hap.py
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20 hours ago •
Illumina
Illumina
ERROR preprocess: vcf.c:3472: bcf_update_format: Assertion `!fmt->p_free' failed.
I can't get rid of this:
root@86876e01e030:/outputs# /opt/hap.py/bin/hap.py --threads $(nproc) --gender auto --reference /outputs/ref/human_g1k_v37/human_g1k_v37.fasta --false-positives /outputs/precFDA/challenge4-fullset.bed --report-prefix /outputs/test012_07_NovoalignGATKHC_1_src /outputs/precFDA/challenge4-fullset.vcf.gz /outputs/precFDA/challenge_results/NovoalignGATKHC_1.vcf.gz
2019-09-10 15:26:22,969 WARNING No reference file found at default locations. You can set the environment variable 'HGREF' or 'HG19' to point to a suitable Fasta file.
2019-09-10 15:26:22,971 WARNING No reference file found at default locations. You can set the environment variable 'HGREF' or 'HG19' to point to a suitable Fasta file.
[I] Total VCF records: 3775169
[I] Non-reference VCF records: 3775169
[W] overlapping records at 1:174769081 for sample 1
[W] Variants that overlap on the reference allele: 5
[I] Total VCF records: 3806019
[I] Non-reference VCF records: 3806019
2019-09-10 15:29:26,126 ERROR Preprocess command preprocess /tmp/tmpxX3Rhw.vcf.gz:* -l 11:108967048-113135716 -o /tmp/input.11:108967048-113135716vF5dc8.prep.vcf.gz -V 1 -L 1 -r /outputs/ref/human_g1k_v37/human_g1k_v37.fasta failed. Outputs are here /tmp/stdout9S5jwA.log / /tmp/stderrbk5UHs.log
2019-09-10 15:29:26,127 ERROR preprocess: vcf.c:3472: bcf_update_format: Assertion `!fmt->p_free' failed.
2019-09-10 15:29:26,128 ERROR Aborted (core dumped)
2019-09-10 15:29:26,128 ERROR Exception when running <function preprocessWrapper at 0x7f35bab28140>:
2019-09-10 15:29:26,128 ERROR ------------------------------------------------------------
2019-09-10 15:29:26,129 ERROR Traceback (most recent call last):
2019-09-10 15:29:26,129 ERROR File "/opt/hap.py/lib/python27/Tools/parallel.py", line 72, in parMapper
2019-09-10 15:29:26,130 ERROR return arg[1]['fun'](arg[0], *arg[1]['args'], **arg[1]['kwargs'])
2019-09-10 15:29:26,130 ERROR File "/opt/hap.py/lib/python27/Haplo/partialcredit.py", line 67, in preprocessWrapper
2019-09-10 15:29:26,131 ERROR subprocess.check_call(to_run, shell=True, stdout=tfo, stderr=tfe)
2019-09-10 15:29:26,131 ERROR File "/usr/lib/python2.7/subprocess.py", line 541, in check_call
2019-09-10 15:29:26,132 ERROR raise CalledProcessError(retcode, cmd)
2019-09-10 15:29:26,132 ERROR CalledProcessError: Command 'preprocess /tmp/tmpxX3Rhw.vcf.gz:* -l 11:108967048-113135716 -o /tmp/input.11:108967048-113135716vF5dc8.prep.vcf.gz -V 1 -L 1 -r /outputs/ref/human_g1k_v37/human_g1k_v37.fasta' returned non-zero exit status 134
2019-09-10 15:29:26,133 ERROR ------------------------------------------------------------
2019-09-10 15:29:27,655 ERROR Preprocess command preprocess /tmp/tmpxX3Rhw.vcf.gz:* -l 11:1-3276637 -o /tmp/input.11:1-3276637rsaKGx.prep.vcf.gz -V 1 -L 1 -r /outputs/ref/human_g1k_v37/human_g1k_v37.fasta failed. Outputs are here /tmp/stdoutsQED2h.log / /tmp/stderrQsZnXG.log
2019-09-10 15:29:27,656 ERROR preprocess: vcf.c:3472: bcf_update_format: Assertion `!fmt->p_free' failed.
