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2024-09-10 11:49:55,246 - Running chopper
2024-09-10 11:49:55,246 - Finished running chopper
2024-09-10 11:49:55,246 - Running MiniMap2
2024-09-10 11:49:55,247 - Finished running Minimap2
2024-09-10 11:49:55,247 - Running Samtools View
2024-09-10 11:49:55,247 - Finished running Samtools View
2024-09-10 11:49:55,247 - Running PEPPER-Margin-DeepVariant
2024-09-10 11:49:55,247 - running command: docker pull jmcdani20/hap.py:v0.3.12
2024-09-10 11:49:55,247 - running command: docker pull kishwars/pepper_deepvariant:r0.8
2024-09-10 11:49:55,247 - running command: docker run --ipc=host -v /home/giuli/Documents/NGPAT/data/tests:/data-u `id -u $USER`:`id -g $USER` kishwars/pepper_deepvariant:r0.8 run_pepper_margin_deepvariant call_variant -b data/alignments.bam -f data/reference.fasta -o data/variantcalls -t 1 --ont_r9_guppy5_sup
2024-09-10 11:50:13,036 - Finished running PEPPER-Margin-DeepVariant
2024-09-10 11:53:54,859 - Running chopper
2024-09-10 11:53:54,859 - Finished running chopper
2024-09-10 11:53:54,859 - Running MiniMap2
2024-09-10 11:53:54,859 - Finished running Minimap2
2024-09-10 11:53:54,859 - Running Samtools View
2024-09-10 11:53:54,859 - Finished running Samtools View
2024-09-10 11:53:54,859 - Running PEPPER-Margin-DeepVariant
2024-09-10 11:53:54,859 - running command: docker pull jmcdani20/hap.py:v0.3.12
2024-09-10 11:53:54,859 - running command: docker pull kishwars/pepper_deepvariant:r0.8
2024-09-10 11:53:54,859 - running command: docker run --ipc=host -v /home/giuli/Documents/NGPAT/data/tests:/datakishwars/pepper_deepvariant:r0.8 run_pepper_margin_deepvariant call_variant -b data/alignments.bam -f data/reference.fasta -o data/variantcalls -t 1 --ont_r9_guppy5_sup
2024-09-10 11:54:08,293 - Finished running PEPPER-Margin-DeepVariant
2024-09-10 11:55:47,316 - Running chopper
2024-09-10 11:55:47,316 - Finished running chopper
2024-09-10 11:55:47,316 - Running MiniMap2
2024-09-10 11:55:47,316 - Finished running Minimap2
2024-09-10 11:55:47,316 - Running Samtools View
2024-09-10 11:55:47,316 - Finished running Samtools View
2024-09-10 11:55:47,316 - Running PEPPER-Margin-DeepVariant
2024-09-10 11:55:47,316 - running command: docker pull jmcdani20/hap.py:v0.3.12
2024-09-10 11:55:47,316 - running command: docker pull kishwars/pepper_deepvariant:r0.8
2024-09-10 11:55:47,316 - running command: docker run --ipc=host -v /home/giuli/Documents/NGPAT/data/tests:/data kishwars/pepper_deepvariant:r0.8 run_pepper_margin_deepvariant call_variant -b data/alignments.bam -f data/reference.fasta -o data/variantcalls -t 1 --ont_r9_guppy5_sup
2024-09-10 11:56:02,111 - Finished running PEPPER-Margin-DeepVariant
2024-09-10 11:57:19,036 - Running chopper
2024-09-10 11:57:19,036 - Finished running chopper
2024-09-10 11:57:19,036 - Running MiniMap2
2024-09-10 11:57:19,036 - Finished running Minimap2
2024-09-10 11:57:19,036 - Running Samtools View
2024-09-10 11:57:19,036 - Finished running Samtools View
2024-09-10 11:57:19,036 - Running PEPPER-Margin-DeepVariant
2024-09-10 11:57:19,036 - running command: docker pull jmcdani20/hap.py:v0.3.12
2024-09-10 11:57:19,036 - running command: docker pull kishwars/pepper_deepvariant:r0.8
2024-09-10 11:57:19,037 - running command: docker run --ipc=host -v /home/giuli/Documents/NGPAT/data/tests:/data kishwars/pepper_deepvariant:r0.8 run_pepper_margin_deepvariant call_variant -b /data/alignments.bam -f /data/reference.fasta -o /data/variantcalls -t 1 --ont_r9_guppy5_sup
2024-09-10 11:57:31,518 - Finished running PEPPER-Margin-DeepVariant
2024-09-10 12:00:19,420 - Running chopper
2024-09-10 12:00:19,420 - Finished running chopper
2024-09-10 12:00:19,420 - Running MiniMap2
2024-09-10 12:00:19,420 - Finished running Minimap2
2024-09-10 12:00:19,420 - Running Samtools View
2024-09-10 12:00:19,420 - running command: samtools view -Sb data/tests/alignments.sam > data/tests/alignments.bam
2024-09-10 12:01:35,006 - Finished running Samtools View
2024-09-10 12:01:35,007 - Running PEPPER-Margin-DeepVariant
2024-09-10 12:01:35,007 - running command: docker pull jmcdani20/hap.py:v0.3.12
2024-09-10 12:01:35,007 - running command: docker pull kishwars/pepper_deepvariant:r0.8
2024-09-10 12:01:35,007 - running command: docker run --ipc=host -v /home/giuli/Documents/NGPAT/data/tests:/data kishwars/pepper_deepvariant:r0.8 run_pepper_margin_deepvariant call_variant -b /data/alignments.bam -f /data/reference.fasta -o /data/variantcalls -t 1 --ont_r9_guppy5_sup
2024-09-10 12:01:42,742 - Finished running PEPPER-Margin-DeepVariant
2024-09-10 12:06:55,544 - Running chopper
2024-09-10 12:06:55,544 - Finished running chopper
2024-09-10 12:06:55,544 - Running MiniMap2
