praneetha92
commented
3 years ago Hi @hannyxie I am facing this same error,can you please tell me how did you solve this problem? QTL-seq version:-2.1.2
Closed hannyxie closed 3 years ago
praneetha92
commented
3 years ago Hi @hannyxie I am facing this same error,can you please tell me how did you solve this problem? QTL-seq version:-2.1.2
hannyxie
commented
3 years ago reinstall bcftools and make sure input sample name correctly
I used it well before, but this time I don’t know what happened. the version is qtlseq 2.1.2。 [QTL-seq:2020-09-08 00:03:05] [QTL-seq:2020-09-08 00:03:05] !!ERROR!! bcftools mpileup -a AD,ADF,ADR -B -q 40 -Q 18 -C 50 -O u -r chr03 -f stigma3/10_ref/IRGSP-1.0_genome.fasta --ignore-RG stigma3/20_bam/parent.filt.bam stigma3/20_bam/bulk1.filt.bam stigma3/20_bam/bulk2.filt.bam | bcftools call -vm -f GQ,GP -O u | bcftools filter -i "INFO/MQ>=40" -O z -o stigma3/30_vcf/qtlseq.chr03.vcf.gz >> stigma3/log/bcftools.chr03.log 2>&1 please check below:
please check below:
multiprocessing.pool.RemoteTraceback: """ Traceback (most recent call last): File "/home/xiehan1223/miniconda3/envs/bioinfo/lib/python3.7/site-packages/qtlseq/mpileup.py", line 144, in mpileup check=True) File "/home/xiehan1223/miniconda3/envs/bioinfo/lib/python3.7/subprocess.py", line 512, in run output=stdout, stderr=stderr) subprocess.CalledProcessError: Command 'bcftools mpileup -a AD,ADF,ADR -B -q 40 -Q 18 -C 50 -O u -r chr09 -f stigma3/10_ref/IRGSP-1.0_genome.fasta --ignore-RG stigma3/20_bam/parent.filt.bam stigma3/20_bam/bulk1.filt.bam stigma3/20_bam/bulk2.filt.bam | bcftools call -vm -f GQ,GP -O u | bcftools filter -i "INFO/MQ>=40" -O z -o stigma3/30_vcf/qtlseq.chr09.vcf.gz >> stigma3/log/bcftools.chr09.log 2>&1' returned non-zero exit status 255.
During handling of the above exception, another exception occurred:
Traceback (most recent call last): File "/home/xiehan1223/miniconda3/envs/bioinfo/lib/python3.7/multiprocessing/pool.py", line 121, in worker result = (True, func(*args, *kwds)) File "/home/xiehan1223/miniconda3/envs/bioinfo/lib/python3.7/multiprocessing/pool.py", line 44, in mapstar return list(map(args)) File "/home/xiehan1223/miniconda3/envs/bioinfo/lib/python3.7/site-packages/qtlseq/mpileup.py", line 146, in mpileup call_log(self.out, 'bcftools', cmd1) File "/home/xiehan1223/miniconda3/envs/bioinfo/lib/python3.7/site-packages/qtlseq/utils.py", line 20, in call_log with open('{}/log/{}.log'.format(out_dir, name)) as log: FileNotFoundError: [Errno 2] No such file or directory: 'stigma3/log/bcftools.log' """
The above exception was the direct cause of the following exception:
Traceback (most recent call last): File "/home/xiehan1223/miniconda3/envs/bioinfo/bin/qtlseq", line 10, in
sys.exit(main())
File "/home/xiehan1223/miniconda3/envs/bioinfo/lib/python3.7/site-packages/qtlseq/qtlseq.py", line 173, in main
QTLseq(args).run()
File "/home/xiehan1223/miniconda3/envs/bioinfo/lib/python3.7/site-packages/qtlseq/qtlseq.py", line 168, in run
self.mpileup()
File "/home/xiehan1223/miniconda3/envs/bioinfo/lib/python3.7/site-packages/qtlseq/qtlseq.py", line 123, in mpileup
mp.run()
File "/home/xiehan1223/miniconda3/envs/bioinfo/lib/python3.7/site-packages/qtlseq/mpileup.py", line 229, in run
p.map(self.mpileup, chr_names)
