Process map_reads (1) terminated with an error exit status (1)
#2
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This may be an issue with clockwork being unable to load its database into memory. How much memory does the machine you were trying this on have? |
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../tools/Varpipeline -q JTT20001087-FL-M04613-200220_S40_R1_001.fastq.gz -r ../tools/ref2.fa -n JTT20001087-FL-M04613-200220_S40 -q2 JTT20001087-FL-M04613-200220_S40_R2_001.fastq.gz -a -v
---[ nextflow remove contamination ]---
Command:
/varpipe_wgs/tools/clockwork-0.11.3/results/nextflow run /varpipe_wgs/tools/clockwork-0.11.3/nextflow/remove_contam.nf --ref_fasta /varpipe_wgs/tools/clockwork-0.11.3/OUT/ref.fa --ref_metadata_tsv /varpipe_wgs/tools/clockwork-0.11.3/OUT/remove_contam_metadata.tsv --reads_in1 JTT20001087-FL-M04613-200220_S40_R1_001.fastq.gz --reads_in2 JTT20001087-FL-M04613-200220_S40_R2_001.fastq.gz --outprefix Output_01_30_2023/JTT20001087-FL-M04613-200220_S40/clockwork/JTT20001087-FL-M04613-200220_S40 --mapping_threads 12
Standard Output:
N E X T F L O W ~ version 20.07.1
Launching
/varpipe_wgs/tools/clockwork-0.11.3/nextflow/remove_contam.nf[berserk_mahavira] - revision: b5b8e4e89e[- ] process > make_jobs_tsv -
[- ] process > map_reads -
[- ] process > sam_to_fastq_files -
executor > local (1)
[ea/bd3185] process > make_jobs_tsv [100%] 1 of 1 ✔
[- ] process > map_reads [ 0%] 0 of 1
[- ] process > sam_to_fastq_files -
executor > local (2)
[ea/bd3185] process > make_jobs_tsv [100%] 1 of 1 ✔
[19/887305] process > map_reads (1) [ 0%] 0 of 1
[- ] process > sam_to_fastq_files -
executor > local (2)
[ea/bd3185] process > make_jobs_tsv [100%] 1 of 1 ✔
[19/887305] process > map_reads (1) [ 0%] 0 of 1
[- ] process > sam_to_fastq_files -
Error executing process > 'map_reads (1)'
Caused by:
Process
map_reads (1)terminated with an error exit status (1)Command executed:
clockwork map_reads --threads 12 --unsorted_sam sample_name /varpipe_wgs/tools/clockwork-0.11.3/OUT/ref.fa contam_sam /varpipe_wgs/data/JTT20001087-FL-M04613-200220_S40_R1_001.fastq.gz /varpipe_wgs/data/JTT20001087-FL-M04613-200220_S40_R2_001.fastq.gz
Command exit status:
1
Command output:
(empty)
Command error:
[2023-01-30T10:15:03 - clockwork map_reads - INFO] Run command: fqtools count /varpipe_wgs/data/JTT20001087-FL-M04613-200220_S40_R1_001.fastq.gz /varpipe_wgs/data/JTT20001087-FL-M04613-200220_S40_R2_001.fastq.gz
[2023-01-30T10:15:08 - clockwork map_reads - INFO] Return code: 0
[2023-01-30T10:15:08 - clockwork map_reads - INFO] stdout:
493552
[2023-01-30T10:15:08 - clockwork map_reads - INFO] stderr:
[2023-01-30T10:15:08 - clockwork map_reads - INFO] Run command: minimap2 --split-prefix contam_sam.tmp.map_reads_set.i4vo5o1q/map.0.tmp -a -t 12 -x sr -R '@rg\tLB:LIB\tID:1\tSM:sample_name' /varpipe_wgs/tools/clockwork-0.11.3/OUT/ref.fa /varpipe_wgs/data/JTT20001087-FL-M04613-200220_S40_R1_001.fastq.gz /varpipe_wgs/data/JTT20001087-FL-M04613-200220_S40_R2_001.fastq.gz | awk '/^@/ || !(and($2,256) || and($2,2048))' > contam_sam.tmp.map_reads_set.i4vo5o1q/map.0
[2023-01-30T10:17:30 - clockwork map_reads - INFO] Return code: 0
[2023-01-30T10:17:31 - clockwork map_reads - INFO] stdout:
[2023-01-30T10:17:31 - clockwork map_reads - INFO] stderr:
[M::mm_idx_gen::93.012*1.85] collected minimizers
Killed
[2023-01-30T10:17:31 - clockwork map_reads - INFO] Run command: grep -c -v '^@' contam_sam.tmp.map_reads_set.i4vo5o1q/map.0
[2023-01-30T10:17:32 - clockwork map_reads - INFO] Return code: 1
Error running this command: grep -c -v '^@' contam_sam.tmp.map_reads_set.i4vo5o1q/map.0
Return code: 1
Output from stdout:
0
Output from stderr:
Traceback (most recent call last):
File "/usr/local/bin/clockwork", line 4, in
import('pkg_resources').run_script('clockwork==0.11.3', 'clockwork')
File "/usr/lib/python3/dist-packages/pkg_resources/init.py", line 667, in run_script
self.require(requires)[0].run_script(script_name, ns)
File "/usr/lib/python3/dist-packages/pkg_resources/init.py", line 1470, in run_script
exec(script_code, namespace, namespace)
File "/usr/local/lib/python3.8/dist-packages/clockwork-0.11.3-py3.8.egg/EGG-INFO/scripts/clockwork", line 1019, in
File "/usr/local/lib/python3.8/dist-packages/clockwork-0.11.3-py3.8.egg/clockwork/tasks/map_reads.py", line 13, in run
File "/usr/local/lib/python3.8/dist-packages/clockwork-0.11.3-py3.8.egg/clockwork/read_map.py", line 133, in map_reads_set
File "/usr/local/lib/python3.8/dist-packages/clockwork-0.11.3-py3.8.egg/clockwork/read_map.py", line 74, in map_reads
File "/usr/local/lib/python3.8/dist-packages/clockwork-0.11.3-py3.8.egg/clockwork/utils.py", line 124, in sam_record_count
File "/usr/local/lib/python3.8/dist-packages/clockwork-0.11.3-py3.8.egg/clockwork/utils.py", line 36, in syscall
Exception: Error in system call. Cannot continue
Work dir:
/varpipe_wgs/data/work/19/887305a2a7107db282285662fdf09d
Tip: you can replicate the issue by changing to the process work dir and entering the command
bash .command.runexecutor > local (2)
[ea/bd3185] process > make_jobs_tsv [100%] 1 of 1 ✔
[19/887305] process > map_reads (1) [ 0%] 0 of 1 ✔
[- ] process > sam_to_fastq_files -
Error executing process > 'map_reads (1)'
Caused by:
Process
map_reads (1)terminated with an error exit status (1)Command executed:
clockwork map_reads --threads 12 --unsorted_sam sample_name /varpipe_wgs/tools/clockwork-0.11.3/OUT/ref.fa contam_sam /varpipe_wgs/data/JTT20001087-FL-M04613-200220_S40_R1_001.fastq.gz /varpipe_wgs/data/JTT20001087-FL-M04613-200220_S40_R2_001.fastq.gz
Command exit status:
1
Command output:
(empty)
Command error:
[2023-01-30T10:15:03 - clockwork map_reads - INFO] Run command: fqtools count /varpipe_wgs/data/JTT20001087-FL-M04613-200220_S40_R1_001.fastq.gz /varpipe_wgs/data/JTT20001087-FL-M04613-200220_S40_R2_001.fastq.gz
[2023-01-30T10:15:08 - clockwork map_reads - INFO] Return code: 0
[2023-01-30T10:15:08 - clockwork map_reads - INFO] stdout:
493552
[2023-01-30T10:15:08 - clockwork map_reads - INFO] stderr:
[2023-01-30T10:15:08 - clockwork map_reads - INFO] Run command: minimap2 --split-prefix contam_sam.tmp.map_reads_set.i4vo5o1q/map.0.tmp -a -t 12 -x sr -R '@rg\tLB:LIB\tID:1\tSM:sample_name' /varpipe_wgs/tools/clockwork-0.11.3/OUT/ref.fa /varpipe_wgs/data/JTT20001087-FL-M04613-200220_S40_R1_001.fastq.gz /varpipe_wgs/data/JTT20001087-FL-M04613-200220_S40_R2_001.fastq.gz | awk '/^@/ || !(and($2,256) || and($2,2048))' > contam_sam.tmp.map_reads_set.i4vo5o1q/map.0
[2023-01-30T10:17:30 - clockwork map_reads - INFO] Return code: 0
[2023-01-30T10:17:31 - clockwork map_reads - INFO] stdout:
[2023-01-30T10:17:31 - clockwork map_reads - INFO] stderr:
[M::mm_idx_gen::93.012*1.85] collected minimizers
Killed
[2023-01-30T10:17:31 - clockwork map_reads - INFO] Run command: grep -c -v '^@' contam_sam.tmp.map_reads_set.i4vo5o1q/map.0
[2023-01-30T10:17:32 - clockwork map_reads - INFO] Return code: 1
Error running this command: grep -c -v '^@' contam_sam.tmp.map_reads_set.i4vo5o1q/map.0
Return code: 1
Output from stdout:
0
Output from stderr:
Traceback (most recent call last):
File "/usr/local/bin/clockwork", line 4, in
import('pkg_resources').run_script('clockwork==0.11.3', 'clockwork')
File "/usr/lib/python3/dist-packages/pkg_resources/init.py", line 667, in run_script
self.require(requires)[0].run_script(script_name, ns)
File "/usr/lib/python3/dist-packages/pkg_resources/init.py", line 1470, in run_script
