skip orientation RF
[M::mem_pestat] skip orientation RR
[M::mem_process_seqs] Processed 400000 reads in 29.671 CPU sec, 7.584 real sec
[M::process] read 400000 sequences (40000000 bp)...
[M::mem_pestat] # candidate unique pairs for (FF, FR, RF, RR): (151, 179116, 18, 99)
[M::mem_pestat] analyzing insert size distribution for orientation FF...
[M::mem_pestat] (25, 50, 75) percentile: (91, 175, 260)
[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 598)
[M::mem_pestat] mean and std.dev: (182.17, 114.19)
[M::mem_pestat] low and high boundaries for proper pairs: (1, 767)
[M::mem_pestat] analyzing insert size distribution for orientation FR...
[M::mem_pestat] (25, 50, 75) percentile: (149, 214, 301)
[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 605)
[M::mem_pestat] mean and std.dev: (232.33, 110.96)
[M::mem_pestat] low and high boundaries for proper pairs: (1, 757)
[M::mem_pestat] analyzing insert size distribution for orientation RF...
[M::mem_pestat] (25, 50, 75) percentile: (77, 251, 460)
[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 1226)
[M::mem_pestat] mean and std.dev: (254.27, 277.52)
[M::mem_pestat] low and high boundaries for proper pairs: (1, 1609)
[M::mem_pestat] analyzing insert size distribution for orientation RR...
[M::mem_pestat] (25, 50, 75) percentile: (102, 171, 249)
[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 543)
[M::mem_pestat] mean and std.dev: (181.99, 110.54)
[M::mem_pestat] low and high boundaries for proper pairs: (1, 690)
[M::mem_pestat] skip orientation FF
[M::mem_pestat] skip orientation RF
[M::mem_pestat] skip orientation RR
[M::mem_process_seqs] Processed 400000 reads in 32.750 CPU sec, 8.590 real sec
[M::process] read 400000 sequences (40000000 bp)...
[M::mem_pestat] # candidate unique pairs for (FF, FR, RF, RR): (139, 179271, 17, 113)
[M::mem_pestat] analyzing insert size distribution for orientation FF...
[M::mem_pestat] (25, 50, 75) percentile: (94, 146, 229)
[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 499)
[M::mem_pestat] mean and std.dev: (161.79, 89.54)
[M::mem_pestat] low and high boundaries for proper pairs: (1, 634)
[M::mem_pestat] analyzing insert size distribution for orientation FR...
[M::mem_pestat] (25, 50, 75) percentile: (149, 213, 299)
[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 599)
[M::mem_pestat] mean and std.dev: (231.10, 110.11)
[M::mem_pestat] low and high boundaries for proper pairs: (1, 749)
[M::mem_pestat] analyzing insert size distribution for orientation RF...
[M::mem_pestat] (25, 50, 75) percentile: (168, 433, 3873)
[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 11283)
[M::mem_pestat] mean and std.dev: (1986.18, 2346.88)
[M::mem_pestat] low and high boundaries for proper pairs: (1, 14988)
[M::mem_pestat] analyzing insert size distribution for orientation RR...
[M::mem_pestat] (25, 50, 75) percentile: (93, 133, 201)
[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 417)
[M::mem_pestat] mean and std.dev: (152.65, 83.65)
[M::mem_pestat] low and high boundaries for proper pairs: (1, 525)
[M::mem_pestat] skip orientation FF
[M::mem_pestat] skip orientation RF
[M::mem_pestat] skip orientation RR
[M::mem_process_seqs] Processed 400000 reads in 26.350 CPU sec, 6.731 real sec
[M::process] read 400000 sequences (40000000 bp)...
[M::mem_pestat] # candidate unique pairs for (FF, FR, RF, RR): (125, 178993, 11, 155)
[M::mem_pestat] analyzing insert size distribution for orientation FF...
[M::mem_pestat] (25, 50, 75) percentile: (104, 149, 244)
[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 524)
[M::mem_pestat] mean and std.dev: (170.03, 100.99)
[M::mem_pestat] low and high boundaries for proper pairs: (1, 664)
[M::mem_pestat] analyzing insert size distribution for orientation FR...
