In [30]:
!python /root/Euplotid/pipelines/buildAnnotatteINs.py --help
usage: buildAnnotatteINs.py [-h] -i INPUT_DIRECTORY -o OUTPUT_DIRECTORY
[-t INSULATED_NEIGH] -c DNA_INT_CELL_TYPE -q
EQTL_TISSUE [-g TOP_GENE_FPKM] -n NAME_OUTPUT
[-m MARKER_REGION]
Pipeline to output graphical genomic model from 2D data
optional arguments:
-h, --help show this help message and exit
-i INPUT_DIRECTORY, --input_directory INPUT_DIRECTORY
Where all the input data lives
-o OUTPUT_DIRECTORY, --output_directory OUTPUT_DIRECTORY
Output directory of graphs
-t INSULATED_NEIGH, --insulated_neigh INSULATED_NEIGH
Comma separated list of Insulated Neighborhoods to
build
-c DNA_INT_CELL_TYPE, --dna_int_cell_type DNA_INT_CELL_TYPE
Cell type to use in building Insulated Neighborhoods
-q EQTL_TISSUE, --eQTL_tissue EQTL_TISSUE
What tissue from GTeX to do eQTL analysis w/.
Available tissues:
Adipose_Subcutaneous,Adipose_Visceral_Omentum,
Adrenal_Gland, Artery_Aorta, Artery_Coronary,
Artery_Tibial, Brain_Anterior_cingulate_cortex_BA24,
Brain_Caudate_basal_ganglia,
Brain_Cerebellar_Hemisphere, Brain_Cerebellum,
Brain_Cortex, Brain_Frontal_Cortex_BA9,
Brain_Hippocampus, Brain_Hypothalamus,
Brain_Nucleus_accumbens_basal_ganglia,
Brain_Putamen_basal_ganglia,Breast_Mammary_Tissue,
Cells_EBV-transformed_lymphocytes,
Cells_Transformed_fibroblasts, Colon_Sigmoid,
Colon_Transverse, Esophagus_Gastroesophageal_Junction,
Esophagus_Mucosa, Esophagus_Muscularis,
Heart_Atrial_Appendage, Heart_Left_Ventricle, Liver,
Lung, Muscle_Skeletal, Nerve_Tibial, Ovary, Pancreas,
Pituitary, Prostate, Skin_Not_Sun_Exposed_Suprapubic,
Skin_Sun_Exposed_Lower_leg,
Small_Intestine_Terminal_Ileum, Spleen, Stomach,
Testis, Thyroid, Uterus, Vagina, Whole_Blood
-g TOP_GENE_FPKM, --top_gene_fpkm TOP_GENE_FPKM
Instead of defining Insulated Neighborhoods take genes
expressed above FPKM cutoff
-n NAME_OUTPUT, --name_output NAME_OUTPUT
Output prefix for all output files
-m MARKER_REGION, --marker_region MARKER_REGION
Build all Insulated Neighborhoods of genes which fall
within this chromosomal region (ex:
chr1:54996039-55996039)
In [7]:
!python /root/Euplotid/euplotid/buildAnnotateINs.py \
-i /input_dir/ -o /output_dir/ -a /annotation_dir \
-c primed -q Adipose_Visceral_Omentum \
-n example -t IRX3,FTO,CHD9
Traceback (most recent call last):
File "/root/Euplotid/euplotid/buildAnnotateINs.py", line 1023, in <module>
homo_gen = pysam.FastaFile(genome_fa)
File "pysam/libcfaidx.pyx", line 114, in pysam.libcfaidx.FastaFile.__cinit__ (pysam/libcfaidx.c:2166)
File "pysam/libcfaidx.pyx", line 149, in pysam.libcfaidx.FastaFile._open (pysam/libcfaidx.c:2675)
IOError: file `/annotation_dirhg19.fa` not found
In [11]:
#Default Insulated Neighborhoods to
!python /root/Euplotid/euplotid/buildAnnotateINs.py -i /input_dir/ -o /output_dir/ -a /annotation_dir/ \
-c primed -q Adipose_Visceral_Omentum -n default
#!python generate_draft_JSONs_all_funcs.py -i /input_data/ -o /root/Euplotid/pipelines/example_output/output_IN_graphs/ \
# -c jurkatt -q Cells_EBV-transformed_lymphocytes -n default
#!python generate_draft_JSONs_all_funcs.py -i /input_data/ -o /root/Euplotid/pipelines/example_output/output_IN_graphs/ \
# -c neuron -q Brain_Cortex -n default
#!python generate_draft_JSONs_all_funcs.py -i /input_data/ -o /root/Euplotid/pipelines/example_output/output_IN_graphs/ \
# -c mesc -q Brain_Cortex -n default
Number of Target Genes: 19
Target Genes to build Insulated Neighborhoods: TMEM63A,NANOGNB,DUSP6,NANOG,SOX17,HMGB3,HIF1A-AS2,PRDM14,HIF1A,SMAD3,TBX3,KLF4,CCDC140,PAX3,SOX2,PYCR2,LEFTY1,IRX3,DD413687
Checking resolution parameter against CTCF-CTCF loop
Annotating 13 Neighborhoods
Annotating the following Insulated Neighborhoods: NANOGNB,NANOG|PRDM14|DUSP6|PYCR2,LEFTY1,TMEM63A,LEFTY1|HMGB3|SMAD3,SMAD3|SOX17|TBX3|KLF4|SOX2|HIF1A,HIF1A,HIF1A-AS2|CCDC140,PAX3,DD413687|IRX3
Annotating Insulated Neighborhood: NANOGNB,NANOG
Annotating Open Regions
Annotating SNPs/CNVs
querying 1-2...done.
Fetching 133 variant(s) . . .
Annotating Insulated Neighborhood: PRDM14
Annotating Open Regions
Annotating SNPs/CNVs
querying 1-1...done.
Fetching 20 variant(s) . . .
Annotating Insulated Neighborhood: PYCR2,LEFTY1,TMEM63A,LEFTY1
Annotating Open Regions
Annotating SNPs/CNVs
querying 1-4...done.
No results to return
Fetching 54 variant(s) . . .
Fetching 80 variant(s) . . .
Annotating Insulated Neighborhood: TBX3
Annotating Open Regions
Annotating SNPs/CNVs
querying 1-1...done.
Annotating Insulated Neighborhood: SMAD3,SMAD3
Annotating Open Regions
Fetching 44 variant(s) . . .
No results to return
Annotating SNPs/CNVs
querying 1-2...done.
Fetching 27 variant(s) . . .
No results to return
No results to return
Annotating Insulated Neighborhood: CCDC140,PAX3,DD413687
Annotating Open Regions
Fetching 37 variant(s) . . .
Fetching 49 variant(s) . . .
Fetching 99 variant(s) . . .