2024-09-10 12:06:55,544 - Finished running Minimap2
2024-09-10 12:06:55,545 - Running Samtools View
2024-09-10 12:06:55,545 - running command: samtools view -u -h -F 1 data/tests/alignments.sam | samtools sort - > data/tests/alignments.bam
2024-09-10 12:09:21,873 - running command: samtools index data/tests/alignments.bam
2024-09-10 12:09:33,022 - Finished running Samtools View
2024-09-10 12:09:33,023 - Running PEPPER-Margin-DeepVariant
2024-09-10 12:09:33,023 - running command: docker pull jmcdani20/hap.py:v0.3.12
2024-09-10 12:09:33,023 - running command: docker pull kishwars/pepper_deepvariant:r0.8
2024-09-10 12:09:33,023 - running command: docker run --ipc=host -v /home/giuli/Documents/NGPAT/data/tests:/data kishwars/pepper_deepvariant:r0.8 run_pepper_margin_deepvariant call_variant -b /data/alignments.bam -f /data/reference.fasta -o /data/variantcalls -t 1 --ont_r9_guppy5_sup
2024-09-10 14:37:22,549 - Finished running PEPPER-Margin-DeepVariant
2024-09-10 15:20:37,801 - Running chopper
2024-09-10 15:20:37,802 - Finished running chopper
2024-09-10 15:20:37,802 - Running MiniMap2
2024-09-10 15:20:37,802 - Finished running Minimap2
2024-09-10 15:20:37,802 - Running Samtools View
2024-09-10 15:20:37,802 - running command: samtools view -u -h -F 1 data/tests/alignments.sam | samtools sort - > data/tests/alignments.bam
2024-09-10 15:21:32,606 - Running chopper
2024-09-10 15:21:32,606 - Finished running chopper
2024-09-10 15:21:32,607 - Running MiniMap2
2024-09-10 15:21:32,607 - Finished running Minimap2
2024-09-10 15:21:32,607 - Running Samtools View
2024-09-10 15:21:32,607 - running command: samtools view -u -h -F 1 data/tests/alignments.sam | samtools sort - > data/tests/alignments.bam
2024-09-10 15:24:11,200 - Running chopper
2024-09-10 15:24:11,200 - Finished running chopper
2024-09-10 15:24:11,200 - Running MiniMap2
2024-09-10 15:24:11,200 - Finished running Minimap2
2024-09-10 15:24:11,200 - Running Samtools View
2024-09-10 15:24:11,200 - Finished running Samtools View
2024-09-10 15:24:11,200 - Running PEPPER-Margin-DeepVariant
2024-09-10 15:24:11,200 - running command: docker pull kishwars/pepper_deepvariant:r0.8
2024-09-10 15:24:11,201 - running command: docker run --ipc=host -v /home/giuli/Documents/NGPAT/data/tests:/data kishwars/pepper_deepvariant:r0.8 run_pepper_margin_deepvariant call_variant -b /data/alignments.bam -f /data/reference.fasta -o /data/variantcalls -t 1 --ont_r9_guppy5_sup
2024-09-10 15:24:11,201 - running command: gunzip -dk /variantcalls/PEPPER_MARGIN_DEEPVARIANT_FINAL_OUTPUT.vcf.gz > /home/giuli/Documents/NGPAT/data/tests
2024-09-10 15:24:11,204 - Finished running PEPPER-Margin-DeepVariant
2024-09-10 15:26:35,624 - Running chopper
2024-09-10 15:26:35,624 - Finished running chopper
2024-09-10 15:26:35,715 - Running MiniMap2
2024-09-10 15:26:35,715 - Finished running Minimap2
2024-09-10 15:26:35,715 - Running Samtools View
2024-09-10 15:26:35,716 - Finished running Samtools View
2024-09-10 15:26:35,716 - Running PEPPER-Margin-DeepVariant
2024-09-10 15:26:35,716 - running command: docker pull kishwars/pepper_deepvariant:r0.8
2024-09-10 15:26:35,716 - running command: docker run --ipc=host -v /home/giuli/Documents/NGPAT/data/tests:/data kishwars/pepper_deepvariant:r0.8 run_pepper_margin_deepvariant call_variant -b /data/alignments.bam -f /data/reference.fasta -o /data/variantcalls -t 1 --ont_r9_guppy5_sup
2024-09-10 15:26:35,716 - running command: gunzip -dk /home/giuli/Documents/NGPAT/data/tests/variantcalls/PEPPER_MARGIN_DEEPVARIANT_FINAL_OUTPUT.vcf.gz > data/tests/variants.vcf
2024-09-10 15:26:36,766 - Finished running PEPPER-Margin-DeepVariant
2024-09-10 15:29:27,696 - Running chopper
2024-09-10 15:29:27,696 - Finished running chopper
2024-09-10 15:29:27,696 - Running MiniMap2
2024-09-10 15:29:27,696 - Finished running Minimap2
2024-09-10 15:29:27,696 - Running Samtools View
2024-09-10 15:29:27,696 - Finished running Samtools View
2024-09-10 15:29:27,696 - Running PEPPER-Margin-DeepVariant
2024-09-10 15:29:27,696 - running command: docker pull kishwars/pepper_deepvariant:r0.8
2024-09-10 15:29:27,696 - running command: docker run --ipc=host -v /home/giuli/Documents/NGPAT/data/tests:/data kishwars/pepper_deepvariant:r0.8 run_pepper_margin_deepvariant call_variant -b /data/alignments.bam -f /data/reference.fasta -o /data/variantcalls -t 1 --ont_r9_guppy5_sup
2024-09-10 15:29:27,696 - running command: zcat /home/giuli/Documents/NGPAT/data/tests/variantcalls/PEPPER_MARGIN_DEEPVARIANT_FINAL_OUTPUT.vcf.gz > data/tests/variants.vcf
2024-09-10 15:29:28,966 - Finished running PEPPER-Margin-DeepVariant
2024-09-17 10:01:05,573 - Running chopper
2024-09-17 10:01:05,573 - Finished running chopper