2019-09-10 15:29:27,657 ERROR Aborted (core dumped)
2019-09-10 15:29:27,658 ERROR Exception when running <function preprocessWrapper at 0x7f35bab28140>:
2019-09-10 15:29:27,658 ERROR ------------------------------------------------------------
2019-09-10 15:29:27,659 ERROR Traceback (most recent call last):
2019-09-10 15:29:27,659 ERROR File "/opt/hap.py/lib/python27/Tools/parallel.py", line 72, in parMapper
2019-09-10 15:29:27,660 ERROR return arg[1]['fun'](arg[0], *arg[1]['args'], **arg[1]['kwargs'])
2019-09-10 15:29:27,661 ERROR File "/opt/hap.py/lib/python27/Haplo/partialcredit.py", line 67, in preprocessWrapper
2019-09-10 15:29:27,661 ERROR subprocess.check_call(to_run, shell=True, stdout=tfo, stderr=tfe)
2019-09-10 15:29:27,662 ERROR File "/usr/lib/python2.7/subprocess.py", line 541, in check_call
2019-09-10 15:29:27,663 ERROR raise CalledProcessError(retcode, cmd)
2019-09-10 15:29:27,663 ERROR CalledProcessError: Command 'preprocess /tmp/tmpxX3Rhw.vcf.gz:* -l 11:1-3276637 -o /tmp/input.11:1-3276637rsaKGx.prep.vcf.gz -V 1 -L 1 -r /outputs/ref/human_g1k_v37/human_g1k_v37.fasta' returned non-zero exit status 134
2019-09-10 15:29:27,664 ERROR ------------------------------------------------------------
2019-09-10 15:29:28,683 ERROR Preprocess command preprocess /tmp/tmpxX3Rhw.vcf.gz:* -l 11:58779876-63175827 -o /tmp/input.11:58779876-63175827BdYbzZ.prep.vcf.gz -V 1 -L 1 -r /outputs/ref/human_g1k_v37/human_g1k_v37.fasta failed. Outputs are here /tmp/stdoutRAtLlb.log / /tmp/stderre8hq0m.log
2019-09-10 15:29:28,684 ERROR preprocess: vcf.c:3472: bcf_update_format: Assertion `!fmt->p_free' failed.
2019-09-10 15:29:28,684 ERROR Aborted (core dumped)
2019-09-10 15:29:28,684 ERROR Exception when running <function preprocessWrapper at 0x7f35bab28140>:
2019-09-10 15:29:28,684 ERROR ------------------------------------------------------------
2019-09-10 15:29:28,684 ERROR Traceback (most recent call last):
2019-09-10 15:29:28,684 ERROR File "/opt/hap.py/lib/python27/Tools/parallel.py", line 72, in parMapper
2019-09-10 15:29:28,684 ERROR return arg[1]['fun'](arg[0], *arg[1]['args'], **arg[1]['kwargs'])
2019-09-10 15:29:28,685 ERROR File "/opt/hap.py/lib/python27/Haplo/partialcredit.py", line 67, in preprocessWrapper
2019-09-10 15:29:28,685 ERROR subprocess.check_call(to_run, shell=True, stdout=tfo, stderr=tfe)
2019-09-10 15:29:28,685 ERROR File "/usr/lib/python2.7/subprocess.py", line 541, in check_call
2019-09-10 15:29:28,686 ERROR raise CalledProcessError(retcode, cmd)
2019-09-10 15:29:28,686 ERROR CalledProcessError: Command 'preprocess /tmp/tmpxX3Rhw.vcf.gz:* -l 11:58779876-63175827 -o /tmp/input.11:58779876-63175827BdYbzZ.prep.vcf.gz -V 1 -L 1 -r /outputs/ref/human_g1k_v37/human_g1k_v37.fasta' returned non-zero exit status 134
2019-09-10 15:29:28,686 ERROR ------------------------------------------------------------
2019-09-10 15:29:35,427 ERROR Preprocess command preprocess /tmp/tmpxX3Rhw.vcf.gz:* -l 11:82545964-86758629 -o /tmp/input.11:82545964-86758629ZxuNke.prep.vcf.gz -V 1 -L 1 -r /outputs/ref/human_g1k_v37/human_g1k_v37.fasta failed. Outputs are here /tmp/stdoutU0SVZQ.log / /tmp/stderrM5Kkhn.log
2019-09-10 15:29:35,427 ERROR preprocess: vcf.c:3472: bcf_update_format: Assertion `!fmt->p_free' failed.