Annotating SNPs/CNVs
No results to return
querying 1-3...done.
No results to return
Annotating Insulated Neighborhood: HIF1A,HIF1A,HIF1A-AS2
Annotating Open Regions
Fetching 625 variant(s) . . .
Fetching 41 variant(s) . . .
Fetching 48 variant(s) . . .
No results to return
Annotating SNPs/CNVs
querying 1-3...done.
Fetching 56 variant(s) . . .
No results to return
Fetching 91 variant(s) . . .
Fetching 29 variant(s) . . .
Annotating Insulated Neighborhood: DUSP6
Annotating Open Regions
Annotating SNPs/CNVs
No results to return
querying 1-1...done.
No results to return
Deepbind SNP prediction of: chr8:70983017-70984817
Fetching 37 variant(s) . . .
No results to return
Annotating Insulated Neighborhood: SOX2
Annotating Open Regions
No results to return
Fetching 24 variant(s) . . .
No results to return
Deepbind SNP prediction of: chr12:7958831-7960358
Fetching 38 variant(s) . . .
Annotating SNPs/CNVs
No results to return
querying 1-1...done.
Fetching 101 variant(s) . . .
Fetching 39 variant(s) . . .
No results to return
Annotating Insulated Neighborhood: HMGB3
Annotating Open Regions
Fetching 35 variant(s) . . .
Fetching 27 variant(s) . . .
No results to return
No results to return
Deepbind SNP prediction of: chr14:62216285-62218561
Annotating SNPs/CNVs
querying 1-1...done.
No results to return
Fetching 76 variant(s) . . .
Annotating Insulated Neighborhood: KLF4
Annotating Open Regions
No results to return
Fetching 7 variant(s) . . .
Annotating SNPs/CNVs
querying 1-1...done.
No results to return
Fetching 67 variant(s) . . .
No results to return
No results to return
Annotating Insulated Neighborhood: IRX3
Annotating Open Regions
Fetching 993 variant(s) . . .
Fetching 51 variant(s) . . .
Fetching 39 variant(s) . . .
Fetching 45 variant(s) . . .
Annotating SNPs/CNVs
querying 1-1...done.
Fetching 20 variant(s) . . .
No results to return
Fetching 12 variant(s) . . .
Annotating Insulated Neighborhood: SOX17
Annotating Open Regions
Fetching 56 variant(s) . . .
No results to return
Annotating SNPs/CNVs
querying 1-1...done.
No results to return
No results to return
Deepbind SNP prediction of: chrX:150150585-150152257
No results to return
No results to return
Fetching 45 variant(s) . . .
No results to return
Fetching 50 variant(s) . . .
Fetching 87 variant(s) . . .
No results to return
No results to return
Fetching 31 variant(s) . . .
Fetching 36 variant(s) . . .
Fetching 78 variant(s) . . .
Fetching 134 variant(s) . . .
Fetching 179 variant(s) . . .
No results to return
Fetching 30 variant(s) . . .
No results to return
No results to return
No results to return
No results to return
Fetching 35 variant(s) . . .
Fetching 64 variant(s) . . .
No results to return
Deepbind SNP prediction of: chr1:226068359-226071203
Fetching 72 variant(s) . . .
Fetching 54 variant(s) . . .
No results to return
Deepbind SNP prediction of: chr8:55370260-55371257
No results to return
Fetching 47 variant(s) . . .
No results to return
Deepbind SNP prediction of: chr12:89745241-89748630
No results to return
No results to return
No results to return
No results to return
Fetching 34 variant(s) . . .
Fetching 42 variant(s) . . .
No results to return
Fetching 24 variant(s) . . .
Fetching 56 variant(s) . . .
No results to return
Fetching 59 variant(s) . . .
Fetching 46 variant(s) . . .
No results to return
No results to return
Deepbind SNP prediction of: chr12:115119911-115123081
Fetching 42 variant(s) . . .
No results to return
Fetching 49 variant(s) . . .
No results to return
No results to return
No results to return
Fetching 92 variant(s) . . .
Fetching 29 variant(s) . . .
No results to return
Fetching 78 variant(s) . . .
No results to return
Fetching 27 variant(s) . . .
Fetching 49 variant(s) . . .
No results to return
Fetching 19 variant(s) . . .
No results to return
Deepbind SNP prediction of: chr15:67355982-67361149
No results to return
Fetching 26 variant(s) . . .
No results to return
Fetching 32 variant(s) . . .
No results to return
No results to return
Deepbind SNP prediction of: chr2:223162665-223165357
Fetching 50 variant(s) . . .
No results to return
Fetching 22 variant(s) . . .
No results to return
Fetching 73 variant(s) . . .
No results to return
No results to return
Fetching 20 variant(s) . . .
Fetching 81 variant(s) . . .
No results to return
Fetching 23 variant(s) . . .
No results to return
No results to return
Fetching 63 variant(s) . . .
Fetching 39 variant(s) . . .
No results to return
Fetching 141 variant(s) . . .
No results to return
Fetching 40 variant(s) . . .
No results to return
Deepbind SNP prediction of: chr16:54315183-54322626
No results to return
Fetching 55 variant(s) . . .
No results to return
Fetching 50 variant(s) . . .
No results to return
Fetching 43 variant(s) . . .
Basset SNP prediction of: chrX:150150585-150152257
/root/Basset/src/basset_sad.py -f /annotation_dir/hg19.fa -l 600 -o /output_dir//primed/default//chrX_150150585_150152257_basset -t /root/Basset/tutorials/sad_eg/sample_beds.txt /input_dir/pretrained_model.th /output_dir//primed/default//chrX_150150585_150152257_basset/open_variants.vcf
No results to return
No results to return
WARNING: Skipping chrX:g.150012231del - neither allele matches reference genome: AT vs TC
/root/Basset/src/basset_predict.lua -rc /input_dir/pretrained_model.th /output_dir//primed/default//chrX_150150585_150152257_basset/model_in.h5 /output_dir//primed/default//chrX_150150585_150152257_basset/model_out.txt
Fetching 54 variant(s) . . .
Fetching 27 variant(s) . . .
No results to return
Deepbind SNP prediction of: chr3:181426680-181430164
No results to return
Fetching 13 variant(s) . . .
No results to return
Fetching 97 variant(s) . . .
/root/anaconda2/lib/python2.7/site-packages/matplotlib/__init__.py:1357: UserWarning: This call to matplotlib.use() has no effect
because the backend has already been chosen;
matplotlib.use() must be called *before* pylab, matplotlib.pyplot,
or matplotlib.backends is imported for the first time.
warnings.warn(_use_error_msg)
Predicting sequence 1 variants
No results to return
Fetching 66 variant(s) . . .
No results to return
Fetching 141 variant(s) . . .
No results to return
Fetching 138 variant(s) . . .