exec(script_code, namespace, namespace)
File "/usr/local/lib/python3.8/dist-packages/clockwork-0.11.3-py3.8.egg/EGG-INFO/scripts/clockwork", line 1019, in
File "/usr/local/lib/python3.8/dist-packages/clockwork-0.11.3-py3.8.egg/clockwork/tasks/map_reads.py", line 13, in run
File "/usr/local/lib/python3.8/dist-packages/clockwork-0.11.3-py3.8.egg/clockwork/read_map.py", line 133, in map_reads_set
File "/usr/local/lib/python3.8/dist-packages/clockwork-0.11.3-py3.8.egg/clockwork/read_map.py", line 74, in map_reads
File "/usr/local/lib/python3.8/dist-packages/clockwork-0.11.3-py3.8.egg/clockwork/utils.py", line 124, in sam_record_count
File "/usr/local/lib/python3.8/dist-packages/clockwork-0.11.3-py3.8.egg/clockwork/utils.py", line 36, in syscall
Exception: Error in system call. Cannot continue
Work dir:
/varpipe_wgs/data/work/19/887305a2a7107db282285662fdf09d
Tip: you can replicate the issue by changing to the process work dir and entering the command
bash .command.runexecutor > local (2)
[ea/bd3185] process > make_jobs_tsv [100%] 1 of 1 ✔
[19/887305] process > map_reads (1) [100%] 1 of 1, failed: 1 ✘
[- ] process > sam_to_fastq_files -
Error executing process > 'map_reads (1)'
Caused by:
Process
map_reads (1)terminated with an error exit status (1)Command executed:
clockwork map_reads --threads 12 --unsorted_sam sample_name /varpipe_wgs/tools/clockwork-0.11.3/OUT/ref.fa contam_sam /varpipe_wgs/data/JTT20001087-FL-M04613-200220_S40_R1_001.fastq.gz /varpipe_wgs/data/JTT20001087-FL-M04613-200220_S40_R2_001.fastq.gz
Command exit status:
1
Command output:
(empty)
Command error:
[2023-01-30T10:15:03 - clockwork map_reads - INFO] Run command: fqtools count /varpipe_wgs/data/JTT20001087-FL-M04613-200220_S40_R1_001.fastq.gz /varpipe_wgs/data/JTT20001087-FL-M04613-200220_S40_R2_001.fastq.gz
[2023-01-30T10:15:08 - clockwork map_reads - INFO] Return code: 0
[2023-01-30T10:15:08 - clockwork map_reads - INFO] stdout:
493552
[2023-01-30T10:15:08 - clockwork map_reads - INFO] stderr:
[2023-01-30T10:15:08 - clockwork map_reads - INFO] Run command: minimap2 --split-prefix contam_sam.tmp.map_reads_set.i4vo5o1q/map.0.tmp -a -t 12 -x sr -R '@rg\tLB:LIB\tID:1\tSM:sample_name' /varpipe_wgs/tools/clockwork-0.11.3/OUT/ref.fa /varpipe_wgs/data/JTT20001087-FL-M04613-200220_S40_R1_001.fastq.gz /varpipe_wgs/data/JTT20001087-FL-M04613-200220_S40_R2_001.fastq.gz | awk '/^@/ || !(and($2,256) || and($2,2048))' > contam_sam.tmp.map_reads_set.i4vo5o1q/map.0
[2023-01-30T10:17:30 - clockwork map_reads - INFO] Return code: 0
[2023-01-30T10:17:31 - clockwork map_reads - INFO] stdout:
[2023-01-30T10:17:31 - clockwork map_reads - INFO] stderr:
[M::mm_idx_gen::93.012*1.85] collected minimizers
Killed
[2023-01-30T10:17:31 - clockwork map_reads - INFO] Run command: grep -c -v '^@' contam_sam.tmp.map_reads_set.i4vo5o1q/map.0
[2023-01-30T10:17:32 - clockwork map_reads - INFO] Return code: 1
Error running this command: grep -c -v '^@' contam_sam.tmp.map_reads_set.i4vo5o1q/map.0
Return code: 1
Output from stdout:
0
Output from stderr:
Traceback (most recent call last):
File "/usr/local/bin/clockwork", line 4, in
import('pkg_resources').run_script('clockwork==0.11.3', 'clockwork')
File "/usr/lib/python3/dist-packages/pkg_resources/init.py", line 667, in run_script
self.require(requires)[0].run_script(script_name, ns)
File "/usr/lib/python3/dist-packages/pkg_resources/init.py", line 1470, in run_script
exec(script_code, namespace, namespace)
File "/usr/local/lib/python3.8/dist-packages/clockwork-0.11.3-py3.8.egg/EGG-INFO/scripts/clockwork", line 1019, in
File "/usr/local/lib/python3.8/dist-packages/clockwork-0.11.3-py3.8.egg/clockwork/tasks/map_reads.py", line 13, in run
File "/usr/local/lib/python3.8/dist-packages/clockwork-0.11.3-py3.8.egg/clockwork/read_map.py", line 133, in map_reads_set
File "/usr/local/lib/python3.8/dist-packages/clockwork-0.11.3-py3.8.egg/clockwork/read_map.py", line 74, in map_reads
File "/usr/local/lib/python3.8/dist-packages/clockwork-0.11.3-py3.8.egg/clockwork/utils.py", line 124, in sam_record_count
File "/usr/local/lib/python3.8/dist-packages/clockwork-0.11.3-py3.8.egg/clockwork/utils.py", line 36, in syscall
Exception: Error in system call. Cannot continue
Work dir:
/varpipe_wgs/data/work/19/887305a2a7107db282285662fdf09d
Tip: you can replicate the issue by changing to the process work dir and entering the command
bash .command.runexecutor > local (2)
[ea/bd3185] process > make_jobs_tsv [100%] 1 of 1 ✔
[19/887305] process > map_reads (1) [100%] 1 of 1, failed: 1 ✘
[- ] process > sam_to_fastq_files -
Error executing process > 'map_reads (1)'
Caused by:
Process
map_reads (1)terminated with an error exit status (1)Command executed:
clockwork map_reads --threads 12 --unsorted_sam sample_name /varpipe_wgs/tools/clockwork-0.11.3/OUT/ref.fa contam_sam /varpipe_wgs/data/JTT20001087-FL-M04613-200220_S40_R1_001.fastq.gz /varpipe_wgs/data/JTT20001087-FL-M04613-200220_S40_R2_001.fastq.gz
Command exit status:
1
Command output:
(empty)
Command error:
[2023-01-30T10:15:03 - clockwork map_reads - INFO] Run command: fqtools count /varpipe_wgs/data/JTT20001087-FL-M04613-200220_S40_R1_001.fastq.gz /varpipe_wgs/data/JTT20001087-FL-M04613-200220_S40_R2_001.fastq.gz
[2023-01-30T10:15:08 - clockwork map_reads - INFO] Return code: 0
[2023-01-30T10:15:08 - clockwork map_reads - INFO] stdout:
493552
[2023-01-30T10:15:08 - clockwork map_reads - INFO] stderr:
[2023-01-30T10:15:08 - clockwork map_reads - INFO] Run command: minimap2 --split-prefix contam_sam.tmp.map_reads_set.i4vo5o1q/map.0.tmp -a -t 12 -x sr -R '@rg\tLB:LIB\tID:1\tSM:sample_name' /varpipe_wgs/tools/clockwork-0.11.3/OUT/ref.fa /varpipe_wgs/data/JTT20001087-FL-M04613-200220_S40_R1_001.fastq.gz /varpipe_wgs/data/JTT20001087-FL-M04613-200220_S40_R2_001.fastq.gz | awk '/^@/ || !(and($2,256) || and($2,2048))' > contam_sam.tmp.map_reads_set.i4vo5o1q/map.0
[2023-01-30T10:17:30 - clockwork map_reads - INFO] Return code: 0
[2023-01-30T10:17:31 - clockwork map_reads - INFO] stdout:
[2023-01-30T10:17:31 - clockwork map_reads - INFO] stderr:
[M::mm_idx_gen::93.012*1.85] collected minimizers
Killed
[2023-01-30T10:17:31 - clockwork map_reads - INFO] Run command: grep -c -v '^@' contam_sam.tmp.map_reads_set.i4vo5o1q/map.0
[2023-01-30T10:17:32 - clockwork map_reads - INFO] Return code: 1
Error running this command: grep -c -v '^@' contam_sam.tmp.map_reads_set.i4vo5o1q/map.0
Return code: 1
Output from stdout:
0
Output from stderr:
Traceback (most recent call last):
File "/usr/local/bin/clockwork", line 4, in
import('pkg_resources').run_script('clockwork==0.11.3', 'clockwork')
File "/usr/lib/python3/dist-packages/pkg_resources/init.py", line 667, in run_script
self.require(requires)[0].run_script(script_name, ns)
File "/usr/lib/python3/dist-packages/pkg_resources/init.py", line 1470, in run_script
exec(script_code, namespace, namespace)
File "/usr/local/lib/python3.8/dist-packages/clockwork-0.11.3-py3.8.egg/EGG-INFO/scripts/clockwork", line 1019, in
File "/usr/local/lib/python3.8/dist-packages/clockwork-0.11.3-py3.8.egg/clockwork/tasks/map_reads.py", line 13, in run
File "/usr/local/lib/python3.8/dist-packages/clockwork-0.11.3-py3.8.egg/clockwork/read_map.py", line 133, in map_reads_set
File "/usr/local/lib/python3.8/dist-packages/clockwork-0.11.3-py3.8.egg/clockwork/read_map.py", line 74, in map_reads
File "/usr/local/lib/python3.8/dist-packages/clockwork-0.11.3-py3.8.egg/clockwork/utils.py", line 124, in sam_record_count