2024-09-17 10:01:05,574 - Running MiniMap2
2024-09-17 10:01:05,574 - Finished running Minimap2
2024-09-17 10:01:05,574 - Running Samtools View
2024-09-17 10:01:05,574 - Finished running Samtools View
2024-09-17 10:01:05,574 - Running PEPPER-Margin-DeepVariant
2024-09-17 10:01:05,574 - running command: docker pull kishwars/pepper_deepvariant:r0.8
2024-09-17 10:01:05,574 - running command: docker run --ipc=host -v /home/giuli/Documents/NGPAT/data/tests:/data kishwars/pepper_deepvariant:r0.8 run_pepper_margin_deepvariant call_variant -b /data/alignments.bam -f /data/reference.fasta -o /data/variantcalls -t 1 --ont_r9_guppy5_sup
2024-09-17 10:02:04,358 - Running chopper
2024-09-17 10:02:04,358 - Finished running chopper
2024-09-17 10:02:04,358 - Running MiniMap2
2024-09-17 10:02:04,358 - Finished running Minimap2
2024-09-17 10:02:04,358 - Running Samtools View
2024-09-17 10:02:04,358 - Finished running Samtools View
2024-09-17 10:02:04,358 - Running PEPPER-Margin-DeepVariant
2024-09-17 10:02:04,358 - Finished running PEPPER-Margin-DeepVariant
2024-09-17 10:02:04,358 - Running VEP
2024-09-17 10:02:04,358 - running command: docker pull ensemblorg/ensembl-vep
2024-09-17 10:09:12,430 - Finished running VEP
2024-09-17 10:13:43,495 - Running chopper
2024-09-17 10:13:43,495 - Finished running chopper
2024-09-17 10:13:43,495 - Running MiniMap2
2024-09-17 10:13:43,495 - Finished running Minimap2
2024-09-17 10:13:43,496 - Running Samtools View
2024-09-17 10:13:43,496 - Finished running Samtools View
2024-09-17 10:13:43,496 - Running PEPPER-Margin-DeepVariant
2024-09-17 10:13:43,496 - Finished running PEPPER-Margin-DeepVariant
2024-09-17 10:13:43,496 - Running VEP
2024-09-17 10:13:43,496 - running command: docker pull ensemblorg/ensembl-vep
2024-09-17 10:13:45,964 - running command: docker run -t -i -v /home/giuli/Documents/NGPAT/data/tests/vep_cache:/data ensemblorg/ensembl-vep INSTALL.pl -a cf -s homo_sapiens -y GRCh38
2024-09-17 10:19:55,286 - running command: docker run -v /home/giuli/Documents/NGPAT/data/tests/vep_cache:/data ensemblorg/ensembl-vep vep --cache --offline --format vcf --vcf --force_overwrite --input_file /data/variants.vcf --output_file /data/annotations.vcf --plugin NMD
2024-09-17 10:20:00,207 - Finished running VEP
2024-09-17 10:24:19,540 - Running chopper
2024-09-17 10:24:19,541 - Finished running chopper
2024-09-17 10:24:19,541 - Running MiniMap2
2024-09-17 10:24:19,541 - Finished running Minimap2
2024-09-17 10:24:19,541 - Running Samtools View
2024-09-17 10:24:19,541 - Finished running Samtools View
2024-09-17 10:24:19,541 - Running PEPPER-Margin-DeepVariant
2024-09-17 10:24:19,541 - Finished running PEPPER-Margin-DeepVariant
2024-09-17 10:24:19,541 - Running VEP
2024-09-17 10:24:19,541 - running command: docker pull ensemblorg/ensembl-vep
2024-09-17 10:24:22,003 - running command: docker run -t -i -v /home/giuli/Documents/NGPAT/data/tests/vep_cache:/data ensemblorg/ensembl-vep INSTALL.pl -a cf -s homo_sapiens -y GRCh38
2024-09-17 10:30:28,753 - running command: docker run -v /home/giuli/Documents/NGPAT/data/tests/vep_cache:/data ensemblorg/ensembl-vep vep --cache --offline --format vcf --vcf --force_overwrite --input_file /data/variants.vcf --output_file /data/vep_data --plugin NMD
2024-09-17 10:30:30,582 - Finished running VEP
2024-09-17 10:32:11,139 - Running chopper
2024-09-17 10:32:11,139 - Finished running chopper
2024-09-17 10:32:11,139 - Running MiniMap2
2024-09-17 10:32:11,139 - Finished running Minimap2
2024-09-17 10:32:11,139 - Running Samtools View
2024-09-17 10:32:11,139 - Finished running Samtools View
2024-09-17 10:32:11,139 - Running PEPPER-Margin-DeepVariant
2024-09-17 10:32:11,139 - Finished running PEPPER-Margin-DeepVariant
2024-09-17 10:32:11,139 - Running VEP
2024-09-17 10:32:11,139 - running command: docker pull ensemblorg/ensembl-vep
2024-09-17 10:32:14,131 - running command: docker run -t -i -v /home/giuli/Documents/NGPAT/data/tests/vep_cache:/data ensemblorg/ensembl-vep INSTALL.pl -a cf -s homo_sapiens -y GRCh38
2024-09-17 10:38:20,981 - running command: docker run -v /home/giuli/Documents/NGPAT/data/tests/vep_cache:/data ensemblorg/ensembl-vep vep --cache --offline --format vcf --vcf --force_overwrite --input_file /data/variants.vcf --output_file /data/vep_data --plugin NMD
2024-09-17 10:38:23,750 - Finished running VEP
2024-09-17 11:31:31,780 - Running chopper
2024-09-17 11:31:31,780 - Finished running chopper
2024-09-17 11:31:31,780 - Running MiniMap2
2024-09-17 11:31:31,780 - Finished running Minimap2
2024-09-17 11:31:31,780 - Running Samtools View
2024-09-17 11:31:31,780 - Finished running Samtools View
2024-09-17 11:31:31,781 - Running PEPPER-Margin-DeepVariant
2024-09-17 11:31:31,781 - Finished running PEPPER-Margin-DeepVariant