No results to return
Fetching 50 variant(s) . . .
No results to return
Fetching 27 variant(s) . . .
No results to return
Fetching 112 variant(s) . . .
No results to return
Fetching 71 variant(s) . . .
Predicting sequence 2 variants
No results to return
Fetching 113 variant(s) . . .
No results to return
Fetching 68 variant(s) . . .
No results to return
Fetching 36 variant(s) . . .
No results to return
Fetching 47 variant(s) . . .
No results to return
Fetching 45 variant(s) . . .
No results to return
Fetching 50 variant(s) . . .
No results to return
Fetching 84 variant(s) . . .
No results to return
Deepbind SNP prediction of: chr9:110248986-110254279
Basset SNP prediction of: chr14:62216285-62218561
/root/Basset/src/basset_sad.py -f /annotation_dir/hg19.fa -l 600 -o /output_dir//primed/default//chr14_62216285_62218561_basset -t /root/Basset/tutorials/sad_eg/sample_beds.txt /input_dir/pretrained_model.th /output_dir//primed/default//chr14_62216285_62218561_basset/open_variants.vcf
WARNING: Skipping chr14:g.62214687del - neither allele matches reference genome: GA vs AA
WARNING: Skipping chr14:g.62214784del - neither allele matches reference genome: CT vs TT
WARNING: Skipping chr14:g.62214579del - neither allele matches reference genome: AC vs CC
WARNING: Skipping chr14:g.62214472del - neither allele matches reference genome: TA vs AT
WARNING: Skipping chr14:g.62214204del - neither allele matches reference genome: CT vs TT
WARNING: Skipping chr14:g.62215153_62215155del - neither allele matches reference genome: AAAT vs AATA
WARNING: Skipping chr14:g.62215159_62215161del - neither allele matches reference genome: TAAC vs AACA
WARNING: Skipping chr14:g.62213865del - neither allele matches reference genome: AT vs TT
WARNING: Skipping chr14:g.62214221del - neither allele matches reference genome: AC vs CA
/root/Basset/src/basset_predict.lua -rc /input_dir/pretrained_model.th /output_dir//primed/default//chr14_62216285_62218561_basset/model_in.h5 /output_dir//primed/default//chr14_62216285_62218561_basset/model_out.txt
Basset SNP prediction of: chr8:55370260-55371257
/root/Basset/src/basset_sad.py -f /annotation_dir/hg19.fa -l 600 -o /output_dir//primed/default//chr8_55370260_55371257_basset -t /root/Basset/tutorials/sad_eg/sample_beds.txt /input_dir/pretrained_model.th /output_dir//primed/default//chr8_55370260_55371257_basset/open_variants.vcf
WARNING: Skipping chr8:g.55374474_55374477del - neither allele matches reference genome: TTAAC vs TAACT
WARNING: Skipping chr8:g.55374701del - neither allele matches reference genome: AG vs GG
WARNING: Skipping chr8:g.55374545_55374548del - neither allele matches reference genome: CATGG vs ATGGA
WARNING: Skipping chr8:g.55374520_55374524del - neither allele matches reference genome: TGTTAA vs GTTAAG
WARNING: Skipping chr8:g.55374876_55374877del - neither allele matches reference genome: ACT vs CTC
WARNING: Skipping chr8:g.55374830_55374833del - neither allele matches reference genome: CTTAG vs TTAGT
WARNING: Skipping chr8:g.55374508_55374509del - neither allele matches reference genome: AAG vs AGA
/root/Basset/src/basset_predict.lua -rc /input_dir/pretrained_model.th /output_dir//primed/default//chr8_55370260_55371257_basset/model_in.h5 /output_dir//primed/default//chr8_55370260_55371257_basset/model_out.txt
/root/anaconda2/lib/python2.7/site-packages/matplotlib/__init__.py:1357: UserWarning: This call to matplotlib.use() has no effect
because the backend has already been chosen;
matplotlib.use() must be called *before* pylab, matplotlib.pyplot,
or matplotlib.backends is imported for the first time.
warnings.warn(_use_error_msg)
Predicting sequence 1 variants
/root/anaconda2/lib/python2.7/site-packages/matplotlib/__init__.py:1357: UserWarning: This call to matplotlib.use() has no effect
because the backend has already been chosen;
matplotlib.use() must be called *before* pylab, matplotlib.pyplot,
or matplotlib.backends is imported for the first time.
warnings.warn(_use_error_msg)
Predicting sequence 1 variants
Predicting sequence 2 variants
Predicting sequence 2 variants
Basset SNP prediction of: chr8:70983017-70984817
/root/Basset/src/basset_sad.py -f /annotation_dir/hg19.fa -l 600 -o /output_dir//primed/default//chr8_70983017_70984817_basset -t /root/Basset/tutorials/sad_eg/sample_beds.txt /input_dir/pretrained_model.th /output_dir//primed/default//chr8_70983017_70984817_basset/open_variants.vcf
WARNING: Skipping chr8:g.70668272del - neither allele matches reference genome: CT vs TT
WARNING: Skipping chr8:g.70616167_70616169del - neither allele matches reference genome: CATT vs ATTA
/root/Basset/src/basset_predict.lua -rc /input_dir/pretrained_model.th /output_dir//primed/default//chr8_70983017_70984817_basset/model_in.h5 /output_dir//primed/default//chr8_70983017_70984817_basset/model_out.txt
/root/anaconda2/lib/python2.7/site-packages/matplotlib/__init__.py:1357: UserWarning: This call to matplotlib.use() has no effect
because the backend has already been chosen;
matplotlib.use() must be called *before* pylab, matplotlib.pyplot,
or matplotlib.backends is imported for the first time.
warnings.warn(_use_error_msg)
Predicting sequence 1 variants
Basset SNP prediction of: chr12:89745241-89748630
/root/Basset/src/basset_sad.py -f /annotation_dir/hg19.fa -l 600 -o /output_dir//primed/default//chr12_89745241_89748630_basset -t /root/Basset/tutorials/sad_eg/sample_beds.txt /input_dir/pretrained_model.th /output_dir//primed/default//chr12_89745241_89748630_basset/open_variants.vcf
WARNING: Skipping chr12:g.89367775del - neither allele matches reference genome: CT vs TT
WARNING: Skipping chr12:g.89368130del - neither allele matches reference genome: TA vs AG
WARNING: Skipping chr12:g.89368002_89368003del - neither allele matches reference genome: CTT vs TTA
WARNING: Skipping chr12:g.89368412_89368416del - neither allele matches reference genome: CTCCTT vs TCCTTT
WARNING: Skipping chr12:g.89367775_89367776del - neither allele matches reference genome: CTT vs TTT
WARNING: Skipping chr12:g.89367787del - neither allele matches reference genome: TG vs GG
WARNING: Skipping chr12:g.89886316_89886317del - neither allele matches reference genome: CAT vs ATA
/root/Basset/src/basset_predict.lua -rc /input_dir/pretrained_model.th /output_dir//primed/default//chr12_89745241_89748630_basset/model_in.h5 /output_dir//primed/default//chr12_89745241_89748630_basset/model_out.txt
Predicting sequence 2 variants
/root/anaconda2/lib/python2.7/site-packages/matplotlib/__init__.py:1357: UserWarning: This call to matplotlib.use() has no effect
because the backend has already been chosen;
matplotlib.use() must be called *before* pylab, matplotlib.pyplot,
or matplotlib.backends is imported for the first time.