[M::mem_pestat] (25, 50, 75) percentile: (148, 211, 296)
[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 592)
[M::mem_pestat] mean and std.dev: (228.93, 108.66)
[M::mem_pestat] low and high boundaries for proper pairs: (1, 740)
[M::mem_pestat] analyzing insert size distribution for orientation RF...
[M::mem_pestat] (25, 50, 75) percentile: (434, 650, 2502)
[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 6638)
[M::mem_pestat] mean and std.dev: (924.78, 812.21)
[M::mem_pestat] low and high boundaries for proper pairs: (1, 8706)
[M::mem_pestat] analyzing insert size distribution for orientation RR...
[M::mem_pestat] (25, 50, 75) percentile: (86, 125, 185)
[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 383)
[M::mem_pestat] mean and std.dev: (137.03, 74.23)
[M::mem_pestat] low and high boundaries for proper pairs: (1, 482)
[M::mem_pestat] skip orientation FF
[M::mem_pestat] skip orientation RF
[M::mem_pestat] skip orientation RR
[M::mem_process_seqs] Processed 400000 reads in 33.988 CPU sec, 9.055 real sec
[M::process] read 340356 sequences (34035600 bp)...
[M::mem_pestat] # candidate unique pairs for (FF, FR, RF, RR): (108, 152822, 10, 101)
[M::mem_pestat] analyzing insert size distribution for orientation FF...
[M::mem_pestat] (25, 50, 75) percentile: (78, 134, 211)
[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 477)
[M::mem_pestat] mean and std.dev: (154.47, 94.22)
[M::mem_pestat] low and high boundaries for proper pairs: (1, 610)
[M::mem_pestat] analyzing insert size distribution for orientation FR...
[M::mem_pestat] (25, 50, 75) percentile: (147, 209, 294)
[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 588)
[M::mem_pestat] mean and std.dev: (227.35, 107.35)
[M::mem_pestat] low and high boundaries for proper pairs: (1, 735)
[M::mem_pestat] analyzing insert size distribution for orientation RF...
[M::mem_pestat] (25, 50, 75) percentile: (251, 778, 3023)
[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 8567)
[M::mem_pestat] mean and std.dev: (1778.80, 1876.74)
[M::mem_pestat] low and high boundaries for proper pairs: (1, 11339)
[M::mem_pestat] analyzing insert size distribution for orientation RR...
[M::mem_pestat] (25, 50, 75) percentile: (79, 138, 210)
[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 472)
[M::mem_pestat] mean and std.dev: (147.41, 81.06)
[M::mem_pestat] low and high boundaries for proper pairs: (1, 603)
[M::mem_pestat] skip orientation FF
[M::mem_pestat] skip orientation RF
[M::mem_pestat] skip orientation RR
[M::mem_process_seqs] Processed 340356 reads in 22.990 CPU sec, 5.839 real sec
[main] Version: 0.7.17-r1188
[main] CMD: bwa mem -M -t 4 -R @RG\tID:1\tSM:1\tPL:illumina -T 30 S_pombe.fa M14-19_J29_01_TAAGGCGA-TATCCTCT_L002_R1_001.fastq.gz M14-19_J29_01_TAAGGCGA-TATCCTCT_L002_R2_001.fastq.gz
[main] Real time: 760.408 sec; CPU: 1458.667 sec
[bam_sort_core] merging from 12 files...
real 18m6.151s
user 52m11.575s
sys 0m39.006s
In [9]:
# Build the BED file (unfiltered)
! time samtools depth -d 30000 S_pombe.fa.sorted.bam -aa > S_pombe.bed
real 2m5.143s
user 2m1.488s
sys 0m1.150s
In [22]:
%%time
from sequana import GenomeCov
# If chromosome length is >5Mb, we split the data. Here we now it is 5.5Mb, so let us
#slightly increase the chunksize.