2024-09-17 11:31:31,781 - Running cuteSV
2024-09-17 11:31:31,781 - running command: cuteSV data/tests/alignments.bam data/tests/reference.fasta data/tests/strucvar.vcf /home/giuli/Documents/NGPAT/data/tests
2024-09-17 11:31:33,078 - Finished running cuteSV
2024-09-17 11:31:33,078 - Running VEP
2024-09-17 11:31:33,078 - Finished running VEP
2024-09-17 11:44:44,475 - Running chopper
2024-09-17 11:44:44,475 - Finished running chopper
2024-09-17 11:44:44,475 - Running MiniMap2
2024-09-17 11:44:44,475 - Finished running Minimap2
2024-09-17 11:44:44,475 - Running Samtools View
2024-09-17 11:44:44,475 - Finished running Samtools View
2024-09-17 11:44:44,476 - Running PEPPER-Margin-DeepVariant
2024-09-17 11:44:44,476 - Finished running PEPPER-Margin-DeepVariant
2024-09-17 11:44:44,476 - Running cuteSV
2024-09-17 11:44:44,476 - running command: cuteSV data/tests/alignments.bam.gz data/tests/reference.fasta data/tests/strucvar.vcf /home/giuli/Documents/NGPAT/data/tests
2024-09-17 11:44:44,863 - Finished running cuteSV
2024-09-17 11:44:44,863 - Running VEP
2024-09-17 11:44:44,863 - Finished running VEP
2024-09-17 11:54:00,620 - Running chopper
2024-09-17 11:54:00,621 - Finished running chopper
2024-09-17 11:54:00,621 - Running MiniMap2
2024-09-17 11:54:00,621 - Finished running Minimap2
2024-09-17 11:54:00,621 - Running Samtools View
2024-09-17 11:54:00,621 - running command: samtools view data/tests/alignments.sam | samtools sort - > data/tests/alignments.bam
2024-09-17 11:54:00,926 - running command: samtools index data/tests/alignments.bam
2024-09-17 11:54:00,931 - Finished running Samtools View
2024-09-17 11:54:00,931 - Running PEPPER-Margin-DeepVariant
2024-09-17 11:54:00,931 - running command: docker pull kishwars/pepper_deepvariant:r0.8
2024-09-17 11:54:00,931 - running command: docker run --ipc=host -v /home/giuli/Documents/NGPAT/data/tests:/data kishwars/pepper_deepvariant:r0.8 run_pepper_margin_deepvariant call_variant -b /data/alignments.bam -f /data/reference.fasta -o /data/variantcalls -t 1 --ont_r9_guppy5_sup
2024-09-17 11:54:08,348 - running command: zcat /home/giuli/Documents/NGPAT/data/tests/variantcalls/PEPPER_MARGIN_DEEPVARIANT_FINAL_OUTPUT.vcf.gz > data/tests/variants.vcf
2024-09-17 11:54:09,295 - Finished running PEPPER-Margin-DeepVariant
2024-09-17 11:54:09,295 - Running cuteSV
2024-09-17 11:54:09,295 - running command: cuteSV data/tests/alignments.bam data/tests/reference.fasta data/tests/strucvar.vcf /home/giuli/Documents/NGPAT/data/tests
2024-09-17 11:54:09,690 - Finished running cuteSV
2024-09-17 11:54:09,690 - Running VEP
2024-09-17 11:54:09,690 - Finished running VEP
2024-09-17 11:55:57,175 - Running chopper
2024-09-17 11:55:57,175 - Finished running chopper
2024-09-17 11:55:57,175 - Running MiniMap2
2024-09-17 11:55:57,175 - running command: minimap2 -ax map-ont -t 1 data/tests/reference.fasta data/reads.fastq > data/tests/alignments.sam
2024-09-17 12:26:28,467 - Finished running Minimap2
2024-09-17 12:26:28,467 - Running Samtools View
2024-09-17 12:26:28,467 - running command: samtools view data/tests/alignments.sam | samtools sort - > data/tests/alignments.bam
2024-09-17 12:26:28,577 - running command: samtools index data/tests/alignments.bam
2024-09-17 12:26:28,584 - Finished running Samtools View
2024-09-17 12:51:32,337 - Running chopper
2024-09-17 12:51:32,337 - Finished running chopper
2024-09-17 12:51:32,337 - Running MiniMap2
2024-09-17 12:51:32,337 - running command: minimap2 -ax map-ont -t 1 data/tests/reference.fasta data/reads.fastq > data/tests/alignments.sam
2024-09-17 13:17:02,153 - Running chopper
2024-09-17 13:17:02,153 - Finished running chopper
2024-09-17 13:17:02,153 - Running MiniMap2
2024-09-17 13:17:02,153 - running command: minimap2 -ax map-ont -t 16 data/tests/reference.fasta data/reads.fastq > data/tests/alignments.sam
2024-09-17 13:21:23,155 - Finished running Minimap2
2024-09-17 13:21:23,155 - Running Samtools View
2024-09-17 13:21:23,156 - running command: samtools view -Sb data/tests/alignments.sam > data/tests/alignments.unsorted.bam
2024-09-17 13:22:32,418 - Finished running Samtools View
2024-09-17 13:22:32,418 - Running SamtoolsView Sort
2024-09-17 13:22:32,419 - running command: samtools sort -o data/tests/alignments.sorted.bam data/tests/alignments.unsorted.bam
2024-09-17 13:24:52,583 - running command: samtools index data/tests/alignments.sorted.bam
2024-09-17 13:25:04,147 - Finished running SamtoolsView Sort
2024-09-17 13:25:04,148 - Running PEPPER-Margin-DeepVariant
2024-09-17 13:25:04,148 - running command: docker pull kishwars/pepper_deepvariant:r0.8