2019-09-10 15:29:35,428 ERROR Aborted (core dumped)
2019-09-10 15:29:35,428 ERROR Exception when running <function preprocessWrapper at 0x7f35bab28140>:
2019-09-10 15:29:35,428 ERROR ------------------------------------------------------------
2019-09-10 15:29:35,428 ERROR Traceback (most recent call last):
2019-09-10 15:29:35,428 ERROR File "/opt/hap.py/lib/python27/Tools/parallel.py", line 72, in parMapper
2019-09-10 15:29:35,428 ERROR return arg[1]['fun'](arg[0], *arg[1]['args'], **arg[1]['kwargs'])
2019-09-10 15:29:35,428 ERROR File "/opt/hap.py/lib/python27/Haplo/partialcredit.py", line 67, in preprocessWrapper
2019-09-10 15:29:35,428 ERROR subprocess.check_call(to_run, shell=True, stdout=tfo, stderr=tfe)
2019-09-10 15:29:35,428 ERROR File "/usr/lib/python2.7/subprocess.py", line 541, in check_call
2019-09-10 15:29:35,428 ERROR raise CalledProcessError(retcode, cmd)
2019-09-10 15:29:35,428 ERROR CalledProcessError: Command 'preprocess /tmp/tmpxX3Rhw.vcf.gz:* -l 11:82545964-86758629 -o /tmp/input.11:82545964-86758629ZxuNke.prep.vcf.gz -V 1 -L 1 -r /outputs/ref/human_g1k_v37/human_g1k_v37.fasta' returned non-zero exit status 134
2019-09-10 15:29:35,428 ERROR ------------------------------------------------------------
2019-09-10 15:29:39,639 ERROR Preprocess command preprocess /tmp/tmpxX3Rhw.vcf.gz:* -l 14:33500303-35755642 -o /tmp/input.14:33500303-35755642EoFLxK.prep.vcf.gz -V 1 -L 1 -r /outputs/ref/human_g1k_v37/human_g1k_v37.fasta failed. Outputs are here /tmp/stdoutvORDME.log / /tmp/stderrx6ZThu.log
2019-09-10 15:29:39,639 ERROR preprocess: vcf.c:3472: bcf_update_format: Assertion `!fmt->p_free' failed.
2019-09-10 15:29:39,639 ERROR Aborted (core dumped)
2019-09-10 15:29:39,639 ERROR Exception when running <function preprocessWrapper at 0x7f35bab28140>:
2019-09-10 15:29:39,640 ERROR ------------------------------------------------------------
2019-09-10 15:29:39,640 ERROR Traceback (most recent call last):
2019-09-10 15:29:39,640 ERROR File "/opt/hap.py/lib/python27/Tools/parallel.py", line 72, in parMapper
2019-09-10 15:29:39,640 ERROR return arg[1]['fun'](arg[0], *arg[1]['args'], **arg[1]['kwargs'])
2019-09-10 15:29:39,640 ERROR File "/opt/hap.py/lib/python27/Haplo/partialcredit.py", line 67, in preprocessWrapper
2019-09-10 15:29:39,640 ERROR subprocess.check_call(to_run, shell=True, stdout=tfo, stderr=tfe)
2019-09-10 15:29:39,641 ERROR File "/usr/lib/python2.7/subprocess.py", line 541, in check_call
2019-09-10 15:29:39,642 ERROR raise CalledProcessError(retcode, cmd)
2019-09-10 15:29:39,642 ERROR CalledProcessError: Command 'preprocess /tmp/tmpxX3Rhw.vcf.gz:* -l 14:33500303-35755642 -o /tmp/input.14:33500303-35755642EoFLxK.prep.vcf.gz -V 1 -L 1 -r /outputs/ref/human_g1k_v37/human_g1k_v37.fasta' returned non-zero exit status 134
2019-09-10 15:29:39,642 ERROR ------------------------------------------------------------
2019-09-10 15:29:41,921 ERROR Preprocess command preprocess /tmp/tmpxX3Rhw.vcf.gz:* -l 10:72802430-78655067 -o /tmp/input.10:72802430-7865506718FRzq.prep.vcf.gz -V 1 -L 1 -r /outputs/ref/human_g1k_v37/human_g1k_v37.fasta failed. Outputs are here /tmp/stdout6Re9HN.log / /tmp/stderrKm1Csb.log
2019-09-10 15:29:41,922 ERROR preprocess: vcf.c:3472: bcf_update_format: Assertion `!fmt->p_free' failed.