b = GenomeCov("S_pombe.bed", "S_pombe.gbk", chunksize=6000000, low_threshold=-4, high_threshold=4)
CPU times: user 16.3 s, sys: 336 ms, total: 16.6 s
Wall time: 16.6 s
In [23]:
b.compute_gc_content("S_pombe.fa")
This data set contains several chromosomes. We can select them one by one and anlyse them as follows:
In [25]:
chrom = b.chr_list[0]
chrom.run(20001, circular=True)
chrom.plot_coverage()
_ = ylim([0, 400])
In [26]:
chrom.plot_rois(0,1000000)
In [27]:
chrom.plot_gc_vs_coverage(bins=[80, 60], Nlevels=6)
Computing 2D histogram. Please wait
In [25]:
!sequana_coverage --input S_pombe.filtered.bed --genbank S_pombe.gbk --reference S_pombe.fa
INFO [sequana]: Reading S_pombe.filtered.bed. This may take time depending on your input file
INFO [sequana]: Scanning input file (chunk of 5000000 rows)
[-----------------100%-----------------] 2 of 2 complete in 3.1 sec
INFO [sequana]: Computing GC content
INFO [sequana]: There are 4 chromosomes/contigs.
INFO [sequana]: CU329670.1 (starting pos: 0, ending pos: 5579132)
INFO [sequana]: CU329671.1 (starting pos: 5579133, ending pos: 10118936)
INFO [sequana]: CU329672.1 (starting pos: 10118937, ending pos: 12571819)
INFO [sequana]: X54421.1 (starting pos: 12571820, ending pos: 12591250)
INFO [sequana]: ==================== analysing chrom/contig 1/4 (CU329670.1)
INFO [sequana]: Computing some metrics
INFO [sequana]:
Genome length: 5579133
!!!! Information based on a sample of 5000000 points
Sequencing depth (DOC): 105.29
Sequencing depth (median): 105.00
Breadth of coverage (BOC) (percent): 100.00
Genome coverage standard deviation : 19.91
Genome coverage coefficient variation : 0.19
Exact values will be available in the summary file (json)
INFO [sequana]: Using running median (w=20001)
INFO [sequana]: Number of mixture models 2
[-----------------100%-----------------] 2 of 2 complete in 21.1 sec
INFO [sequana]: Fitted central distribution (first chunk): mu=1.002, sigma=0.158, pi=0.89
INFO [sequana]: Searching for ROIs (threshold=[-4,4] ; double =[-2.0,2.0])
INFO [sequana]: Number of ROIs found: 463
INFO [sequana]: - below average: 172
INFO [sequana]: - above average: 291
INFO [sequana]: Computing extra metrics
INFO [sequana]: Evenness: 0.9302
INFO [sequana]: Centralness (3 sigma): 0.98105
INFO [sequana]: Centralness (4 sigma): 0.99605
INFO [sequana]: Creating report in report. Please wait
WARNING [sequana]: This chromosome is large (more than 5000000). Producing plots and HTML sub coverage plots only for data from 0 to 5000000 bases. Neccesitate to recompute some metrics. Please wait
WARNING [sequana]:
Found mixture model parameters (k=2) where |mu0-mu1| < sigma0. k=1 could be a better choice.mu0=1.0035266702770107, m1=0.983266870441364, sigma0=0.1604588521928874, sigma1=0.3009729239624961
INFO [sequana]: sub sample data for plotting the coverage
Computing 2D histogram. Please wait
INFO [sequana]: ==================== analysing chrom/contig 2/4 (CU329671.1)
INFO [sequana]: Computing some metrics
INFO [sequana]:
Genome length: 4539804
Sequencing depth (DOC): 106.07
Sequencing depth (median): 105.00
Breadth of coverage (BOC) (percent): 99.99
Genome coverage standard deviation : 27.20
Genome coverage coefficient variation : 0.26
INFO [sequana]: Using running median (w=20001)
INFO [sequana]: Number of mixture models 2
INFO [sequana]: Fitted central distribution (first chunk): mu=1.0, sigma=0.167, pi=0.971
INFO [sequana]: Searching for ROIs (threshold=[-4,4] ; double =[-2.0,2.0])