2024-09-17 13:25:04,148 - running command: docker run --ipc=host -v /home/giuli/Documents/NGPAT/data/tests:/data kishwars/pepper_deepvariant:r0.8 run_pepper_margin_deepvariant call_variant -b /data/alignments.sorted.bam -f /data/reference.fasta -o /data/variantcalls -t 16 --ont_r9_guppy5_sup
2024-09-17 14:26:14,255 - running command: zcat /home/giuli/Documents/NGPAT/data/tests/variantcalls/PEPPER_MARGIN_DEEPVARIANT_FINAL_OUTPUT.vcf.gz > data/tests/variants.vcf
2024-09-17 14:26:14,849 - Finished running PEPPER-Margin-DeepVariant
2024-09-17 14:26:14,849 - Running cuteSV
2024-09-17 14:26:14,850 - running command: cuteSV data/tests/alignments.sorted.bam data/tests/reference.fasta data/tests/strucvar.vcf /home/giuli/Documents/NGPAT/data/tests
2024-09-17 14:26:29,133 - Finished running cuteSV
2024-09-17 14:26:29,133 - Running VEP
2024-09-17 14:26:29,133 - Finished running VEP
2024-11-14 11:51:37,284 - Running chopper
2024-11-14 11:51:37,343 - Finished running chopper
2024-11-14 11:51:37,343 - Running MiniMap2
2024-11-14 11:51:37,344 - Running VEP
2024-11-14 11:51:37,344 - running command: docker pull ensemblorg/ensembl-vep
2024-11-14 11:52:18,554 - running command: docker run -t -i -v /home/giuli/Documents/NGPAT/data/tests/vep_cache:/data ensemblorg/ensembl-vep INSTALL.pl -a cf -s homo_sapiens -y GRCh38
2024-11-14 11:52:18,555 - running command: docker run -v /home/giuli/Documents/NGPAT/data/tests/vep_cache:/data ensemblorg/ensembl-vep vep --cache --offline --format vcf --vcf --force_overwrite --input_file /data/variants.vcf --output_file /data/vep_data --plugin NMD
2024-11-14 11:52:29,732 - Finished running VEP
2024-11-14 12:02:16,084 - Running chopper
2024-11-14 12:02:16,084 - Finished running chopper
2024-11-14 12:02:16,085 - Running MiniMap2
2024-11-14 12:02:16,085 - Running VEP
2024-11-14 12:02:16,085 - running command: docker pull ensemblorg/ensembl-vep
2024-11-14 12:02:19,019 - running command: docker run -t -i -v /home/giuli/Documents/NGPAT/data/tests/vep_cache:/data -v /home/giuli/Documents/NGPAT/data/tests:/data_ngpat ensemblorg/ensembl-vep INSTALL.pl -a cf -s homo_sapiens -y GRCh38
2024-11-14 12:02:19,019 - running command: docker run -v /home/giuli/Documents/NGPAT/data/tests/vep_cache:/data -v /home/giuli/Documents/NGPAT/data/tests:/data_ngpat ensemblorg/ensembl-vep vep --cache --offline --format vcf --vcf --force_overwrite --input_file /data_ngpat/variants.vcf --output_file /data_ngpat/vep_data --plugin NMD
2024-11-14 12:02:22,038 - Finished running VEP
2024-11-14 12:04:20,527 - Running chopper
2024-11-14 12:04:20,527 - Finished running chopper
2024-11-14 12:04:20,527 - Running MiniMap2
2024-11-14 12:04:20,527 - Running VEP
2024-11-14 12:04:20,527 - running command: docker pull ensemblorg/ensembl-vep
2024-11-14 12:04:23,217 - running command: docker run -t -i -v /home/giuli/Documents/NGPAT/data/tests/vep_cache:/data -v /home/giuli/Documents/NGPAT/data/tests:/data_ngpat ensemblorg/ensembl-vep INSTALL.pl -a cf -s homo_sapiens -y GRCh38
2024-11-14 12:04:23,217 - running command: docker run -v /home/giuli/Documents/NGPAT/data/tests/vep_cache:/data -v /home/giuli/Documents/NGPAT/data/tests:/data_ngpat/ ensemblorg/ensembl-vep vep --cache --offline --format vcf --vcf --force_overwrite --input_file /data_ngpat/variants.vcf --output_file /data_ngpat/vep_data --plugin NMD
2024-11-14 12:04:23,217 - Finished running VEP
2024-11-14 12:35:13,498 - Running chopper
2024-11-14 12:35:13,498 - Finished running chopper
2024-11-14 12:35:13,498 - Running MiniMap2
2024-11-14 12:35:13,498 - Running VEP
2024-11-14 12:35:13,498 - running command: docker pull ensemblorg/ensembl-vep
2024-11-14 12:35:16,448 - running command: docker run -t -i -v /home/giuli/Documents/NGPAT/data/tests/vep_cache:/data -v /home/giuli/Documents/NGPAT/data/tests:/data_ngpat ensemblorg/ensembl-vep INSTALL.pl -a cf -s homo_sapiens -y GRCh38
2024-11-14 12:35:16,448 - running command: docker run -v /home/giuli/Documents/NGPAT/data/tests/vep_cache:/data -v /home/giuli/Documents/NGPAT/data/tests:/data_ngpat/ --ipc=host ensemblorg/ensembl-vep vep --cache --offline --format vcf --vcf --force_overwrite --input_file /data_ngpat/variants.vcf --output_file /data_ngpat/variants_vep.vcf --plugin NMD
2024-11-14 12:35:16,448 - Finished running VEP
2024-11-14 12:37:04,240 - Running chopper
2024-11-14 12:37:04,240 - Finished running chopper
2024-11-14 12:37:04,240 - Running MiniMap2
2024-11-14 12:37:04,240 - Running VEP
2024-11-14 12:37:04,240 - running command: docker pull ensemblorg/ensembl-vep
2024-11-14 12:37:07,838 - running command: docker run -t -i -v /home/giuli/Documents/NGPAT/data/tests/vep_cache:/data -v /home/giuli/Documents/NGPAT/data/tests:/data_ngpat ensemblorg/ensembl-vep INSTALL.pl -a cf -s homo_sapiens -y GRCh38