2019-09-10 15:29:41,922 ERROR Aborted (core dumped)
2019-09-10 15:29:41,922 ERROR Exception when running <function preprocessWrapper at 0x7f35bab28140>:
2019-09-10 15:29:41,922 ERROR ------------------------------------------------------------
2019-09-10 15:29:41,922 ERROR Traceback (most recent call last):
2019-09-10 15:29:41,922 ERROR File "/opt/hap.py/lib/python27/Tools/parallel.py", line 72, in parMapper
2019-09-10 15:29:41,922 ERROR return arg[1]['fun'](arg[0], *arg[1]['args'], **arg[1]['kwargs'])
2019-09-10 15:29:41,922 ERROR File "/opt/hap.py/lib/python27/Haplo/partialcredit.py", line 67, in preprocessWrapper
2019-09-10 15:29:41,922 ERROR subprocess.check_call(to_run, shell=True, stdout=tfo, stderr=tfe)
2019-09-10 15:29:41,922 ERROR File "/usr/lib/python2.7/subprocess.py", line 541, in check_call
2019-09-10 15:29:41,923 ERROR raise CalledProcessError(retcode, cmd)
2019-09-10 15:29:41,923 ERROR CalledProcessError: Command 'preprocess /tmp/tmpxX3Rhw.vcf.gz:* -l 10:72802430-78655067 -o /tmp/input.10:72802430-7865506718FRzq.prep.vcf.gz -V 1 -L 1 -r /outputs/ref/human_g1k_v37/human_g1k_v37.fasta' returned non-zero exit status 134
2019-09-10 15:29:41,923 ERROR ------------------------------------------------------------
2019-09-10 15:29:45,156 ERROR Preprocess command preprocess /tmp/tmpxX3Rhw.vcf.gz:* -l 16:1-2098417 -o /tmp/input.16:1-2098417hbEOn2.prep.vcf.gz -V 1 -L 1 -r /outputs/ref/human_g1k_v37/human_g1k_v37.fasta failed. Outputs are here /tmp/stdoutbWYari.log / /tmp/stderrRuh18k.log
2019-09-10 15:29:45,160 ERROR preprocess: vcf.c:3472: bcf_update_format: Assertion `!fmt->p_free' failed.
2019-09-10 15:29:45,160 ERROR Aborted (core dumped)
2019-09-10 15:29:45,161 ERROR Exception when running <function preprocessWrapper at 0x7f35bab28140>:
2019-09-10 15:29:45,161 ERROR ------------------------------------------------------------
2019-09-10 15:29:45,161 ERROR Traceback (most recent call last):
2019-09-10 15:29:45,161 ERROR File "/opt/hap.py/lib/python27/Tools/parallel.py", line 72, in parMapper
2019-09-10 15:29:45,162 ERROR return arg[1]['fun'](arg[0], *arg[1]['args'], **arg[1]['kwargs'])
2019-09-10 15:29:45,162 ERROR File "/opt/hap.py/lib/python27/Haplo/partialcredit.py", line 67, in preprocessWrapper
2019-09-10 15:29:45,162 ERROR subprocess.check_call(to_run, shell=True, stdout=tfo, stderr=tfe)
2019-09-10 15:29:45,162 ERROR File "/usr/lib/python2.7/subprocess.py", line 541, in check_call
2019-09-10 15:29:45,162 ERROR raise CalledProcessError(retcode, cmd)
2019-09-10 15:29:45,163 ERROR CalledProcessError: Command 'preprocess /tmp/tmpxX3Rhw.vcf.gz:* -l 16:1-2098417 -o /tmp/input.16:1-2098417hbEOn2.prep.vcf.gz -V 1 -L 1 -r /outputs/ref/human_g1k_v37/human_g1k_v37.fasta' returned non-zero exit status 134
2019-09-10 15:29:45,163 ERROR ------------------------------------------------------------
2019-09-10 15:29:46,915 ERROR Preprocess command preprocess /tmp/tmpxX3Rhw.vcf.gz:* -l 17:66090351-67974619 -o /tmp/input.17:66090351-67974619teIX1z.prep.vcf.gz -V 1 -L 1 -r /outputs/ref/human_g1k_v37/human_g1k_v37.fasta failed. Outputs are here /tmp/stdoutZn5fVY.log / /tmp/stderrTCGTvy.log
2019-09-10 15:29:46,916 ERROR preprocess: vcf.c:3472: bcf_update_format: Assertion `!fmt->p_free' failed.