File "/usr/local/lib/python3.8/dist-packages/clockwork-0.11.3-py3.8.egg/clockwork/utils.py", line 36, in syscall
Exception: Error in system call. Cannot continue
Work dir:
/varpipe_wgs/data/work/19/887305a2a7107db282285662fdf09d
Tip: you can replicate the issue by changing to the process work dir and entering the command
bash .command.runexecutor > local (2)
[ea/bd3185] process > make_jobs_tsv [100%] 1 of 1 ✔
[19/887305] process > map_reads (1) [100%] 1 of 1, failed: 1 ✘
[- ] process > sam_to_fastq_files -
Error executing process > 'map_reads (1)'
Caused by:
Process
map_reads (1)terminated with an error exit status (1)Command executed:
clockwork map_reads --threads 12 --unsorted_sam sample_name /varpipe_wgs/tools/clockwork-0.11.3/OUT/ref.fa contam_sam /varpipe_wgs/data/JTT20001087-FL-M04613-200220_S40_R1_001.fastq.gz /varpipe_wgs/data/JTT20001087-FL-M04613-200220_S40_R2_001.fastq.gz
Command exit status:
1
Command output:
(empty)
Command error:
[2023-01-30T10:15:03 - clockwork map_reads - INFO] Run command: fqtools count /varpipe_wgs/data/JTT20001087-FL-M04613-200220_S40_R1_001.fastq.gz /varpipe_wgs/data/JTT20001087-FL-M04613-200220_S40_R2_001.fastq.gz
[2023-01-30T10:15:08 - clockwork map_reads - INFO] Return code: 0
[2023-01-30T10:15:08 - clockwork map_reads - INFO] stdout:
493552
[2023-01-30T10:15:08 - clockwork map_reads - INFO] stderr:
[2023-01-30T10:15:08 - clockwork map_reads - INFO] Run command: minimap2 --split-prefix contam_sam.tmp.map_reads_set.i4vo5o1q/map.0.tmp -a -t 12 -x sr -R '@rg\tLB:LIB\tID:1\tSM:sample_name' /varpipe_wgs/tools/clockwork-0.11.3/OUT/ref.fa /varpipe_wgs/data/JTT20001087-FL-M04613-200220_S40_R1_001.fastq.gz /varpipe_wgs/data/JTT20001087-FL-M04613-200220_S40_R2_001.fastq.gz | awk '/^@/ || !(and($2,256) || and($2,2048))' > contam_sam.tmp.map_reads_set.i4vo5o1q/map.0
[2023-01-30T10:17:30 - clockwork map_reads - INFO] Return code: 0
[2023-01-30T10:17:31 - clockwork map_reads - INFO] stdout:
[2023-01-30T10:17:31 - clockwork map_reads - INFO] stderr:
[M::mm_idx_gen::93.012*1.85] collected minimizers
Killed
[2023-01-30T10:17:31 - clockwork map_reads - INFO] Run command: grep -c -v '^@' contam_sam.tmp.map_reads_set.i4vo5o1q/map.0
[2023-01-30T10:17:32 - clockwork map_reads - INFO] Return code: 1
Error running this command: grep -c -v '^@' contam_sam.tmp.map_reads_set.i4vo5o1q/map.0
Return code: 1
Output from stdout:
0
Output from stderr:
Traceback (most recent call last):
File "/usr/local/bin/clockwork", line 4, in
import('pkg_resources').run_script('clockwork==0.11.3', 'clockwork')
File "/usr/lib/python3/dist-packages/pkg_resources/init.py", line 667, in run_script
self.require(requires)[0].run_script(script_name, ns)
File "/usr/lib/python3/dist-packages/pkg_resources/init.py", line 1470, in run_script
exec(script_code, namespace, namespace)
File "/usr/local/lib/python3.8/dist-packages/clockwork-0.11.3-py3.8.egg/EGG-INFO/scripts/clockwork", line 1019, in
File "/usr/local/lib/python3.8/dist-packages/clockwork-0.11.3-py3.8.egg/clockwork/tasks/map_reads.py", line 13, in run
File "/usr/local/lib/python3.8/dist-packages/clockwork-0.11.3-py3.8.egg/clockwork/read_map.py", line 133, in map_reads_set
File "/usr/local/lib/python3.8/dist-packages/clockwork-0.11.3-py3.8.egg/clockwork/read_map.py", line 74, in map_reads
File "/usr/local/lib/python3.8/dist-packages/clockwork-0.11.3-py3.8.egg/clockwork/utils.py", line 124, in sam_record_count
File "/usr/local/lib/python3.8/dist-packages/clockwork-0.11.3-py3.8.egg/clockwork/utils.py", line 36, in syscall
Exception: Error in system call. Cannot continue
Work dir:
/varpipe_wgs/data/work/19/887305a2a7107db282285662fdf09d
Tip: you can replicate the issue by changing to the process work dir and entering the command
bash .command.run---[ trimmomatic ]---
Command:
java -jar /varpipe_wgs/tools/trimmomatic-0.39.jar PE -threads 12 -trimlog Output_01_30_2023/JTT20001087-FL-M04613-200220_S40/trimmomatic/trimLog.txt Output_01_30_2023/JTT20001087-FL-M04613-200220_S40/clockwork/JTT20001087-FL-M04613-200220_S40.remove_contam.1.fq.gz Output_01_30_2023/JTT20001087-FL-M04613-200220_S40/clockwork/JTT20001087-FL-M04613-200220_S40.remove_contam.2.fq.gz Output_01_30_2023/JTT20001087-FL-M04613-200220_S40/trimmomatic/JTT20001087-FL-M04613-200220_S40_paired_1.fastq.gz Output_01_30_2023/JTT20001087-FL-M04613-200220_S40/trimmomatic/JTT20001087-FL-M04613-200220_S40_unpaired_1.fastq.gz Output_01_30_2023/JTT20001087-FL-M04613-200220_S40/trimmomatic/JTT20001087-FL-M04613-200220_S40_paired_2.fastq.gz Output_01_30_2023/JTT20001087-FL-M04613-200220_S40/trimmomatic/JTT20001087-FL-M04613-200220_S40_unpaired_2.fastq.gz LEADING:3 TRAILING:3 SLIDINGWINDOW:4:15 MINLEN:40
Standard Error:
TrimmomaticPE: Started with arguments:
-threads 12 -trimlog Output_01_30_2023/JTT20001087-FL-M04613-200220_S40/trimmomatic/trimLog.txt Output_01_30_2023/JTT20001087-FL-M04613-200220_S40/clockwork/JTT20001087-FL-M04613-200220_S40.remove_contam.1.fq.gz Output_01_30_2023/JTT20001087-FL-M04613-200220_S40/clockwork/JTT20001087-FL-M04613-200220_S40.remove_contam.2.fq.gz Output_01_30_2023/JTT20001087-FL-M04613-200220_S40/trimmomatic/JTT20001087-FL-M04613-200220_S40_paired_1.fastq.gz Output_01_30_2023/JTT20001087-FL-M04613-200220_S40/trimmomatic/JTT20001087-FL-M04613-200220_S40_unpaired_1.fastq.gz Output_01_30_2023/JTT20001087-FL-M04613-200220_S40/trimmomatic/JTT20001087-FL-M04613-200220_S40_paired_2.fastq.gz Output_01_30_2023/JTT20001087-FL-M04613-200220_S40/trimmomatic/JTT20001087-FL-M04613-200220_S40_unpaired_2.fastq.gz LEADING:3 TRAILING:3 SLIDINGWINDOW:4:15 MINLEN:40
Exception in thread "main" java.io.FileNotFoundException: Output_01_30_2023/JTT20001087-FL-M04613-200220_S40/clockwork/JTT20001087-FL-M04613-200220_S40.remove_contam.1.fq.gz (No such file or directory)
at java.base/java.io.FileInputStream.open0(Native Method)
at java.base/java.io.FileInputStream.open(FileInputStream.java:216)
at java.base/java.io.FileInputStream.(FileInputStream.java:157)
at org.usadellab.trimmomatic.fastq.FastqParser.parse(FastqParser.java:135)
at org.usadellab.trimmomatic.TrimmomaticPE.process(TrimmomaticPE.java:265)
at org.usadellab.trimmomatic.TrimmomaticPE.run(TrimmomaticPE.java:555)
at org.usadellab.trimmomatic.Trimmomatic.main(Trimmomatic.java:80)
---[ rm ]---
Command:
rm Output_01_30_2023/JTT20001087-FL-M04613-200220_S40/trimmomatic/JTT20001087-FL-M04613-200220_S40_unpaired_1.fastq.gz Output_01_30_2023/JTT20001087-FL-M04613-200220_S40/trimmomatic/JTT20001087-FL-M04613-200220_S40_unpaired_2.fastq.gz
Standard Error:
rm: cannot remove 'Output_01_30_2023/JTT20001087-FL-M04613-200220_S40/trimmomatic/JTT20001087-FL-M04613-200220_S40_unpaired_1.fastq.gz': No such file or directory
rm: cannot remove 'Output_01_30_2023/JTT20001087-FL-M04613-200220_S40/trimmomatic/JTT20001087-FL-M04613-200220_S40_unpaired_2.fastq.gz': No such file or directory
########## Running BWA. ##########
---[ mkdir ]---
Command:
mkdir -p Output_01_30_2023/JTT20001087-FL-M04613-200220_S40/tmp/bwa
---[ mkdir ]---
Command:
mkdir -p Output_01_30_2023/JTT20001087-FL-M04613-200220_S40/tmp/bwa/index
---[ cp ]---
Command:
cp ../tools/ref2.fa Output_01_30_2023/JTT20001087-FL-M04613-200220_S40/tmp/bwa/index/ref.fa
---[ bwa index ]---
Command:
/varpipe_wgs/tools/bwa index Output_01_30_2023/JTT20001087-FL-M04613-200220_S40/tmp/bwa/index/ref.fa
Standard Error:
[bwa_index] Pack FASTA... 0.05 sec
[bwa_index] Construct BWT for the packed sequence...