2024-11-14 12:37:07,838 - running command: docker run -v /home/giuli/Documents/NGPAT/data/tests/vep_cache:/data -v /home/giuli/Documents/NGPAT/data/tests:/data_ngpat/ --ipc=host ensemblorg/ensembl-vep vep --cache --offline --format vcf --vcf --force_overwrite --input_file /data_ngpat/variants.vcf --output_file /data_ngpat/variants_vep.vcf --plugin NMD
2024-11-14 12:50:58,408 - Finished running VEP
2025-03-20 10:59:02,916 - Running chopper
2025-03-20 10:59:02,919 - running command: chopper -i data/projects/1/reads.fastq > data/projects/1/reads.clean.fastq
2025-03-20 11:01:30,711 - Finished running chopper
2025-03-20 11:01:30,712 - Running MiniMap2
2025-03-20 11:01:30,712 - running command: minimap2 -ax map-ont -t 4 data/projects/1/reference.fasta data/projects/1/reads.fastq > data/projects/1/alignments.sam
2025-05-06 10:37:44,783 - Running FastP SE
2025-05-06 10:37:44,783 - Running FastP SE
2025-05-06 10:37:44,784 - running command: fastp -i data/rereadsillu.fastq -o data/testsillu/reads.clean.fastq
2025-05-06 10:37:44,784 - running command: fastp -i data/rereadsillu.fastq -o data/testsillu/reads.clean.fastq
2025-05-06 10:37:44,801 - Finished running FastP SE
2025-05-06 10:37:44,801 - Finished running FastP SE
2025-05-06 10:37:44,801 - Running BWA Single End
2025-05-06 10:37:44,801 - Running BWA Single End
2025-05-06 10:37:44,801 - running command: bwa index data/testsillu/reference.fasta
2025-05-06 10:37:44,801 - running command: bwa index data/testsillu/reference.fasta
2025-05-06 11:39:12,650 - running command: bwa mem data/testsillu/reference.fasta data/testsillu/reads.clean.fastq > data/testsillu/alignments.sam
2025-05-06 11:39:12,650 - running command: bwa mem data/testsillu/reference.fasta data/testsillu/reads.clean.fastq > data/testsillu/alignments.sam
2025-05-06 11:39:28,900 - Finished running BWA Single End
2025-05-06 11:39:28,900 - Finished running BWA Single End
2025-05-06 11:39:28,902 - Running Samtools View
2025-05-06 11:39:28,902 - Running Samtools View
2025-05-06 11:39:28,904 - running command: samtools view -Sb data/testsillu/alignments.sam > data/testsillu/alignments.unsorted.bam
2025-05-06 11:39:28,904 - running command: samtools view -Sb data/testsillu/alignments.sam > data/testsillu/alignments.unsorted.bam
2025-05-06 11:39:28,933 - Finished running Samtools View
2025-05-06 11:39:28,933 - Finished running Samtools View
2025-05-06 11:39:28,934 - Running SamtoolsView Sort
2025-05-06 11:39:28,934 - Running SamtoolsView Sort
2025-05-06 11:39:28,936 - running command: samtools sort -o data/testsillu/alignments.sorted.bam data/testsillu/alignments.unsorted.bam
2025-05-06 11:39:28,936 - running command: samtools sort -o data/testsillu/alignments.sorted.bam data/testsillu/alignments.unsorted.bam
2025-05-06 11:39:28,942 - running command: samtools index data/testsillu/alignments.sorted.bam
2025-05-06 11:39:28,942 - running command: samtools index data/testsillu/alignments.sorted.bam
2025-05-06 11:39:28,947 - Finished running SamtoolsView Sort
2025-05-06 11:39:28,947 - Finished running SamtoolsView Sort
2025-05-06 11:39:28,948 - Runninng Picard
2025-05-06 11:39:28,948 - Runninng Picard
2025-05-06 11:39:28,949 - running command: docker pull broadinstitute/picard
2025-05-06 11:39:28,949 - running command: docker pull broadinstitute/picard
2025-05-06 12:01:25,587 - Running FastP SE
2025-05-06 12:01:25,587 - Running FastP SE
2025-05-06 12:01:25,621 - running command: fastp -i data/rereadsillu.fastq -o data/testsillu/reads.clean.fastq
2025-05-06 12:01:25,621 - running command: fastp -i data/rereadsillu.fastq -o data/testsillu/reads.clean.fastq
2025-05-06 12:01:25,740 - Finished running FastP SE
2025-05-06 12:01:25,740 - Finished running FastP SE
2025-05-06 12:01:25,741 - Running BWA Single End
2025-05-06 12:01:25,741 - Running BWA Single End
2025-05-06 12:01:25,744 - running command: bwa index data/testsillu/reference.fasta
2025-05-06 12:01:25,744 - running command: bwa index data/testsillu/reference.fasta
2025-05-06 13:03:57,044 - running command: bwa mem data/testsillu/reference.fasta data/testsillu/reads.clean.fastq > data/testsillu/alignments.sam
2025-05-06 13:03:57,044 - running command: bwa mem data/testsillu/reference.fasta data/testsillu/reads.clean.fastq > data/testsillu/alignments.sam
2025-05-06 13:04:14,041 - Finished running BWA Single End
2025-05-06 13:04:14,041 - Finished running BWA Single End
2025-05-06 13:04:14,045 - Running Samtools View
2025-05-06 13:04:14,045 - Running Samtools View
2025-05-06 13:04:14,048 - running command: samtools view -Sb data/testsillu/alignments.sam > data/testsillu/alignments.unsorted.bam
2025-05-06 13:04:14,048 - running command: samtools view -Sb data/testsillu/alignments.sam > data/testsillu/alignments.unsorted.bam