2019-09-10 15:29:46,916 ERROR Aborted (core dumped)
2019-09-10 15:29:46,916 ERROR Exception when running <function preprocessWrapper at 0x7f35bab28140>:
2019-09-10 15:29:46,917 ERROR ------------------------------------------------------------
2019-09-10 15:29:46,917 ERROR Traceback (most recent call last):
2019-09-10 15:29:46,917 ERROR File "/opt/hap.py/lib/python27/Tools/parallel.py", line 72, in parMapper
2019-09-10 15:29:46,917 ERROR return arg[1]['fun'](arg[0], *arg[1]['args'], **arg[1]['kwargs'])
2019-09-10 15:29:46,917 ERROR File "/opt/hap.py/lib/python27/Haplo/partialcredit.py", line 67, in preprocessWrapper
2019-09-10 15:29:46,918 ERROR subprocess.check_call(to_run, shell=True, stdout=tfo, stderr=tfe)
2019-09-10 15:29:46,918 ERROR File "/usr/lib/python2.7/subprocess.py", line 541, in check_call
2019-09-10 15:29:46,918 ERROR raise CalledProcessError(retcode, cmd)
2019-09-10 15:29:46,919 ERROR CalledProcessError: Command 'preprocess /tmp/tmpxX3Rhw.vcf.gz:* -l 17:66090351-67974619 -o /tmp/input.17:66090351-67974619teIX1z.prep.vcf.gz -V 1 -L 1 -r /outputs/ref/human_g1k_v37/human_g1k_v37.fasta' returned non-zero exit status 134
2019-09-10 15:29:46,919 ERROR ------------------------------------------------------------
2019-09-10 15:30:01,823 ERROR Preprocess command preprocess /tmp/tmpxX3Rhw.vcf.gz:* -l 3:130994975-135491782 -o /tmp/input.3:130994975-1354917820FkeoI.prep.vcf.gz -V 1 -L 1 -r /outputs/ref/human_g1k_v37/human_g1k_v37.fasta failed. Outputs are here /tmp/stdout_ZR1n9.log / /tmp/stderrd8oeMY.log
2019-09-10 15:30:01,824 ERROR preprocess: vcf.c:3472: bcf_update_format: Assertion `!fmt->p_free' failed.
2019-09-10 15:30:01,825 ERROR Aborted (core dumped)
2019-09-10 15:30:01,825 ERROR Exception when running <function preprocessWrapper at 0x7f35bab28140>:
2019-09-10 15:30:01,825 ERROR ------------------------------------------------------------
2019-09-10 15:30:01,826 ERROR Traceback (most recent call last):
2019-09-10 15:30:01,826 ERROR File "/opt/hap.py/lib/python27/Tools/parallel.py", line 72, in parMapper
2019-09-10 15:30:01,827 ERROR return arg[1]['fun'](arg[0], *arg[1]['args'], **arg[1]['kwargs'])
2019-09-10 15:30:01,827 ERROR File "/opt/hap.py/lib/python27/Haplo/partialcredit.py", line 67, in preprocessWrapper
2019-09-10 15:30:01,828 ERROR subprocess.check_call(to_run, shell=True, stdout=tfo, stderr=tfe)
2019-09-10 15:30:01,828 ERROR File "/usr/lib/python2.7/subprocess.py", line 541, in check_call
2019-09-10 15:30:01,828 ERROR raise CalledProcessError(retcode, cmd)
2019-09-10 15:30:01,829 ERROR CalledProcessError: Command 'preprocess /tmp/tmpxX3Rhw.vcf.gz:* -l 3:130994975-135491782 -o /tmp/input.3:130994975-1354917820FkeoI.prep.vcf.gz -V 1 -L 1 -r /outputs/ref/human_g1k_v37/human_g1k_v37.fasta' returned non-zero exit status 134
2019-09-10 15:30:01,829 ERROR ------------------------------------------------------------
2019-09-10 15:30:07,729 ERROR Preprocess command preprocess /tmp/tmpxX3Rhw.vcf.gz:* -l 21:35624759-37021956 -o /tmp/input.21:35624759-37021956oLRvHY.prep.vcf.gz -V 1 -L 1 -r /outputs/ref/human_g1k_v37/human_g1k_v37.fasta failed. Outputs are here /tmp/stdoutmCBtYP.log / /tmp/stderr8iCZbH.log
2019-09-10 15:30:07,729 ERROR preprocess: vcf.c:3472: bcf_update_format: Assertion `!fmt->p_free' failed.