[bwa_index] 1.31 seconds elapse.
[bwa_index] Update BWT... 0.03 sec
[bwa_index] Pack forward-only FASTA... 0.03 sec
[bwa_index] Construct SA from BWT and Occ... 0.60 sec
[main] Version: 0.7.17-r1188
[main] CMD: /varpipe_wgs/tools/bwa index Output_01_30_2023/JTT20001087-FL-M04613-200220_S40/tmp/bwa/index/ref.fa
[main] Real time: 2.102 sec; CPU: 2.020 sec
---[ CreateSequenceDictionary ]---
Command:
java -jar /varpipe_wgs/tools/picard.jar CreateSequenceDictionary R=Output_01_30_2023/JTT20001087-FL-M04613-200220_S40/tmp/bwa/index/ref.fa O=Output_01_30_2023/JTT20001087-FL-M04613-200220_S40/tmp/bwa/index/ref.dict
Standard Error:
INFO 2023-01-30 15:18:19 CreateSequenceDictionary
********** NOTE: Picard's command line syntax is changing.
********** For more information, please see:
********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition)
********** The command line looks like this in the new syntax:
********** CreateSequenceDictionary -R Output_01_30_2023/JTT20001087-FL-M04613-200220_S40/tmp/bwa/index/ref.fa -O Output_01_30_2023/JTT20001087-FL-M04613-200220_S40/tmp/bwa/index/ref.dict
15:18:21.156 INFO NativeLibraryLoader - Loading libgkl_compression.so from jar:file:/varpipe_wgs/tools/picard.jar!/com/intel/gkl/native/libgkl_compression.so
[Mon Jan 30 15:18:21 UTC 2023] CreateSequenceDictionary OUTPUT=Output_01_30_2023/JTT20001087-FL-M04613-200220_S40/tmp/bwa/index/ref.dict REFERENCE=Output_01_30_2023/JTT20001087-FL-M04613-200220_S40/tmp/bwa/index/ref.fa TRUNCATE_NAMES_AT_WHITESPACE=true NUM_SEQUENCES=2147483647 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false
[Mon Jan 30 15:18:21 UTC 2023] Executing as dongyibo@login6.ufhpc on Linux 3.10.0-1160.80.1.el7.x86_64 amd64; OpenJDK 64-Bit Server VM 17.0.4+8-Ubuntu-120.04; Deflater: Intel; Inflater: Intel; Provider GCS is not available; Picard version: 2.26.10
[Mon Jan 30 15:18:21 UTC 2023] picard.sam.CreateSequenceDictionary done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=432013312
---[ samtools faidx ]---
Command:
samtools faidx Output_01_30_2023/JTT20001087-FL-M04613-200220_S40/tmp/bwa/index/ref.fa
---[ bwa mem ]---
Command:
/varpipe_wgs/tools/bwa mem -t 12 -R @rg\tID:JTT20001087-FL-M04613-200220_S40\tSM:JTT20001087-FL-M04613-200220_S40\tPL:ILLUMINA Output_01_30_2023/JTT20001087-FL-M04613-200220_S40/tmp/bwa/index/ref.fa Output_01_30_2023/JTT20001087-FL-M04613-200220_S40/trimmomatic/JTT20001087-FL-M04613-200220_S40_paired_1.fastq.gz Output_01_30_2023/JTT20001087-FL-M04613-200220_S40/trimmomatic/JTT20001087-FL-M04613-200220_S40_paired_2.fastq.gz
Standard Error:
[M::bwa_idx_load_from_disk] read 0 ALT contigs
[E::main_mem] fail to open file `Output_01_30_2023/JTT20001087-FL-M04613-200220_S40/trimmomatic/JTT20001087-FL-M04613-200220_S40_paired_1.fastq.gz'.
########## Filtering alignment with GATK and Picard-Tools. ##########
---[ mkdir ]---
Command:
mkdir -p Output_01_30_2023/JTT20001087-FL-M04613-200220_S40/tmp/GATK
---[ mkdir ]---
Command:
mkdir -p Output_01_30_2023/JTT20001087-FL-M04613-200220_S40/tmp/SamTools
---[ SamFormatConverter ]---
Command:
java -Xmx4g -jar /varpipe_wgs/tools/picard.jar SamFormatConverter INPUT=Output_01_30_2023/JTT20001087-FL-M04613-200220_S40/tmp/bwa/bwa.sam VALIDATION_STRINGENCY=LENIENT OUTPUT=Output_01_30_2023/JTT20001087-FL-M04613-200220_S40/tmp/GATK/GATK.bam
Standard Error:
INFO 2023-01-30 15:18:22 SamFormatConverter
********** NOTE: Picard's command line syntax is changing.
********** For more information, please see:
********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition)
********** The command line looks like this in the new syntax:
********** SamFormatConverter -INPUT Output_01_30_2023/JTT20001087-FL-M04613-200220_S40/tmp/bwa/bwa.sam -VALIDATION_STRINGENCY LENIENT -OUTPUT Output_01_30_2023/JTT20001087-FL-M04613-200220_S40/tmp/GATK/GATK.bam
15:18:22.658 INFO NativeLibraryLoader - Loading libgkl_compression.so from jar:file:/varpipe_wgs/tools/picard.jar!/com/intel/gkl/native/libgkl_compression.so
[Mon Jan 30 15:18:22 UTC 2023] SamFormatConverter INPUT=Output_01_30_2023/JTT20001087-FL-M04613-200220_S40/tmp/bwa/bwa.sam OUTPUT=Output_01_30_2023/JTT20001087-FL-M04613-200220_S40/tmp/GATK/GATK.bam VALIDATION_STRINGENCY=LENIENT VERBOSITY=INFO QUIET=false COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false
[Mon Jan 30 15:18:22 UTC 2023] Executing as dongyibo@login6.ufhpc on Linux 3.10.0-1160.80.1.el7.x86_64 amd64; OpenJDK 64-Bit Server VM 17.0.4+8-Ubuntu-120.04; Deflater: Intel; Inflater: Intel; Provider GCS is not available; Picard version: 2.26.10
[Mon Jan 30 15:18:22 UTC 2023] picard.sam.SamFormatConverter done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=425721856
---[ SortSam ]---
Command:
java -Xmx8g -Djava.io.tmpdir=Output_01_30_2023/JTT20001087-FL-M04613-200220_S40/tmp/tmp -jar /varpipe_wgs/tools/picard.jar SortSam INPUT=Output_01_30_2023/JTT20001087-FL-M04613-200220_S40/tmp/GATK/GATK.bam SORT_ORDER=coordinate OUTPUT=Output_01_30_2023/JTT20001087-FL-M04613-200220_S40/tmp/GATK/GATK_s.bam VALIDATION_STRINGENCY=LENIENT TMP_DIR=Output_01_30_2023/JTT20001087-FL-M04613-200220_S40/tmp/tmp
Standard Error:
INFO 2023-01-30 15:18:23 SortSam
********** NOTE: Picard's command line syntax is changing.
********** For more information, please see:
********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition)
********** The command line looks like this in the new syntax:
********** SortSam -INPUT Output_01_30_2023/JTT20001087-FL-M04613-200220_S40/tmp/GATK/GATK.bam -SORT_ORDER coordinate -OUTPUT Output_01_30_2023/JTT20001087-FL-M04613-200220_S40/tmp/GATK/GATK_s.bam -VALIDATION_STRINGENCY LENIENT -TMP_DIR Output_01_30_2023/JTT20001087-FL-M04613-200220_S40/tmp/tmp
15:18:23.545 INFO NativeLibraryLoader - Loading libgkl_compression.so from jar:file:/varpipe_wgs/tools/picard.jar!/com/intel/gkl/native/libgkl_compression.so
[Mon Jan 30 15:18:23 UTC 2023] SortSam INPUT=Output_01_30_2023/JTT20001087-FL-M04613-200220_S40/tmp/GATK/GATK.bam OUTPUT=Output_01_30_2023/JTT20001087-FL-M04613-200220_S40/tmp/GATK/GATK_s.bam SORT_ORDER=coordinate TMP_DIR=[Output_01_30_2023/JTT20001087-FL-M04613-200220_S40/tmp/tmp] VALIDATION_STRINGENCY=LENIENT VERBOSITY=INFO QUIET=false COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false
[Mon Jan 30 15:18:23 UTC 2023] Executing as dongyibo@login6.ufhpc on Linux 3.10.0-1160.80.1.el7.x86_64 amd64; OpenJDK 64-Bit Server VM 17.0.4+8-Ubuntu-120.04; Deflater: Intel; Inflater: Intel; Provider GCS is not available; Picard version: 2.26.10
INFO 2023-01-30 15:18:23 SortSam Finished reading inputs, merging and writing to output now.