File "/home/xiehan1223/miniconda3/envs/bioinfo/lib/python3.7/multiprocessing/pool.py", line 268, in map
return self._map_async(func, iterable, mapstar, chunksize).get()
File "/home/xiehan1223/miniconda3/envs/bioinfo/lib/python3.7/multiprocessing/pool.py", line 657, in get
raise self._value
FileNotFoundError: [Errno 2] No such file or directory: 'stigma3/log/bcftools.log'stigma3/20_bam/parent.filt.bam stigma3/20_bam/bulk1.filt.bam stigma3/20_bam/bulk2.filt.bam | bcftools call -vm -f GQ,GP -O u | bcftools filter -i "INFO/MQ>=40" -O z -o stigma3/30_vcf/qtlseq.chr03.vcf.gz >> stigma3/log/bcftools.chr03.log 2>&1
please check below:
please check below:
multiprocessing.pool.RemoteTraceback: """ Traceback (most recent call last): File "/home/xiehan1223/miniconda3/envs/bioinfo/lib/python3.7/site-packages/qtlseq/mpileup.py", line 144, in mpileup check=True) File "/home/xiehan1223/miniconda3/envs/bioinfo/lib/python3.7/subprocess.py", line 512, in run output=stdout, stderr=stderr) subprocess.CalledProcessError: Command 'bcftools mpileup -a AD,ADF,ADR -B -q 40 -Q 18 -C 50 -O u -r chr09 -f stigma3/10_ref/IRGSP-1.0_genome.fasta --ignore-RG stigma3/20_bam/parent.filt.bam stigma3/20_bam/bulk1.filt.bam stigma3/20_bam/bulk2.filt.bam | bcftools call -vm -f GQ,GP -O u | bcftools filter -i "INFO/MQ>=40" -O z -o stigma3/30_vcf/qtlseq.chr09.vcf.gz >> stigma3/log/bcftools.chr09.log 2>&1' returned non-zero exit status 255.
During handling of the above exception, another exception occurred:
Traceback (most recent call last): File "/home/xiehan1223/miniconda3/envs/bioinfo/lib/python3.7/multiprocessing/pool.py", line 121, in worker result = (True, func(*args, *kwds)) File "/home/xiehan1223/miniconda3/envs/bioinfo/lib/python3.7/multiprocessing/pool.py", line 44, in mapstar return list(map(args)) File "/home/xiehan1223/miniconda3/envs/bioinfo/lib/python3.7/site-packages/qtlseq/mpileup.py", line 146, in mpileup call_log(self.out, 'bcftools', cmd1) File "/home/xiehan1223/miniconda3/envs/bioinfo/lib/python3.7/site-packages/qtlseq/utils.py", line 20, in call_log with open('{}/log/{}.log'.format(out_dir, name)) as log: FileNotFoundError: [Errno 2] No such file or directory: 'stigma3/log/bcftools.log' """
The above exception was the direct cause of the following exception:
Traceback (most recent call last): File "/home/xiehan1223/miniconda3/envs/bioinfo/bin/qtlseq", line 10, in
sys.exit(main())
File "/home/xiehan1223/miniconda3/envs/bioinfo/lib/python3.7/site-packages/qtlseq/qtlseq.py", line 173, in main
QTLseq(args).run()
File "/home/xiehan1223/miniconda3/envs/bioinfo/lib/python3.7/site-packages/qtlseq/qtlseq.py", line 168, in run
self.mpileup()
File "/home/xiehan1223/miniconda3/envs/bioinfo/lib/python3.7/site-packages/qtlseq/qtlseq.py", line 123, in mpileup
mp.run()
File "/home/xiehan1223/miniconda3/envs/bioinfo/lib/python3.7/site-packages/qtlseq/mpileup.py", line 229, in run
p.map(self.mpileup, chr_names)
File "/home/xiehan1223/miniconda3/envs/bioinfo/lib/python3.7/multiprocessing/pool.py", line 268, in map
return self._map_async(func, iterable, mapstar, chunksize).get()
File "/home/xiehan1223/miniconda3/envs/bioinfo/lib/python3.7/multiprocessing/pool.py", line 657, in get
raise self._value
FileNotFoundError: [Errno 2] No such file or directory: 'stigma3/log/bcftools.log'