warnings.warn(_use_error_msg)
Predicting sequence 1 variants
Basset SNP prediction of: chr12:7958831-7960358
/root/Basset/src/basset_sad.py -f /annotation_dir/hg19.fa -l 600 -o /output_dir//primed/default//chr12_7958831_7960358_basset -t /root/Basset/tutorials/sad_eg/sample_beds.txt /input_dir/pretrained_model.th /output_dir//primed/default//chr12_7958831_7960358_basset/open_variants.vcf
WARNING: Skipping chr12:g.7933946_7933947del - neither allele matches reference genome: CAA vs AAA
WARNING: Skipping chr12:g.7934314_7934315del - neither allele matches reference genome: CAT vs ATG
WARNING: Skipping chr12:g.7933809del - neither allele matches reference genome: CT vs TG
WARNING: Skipping chr12:g.7933773del - neither allele matches reference genome: GA vs AA
WARNING: Skipping chr12:g.7934071del - neither allele matches reference genome: TA vs AA
WARNING: Skipping chr12:g.7933945_7933946del - neither allele matches reference genome: TCA vs CAA
WARNING: Skipping chr12:g.7934158_7934163del - neither allele matches reference genome: AGAACTT vs GAACTTG
WARNING: Skipping chr12:g.7933537del - neither allele matches reference genome: GC vs CC
WARNING: Skipping chr12:g.7933933_7933934del - neither allele matches reference genome: CAG vs AGA
WARNING: Skipping chr12:g.7943340_7943348del - neither allele matches reference genome: CCCTGCTTTT vs CCTGCTTTTC
WARNING: Skipping chr12:g.7943353_7943354del - neither allele matches reference genome: CTT vs TTT
WARNING: Skipping chr12:g.7943710del - neither allele matches reference genome: CT vs TT
WARNING: Skipping chr12:g.7943706_7943710del - neither allele matches reference genome: CTTTCT vs TTTCTT
WARNING: Skipping chr12:g.7943821del - neither allele matches reference genome: CT vs TC
WARNING: Skipping chr12:g.7943706_7943711del - neither allele matches reference genome: CTTTCTT vs TTTCTTT
/root/Basset/src/basset_predict.lua -rc /input_dir/pretrained_model.th /output_dir//primed/default//chr12_7958831_7960358_basset/model_in.h5 /output_dir//primed/default//chr12_7958831_7960358_basset/model_out.txt
Predicting sequence 2 variants
/root/anaconda2/lib/python2.7/site-packages/matplotlib/__init__.py:1357: UserWarning: This call to matplotlib.use() has no effect
because the backend has already been chosen;
matplotlib.use() must be called *before* pylab, matplotlib.pyplot,
or matplotlib.backends is imported for the first time.
warnings.warn(_use_error_msg)
Predicting sequence 1 variants
Predicting sequence 2 variants
Basset SNP prediction of: chr1:226068359-226071203
/root/Basset/src/basset_sad.py -f /annotation_dir/hg19.fa -l 600 -o /output_dir//primed/default//chr1_226068359_226071203_basset -t /root/Basset/tutorials/sad_eg/sample_beds.txt /input_dir/pretrained_model.th /output_dir//primed/default//chr1_226068359_226071203_basset/open_variants.vcf
WARNING: Skipping chr1:g.225840609del - neither allele matches reference genome: AG vs GG
WARNING: Skipping chr1:g.225840452del - neither allele matches reference genome: AG vs GG
WARNING: Skipping chr1:g.225840298del - neither allele matches reference genome: CG vs GG
WARNING: Skipping chr1:g.225803730del - neither allele matches reference genome: AC vs CC
WARNING: Skipping chr1:g.225850545del - neither allele matches reference genome: TG vs GA
WARNING: Skipping chr1:g.225850873_225850875del - neither allele matches reference genome: TAAC vs AACT
WARNING: Skipping chr1:g.225850750_225850763del - neither allele matches reference genome: CAAAAAAAAAAAAAA vs AAAAAAAAAAAAAAA
WARNING: Skipping chr1:g.225813385_225813388del - neither allele matches reference genome: ATTGT vs TTGTT
WARNING: Skipping chr1:g.225813259_225813260del - neither allele matches reference genome: CTT vs TTG
WARNING: Skipping chr1:g.225813669_225813671del - neither allele matches reference genome: AAAG vs AAGA
WARNING: Skipping chr1:g.226028981_226028984del - neither allele matches reference genome: CTTTA vs TTTAT
WARNING: Skipping chr1:g.226028610_226028613del - neither allele matches reference genome: AAGTC vs AGTCA
WARNING: Skipping chr1:g.226028796del - neither allele matches reference genome: TG vs GG
WARNING: Skipping chr1:g.226028622_226028623del - neither allele matches reference genome: TTC vs TCT
WARNING: Skipping chr1:g.226028641_226028643del - neither allele matches reference genome: ATGT vs TGTT
WARNING: Skipping chr1:g.226028127del - neither allele matches reference genome: TC vs CC
WARNING: Skipping chr1:g.226028749del - neither allele matches reference genome: AT vs TT
/root/Basset/src/basset_predict.lua -rc /input_dir/pretrained_model.th /output_dir//primed/default//chr1_226068359_226071203_basset/model_in.h5 /output_dir//primed/default//chr1_226068359_226071203_basset/model_out.txt
/root/anaconda2/lib/python2.7/site-packages/matplotlib/__init__.py:1357: UserWarning: This call to matplotlib.use() has no effect
because the backend has already been chosen;
matplotlib.use() must be called *before* pylab, matplotlib.pyplot,
or matplotlib.backends is imported for the first time.