[Mon Jan 30 15:18:23 UTC 2023] picard.sam.SortSam done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=432013312
---[ MarkDuplicates ]---
Command:
java -Xmx8g -jar /varpipe_wgs/tools/picard.jar MarkDuplicates INPUT=Output_01_30_2023/JTT20001087-FL-M04613-200220_S40/tmp/GATK/GATK_s.bam OUTPUT=Output_01_30_2023/JTT20001087-FL-M04613-200220_S40/tmp/GATK/GATK_sdr.bam METRICS_FILE=Output_01_30_2023/JTT20001087-FL-M04613-200220_S40/tmp/GATK/MarkDupes.metrics ASSUME_SORTED=true REMOVE_DUPLICATES=false VALIDATION_STRINGENCY=LENIENT
Standard Error:
INFO 2023-01-30 15:18:24 MarkDuplicates
********** NOTE: Picard's command line syntax is changing.
********** For more information, please see:
********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition)
********** The command line looks like this in the new syntax:
********** MarkDuplicates -INPUT Output_01_30_2023/JTT20001087-FL-M04613-200220_S40/tmp/GATK/GATK_s.bam -OUTPUT Output_01_30_2023/JTT20001087-FL-M04613-200220_S40/tmp/GATK/GATK_sdr.bam -METRICS_FILE Output_01_30_2023/JTT20001087-FL-M04613-200220_S40/tmp/GATK/MarkDupes.metrics -ASSUME_SORTED true -REMOVE_DUPLICATES false -VALIDATION_STRINGENCY LENIENT
15:18:24.487 INFO NativeLibraryLoader - Loading libgkl_compression.so from jar:file:/varpipe_wgs/tools/picard.jar!/com/intel/gkl/native/libgkl_compression.so
[Mon Jan 30 15:18:24 UTC 2023] MarkDuplicates INPUT=[Output_01_30_2023/JTT20001087-FL-M04613-200220_S40/tmp/GATK/GATK_s.bam] OUTPUT=Output_01_30_2023/JTT20001087-FL-M04613-200220_S40/tmp/GATK/GATK_sdr.bam METRICS_FILE=Output_01_30_2023/JTT20001087-FL-M04613-200220_S40/tmp/GATK/MarkDupes.metrics REMOVE_DUPLICATES=false ASSUME_SORTED=true VALIDATION_STRINGENCY=LENIENT MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false TAGGING_POLICY=DontTag CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true DUPLICATE_SCORING_STRATEGY=SUM_OF_BASE_QUALITIES PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX=<optimized capture of last three ':' separated fields as numeric values> OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false
[Mon Jan 30 15:18:24 UTC 2023] Executing as dongyibo@login6.ufhpc on Linux 3.10.0-1160.80.1.el7.x86_64 amd64; OpenJDK 64-Bit Server VM 17.0.4+8-Ubuntu-120.04; Deflater: Intel; Inflater: Intel; Provider GCS is not available; Picard version: 2.26.10
INFO 2023-01-30 15:18:24 MarkDuplicates Start of doWork freeMemory: 115732352; totalMemory: 125829120; maxMemory: 8589934592
INFO 2023-01-30 15:18:24 MarkDuplicates Reading input file and constructing read end information.
INFO 2023-01-30 15:18:24 MarkDuplicates Will retain up to 31122951 data points before spilling to disk.
INFO 2023-01-30 15:18:24 MarkDuplicates Read 0 records. 0 pairs never matched.
INFO 2023-01-30 15:18:24 MarkDuplicates After buildSortedReadEndLists freeMemory: 227800464; totalMemory: 490733568; maxMemory: 8589934592
INFO 2023-01-30 15:18:24 MarkDuplicates Will retain up to 268435456 duplicate indices before spilling to disk.
INFO 2023-01-30 15:18:26 MarkDuplicates Traversing read pair information and detecting duplicates.
INFO 2023-01-30 15:18:26 MarkDuplicates Traversing fragment information and detecting duplicates.
INFO 2023-01-30 15:18:26 MarkDuplicates Sorting list of duplicate records.
INFO 2023-01-30 15:18:26 MarkDuplicates After generateDuplicateIndexes freeMemory: 1921945376; totalMemory: 4085252096; maxMemory: 8589934592
INFO 2023-01-30 15:18:26 MarkDuplicates Marking 0 records as duplicates.
INFO 2023-01-30 15:18:26 MarkDuplicates Found 0 optical duplicate clusters.
INFO 2023-01-30 15:18:26 MarkDuplicates Reads are assumed to be ordered by: coordinate
INFO 2023-01-30 15:18:26 MarkDuplicates Writing complete. Closing input iterator.
INFO 2023-01-30 15:18:26 MarkDuplicates Duplicate Index cleanup.
INFO 2023-01-30 15:18:26 MarkDuplicates Getting Memory Stats.
INFO 2023-01-30 15:18:26 MarkDuplicates Before output close freeMemory: 173314320; totalMemory: 184549376; maxMemory: 8589934592
INFO 2023-01-30 15:18:26 MarkDuplicates Closed outputs. Getting more Memory Stats.
INFO 2023-01-30 15:18:26 MarkDuplicates After output close freeMemory: 73334016; totalMemory: 83886080; maxMemory: 8589934592
[Mon Jan 30 15:18:26 UTC 2023] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.03 minutes.
Runtime.totalMemory()=83886080
---[ BuildBamIndex ]---
Command:
java -Xmx8g -jar /varpipe_wgs/tools/picard.jar BuildBamIndex INPUT=Output_01_30_2023/JTT20001087-FL-M04613-200220_S40/tmp/GATK/GATK_sdr.bam VALIDATION_STRINGENCY=LENIENT
Standard Error:
INFO 2023-01-30 15:18:27 BuildBamIndex
********** NOTE: Picard's command line syntax is changing.
********** For more information, please see:
********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition)
********** The command line looks like this in the new syntax:
********** BuildBamIndex -INPUT Output_01_30_2023/JTT20001087-FL-M04613-200220_S40/tmp/GATK/GATK_sdr.bam -VALIDATION_STRINGENCY LENIENT
15:18:27.586 INFO NativeLibraryLoader - Loading libgkl_compression.so from jar:file:/varpipe_wgs/tools/picard.jar!/com/intel/gkl/native/libgkl_compression.so
[Mon Jan 30 15:18:27 UTC 2023] BuildBamIndex INPUT=Output_01_30_2023/JTT20001087-FL-M04613-200220_S40/tmp/GATK/GATK_sdr.bam VALIDATION_STRINGENCY=LENIENT VERBOSITY=INFO QUIET=false COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false
[Mon Jan 30 15:18:27 UTC 2023] Executing as dongyibo@login6.ufhpc on Linux 3.10.0-1160.80.1.el7.x86_64 amd64; OpenJDK 64-Bit Server VM 17.0.4+8-Ubuntu-120.04; Deflater: Intel; Inflater: Intel; Provider GCS is not available; Picard version: 2.26.10
INFO 2023-01-30 15:18:27 BuildBamIndex Successfully wrote bam index file /varpipe_wgs/data/Output_01_30_2023/JTT20001087-FL-M04613-200220_S40/tmp/GATK/GATK_sdr.bai
[Mon Jan 30 15:18:27 UTC 2023] picard.sam.BuildBamIndex done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=432013312
---[ samtools view ]---
Command:
samtools view -c Output_01_30_2023/JTT20001087-FL-M04613-200220_S40/tmp/GATK/GATK_sdr.bam
---[ samtools view ]---
Command:
samtools view -bhF 4 -o Output_01_30_2023/JTT20001087-FL-M04613-200220_S40/JTT20001087-FL-M04613-200220_S40_sdrcsm.bam Output_01_30_2023/JTT20001087-FL-M04613-200220_S40/tmp/GATK/GATK_sdr.bam
---[ BuildBamIndex ]---
Command:
java -Xmx8g -jar /varpipe_wgs/tools/picard.jar BuildBamIndex INPUT=Output_01_30_2023/JTT20001087-FL-M04613-200220_S40/JTT20001087-FL-M04613-200220_S40_sdrcsm.bam VALIDATION_STRINGENCY=LENIENT
Standard Error:
INFO 2023-01-30 15:18:28 BuildBamIndex
********** NOTE: Picard's command line syntax is changing.
********** For more information, please see:
********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition)
********** The command line looks like this in the new syntax:
********** BuildBamIndex -INPUT Output_01_30_2023/JTT20001087-FL-M04613-200220_S40/JTT20001087-FL-M04613-200220_S40_sdrcsm.bam -VALIDATION_STRINGENCY LENIENT
15:18:28.576 INFO NativeLibraryLoader - Loading libgkl_compression.so from jar:file:/varpipe_wgs/tools/picard.jar!/com/intel/gkl/native/libgkl_compression.so
[Mon Jan 30 15:18:28 UTC 2023] BuildBamIndex INPUT=Output_01_30_2023/JTT20001087-FL-M04613-200220_S40/JTT20001087-FL-M04613-200220_S40_sdrcsm.bam VALIDATION_STRINGENCY=LENIENT VERBOSITY=INFO QUIET=false COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false
[Mon Jan 30 15:18:28 UTC 2023] Executing as dongyibo@login6.ufhpc on Linux 3.10.0-1160.80.1.el7.x86_64 amd64; OpenJDK 64-Bit Server VM 17.0.4+8-Ubuntu-120.04; Deflater: Intel; Inflater: Intel; Provider GCS is not available; Picard version: 2.26.10
INFO 2023-01-30 15:18:28 BuildBamIndex Successfully wrote bam index file /varpipe_wgs/data/Output_01_30_2023/JTT20001087-FL-M04613-200220_S40/JTT20001087-FL-M04613-200220_S40_sdrcsm.bai
[Mon Jan 30 15:18:28 UTC 2023] picard.sam.BuildBamIndex done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=432013312
---[ rm ]---
Command:
rm -r Output_01_30_2023/JTT20001087-FL-M04613-200220_S40/tmp/tmp
---[ samtools view ]---
Command:
samtools view -c Output_01_30_2023/JTT20001087-FL-M04613-200220_S40/JTT20001087-FL-M04613-200220_S40_sdrcsm.bam
---[ samtools depth ]---
Command:
samtools depth -a Output_01_30_2023/JTT20001087-FL-M04613-200220_S40/JTT20001087-FL-M04613-200220_S40_sdrcsm.bam
---[ bedtools coverage ]---
Command:
/varpipe_wgs/tools/bedtools coverage -abam Output_01_30_2023/JTT20001087-FL-M04613-200220_S40/JTT20001087-FL-M04613-200220_S40_sdrcsm.bam -b /varpipe_wgs/tools/bed_1.txt
---[ bedtools coverage ]---
Command:
/varpipe_wgs/tools/bedtools coverage -abam Output_01_30_2023/JTT20001087-FL-M04613-200220_S40/JTT20001087-FL-M04613-200220_S40_sdrcsm.bam -b /varpipe_wgs/tools/bed_2.txt
---[ sort ]---
Command:
sort -nk 6 Output_01_30_2023/JTT20001087-FL-M04613-200220_S40/tmp/SamTools/bed_1_coverage.txt
---[ sort ]---
Command:
sort -nk 6 Output_01_30_2023/JTT20001087-FL-M04613-200220_S40/tmp/SamTools/bed_2_coverage.txt
---[ target region coverage estimator ]---
Command:
python /varpipe_wgs/tools/target_coverage_estimator.py /varpipe_wgs/tools/amp_bed.txt Output_01_30_2023/JTT20001087-FL-M04613-200220_S40/tmp/SamTools/coverage.txt JTT20001087-FL-M04613-200220_S40
---[ sort ]---
Command:
sort -nk 3 Output_01_30_2023/JTT20001087-FL-M04613-200220_S40/tmp/SamTools/target_region_coverage_amp.txt
---[ genome stats estimator ]---
Command:
python /varpipe_wgs/tools/genome_stats_estimator.py Output_01_30_2023/JTT20001087-FL-M04613-200220_S40/tmp/SamTools/coverage.txt JTT20001087-FL-M04613-200220_S40
Standard Error:
Traceback (most recent call last):
File "/varpipe_wgs/tools/genome_stats_estimator.py", line 19, in
av_depth = depth/count
ZeroDivisionError: integer division or modulo by zero
---[ genome region coverage estimator ]---
Command:
python /varpipe_wgs/tools/genome_coverage_estimator.py Output_01_30_2023/JTT20001087-FL-M04613-200220_S40/tmp/SamTools/bed_1_sorted_coverage.txt Output_01_30_2023/JTT20001087-FL-M04613-200220_S40/tmp/SamTools/coverage.txt JTT20001087-FL-M04613-200220_S40
---[ genome region coverage estimator ]---
Command:
python /varpipe_wgs/tools/genome_coverage_estimator.py Output_01_30_2023/JTT20001087-FL-M04613-200220_S40/tmp/SamTools/bed_2_sorted_coverage.txt Output_01_30_2023/JTT20001087-FL-M04613-200220_S40/tmp/SamTools/coverage.txt JTT20001087-FL-M04613-200220_S40
---[ cat ]---
Command:
cat Output_01_30_2023/JTT20001087-FL-M04613-200220_S40/tmp/SamTools/genome_region_coverage_1.txt Output_01_30_2023/JTT20001087-FL-M04613-200220_S40/tmp/SamTools/genome_region_coverage_2.txt
---[ sort ]---
Command:
sort -nk 3 Output_01_30_2023/JTT20001087-FL-M04613-200220_S40/tmp/SamTools/genome_region_coverage.txt
---[ sed ]---
Command:
sed -i 1d Output_01_30_2023/JTT20001087-FL-M04613-200220_S40/JTT20001087-FL-M04613-200220_S40_genome_region_coverage.txt
---[ structural variant detector ]---
Command:
python /varpipe_wgs/tools/structvar_parser.py /varpipe_wgs/tools/BED.txt Output_01_30_2023/JTT20001087-FL-M04613-200220_S40/JTT20001087-FL-M04613-200220_S40_genome_region_coverage.txt Output_01_30_2023/JTT20001087-FL-M04613-200220_S40/tmp/SamTools/coverage.txt JTT20001087-FL-M04613-200220_S40
---[ stats estimator ]---
Command:
python /varpipe_wgs/tools/stats_estimator.py Output_01_30_2023/JTT20001087-FL-M04613-200220_S40/tmp/SamTools/unmapped.txt Output_01_30_2023/JTT20001087-FL-M04613-200220_S40/tmp/SamTools/mapped.txt Output_01_30_2023/JTT20001087-FL-M04613-200220_S40/JTT20001087-FL-M04613-200220_S40_target_region_coverage.txt JTT20001087-FL-M04613-200220_S40 Output_01_30_2023/JTT20001087-FL-M04613-200220_S40/tmp/SamTools/JTT20001087-FL-M04613-200220_S40_genome_stats.txt
Standard Error:
Traceback (most recent call last):
File "/varpipe_wgs/tools/stats_estimator.py", line 47, in
percent_mapped = (float(mapped)/float(unmapped))*100.00
ZeroDivisionError: float division by zero
########## Calling SNPs/InDels with Mutect2. ##########
---[ Mutect2 ]---
Command:
/varpipe_wgs/tools/gatk-4.2.4.0/gatk Mutect2 -R Output_01_30_2023/JTT20001087-FL-M04613-200220_S40/tmp/bwa/index/ref.fa -I Output_01_30_2023/JTT20001087-FL-M04613-200220_S40/JTT20001087-FL-M04613-200220_S40_sdrcsm.bam -O Output_01_30_2023/JTT20001087-FL-M04613-200220_S40/tmp/GATK/mutect.vcf --max-mnp-distance 2 -L /varpipe_wgs/tools/intervals.bed
Standard Error:
No local jar was found, please build one by running
or
export GATK_LOCAL_JAR=<path_to_local_jar>
---[ Mutect2 ]---
Command:
/varpipe_wgs/tools/gatk-4.2.4.0/gatk Mutect2 -R Output_01_30_2023/JTT20001087-FL-M04613-200220_S40/tmp/bwa/index/ref.fa -I Output_01_30_2023/JTT20001087-FL-M04613-200220_S40/JTT20001087-FL-M04613-200220_S40_sdrcsm.bam -O Output_01_30_2023/JTT20001087-FL-M04613-200220_S40/tmp/GATK/full_mutect.vcf --max-mnp-distance 2
Standard Error:
No local jar was found, please build one by running
or
export GATK_LOCAL_JAR=<path_to_local_jar>
---[ LeftAlignAndTrimVariants ]---
Command:
/varpipe_wgs/tools/gatk-4.2.4.0/gatk LeftAlignAndTrimVariants -R Output_01_30_2023/JTT20001087-FL-M04613-200220_S40/tmp/bwa/index/ref.fa -V Output_01_30_2023/JTT20001087-FL-M04613-200220_S40/tmp/GATK/mutect.vcf -O Output_01_30_2023/JTT20001087-FL-M04613-200220_S40/tmp/GATK/gatk_mutect.vcf --split-multi-allelics
Standard Error:
No local jar was found, please build one by running
or
export GATK_LOCAL_JAR=<path_to_local_jar>
---[ mv ]---
Command:
mv Output_01_30_2023/JTT20001087-FL-M04613-200220_S40/tmp/GATK/gatk_mutect.vcf Output_01_30_2023/JTT20001087-FL-M04613-200220_S40/tmp/GATK/mutect.vcf
Standard Error:
mv: cannot stat 'Output_01_30_2023/JTT20001087-FL-M04613-200220_S40/tmp/GATK/gatk_mutect.vcf': No such file or directory
---[ LeftAlignAndTrimVariants ]---
Command:
/varpipe_wgs/tools/gatk-4.2.4.0/gatk LeftAlignAndTrimVariants -R Output_01_30_2023/JTT20001087-FL-M04613-200220_S40/tmp/bwa/index/ref.fa -V Output_01_30_2023/JTT20001087-FL-M04613-200220_S40/tmp/GATK/full_mutect.vcf -O Output_01_30_2023/JTT20001087-FL-M04613-200220_S40/tmp/GATK/full_gatk_mutect.vcf --split-multi-allelics