2025-05-06 13:04:14,078 - Finished running Samtools View
2025-05-06 13:04:14,078 - Finished running Samtools View
2025-05-06 13:04:14,078 - Running SamtoolsView Sort
2025-05-06 13:04:14,078 - Running SamtoolsView Sort
2025-05-06 13:04:14,079 - running command: samtools sort -o data/testsillu/alignments.sorted.bam data/testsillu/alignments.unsorted.bam
2025-05-06 13:04:14,079 - running command: samtools sort -o data/testsillu/alignments.sorted.bam data/testsillu/alignments.unsorted.bam
2025-05-06 13:04:14,086 - running command: samtools index data/testsillu/alignments.sorted.bam
2025-05-06 13:04:14,086 - running command: samtools index data/testsillu/alignments.sorted.bam
2025-05-06 13:04:14,093 - Finished running SamtoolsView Sort
2025-05-06 13:04:14,093 - Finished running SamtoolsView Sort
2025-05-06 13:04:14,094 - Runninng Picard
2025-05-06 13:04:14,094 - Runninng Picard
2025-05-06 13:04:14,096 - running command: docker pull broadinstitute/picard
2025-05-06 13:04:14,096 - running command: docker pull broadinstitute/picard
2025-05-06 13:10:58,085 - Running FastP SE
2025-05-06 13:10:58,085 - Running FastP SE
2025-05-06 13:10:58,143 - running command: fastp -i data/rereadsillu.fastq -o data/testsillu/reads.clean.fastq
2025-05-06 13:10:58,143 - running command: fastp -i data/rereadsillu.fastq -o data/testsillu/reads.clean.fastq
2025-05-06 13:10:58,343 - Finished running FastP SE
2025-05-06 13:10:58,343 - Finished running FastP SE
2025-05-06 13:10:58,345 - Running BWA Single End
2025-05-06 13:10:58,345 - Running BWA Single End
2025-05-06 13:10:58,351 - running command: bwa index data/testsillu/reference.fasta
2025-05-06 13:10:58,351 - running command: bwa index data/testsillu/reference.fasta
2025-05-06 14:11:25,060 - running command: bwa mem data/testsillu/reference.fasta data/testsillu/reads.clean.fastq > data/testsillu/alignments.sam
2025-05-06 14:11:25,060 - running command: bwa mem data/testsillu/reference.fasta data/testsillu/reads.clean.fastq > data/testsillu/alignments.sam
2025-05-06 14:11:43,042 - Finished running BWA Single End
2025-05-06 14:11:43,042 - Finished running BWA Single End
2025-05-06 14:11:43,045 - Running Samtools View
2025-05-06 14:11:43,045 - Running Samtools View
2025-05-06 14:11:43,047 - running command: samtools view -Sb data/testsillu/alignments.sam > data/testsillu/alignments.unsorted.bam
2025-05-06 14:11:43,047 - running command: samtools view -Sb data/testsillu/alignments.sam > data/testsillu/alignments.unsorted.bam
2025-05-06 14:11:43,075 - Finished running Samtools View
2025-05-06 14:11:43,075 - Finished running Samtools View
2025-05-06 14:11:43,075 - Running SamtoolsView Sort
2025-05-06 14:11:43,075 - Running SamtoolsView Sort
2025-05-06 14:11:43,078 - running command: samtools sort -o data/testsillu/alignments.sorted.bam data/testsillu/alignments.unsorted.bam
2025-05-06 14:11:43,078 - running command: samtools sort -o data/testsillu/alignments.sorted.bam data/testsillu/alignments.unsorted.bam
2025-05-06 14:11:43,084 - running command: samtools index data/testsillu/alignments.sorted.bam
2025-05-06 14:11:43,084 - running command: samtools index data/testsillu/alignments.sorted.bam
2025-05-06 14:11:43,089 - Finished running SamtoolsView Sort
2025-05-06 14:11:43,089 - Finished running SamtoolsView Sort
2025-05-06 14:11:43,089 - Runninng Picard
2025-05-06 14:11:43,089 - Runninng Picard
2025-05-06 14:11:43,090 - running command: docker pull broadinstitute/picard
2025-05-06 14:11:43,090 - running command: docker pull broadinstitute/picard
2025-05-06 14:11:43,094 - running command: docker run -v /home/giuli/NGPAT/data/testsillu:/data broadinstitute/picard:latest java -jar picard.jar MarkDuplicates REMOVE_DUPLICATES=trueI=alignments.sorted.bam O=alignments.nodups.bam M=marked_dup_metric.txt
2025-05-06 14:11:43,094 - running command: docker run -v /home/giuli/NGPAT/data/testsillu:/data broadinstitute/picard:latest java -jar picard.jar MarkDuplicates REMOVE_DUPLICATES=trueI=alignments.sorted.bam O=alignments.nodups.bam M=marked_dup_metric.txt
2025-05-07 09:46:26,168 - Running FastP SE
2025-05-07 09:46:26,168 - Running FastP SE
2025-05-07 09:46:26,372 - running command: fastp -i data/rereadsillu.fastq -o data/testsillu/reads.clean.fastq
2025-05-07 09:46:26,372 - running command: fastp -i data/rereadsillu.fastq -o data/testsillu/reads.clean.fastq
2025-05-07 09:46:26,726 - Finished running FastP SE
2025-05-07 09:46:26,726 - Finished running FastP SE
2025-05-07 09:46:26,735 - Running BWA Single End
2025-05-07 09:46:26,735 - Running BWA Single End
2025-05-07 09:46:26,741 - running command: bwa index data/testsillu/reference.fasta
2025-05-07 09:46:26,741 - running command: bwa index data/testsillu/reference.fasta