warnings.warn(_use_error_msg)
Predicting sequence 1 variants
Basset SNP prediction of: chr15:67355982-67361149
/root/Basset/src/basset_sad.py -f /annotation_dir/hg19.fa -l 600 -o /output_dir//primed/default//chr15_67355982_67361149_basset -t /root/Basset/tutorials/sad_eg/sample_beds.txt /input_dir/pretrained_model.th /output_dir//primed/default//chr15_67355982_67361149_basset/open_variants.vcf
WARNING: Skipping chr15:g.67292326del - neither allele matches reference genome: TA vs AT
WARNING: Skipping chr15:g.67292329del - neither allele matches reference genome: CT vs TT
WARNING: Skipping chr15:g.67292176_67292177del - neither allele matches reference genome: CTG vs TGT
WARNING: Skipping chr15:g.67283186_67283189del - neither allele matches reference genome: CAAAG vs AAAGA
WARNING: Skipping chr15:g.67283298del - neither allele matches reference genome: GA vs AA
WARNING: Skipping chr15:g.67447857del - neither allele matches reference genome: AG vs GG
WARNING: Skipping chr15:g.67447903del - neither allele matches reference genome: AT vs TT
WARNING: Skipping chr15:g.67447825_67447828del - neither allele matches reference genome: AAGAG vs AGAGA
WARNING: Skipping chr15:g.67388045_67388048del - neither allele matches reference genome: ATTTC vs TTTCT
WARNING: Skipping chr15:g.67387890_67387891del - neither allele matches reference genome: CTT vs TTT
WARNING: Skipping chr15:g.67387890del - neither allele matches reference genome: CT vs TT
WARNING: Skipping chr15:g.67286913_67286944del - neither allele matches reference genome: TCAGTGGCTCATGCCTGTAGTCCCAGCACTTTG vs CAGTGGCTCATGCCTGTAGTCCCAGCACTTTGG
/root/Basset/src/basset_predict.lua -rc /input_dir/pretrained_model.th /output_dir//primed/default//chr15_67355982_67361149_basset/model_in.h5 /output_dir//primed/default//chr15_67355982_67361149_basset/model_out.txt
Predicting sequence 2 variants
Basset SNP prediction of: chr16:54315183-54322626
/root/Basset/src/basset_sad.py -f /annotation_dir/hg19.fa -l 600 -o /output_dir//primed/default//chr16_54315183_54322626_basset -t /root/Basset/tutorials/sad_eg/sample_beds.txt /input_dir/pretrained_model.th /output_dir//primed/default//chr16_54315183_54322626_basset/open_variants.vcf
WARNING: Skipping chr16:g.53932919_53932920del - neither allele matches reference genome: TAA vs AAA
WARNING: Skipping chr16:g.53932930_53932932del - neither allele matches reference genome: CTCT vs TCTT
WARNING: Skipping chr16:g.54399504del - neither allele matches reference genome: GA vs AA
WARNING: Skipping chr16:g.54261748_54261751del - neither allele matches reference genome: CTATA vs TATAT
WARNING: Skipping chr16:g.54261741_54261760del - neither allele matches reference genome: CTATATACTATATATAGTATA vs TATATACTATATATAGTATAT
WARNING: Skipping chr16:g.54261644_54261645del - neither allele matches reference genome: CTA vs TAT
WARNING: Skipping chr16:g.54261806del - neither allele matches reference genome: CA vs AT
WARNING: Skipping chr16:g.54261829_54261841del - neither allele matches reference genome: ATATATGTATACTG vs TATATGTATACTGT
WARNING: Skipping chr16:g.53933428del - neither allele matches reference genome: TC vs CC
WARNING: Skipping chr16:g.54388922del - neither allele matches reference genome: AT vs TT
WARNING: Skipping chr16:g.55188147del - neither allele matches reference genome: CA vs AT
WARNING: Skipping chr16:g.55188201del - neither allele matches reference genome: GA vs AA
WARNING: Skipping chr16:g.54354078del - neither allele matches reference genome: AC vs CT
WARNING: Skipping chr16:g.55124562del - neither allele matches reference genome: AG vs GC
/root/Basset/src/basset_predict.lua -rc /input_dir/pretrained_model.th /output_dir//primed/default//chr16_54315183_54322626_basset/model_in.h5 /output_dir//primed/default//chr16_54315183_54322626_basset/model_out.txt
Basset SNP prediction of: chr2:223162665-223165357
/root/Basset/src/basset_sad.py -f /annotation_dir/hg19.fa -l 600 -o /output_dir//primed/default//chr2_223162665_223165357_basset -t /root/Basset/tutorials/sad_eg/sample_beds.txt /input_dir/pretrained_model.th /output_dir//primed/default//chr2_223162665_223165357_basset/open_variants.vcf
WARNING: Skipping chr2:g.223522739_223522741del - neither allele matches reference genome: TAAC vs AACA
WARNING: Skipping chr2:g.223208242_223208245del - neither allele matches reference genome: TTCTA vs TCTAT
WARNING: Skipping chr2:g.222919042_222919047del - neither allele matches reference genome: TCTGTTC vs CTGTTCC
WARNING: Skipping chr2:g.222919033del - neither allele matches reference genome: GT vs TT
WARNING: Skipping chr2:g.223303104_223303105del - neither allele matches reference genome: ACC vs CCA
WARNING: Skipping chr2:g.223302868del - neither allele matches reference genome: CT vs TT
WARNING: Skipping chr2:g.223302888del - neither allele matches reference genome: GC vs CC
WARNING: Skipping chr2:g.223102049del - neither allele matches reference genome: CA vs AC
WARNING: Skipping chr2:g.223102243_223102245del - neither allele matches reference genome: CAAT vs AATC
WARNING: Skipping chr2:g.223102046_223102049del - neither allele matches reference genome: GCACA vs CACAC
WARNING: Skipping chr2:g.223102046_223102059del - neither allele matches reference genome: GCACACACACACACA vs CACACACACACACAC
WARNING: Skipping chr2:g.223102042_223102045del - neither allele matches reference genome: ACATG vs CATGC
WARNING: Skipping chr2:g.223102046_223102047del - neither allele matches reference genome: GCA vs CAC
WARNING: Skipping chr2:g.223301732del - neither allele matches reference genome: CA vs AG
WARNING: Skipping chr2:g.223301183del - neither allele matches reference genome: TA vs AA
WARNING: Skipping chr2:g.223301970del - neither allele matches reference genome: AT vs TT
/root/Basset/src/basset_predict.lua -rc /input_dir/pretrained_model.th /output_dir//primed/default//chr2_223162665_223165357_basset/model_in.h5 /output_dir//primed/default//chr2_223162665_223165357_basset/model_out.txt
Basset SNP prediction of: chr12:115119911-115123081
/root/Basset/src/basset_sad.py -f /annotation_dir/hg19.fa -l 600 -o /output_dir//primed/default//chr12_115119911_115123081_basset -t /root/Basset/tutorials/sad_eg/sample_beds.txt /input_dir/pretrained_model.th /output_dir//primed/default//chr12_115119911_115123081_basset/open_variants.vcf
WARNING: Skipping chr12:g.115514458_115514460del - neither allele matches reference genome: TCAG vs CAGC
WARNING: Skipping chr12:g.115514724del - neither allele matches reference genome: CT vs TG
WARNING: Skipping chr12:g.115514956_115514958del - neither allele matches reference genome: TAGA vs AGAA
WARNING: Skipping chr12:g.115151539del - neither allele matches reference genome: GA vs AA
WARNING: Skipping chr12:g.115151895_115151899del - neither allele matches reference genome: TCTTTA vs CTTTAG
WARNING: Skipping chr12:g.115151884_115151888del - neither allele matches reference genome: TTCTTA vs TCTTAT
WARNING: Skipping chr12:g.115151395del - neither allele matches reference genome: CA vs AA
WARNING: Skipping chr12:g.115152053_115152056del - neither allele matches reference genome: TTTTC vs TTTCT