Standard Error:
No local jar was found, please build one by running
or
export GATK_LOCAL_JAR=<path_to_local_jar>
---[ mv ]---
Command:
mv Output_01_30_2023/JTT20001087-FL-M04613-200220_S40/tmp/GATK/full_gatk_mutect.vcf Output_01_30_2023/JTT20001087-FL-M04613-200220_S40/tmp/GATK/full_mutect.vcf
Standard Error:
mv: cannot stat 'Output_01_30_2023/JTT20001087-FL-M04613-200220_S40/tmp/GATK/full_gatk_mutect.vcf': No such file or directory
---[ FilterMutectCalls ]---
Command:
/varpipe_wgs/tools/gatk-4.2.4.0/gatk FilterMutectCalls -R Output_01_30_2023/JTT20001087-FL-M04613-200220_S40/tmp/bwa/index/ref.fa -V Output_01_30_2023/JTT20001087-FL-M04613-200220_S40/tmp/GATK/mutect.vcf --min-reads-per-strand 1 --min-median-read-position 10 --min-allele-fraction 0.01 --microbial-mode true -O Output_01_30_2023/JTT20001087-FL-M04613-200220_S40/tmp/GATK/JTT20001087-FL-M04613-200220_S40_filter.vcf
Standard Error:
No local jar was found, please build one by running
or
export GATK_LOCAL_JAR=<path_to_local_jar>
---[ FilterMutectCalls ]---
Command:
/varpipe_wgs/tools/gatk-4.2.4.0/gatk FilterMutectCalls -R Output_01_30_2023/JTT20001087-FL-M04613-200220_S40/tmp/bwa/index/ref.fa -V Output_01_30_2023/JTT20001087-FL-M04613-200220_S40/tmp/GATK/full_mutect.vcf --min-reads-per-strand 1 --min-median-read-position 10 --min-allele-fraction 0.01 --microbial-mode true -O Output_01_30_2023/JTT20001087-FL-M04613-200220_S40/tmp/GATK/JTT20001087-FL-M04613-200220_S40_full_filter.vcf
Standard Error:
No local jar was found, please build one by running
or
export GATK_LOCAL_JAR=<path_to_local_jar>
---[ SnpEff ]---
Command:
java -Xmx4g -jar /varpipe_wgs/tools/snpEff/snpEff.jar NC_000962 Output_01_30_2023/JTT20001087-FL-M04613-200220_S40/tmp/GATK/JTT20001087-FL-M04613-200220_S40_filter.vcf
Standard Error:
Error : Cannot read input file 'Output_01_30_2023/JTT20001087-FL-M04613-200220_S40/tmp/GATK/JTT20001087-FL-M04613-200220_S40_filter.vcf'
Command line : SnpEff NC_000962 Output_01_30_2023/JTT20001087-FL-M04613-200220_S40/tmp/GATK/JTT20001087-FL-M04613-200220_S40_filter.vcf
snpEff version SnpEff 4.3r (build 2017-09-06 16:41), by Pablo Cingolani
Usage: snpEff [eff] [options] genome_version [input_file]
Options:
-chr : Prepend 'string' to chromosome name (e.g. 'chr1' instead of '1'). Only on TXT output.
-classic : Use old style annotations instead of Sequence Ontology and Hgvs.
-csvStats : Create CSV summary file.
-download : Download reference genome if not available. Default: true
-i : Input format [ vcf, bed ]. Default: VCF.
-fileList : Input actually contains a list of files to process.
-o : Ouput format [ vcf, gatk, bed, bedAnn ]. Default: VCF.
-s , -stats, -htmlStats : Create HTML summary file. Default is 'snpEff_summary.html'
-noStats : Do not create stats (summary) file
Results filter options:
-fi , -filterInterval : Only analyze changes that intersect with the intervals specified in this file (you may use this option many times)
-no-downstream : Do not show DOWNSTREAM changes
-no-intergenic : Do not show INTERGENIC changes
-no-intron : Do not show INTRON changes
-no-upstream : Do not show UPSTREAM changes
-no-utr : Do not show 5_PRIME_UTR or 3_PRIME_UTR changes
-no : Do not show 'EffectType'. This option can be used several times.
Annotations options:
-cancer : Perform 'cancer' comparisons (Somatic vs Germline). Default: false
-cancerSamples : Two column TXT file defining 'oringinal \t derived' samples.
-formatEff : Use 'EFF' field compatible with older versions (instead of 'ANN').
-geneId : Use gene ID instead of gene name (VCF output). Default: false
-hgvs : Use HGVS annotations for amino acid sub-field. Default: true
-hgvsOld : Use old HGVS notation. Default: false
-hgvs1LetterAa : Use one letter Amino acid codes in HGVS notation. Default: false
-hgvsTrId : Use transcript ID in HGVS notation. Default: false
-lof : Add loss of function (LOF) and Nonsense mediated decay (NMD) tags.
-noHgvs : Do not add HGVS annotations.
-noLof : Do not add LOF and NMD annotations.
-noShiftHgvs : Do not shift variants according to HGVS notation (most 3prime end).
-oicr : Add OICR tag in VCF file. Default: false
-sequenceOntology : Use Sequence Ontology terms. Default: true
Generic options:
-c , -config : Specify config file
-configOption name=value : Override a config file option
-d , -debug : Debug mode (very verbose).
-dataDir : Override data_dir parameter from config file.
-download : Download a SnpEff database, if not available locally. Default: true
-nodownload : Do not download a SnpEff database, if not available locally.
-h , -help : Show this help and exit
-noLog : Do not report usage statistics to server
-t : Use multiple threads (implies '-noStats'). Default 'off'
-q , -quiet : Quiet mode (do not show any messages or errors)
-v , -verbose : Verbose mode
-version : Show version number and exit
Database options:
-canon : Only use canonical transcripts.
-canonList : Only use canonical transcripts, replace some transcripts using the 'gene_id transcript_id' entries in .
-interaction : Annotate using inteactions (requires interaciton database). Default: true
-interval : Use a custom intervals in TXT/BED/BigBed/VCF/GFF file (you may use this option many times)
-maxTSL <TSL_number> : Only use transcripts having Transcript Support Level lower than <TSL_number>.
-motif : Annotate using motifs (requires Motif database). Default: true
-nextProt : Annotate using NextProt (requires NextProt database).
-noGenome : Do not load any genomic database (e.g. annotate using custom files).
-noExpandIUB : Disable IUB code expansion in input variants
-noInteraction : Disable inteaction annotations
-noMotif : Disable motif annotations.
-noNextProt : Disable NextProt annotations.
-onlyReg : Only use regulation tracks.
-onlyProtein : Only use protein coding transcripts. Default: false
-onlyTr <file.txt> : Only use the transcripts in this file. Format: One transcript ID per line.
-reg : Regulation track to use (this option can be used add several times).
-ss , -spliceSiteSize : Set size for splice sites (donor and acceptor) in bases. Default: 2
-spliceRegionExonSize : Set size for splice site region within exons. Default: 3 bases
-spliceRegionIntronMin : Set minimum number of bases for splice site region within intron. Default: 3 bases
-spliceRegionIntronMax : Set maximum number of bases for splice site region within intron. Default: 8 bases
-strict : Only use 'validated' transcripts (i.e. sequence has been checked). Default: false
-ud , -upDownStreamLen : Set upstream downstream interval length (in bases)
---[ SnpEff ]---
Command:
java -Xmx4g -jar /varpipe_wgs/tools/snpEff/snpEff.jar NC_000962 Output_01_30_2023/JTT20001087-FL-M04613-200220_S40/tmp/GATK/JTT20001087-FL-M04613-200220_S40_full_filter.vcf
Standard Error:
Error : Cannot read input file 'Output_01_30_2023/JTT20001087-FL-M04613-200220_S40/tmp/GATK/JTT20001087-FL-M04613-200220_S40_full_filter.vcf'
Command line : SnpEff NC_000962 Output_01_30_2023/JTT20001087-FL-M04613-200220_S40/tmp/GATK/JTT20001087-FL-M04613-200220_S40_full_filter.vcf
snpEff version SnpEff 4.3r (build 2017-09-06 16:41), by Pablo Cingolani
Usage: snpEff [eff] [options] genome_version [input_file]
Options:
-chr : Prepend 'string' to chromosome name (e.g. 'chr1' instead of '1'). Only on TXT output.