INFO [sequana]: Number of ROIs found: 320
INFO [sequana]: - below average: 146
INFO [sequana]: - above average: 174
INFO [sequana]: Computing extra metrics
INFO [sequana]: Evenness: 0.9257
INFO [sequana]: Centralness (3 sigma): 0.9848
INFO [sequana]: Centralness (4 sigma): 0.9949
INFO [sequana]: Creating report in report. Please wait
INFO [sequana]: sub sample data for plotting the coverage
Computing 2D histogram. Please wait
INFO [sequana]: ==================== analysing chrom/contig 3/4 (CU329672.1)
INFO [sequana]: Computing some metrics
INFO [sequana]:
Genome length: 2452883
Sequencing depth (DOC): 144.10
Sequencing depth (median): 107.00
Breadth of coverage (BOC) (percent): 99.99
Genome coverage standard deviation : 329.91
Genome coverage coefficient variation : 2.29
INFO [sequana]: Using running median (w=20001)
INFO [sequana]: Number of mixture models 2
INFO [sequana]: Fitted central distribution (first chunk): mu=1.0, sigma=0.171, pi=0.985
INFO [sequana]: Searching for ROIs (threshold=[-4,4] ; double =[-2.0,2.0])
INFO [sequana]: Number of ROIs found: 210
INFO [sequana]: - below average: 89
INFO [sequana]: - above average: 121
INFO [sequana]: Computing extra metrics
INFO [sequana]: Evenness: 0.7412
INFO [sequana]: Centralness (3 sigma): 0.9836
INFO [sequana]: Centralness (4 sigma): 0.9933
INFO [sequana]: Creating report in report. Please wait
INFO [sequana]: sub sample data for plotting the coverage
Computing 2D histogram. Please wait
INFO [sequana]: ==================== analysing chrom/contig 4/4 (X54421.1)
INFO [sequana]: Computing some metrics
INFO [sequana]:
Genome length: 19431
Sequencing depth (DOC): 16959.39
Sequencing depth (median): 17265.00
Breadth of coverage (BOC) (percent): 100.00
Genome coverage standard deviation : 2819.64
Genome coverage coefficient variation : 0.17
WARNING [sequana]: median window length is too long.
Setting the window length automatically to a fifth of
the chromosome length (3887)
INFO [sequana]: Using running median (w=3887)
INFO [sequana]: Number of mixture models 2
INFO [sequana]: Fitted central distribution (first chunk): mu=1.017, sigma=0.116, pi=0.879
INFO [sequana]: Searching for ROIs (threshold=[-4,4] ; double =[-2.0,2.0])
INFO [sequana]: Number of ROIs found: 9
INFO [sequana]: - below average: 8
INFO [sequana]: - above average: 1
INFO [sequana]: Computing extra metrics
INFO [sequana]: Evenness: 0.9349
INFO [sequana]: Centralness (3 sigma): 0.9559
INFO [sequana]: Centralness (4 sigma): 0.9965
INFO [sequana]: Creating report in report. Please wait
Computing 2D histogram. Please wait
INFO [sequana]: =========================
INFO [sequana]: Creating multiqc report
[WARNING] multiqc : MultiQC Version v1.4 now available!
[INFO ] multiqc : This is MultiQC v1.0
[INFO ] multiqc : Template : default
[INFO ] multiqc : Report title: Sequana multi summary
[INFO ] multiqc : Searching '.'
[INFO ] multiqc : Only using modules sequana_coverage
Searching 90 files.. [####################################] 100%
[INFO ] coverage : Found 4 reports
[INFO ] multiqc : Compressing plot data
[INFO ] multiqc : Report : multiqc_report.html
[INFO ] multiqc : Data : multiqc_data
[INFO ] multiqc : MultiQC complete
The previous cell should create a directory that contains a HTML file called multiqc_report.html, which can be browsed to look at the different chromosome and results.
Here, all chromosomes are analysed one by one.
In [ ]:
Content source: sequana/resources
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