2019-09-10 15:30:07,730 ERROR Aborted (core dumped)
2019-09-10 15:30:07,730 ERROR Exception when running <function preprocessWrapper at 0x7f35bab28140>:
2019-09-10 15:30:07,730 ERROR ------------------------------------------------------------
2019-09-10 15:30:07,730 ERROR Traceback (most recent call last):
2019-09-10 15:30:07,730 ERROR File "/opt/hap.py/lib/python27/Tools/parallel.py", line 72, in parMapper
2019-09-10 15:30:07,730 ERROR return arg[1]['fun'](arg[0], *arg[1]['args'], **arg[1]['kwargs'])
2019-09-10 15:30:07,730 ERROR File "/opt/hap.py/lib/python27/Haplo/partialcredit.py", line 67, in preprocessWrapper
2019-09-10 15:30:07,730 ERROR subprocess.check_call(to_run, shell=True, stdout=tfo, stderr=tfe)
2019-09-10 15:30:07,731 ERROR File "/usr/lib/python2.7/subprocess.py", line 541, in check_call
2019-09-10 15:30:07,731 ERROR raise CalledProcessError(retcode, cmd)
2019-09-10 15:30:07,731 ERROR CalledProcessError: Command 'preprocess /tmp/tmpxX3Rhw.vcf.gz:* -l 21:35624759-37021956 -o /tmp/input.21:35624759-37021956oLRvHY.prep.vcf.gz -V 1 -L 1 -r /outputs/ref/human_g1k_v37/human_g1k_v37.fasta' returned non-zero exit status 134
2019-09-10 15:30:07,731 ERROR ------------------------------------------------------------
2019-09-10 15:30:08,911 ERROR Preprocess command preprocess /tmp/tmpxX3Rhw.vcf.gz:* -l 3:10807132-16504983 -o /tmp/input.3:10807132-165049833EYGvH.prep.vcf.gz -V 1 -L 1 -r /outputs/ref/human_g1k_v37/human_g1k_v37.fasta failed. Outputs are here /tmp/stdoutswnASQ.log / /tmp/stderrHUZfQc.log
2019-09-10 15:30:08,911 ERROR preprocess: vcf.c:3472: bcf_update_format: Assertion `!fmt->p_free' failed.
2019-09-10 15:30:08,911 ERROR Aborted (core dumped)
2019-09-10 15:30:08,911 ERROR Exception when running <function preprocessWrapper at 0x7f35bab28140>:
2019-09-10 15:30:08,912 ERROR ------------------------------------------------------------
2019-09-10 15:30:08,912 ERROR Traceback (most recent call last):
2019-09-10 15:30:08,912 ERROR File "/opt/hap.py/lib/python27/Tools/parallel.py", line 72, in parMapper
2019-09-10 15:30:08,912 ERROR return arg[1]['fun'](arg[0], *arg[1]['args'], **arg[1]['kwargs'])
2019-09-10 15:30:08,912 ERROR File "/opt/hap.py/lib/python27/Haplo/partialcredit.py", line 67, in preprocessWrapper
2019-09-10 15:30:08,912 ERROR subprocess.check_call(to_run, shell=True, stdout=tfo, stderr=tfe)
2019-09-10 15:30:08,912 ERROR File "/usr/lib/python2.7/subprocess.py", line 541, in check_call
2019-09-10 15:30:08,913 ERROR raise CalledProcessError(retcode, cmd)
2019-09-10 15:30:08,913 ERROR CalledProcessError: Command 'preprocess /tmp/tmpxX3Rhw.vcf.gz:* -l 3:10807132-16504983 -o /tmp/input.3:10807132-165049833EYGvH.prep.vcf.gz -V 1 -L 1 -r /outputs/ref/human_g1k_v37/human_g1k_v37.fasta' returned non-zero exit status 134
2019-09-10 15:30:08,913 ERROR ------------------------------------------------------------
2019-09-10 15:30:16,680 ERROR Preprocess command preprocess /tmp/tmpxX3Rhw.vcf.gz:* -l 3:36998800-44158047 -o /tmp/input.3:36998800-44158047hezEhG.prep.vcf.gz -V 1 -L 1 -r /outputs/ref/human_g1k_v37/human_g1k_v37.fasta failed. Outputs are here /tmp/stdoutYemyKC.log / /tmp/stderrvtkR9y.log
2019-09-10 15:30:16,681 ERROR preprocess: vcf.c:3472: bcf_update_format: Assertion `!fmt->p_free' failed.