WARNING: Skipping chr12:g.115152048del - neither allele matches reference genome: AT vs TT
WARNING: Skipping chr12:g.115152023_115152024del - neither allele matches reference genome: CAT vs ATG
WARNING: Skipping chr12:g.115559536_115559537del - neither allele matches reference genome: CAA vs AAT
WARNING: Skipping chr12:g.115559539_115559543del - neither allele matches reference genome: TCTTTA vs CTTTAC
WARNING: Skipping chr12:g.115062282_115062283del - neither allele matches reference genome: CAA vs AAA
WARNING: Skipping chr12:g.115062282del - neither allele matches reference genome: CA vs AA
WARNING: Skipping chr12:g.115121136_115121139del - neither allele matches reference genome: GAAAA vs AAAAA
WARNING: Skipping chr12:g.115121494_115121498del - neither allele matches reference genome: CCCTAT vs CCTATC
WARNING: Skipping chr12:g.115121513_115121514del - neither allele matches reference genome: CCT vs CTC
WARNING: Skipping chr12:g.115121495_115121498del - neither allele matches reference genome: CCTAT vs CTATC
WARNING: Skipping chr12:g.115121128_115121131del - neither allele matches reference genome: AAAAG vs AAAGA
WARNING: Skipping chr12:g.115121186del - neither allele matches reference genome: AG vs GG
WARNING: Skipping chr12:g.115121496del - neither allele matches reference genome: CT vs TA
WARNING: Skipping chr12:g.115121519_115121522del - neither allele matches reference genome: TCTCG vs CTCGC
WARNING: Skipping chr12:g.115121132_115121138del - neither allele matches reference genome: GAAAGAAA vs AAAGAAAA
WARNING: Skipping chr12:g.115121079_115121082del - neither allele matches reference genome: GTTGT vs TTGTT
WARNING: Skipping chr12:g.115543798_115543799del - neither allele matches reference genome: CTT vs TTT
WARNING: Skipping chr12:g.115543798del - neither allele matches reference genome: CT vs TT
/root/Basset/src/basset_predict.lua -rc /input_dir/pretrained_model.th /output_dir//primed/default//chr12_115119911_115123081_basset/model_in.h5 /output_dir//primed/default//chr12_115119911_115123081_basset/model_out.txt
/root/anaconda2/lib/python2.7/site-packages/matplotlib/__init__.py:1357: UserWarning: This call to matplotlib.use() has no effect
because the backend has already been chosen;
matplotlib.use() must be called *before* pylab, matplotlib.pyplot,
or matplotlib.backends is imported for the first time.
warnings.warn(_use_error_msg)
Predicting sequence 1 variants
/root/anaconda2/lib/python2.7/site-packages/matplotlib/__init__.py:1357: UserWarning: This call to matplotlib.use() has no effect
because the backend has already been chosen;
matplotlib.use() must be called *before* pylab, matplotlib.pyplot,
or matplotlib.backends is imported for the first time.
warnings.warn(_use_error_msg)
Predicting sequence 1 variants
Predicting sequence 2 variants
Predicting sequence 2 variants
/root/anaconda2/lib/python2.7/site-packages/matplotlib/__init__.py:1357: UserWarning: This call to matplotlib.use() has no effect
because the backend has already been chosen;
matplotlib.use() must be called *before* pylab, matplotlib.pyplot,
or matplotlib.backends is imported for the first time.
warnings.warn(_use_error_msg)
Predicting sequence 1 variants
/root/anaconda2/lib/python2.7/site-packages/matplotlib/__init__.py:1357: UserWarning: This call to matplotlib.use() has no effect
because the backend has already been chosen;
matplotlib.use() must be called *before* pylab, matplotlib.pyplot,
or matplotlib.backends is imported for the first time.
warnings.warn(_use_error_msg)
Predicting sequence 1 variants
Predicting sequence 2 variants
Predicting sequence 2 variants
Basset SNP prediction of: chr3:181426680-181430164
/root/Basset/src/basset_sad.py -f /annotation_dir/hg19.fa -l 600 -o /output_dir//primed/default//chr3_181426680_181430164_basset -t /root/Basset/tutorials/sad_eg/sample_beds.txt /input_dir/pretrained_model.th /output_dir//primed/default//chr3_181426680_181430164_basset/open_variants.vcf
WARNING: Skipping chr3:g.181648199del - neither allele matches reference genome: AC vs CC
WARNING: Skipping chr3:g.181762730del - neither allele matches reference genome: AT vs TT
WARNING: Skipping chr3:g.181762664del - neither allele matches reference genome: CT vs TT
WARNING: Skipping chr3:g.182229245_182229248del - neither allele matches reference genome: ATTTT vs TTTTA
WARNING: Skipping chr3:g.182229660_182229669del - neither allele matches reference genome: GCCTACAGTCC vs CCTACAGTCCA
WARNING: Skipping chr3:g.182228434_182228437del - neither allele matches reference genome: CTGTT vs TGTTT
WARNING: Skipping chr3:g.182228396del - neither allele matches reference genome: AT vs TT
WARNING: Skipping chr3:g.182228510_182228511del - neither allele matches reference genome: GAA vs AAA
WARNING: Skipping chr3:g.181673954_181673961del - neither allele matches reference genome: CAAATTGAA vs AAATTGAAA
WARNING: Skipping chr3:g.181673960_181673962del - neither allele matches reference genome: GAAA vs AAAG
WARNING: Skipping chr3:g.181673954_181673958del - neither allele matches reference genome: CAAATT vs AAATTG
WARNING: Skipping chr3:g.181578621_181578628del - neither allele matches reference genome: ACAGGGTTT vs CAGGGTTTC
WARNING: Skipping chr3:g.181578711_181578722del - neither allele matches reference genome: GGCATGAGCCACT vs GCATGAGCCACTG
WARNING: Skipping chr3:g.181936054_181936056del - neither allele matches reference genome: AGAG vs GAGC
WARNING: Skipping chr3:g.181862449del - neither allele matches reference genome: AT vs TT
WARNING: Skipping chr3:g.182416175del - neither allele matches reference genome: AC vs CA
WARNING: Skipping chr3:g.182415952del - neither allele matches reference genome: TG vs GT
WARNING: Skipping chr3:g.181131080del - neither allele matches reference genome: AC vs CG
WARNING: Skipping chr3:g.181836534_181836535del - neither allele matches reference genome: AAG vs AGA
WARNING: Skipping chr3:g.181836535del - neither allele matches reference genome: AG vs GA
WARNING: Skipping chr4:g.145616279_145616282del - neither allele matches reference genome: ACAAG vs CAAGA
WARNING: Skipping chr3:g.181575779del - neither allele matches reference genome: GA vs AA
WARNING: Skipping chr3:g.181861727_181861728del - neither allele matches reference genome: CAG vs AGA
WARNING: Skipping chr3:g.181861661del - neither allele matches reference genome: CT vs TT
WARNING: Skipping chr3:g.181861893del - neither allele matches reference genome: AT vs TT
WARNING: Skipping chr3:g.181861888del - neither allele matches reference genome: GT vs TG
/root/Basset/src/basset_predict.lua -rc /input_dir/pretrained_model.th /output_dir//primed/default//chr3_181426680_181430164_basset/model_in.h5 /output_dir//primed/default//chr3_181426680_181430164_basset/model_out.txt
/root/anaconda2/lib/python2.7/site-packages/matplotlib/__init__.py:1357: UserWarning: This call to matplotlib.use() has no effect
because the backend has already been chosen;
matplotlib.use() must be called *before* pylab, matplotlib.pyplot,
or matplotlib.backends is imported for the first time.