-classic : Use old style annotations instead of Sequence Ontology and Hgvs.
-csvStats : Create CSV summary file.
-download : Download reference genome if not available. Default: true
-i : Input format [ vcf, bed ]. Default: VCF.
-fileList : Input actually contains a list of files to process.
-o : Ouput format [ vcf, gatk, bed, bedAnn ]. Default: VCF.
-s , -stats, -htmlStats : Create HTML summary file. Default is 'snpEff_summary.html'
-noStats : Do not create stats (summary) file
Results filter options:
-fi , -filterInterval : Only analyze changes that intersect with the intervals specified in this file (you may use this option many times)
-no-downstream : Do not show DOWNSTREAM changes
-no-intergenic : Do not show INTERGENIC changes
-no-intron : Do not show INTRON changes
-no-upstream : Do not show UPSTREAM changes
-no-utr : Do not show 5_PRIME_UTR or 3_PRIME_UTR changes
-no : Do not show 'EffectType'. This option can be used several times.
Annotations options:
-cancer : Perform 'cancer' comparisons (Somatic vs Germline). Default: false
-cancerSamples : Two column TXT file defining 'oringinal \t derived' samples.
-formatEff : Use 'EFF' field compatible with older versions (instead of 'ANN').
-geneId : Use gene ID instead of gene name (VCF output). Default: false
-hgvs : Use HGVS annotations for amino acid sub-field. Default: true
-hgvsOld : Use old HGVS notation. Default: false
-hgvs1LetterAa : Use one letter Amino acid codes in HGVS notation. Default: false
-hgvsTrId : Use transcript ID in HGVS notation. Default: false
-lof : Add loss of function (LOF) and Nonsense mediated decay (NMD) tags.
-noHgvs : Do not add HGVS annotations.
-noLof : Do not add LOF and NMD annotations.
-noShiftHgvs : Do not shift variants according to HGVS notation (most 3prime end).
-oicr : Add OICR tag in VCF file. Default: false
-sequenceOntology : Use Sequence Ontology terms. Default: true
Generic options:
-c , -config : Specify config file
-configOption name=value : Override a config file option
-d , -debug : Debug mode (very verbose).
-dataDir : Override data_dir parameter from config file.
-download : Download a SnpEff database, if not available locally. Default: true
-nodownload : Do not download a SnpEff database, if not available locally.
-h , -help : Show this help and exit
-noLog : Do not report usage statistics to server
-t : Use multiple threads (implies '-noStats'). Default 'off'
-q , -quiet : Quiet mode (do not show any messages or errors)
-v , -verbose : Verbose mode
-version : Show version number and exit
Database options:
-canon : Only use canonical transcripts.
-canonList : Only use canonical transcripts, replace some transcripts using the 'gene_id transcript_id' entries in .
-interaction : Annotate using inteactions (requires interaciton database). Default: true
-interval : Use a custom intervals in TXT/BED/BigBed/VCF/GFF file (you may use this option many times)
-maxTSL <TSL_number> : Only use transcripts having Transcript Support Level lower than <TSL_number>.
-motif : Annotate using motifs (requires Motif database). Default: true
-nextProt : Annotate using NextProt (requires NextProt database).
-noGenome : Do not load any genomic database (e.g. annotate using custom files).
-noExpandIUB : Disable IUB code expansion in input variants
-noInteraction : Disable inteaction annotations
-noMotif : Disable motif annotations.
-noNextProt : Disable NextProt annotations.
-onlyReg : Only use regulation tracks.
-onlyProtein : Only use protein coding transcripts. Default: false
-onlyTr <file.txt> : Only use the transcripts in this file. Format: One transcript ID per line.
-reg : Regulation track to use (this option can be used add several times).
-ss , -spliceSiteSize : Set size for splice sites (donor and acceptor) in bases. Default: 2
-spliceRegionExonSize : Set size for splice site region within exons. Default: 3 bases
-spliceRegionIntronMin : Set minimum number of bases for splice site region within intron. Default: 3 bases
-spliceRegionIntronMax : Set maximum number of bases for splice site region within intron. Default: 8 bases
-strict : Only use 'validated' transcripts (i.e. sequence has been checked). Default: false
-ud , -upDownStreamLen : Set upstream downstream interval length (in bases)
---[ create annotation ]---
Command:
python /varpipe_wgs/tools/create_annotation.py Output_01_30_2023/JTT20001087-FL-M04613-200220_S40/JTT20001087-FL-M04613-200220_S40_DR_loci_raw_annotation.txt JTT20001087-FL-M04613-200220_S40
---[ create annotation ]---
Command:
python /varpipe_wgs/tools/create_annotation.py Output_01_30_2023/JTT20001087-FL-M04613-200220_S40/JTT20001087-FL-M04613-200220_S40_full_raw_annotation.txt JTT20001087-FL-M04613-200220_S40
---[ parse annotation ]---
Command:
python /varpipe_wgs/tools/parse_annotation.py Output_01_30_2023/JTT20001087-FL-M04613-200220_S40/JTT20001087-FL-M04613-200220_S40_DR_loci_raw_annotation.txt /varpipe_wgs/tools/mutation_loci.txt JTT20001087-FL-M04613-200220_S40
---[ parse annotation ]---
Command:
python /varpipe_wgs/tools/parse_annotation.py Output_01_30_2023/JTT20001087-FL-M04613-200220_S40/JTT20001087-FL-M04613-200220_S40_full_raw_annotation.txt /varpipe_wgs/tools/mutation_loci.txt JTT20001087-FL-M04613-200220_S40
---[ rm ]---
Command:
rm /varpipe_wgs/data/snpEff_genes.txt
Standard Error:
rm: cannot remove '/varpipe_wgs/data/snpEff_genes.txt': No such file or directory
---[ rm ]---
Command:
rm /varpipe_wgs/data/snpEff_summary.html
Standard Error:
rm: cannot remove '/varpipe_wgs/data/snpEff_summary.html': No such file or directory
---[ lineage parsing ]---
Command:
python /varpipe_wgs/tools/lineage_parser.py /varpipe_wgs/tools/lineage_markers.txt Output_01_30_2023/JTT20001087-FL-M04613-200220_S40/JTT20001087-FL-M04613-200220_S40_full_Final_annotation.txt Output_01_30_2023/JTT20001087-FL-M04613-200220_S40/JTT20001087-FL-M04613-200220_S40.lineage_report.txt JTT20001087-FL-M04613-200220_S40
---[ create summary report ]---
Command:
python /varpipe_wgs/tools/create_report.py Output_01_30_2023/JTT20001087-FL-M04613-200220_S40/JTT20001087-FL-M04613-200220_S40_stats.txt Output_01_30_2023/JTT20001087-FL-M04613-200220_S40/JTT20001087-FL-M04613-200220_S40_target_region_coverage.txt Output_01_30_2023/JTT20001087-FL-M04613-200220_S40/JTT20001087-FL-M04613-200220_S40_DR_loci_Final_annotation.txt
Standard Error:
Traceback (most recent call last):
File "/varpipe_wgs/tools/create_report.py", line 21, in
print matrix[0][0] + ":" + "\t" + matrix[1][0]
IndexError: list index out of range
---[ run interpretation report ]---
Command:
python /varpipe_wgs/tools/interprete.py /varpipe_wgs/tools/reportable.txt Output_01_30_2023/JTT20001087-FL-M04613-200220_S40/JTT20001087-FL-M04613-200220_S40_summary.txt Output_01_30_2023/JTT20001087-FL-M04613-200220_S40/JTT20001087-FL-M04613-200220_S40_structural_variants.txt Output_01_30_2023/JTT20001087-FL-M04613-200220_S40/JTT20001087-FL-M04613-200220_S40_DR_loci_annotation.txt Output_01_30_2023/JTT20001087-FL-M04613-200220_S40/JTT20001087-FL-M04613-200220_S40_target_region_coverage.txt JTT20001087-FL-M04613-200220_S40
---[ print pdf report ]---
Command:
python /varpipe_wgs/tools/pdf_print.py Output_01_30_2023/JTT20001087-FL-M04613-200220_S40/JTT20001087-FL-M04613-200220_S40_summary.txt Output_01_30_2023/JTT20001087-FL-M04613-200220_S40/JTT20001087-FL-M04613-200220_S40_report.pdf
---[ rm ]---
Command:
rm -r Output_01_30_2023/JTT20001087-FL-M04613-200220_S40/tmp
---[ rm ]---
Command:
rm Output_01_30_2023/JTT20001087-FL-M04613-200220_S40/JTT20001087-FL-M04613-200220_S40_sdrcsm.bai
---[ rm ]---
Command:
rm Output_01_30_2023/JTT20001087-FL-M04613-200220_S40/JTT20001087-FL-M04613-200220_S40_sdrcsm.bam
---[ rm ]---
Command:
rm -r Output_01_30_2023/JTT20001087-FL-M04613-200220_S40/trimmomatic
---[ rm ]---
Command:
rm -r Output_01_30_2023/JTT20001087-FL-M04613-200220_S40/clockwork
---[ rm ]---
Command:
rm /varpipe_wgs/data/config.yml
---[ rm ]---
Command:
rm -r /varpipe_wgs/data/work
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