2025-05-07 09:53:43,445 - Running FastP SE
2025-05-07 09:53:43,445 - Running FastP SE
2025-05-07 09:53:43,483 - running command: fastp -i data/readsillu.fastq -o data/testsillu/reads.clean.fastq
2025-05-07 09:53:43,483 - running command: fastp -i data/readsillu.fastq -o data/testsillu/reads.clean.fastq
2025-05-07 09:55:52,860 - Finished running FastP SE
2025-05-07 09:55:52,860 - Finished running FastP SE
2025-05-07 09:55:52,866 - Running BWA Single End
2025-05-07 09:55:52,866 - Running BWA Single End
2025-05-07 09:55:52,866 - running command: bwa index data/testsillu/reference.fasta
2025-05-07 09:55:52,866 - running command: bwa index data/testsillu/reference.fasta
2025-05-07 10:57:32,759 - running command: bwa mem data/testsillu/reference.fasta data/testsillu/reads.clean.fastq > data/testsillu/alignments.sam
2025-05-07 10:57:32,759 - running command: bwa mem data/testsillu/reference.fasta data/testsillu/reads.clean.fastq > data/testsillu/alignments.sam
2025-05-07 12:08:46,748 - Finished running BWA Single End
2025-05-07 12:08:46,748 - Finished running BWA Single End
2025-05-07 12:08:46,787 - Running Samtools View
2025-05-07 12:08:46,787 - Running Samtools View
2025-05-07 12:08:46,790 - running command: samtools view -Sb data/testsillu/alignments.sam > data/testsillu/alignments.unsorted.bam
2025-05-07 12:08:46,790 - running command: samtools view -Sb data/testsillu/alignments.sam > data/testsillu/alignments.unsorted.bam
2025-05-07 12:09:39,373 - Finished running Samtools View
2025-05-07 12:09:39,373 - Finished running Samtools View
2025-05-07 12:09:39,375 - Running SamtoolsView Sort
2025-05-07 12:09:39,375 - Running SamtoolsView Sort
2025-05-07 12:09:39,380 - running command: samtools sort -o data/testsillu/alignments.sorted.bam data/testsillu/alignments.unsorted.bam
2025-05-07 12:09:39,380 - running command: samtools sort -o data/testsillu/alignments.sorted.bam data/testsillu/alignments.unsorted.bam
2025-05-07 12:10:56,865 - running command: samtools index data/testsillu/alignments.sorted.bam
2025-05-07 12:10:56,865 - running command: samtools index data/testsillu/alignments.sorted.bam
2025-05-07 12:11:01,695 - Finished running SamtoolsView Sort
2025-05-07 12:11:01,695 - Finished running SamtoolsView Sort
2025-05-07 12:11:01,697 - Runninng Picard
2025-05-07 12:11:01,697 - Runninng Picard
2025-05-07 12:11:01,700 - running command: docker pull broadinstitute/picard
2025-05-07 12:11:01,700 - running command: docker pull broadinstitute/picard
2025-05-07 12:11:01,704 - running command: docker run -v /home/giuli/NGPAT/data/testsillu:/data broadinstitute/picard:latest java -jar picard.jar MarkDuplicates REMOVE_DUPLICATES=trueI=alignments.sorted.bam O=alignments.nodups.bam M=marked_dup_metric.txt
2025-05-07 12:11:01,704 - running command: docker run -v /home/giuli/NGPAT/data/testsillu:/data broadinstitute/picard:latest java -jar picard.jar MarkDuplicates REMOVE_DUPLICATES=trueI=alignments.sorted.bam O=alignments.nodups.bam M=marked_dup_metric.txt
2025-05-07 12:54:52,925 - Finished running Picard
2025-05-07 12:54:52,925 - Finished running Picard
2025-05-07 12:54:52,926 - Running GATK HaplotypeCaller
2025-05-07 12:54:52,926 - Running GATK HaplotypeCaller
2025-05-07 12:54:52,927 - running command: gatk HaplotypeCaller -R data/testsillu/reference.fasta -I data/testsillu/alignments.nodups.bam -O data/testsillu/variants.vcf
2025-05-07 12:54:52,927 - running command: gatk HaplotypeCaller -R data/testsillu/reference.fasta -I data/testsillu/alignments.nodups.bam -O data/testsillu/variants.vcf
2025-05-07 12:54:52,932 - Finished running GATK HaplotypeCaller
2025-05-07 12:54:52,932 - Finished running GATK HaplotypeCaller
2025-05-07 12:54:52,933 - Running Gridss
2025-05-07 12:54:52,933 - Running Gridss
2025-05-07 12:54:52,934 - running command: docker pull gridss/gridss:latest
2025-05-07 12:54:52,934 - running command: docker pull gridss/gridss:latest
2025-05-07 12:54:52,935 - running command: docker run -v /home/giuli/NGPAT/data/testsillu:/data gridss/gridss:latest grids -r reference.fasta -j gridss-2.X.Y-gridss-jar-with-dependencies.jar -o strucvar.vcf alignments.nodups.bam
2025-05-07 12:54:52,935 - running command: docker run -v /home/giuli/NGPAT/data/testsillu:/data gridss/gridss:latest grids -r reference.fasta -j gridss-2.X.Y-gridss-jar-with-dependencies.jar -o strucvar.vcf alignments.nodups.bam
2025-05-07 15:10:00,954 - Finished running Gridss
2025-05-07 15:10:00,954 - Finished running Gridss
2025-05-07 15:10:00,955 - Running VEP
2025-05-07 15:10:00,955 - Running VEP
2025-05-07 15:10:00,957 - running command: docker pull ensemblorg/ensembl-vep
2025-05-07 15:10:00,957 - running command: docker pull ensemblorg/ensembl-vep