warnings.warn(_use_error_msg)
Predicting sequence 1 variants
Predicting sequence 2 variants
Basset SNP prediction of: chr9:110248986-110254279
/root/Basset/src/basset_sad.py -f /annotation_dir/hg19.fa -l 600 -o /output_dir//primed/default//chr9_110248986_110254279_basset -t /root/Basset/tutorials/sad_eg/sample_beds.txt /input_dir/pretrained_model.th /output_dir//primed/default//chr9_110248986_110254279_basset/open_variants.vcf
WARNING: Skipping chr9:g.110682159del - neither allele matches reference genome: TG vs GC
WARNING: Skipping chr9:g.110682137del - neither allele matches reference genome: TA vs AA
WARNING: Skipping chr9:g.110682024_110682025del - neither allele matches reference genome: CTA vs TAC
WARNING: Skipping chr9:g.110287863del - neither allele matches reference genome: TA vs AA
WARNING: Skipping chr9:g.110287791del - neither allele matches reference genome: AG vs GA
WARNING: Skipping chr9:g.110288007del - neither allele matches reference genome: CA vs AA
WARNING: Skipping chr9:g.110288166_110288168del - neither allele matches reference genome: CAAA vs AAAA
WARNING: Skipping chr9:g.110288140_110288143del - neither allele matches reference genome: CTGGG vs TGGGT
WARNING: Skipping chr9:g.110288169_110288177del - neither allele matches reference genome: AAACAACAAC vs AACAACAACA
WARNING: Skipping chr9:g.110288397_110288409del - neither allele matches reference genome: GTACGGAGATGGAC vs TACGGAGATGGACG
WARNING: Skipping chr9:g.110288169_110288183del - neither allele matches reference genome: AAACAACAACAACAAC vs AACAACAACAACAACA
WARNING: Skipping chr9:g.110288018del - neither allele matches reference genome: AT vs TA
WARNING: Skipping chr9:g.110289066_110289068del - neither allele matches reference genome: ATTT vs TTTT
WARNING: Skipping chr9:g.110288900del - neither allele matches reference genome: TA vs AA
WARNING: Skipping chr9:g.110940143_110940148del - neither allele matches reference genome: GATAGAT vs ATAGATA
WARNING: Skipping chr9:g.111425886_111425887del - neither allele matches reference genome: TGA vs GAG
WARNING: Skipping chr9:g.111402663_111402666del - neither allele matches reference genome: CCTCT vs CTCTC
WARNING: Skipping chr9:g.110485797del - neither allele matches reference genome: TG vs GG
WARNING: Skipping chr9:g.110485907_110485912del - neither allele matches reference genome: CTTTTTT vs TTTTTTT
WARNING: Skipping chr9:g.110485902del - neither allele matches reference genome: TC vs CT
WARNING: Skipping chr9:g.110485886_110485906del - neither allele matches reference genome: TCTCTCTTTCTTTCTTTCTTTC vs CTCTCTTTCTTTCTTTCTTTCT
WARNING: Skipping chr9:g.110485885_110485911del - neither allele matches reference genome: CTCTCTCTTTCTTTCTTTCTTTCTTTTT vs TCTCTCTTTCTTTCTTTCTTTCTTTTTT
WARNING: Skipping chr9:g.110485889_110485892del - neither allele matches reference genome: CTCTT vs TCTTT
WARNING: Skipping chr9:g.110485902_110485906del - neither allele matches reference genome: TCTTTC vs CTTTCT
WARNING: Skipping chr9:g.111218814del - neither allele matches reference genome: TG vs GT
WARNING: Skipping chr9:g.111218820_111218821del - neither allele matches reference genome: TAA vs AAA
WARNING: Skipping chr9:g.111220122_111220125del - neither allele matches reference genome: AAGAG vs AGAGA
WARNING: Skipping chr9:g.111220121_111220122del - neither allele matches reference genome: TAA vs AAG
WARNING: Skipping chr9:g.110518021_110518024del - neither allele matches reference genome: GTTTT vs TTTTT
WARNING: Skipping chr9:g.110518410_110518413del - neither allele matches reference genome: AGATT vs GATTA
WARNING: Skipping chr9:g.110518402_110518405del - neither allele matches reference genome: GGATA vs GATAG
WARNING: Skipping chr9:g.110518381_110518384del - neither allele matches reference genome: TACAC vs ACACA
WARNING: Skipping chr9:g.111082728_111082735del - neither allele matches reference genome: TAGACAGTC vs AGACAGTCC
WARNING: Skipping chr9:g.110452052_110452053del - neither allele matches reference genome: CTT vs TTG
WARNING: Skipping chr9:g.110451954_110451955del - neither allele matches reference genome: TAA vs AAA
WARNING: Skipping chr9:g.110452358_110452361del - neither allele matches reference genome: GAAAC vs AAACA
WARNING: Skipping chr9:g.110400582_110400589del - neither allele matches reference genome: CCTCGCTTT vs CTCGCTTTC
WARNING: Skipping chr9:g.110400714_110400716del - neither allele matches reference genome: GCGC vs CGCC
WARNING: Skipping chr9:g.110400273_110400274del - neither allele matches reference genome: TCC vs CCG
WARNING: Skipping chr9:g.110400713_110400714del - neither allele matches reference genome: TGC vs GCG
WARNING: Skipping chr9:g.110400716del - neither allele matches reference genome: GC vs CC
WARNING: Skipping chr9:g.110400850_110400852del - neither allele matches reference genome: CAGA vs AGAA
WARNING: Skipping chr9:g.110401239_110401240del - neither allele matches reference genome: TTC vs TCA
WARNING: Skipping chr9:g.110400665_110400666del - neither allele matches reference genome: CCT vs CTC
WARNING: Skipping chr9:g.110401282_110401285del - neither allele matches reference genome: TACAC vs ACACA
WARNING: Skipping chr9:g.110401306_110401308del - neither allele matches reference genome: CACA vs ACAC
WARNING: Skipping chr9:g.110401282_110401287del - neither allele matches reference genome: TACACAC vs ACACACA