2019-09-10 15:30:16,681 ERROR Aborted (core dumped)
2019-09-10 15:30:16,682 ERROR Exception when running <function preprocessWrapper at 0x7f35bab28140>:
2019-09-10 15:30:16,682 ERROR ------------------------------------------------------------
2019-09-10 15:30:16,683 ERROR Traceback (most recent call last):
2019-09-10 15:30:16,683 ERROR File "/opt/hap.py/lib/python27/Tools/parallel.py", line 72, in parMapper
2019-09-10 15:30:16,684 ERROR return arg[1]['fun'](arg[0], *arg[1]['args'], **arg[1]['kwargs'])
2019-09-10 15:30:16,684 ERROR File "/opt/hap.py/lib/python27/Haplo/partialcredit.py", line 67, in preprocessWrapper
2019-09-10 15:30:16,684 ERROR subprocess.check_call(to_run, shell=True, stdout=tfo, stderr=tfe)
2019-09-10 15:30:16,685 ERROR File "/usr/lib/python2.7/subprocess.py", line 541, in check_call
2019-09-10 15:30:16,685 ERROR raise CalledProcessError(retcode, cmd)
2019-09-10 15:30:16,686 ERROR CalledProcessError: Command 'preprocess /tmp/tmpxX3Rhw.vcf.gz:* -l 3:36998800-44158047 -o /tmp/input.3:36998800-44158047hezEhG.prep.vcf.gz -V 1 -L 1 -r /outputs/ref/human_g1k_v37/human_g1k_v37.fasta' returned non-zero exit status 134
2019-09-10 15:30:16,686 ERROR ------------------------------------------------------------
2019-09-10 15:30:20,948 ERROR Preprocess command preprocess /tmp/tmpxX3Rhw.vcf.gz:* -l 6:74275294-78208081 -o /tmp/input.6:74275294-782080816Gpqoh.prep.vcf.gz -V 1 -L 1 -r /outputs/ref/human_g1k_v37/human_g1k_v37.fasta failed. Outputs are here /tmp/stdout5d_vb7.log / /tmp/stderrw_vatl.log
2019-09-10 15:30:20,949 ERROR preprocess: vcf.c:3472: bcf_update_format: Assertion `!fmt->p_free' failed.
2019-09-10 15:30:20,950 ERROR Aborted (core dumped)
2019-09-10 15:30:20,950 ERROR Exception when running <function preprocessWrapper at 0x7f35bab28140>:
2019-09-10 15:30:20,950 ERROR ------------------------------------------------------------
2019-09-10 15:30:20,951 ERROR Traceback (most recent call last):
2019-09-10 15:30:20,952 ERROR File "/opt/hap.py/lib/python27/Tools/parallel.py", line 72, in parMapper
2019-09-10 15:30:20,952 ERROR return arg[1]['fun'](arg[0], *arg[1]['args'], **arg[1]['kwargs'])
2019-09-10 15:30:20,952 ERROR File "/opt/hap.py/lib/python27/Haplo/partialcredit.py", line 67, in preprocessWrapper
2019-09-10 15:30:20,953 ERROR subprocess.check_call(to_run, shell=True, stdout=tfo, stderr=tfe)
2019-09-10 15:30:20,953 ERROR File "/usr/lib/python2.7/subprocess.py", line 541, in check_call
2019-09-10 15:30:20,953 ERROR raise CalledProcessError(retcode, cmd)
2019-09-10 15:30:20,954 ERROR CalledProcessError: Command 'preprocess /tmp/tmpxX3Rhw.vcf.gz:* -l 6:74275294-78208081 -o /tmp/input.6:74275294-782080816Gpqoh.prep.vcf.gz -V 1 -L 1 -r /outputs/ref/human_g1k_v37/human_g1k_v37.fasta' returned non-zero exit status 134
2019-09-10 15:30:20,954 ERROR ------------------------------------------------------------
2019-09-10 15:30:23,071 ERROR Preprocess command preprocess /tmp/tmpxX3Rhw.vcf.gz:* -l 3:124713022-130994974 -o /tmp/input.3:124713022-130994974dlXrD0.prep.vcf.gz -V 1 -L 1 -r /outputs/ref/human_g1k_v37/human_g1k_v37.fasta failed. Outputs are here /tmp/stdoutIjqIqq.log / /tmp/stderrns2AJM.log
2019-09-10 15:30:23,072 ERROR preprocess: vcf.c:3472: bcf_update_format: Assertion `!fmt->p_free' failed.
2019-09-10 15:30:23,073 ERROR Aborted (core dumped)
2019-09-10 15:30:23,073 ERROR Exception when running <function preprocessWrapper at 0x7f35bab28140>:
2019-09-10 15:30:23,074 ERROR ------------------------------------------------------------
2019-09-10 15:30:23,074 ERROR Traceback (most recent call last):
2019-09-10 15:30:23,074 ERROR File "/opt/hap.py/lib/python27/Tools/parallel.py", line 72, in parMapper
2019-09-10 15:30:23,075 ERROR return arg[1]['fun'](arg[0], *arg[1]['args'], **arg[1]['kwargs'])
2019-09-10 15:30:23,075 ERROR File "/opt/hap.py/lib/python27/Haplo/partialcredit.py", line 67, in preprocessWrapper
2019-09-10 15:30:23,076 ERROR subprocess.check_call(to_run, shell=True, stdout=tfo, stderr=tfe)
2019-09-10 15:30:23,076 ERROR File "/usr/lib/python2.7/subprocess.py", line 541, in check_call
2019-09-10 15:30:23,077 ERROR raise CalledProcessError(retcode, cmd)
2019-09-10 15:30:23,077 ERROR CalledProcessError: Command 'preprocess /tmp/tmpxX3Rhw.vcf.gz:* -l 3:124713022-130994974 -o /tmp/input.3:124713022-130994974dlXrD0.prep.vcf.gz -V 1 -L 1 -r /outputs/ref/human_g1k_v37/human_g1k_v37.fasta' returned non-zero exit status 134
2019-09-10 15:30:23,077 ERROR ------------------------------------------------------------
2019-09-10 15:30:34,434 ERROR Preprocess command preprocess /tmp/tmpxX3Rhw.vcf.gz:* -l 8:11148861-15121461 -o /tmp/input.8:11148861-15121461mtpYm1.prep.vcf.gz -V 1 -L 1 -r /outputs/ref/human_g1k_v37/human_g1k_v37.fasta failed. Outputs are here /tmp/stdoutqPneyr.log / /tmp/stderrtoTviD.log
2019-09-10 15:30:34,435 ERROR preprocess: vcf.c:3472: bcf_update_format: Assertion `!fmt->p_free' failed.