WARNING: Skipping chr9:g.110400956_110400957del - neither allele matches reference genome: CTG vs TGG
WARNING: Skipping chr9:g.110400628_110400629del - neither allele matches reference genome: TTC vs TCT
WARNING: Skipping chr9:g.110400594_110400601del - neither allele matches reference genome: GCTTTCTCT vs CTTTCTCTC
WARNING: Skipping chr9:g.110400212_110400214del - neither allele matches reference genome: TTTC vs TTCT
WARNING: Skipping chr9:g.110400715del - neither allele matches reference genome: CG vs GC
WARNING: Skipping chr9:g.110401282_110401293del - neither allele matches reference genome: TACACACACACAC vs ACACACACACACA
WARNING: Skipping chr9:g.110973355_110973362del - neither allele matches reference genome: GGGGTGTGT vs GGGTGTGTG
WARNING: Skipping chr9:g.110973355_110973360del - neither allele matches reference genome: GGGGTGT vs GGGTGTG
WARNING: Skipping chr9:g.110972813_110972822del - neither allele matches reference genome: AAAAAAAAAAC vs AAAAAAAAACA
WARNING: Skipping chr9:g.110973355_110973370del - neither allele matches reference genome: GGGGTGTGTGTGTGTGT vs GGGTGTGTGTGTGTGTG
WARNING: Skipping chr9:g.110972274_110972281del - neither allele matches reference genome: CATAAGAGT vs ATAAGAGTA
WARNING: Skipping chr9:g.110973384_110973385del - neither allele matches reference genome: GTA vs TAT
WARNING: Skipping chr9:g.110973380_110973385del - neither allele matches reference genome: GTGTGTA vs TGTGTAT
WARNING: Skipping chr9:g.110973355_110973358del - neither allele matches reference genome: GGGGT vs GGGTG
WARNING: Skipping chr9:g.110973370_110973385del - neither allele matches reference genome: GTGTGTGTGTGTGTGTA vs TGTGTGTGTGTGTGTAT
WARNING: Skipping chr9:g.110972811_110972822del - neither allele matches reference genome: AAAAAAAAAAAAC vs AAAAAAAAAAACA
WARNING: Skipping chr9:g.110973353_110973354del - neither allele matches reference genome: TGG vs GGG
WARNING: Skipping chr9:g.110972814_110972822del - neither allele matches reference genome: AAAAAAAAAC vs AAAAAAAACA
WARNING: Skipping chr9:g.110973357_110973362del - neither allele matches reference genome: GGTGTGT vs GTGTGTG
WARNING: Skipping chr9:g.110973129_110973132del - neither allele matches reference genome: GTCTT vs TCTTT
WARNING: Skipping chr9:g.110973378_110973385del - neither allele matches reference genome: GTGTGTGTA vs TGTGTGTAT
WARNING: Skipping chr9:g.110973350_110973352del - neither allele matches reference genome: GTTT vs TTTG
WARNING: Skipping chr9:g.110272225del - neither allele matches reference genome: CG vs GC
WARNING: Skipping chr9:g.110272905del - neither allele matches reference genome: TC vs CA
WARNING: Skipping chr9:g.110272497del - neither allele matches reference genome: AG vs GG
WARNING: Skipping chr9:g.110450993_110451005del - neither allele matches reference genome: TATGTTCCAGATCC vs ATGTTCCAGATCCA
WARNING: Skipping chr9:g.110451058del - neither allele matches reference genome: TA vs AA
WARNING: Skipping chr9:g.110451075del - neither allele matches reference genome: AT vs TT
WARNING: Skipping chr9:g.110451122del - neither allele matches reference genome: AG vs GG
WARNING: Skipping chr9:g.110451086del - neither allele matches reference genome: CA vs AA
WARNING: Skipping chr9:g.110769531_110769534del - neither allele matches reference genome: ATTTC vs TTTCT
WARNING: Skipping chr9:g.110770377del - neither allele matches reference genome: GC vs CA
WARNING: Skipping chr9:g.110770355_110770358del - neither allele matches reference genome: CTTTG vs TTTGT
WARNING: Skipping chr9:g.110768815del - neither allele matches reference genome: AT vs TT
WARNING: Skipping chr9:g.110769809_110769820del - neither allele matches reference genome: AGAAGTACTAGTT vs GAAGTACTAGTTG
WARNING: Skipping chr9:g.110393804del - neither allele matches reference genome: GA vs AA
WARNING: Skipping chr9:g.110394134_110394135del - neither allele matches reference genome: CAA vs AAA
WARNING: Skipping chr9:g.110673277_110673279del - neither allele matches reference genome: AAAC vs AACA
WARNING: Skipping chr9:g.110673481del - neither allele matches reference genome: GA vs AG
WARNING: Skipping chr9:g.111482674_111482675del - neither allele matches reference genome: CTG vs TGC
WARNING: Skipping chr9:g.110999952_110999954del - neither allele matches reference genome: AAAG vs AAGA
WARNING: Skipping chr9:g.111106449_111106451del - neither allele matches reference genome: TAAG vs AAGA
WARNING: Skipping chr9:g.111106369_111106371del - neither allele matches reference genome: TGAG vs GAGG
/root/Basset/src/basset_predict.lua -rc /input_dir/pretrained_model.th /output_dir//primed/default//chr9_110248986_110254279_basset/model_in.h5 /output_dir//primed/default//chr9_110248986_110254279_basset/model_out.txt
/root/anaconda2/lib/python2.7/site-packages/matplotlib/__init__.py:1357: UserWarning: This call to matplotlib.use() has no effect
because the backend has already been chosen;
matplotlib.use() must be called *before* pylab, matplotlib.pyplot,
or matplotlib.backends is imported for the first time.
warnings.warn(_use_error_msg)
Predicting sequence 1 variants
Predicting sequence 2 variants
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!ls /output_dir
jurkatt local_out mesc neuron primed
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Content source: dborgesr/Euplotid
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