2019-09-10 15:30:34,435 ERROR Aborted (core dumped)
2019-09-10 15:30:34,436 ERROR Exception when running <function preprocessWrapper at 0x7f35bab28140>:
2019-09-10 15:30:34,436 ERROR ------------------------------------------------------------
2019-09-10 15:30:34,436 ERROR Traceback (most recent call last):
2019-09-10 15:30:34,437 ERROR File "/opt/hap.py/lib/python27/Tools/parallel.py", line 72, in parMapper
2019-09-10 15:30:34,437 ERROR return arg[1]['fun'](arg[0], *arg[1]['args'], **arg[1]['kwargs'])
2019-09-10 15:30:34,438 ERROR File "/opt/hap.py/lib/python27/Haplo/partialcredit.py", line 67, in preprocessWrapper
2019-09-10 15:30:34,438 ERROR subprocess.check_call(to_run, shell=True, stdout=tfo, stderr=tfe)
2019-09-10 15:30:34,438 ERROR File "/usr/lib/python2.7/subprocess.py", line 541, in check_call
2019-09-10 15:30:34,439 ERROR raise CalledProcessError(retcode, cmd)
2019-09-10 15:30:34,439 ERROR CalledProcessError: Command 'preprocess /tmp/tmpxX3Rhw.vcf.gz:* -l 8:11148861-15121461 -o /tmp/input.8:11148861-15121461mtpYm1.prep.vcf.gz -V 1 -L 1 -r /outputs/ref/human_g1k_v37/human_g1k_v37.fasta' returned non-zero exit status 134
2019-09-10 15:30:34,439 ERROR ------------------------------------------------------------
2019-09-10 15:30:43,487 ERROR One of the preprocess jobs failed
2019-09-10 15:30:43,487 ERROR Traceback (most recent call last):
2019-09-10 15:30:43,487 ERROR File "/opt/hap.py/bin/hap.py", line 508, in <module>
2019-09-10 15:30:43,488 ERROR main()
2019-09-10 15:30:43,488 ERROR File "/opt/hap.py/bin/hap.py", line 363, in main
2019-09-10 15:30:43,488 ERROR "QUERY")
2019-09-10 15:30:43,488 ERROR File "/opt/hap.py/bin/pre.py", line 203, in preprocess
2019-09-10 15:30:43,488 ERROR haploid_x=gender == "male")
2019-09-10 15:30:43,488 ERROR File "/opt/hap.py/lib/python27/Haplo/partialcredit.py", line 214, in partialCredit
2019-09-10 15:30:43,488 ERROR raise Exception("One of the preprocess jobs failed")
2019-09-10 15:30:43,488 ERROR Exception: One of the preprocess jobs failed
root@86876e01e030:/outputs#
Could you help me, please?
I've found this error too:
preprocess: vcf.c:3496: bcf_update_format: Assertion!fmt->p_free' failed.`
I ran:
hap.py {input.baselin} {input.callset} --roc QUAL -T {input.targets} -r {input.ref} -o {output}/i
(parameter values are in {} because this was part of a Snakefile).
Removing -T <Bed> doesn't solve. I think my target regions overlap, because of the upstream NGS technique (platform = IT PGM machine). My sequences are from 3 loci and they were targeted by different shorter amplicons. The docs say it would fail in such cases where there are overlaps. Does that mean that the only way to use this tool is with WES or WGS?
Plus, I don't have a "truth" dataset. I was comparing different callsets from different algorithms (TVC, platform standard vs. DeepVariant, universal caller).
Thanks in advance.
You can always try running RTG vcfeval directly if you don't need stratification.
