Open shanmugavadivelps opened 3 years ago
This error seems to fail the concatenation of log files. Please check the files in /media/iipruser/Drive_2/FW_qtlseq_icrisat2/log/. If you could find the log file related to bcftools, you may find why bcftools 'mpileup' failed.
kindly mention the organism. If the genome assembly consist of many scaffold or contigs (>15), this could be a reason the QTL-seq throws an error. IN that case, extract maximum10-15 scaffold/contig's variants at a time to generate the graph of QTL-seq.
On Wed, Jul 6, 2022 at 9:14 AM anusinghrao @.***> wrote:
I am using version 2.2.2 installed manually and encountering error during vcf generation after successful completion of bam file generation.
the error as follows
File "/home/iipruser/yes/bin/qtlseq", line 33, in sys.exit(load_entry_point('qtlseq', 'console_scripts', 'qtlseq')()) File "/home/iipruser/QTL-seq/qtlseq/qtlseq.py", line 171, in main QTLseq(args).run() File "/home/iipruser/QTL-seq/qtlseq/qtlseq.py", line 166, in run self.mpileup() File "/home/iipruser/QTL-seq/qtlseq/qtlseq.py", line 122, in mpileup mp.run() File "/home/iipruser/QTL-seq/qtlseq/mpileup.py", line 231, in run self.concat() File "/home/iipruser/QTL-seq/qtlseq/mpileup.py", line 182, in concat sbp.run(cmd1, stdout=sbp.DEVNULL, stderr=sbp.DEVNULL, shell=True, check=True) File "/home/iipruser/yes/lib/python3.8/subprocess.py", line 512, in run raise CalledProcessError(retcode, process.args, subprocess.CalledProcessError: Command 'cat /media/iipruser/Drive_2/FW_qtlseq_icrisat2/log/bcftools.*.log > /media/iipruser/Drive_2/FW_qtlseq_icrisat2/log/bcftools.log' returned non-zero exit status 2.
pls help me to solve
Hello! I am getting the same error. Please share how did you resolve this issue?
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Govt. of India,Kanpur - 208 024. *email: @. @.> https://iipr.icar.gov.in/ https://iipr.icar.gov.in/*
I am using version 2.2.2 installed manually and encountering error during vcf generation after successful completion of bam file generation.
the error as follows
File "/home/iipruser/yes/bin/qtlseq", line 33, in
sys.exit(load_entry_point('qtlseq', 'console_scripts', 'qtlseq')())
File "/home/iipruser/QTL-seq/qtlseq/qtlseq.py", line 171, in main
QTLseq(args).run()
File "/home/iipruser/QTL-seq/qtlseq/qtlseq.py", line 166, in run
self.mpileup()
File "/home/iipruser/QTL-seq/qtlseq/qtlseq.py", line 122, in mpileup
mp.run()
File "/home/iipruser/QTL-seq/qtlseq/mpileup.py", line 231, in run
self.concat()
File "/home/iipruser/QTL-seq/qtlseq/mpileup.py", line 182, in concat
sbp.run(cmd1, stdout=sbp.DEVNULL, stderr=sbp.DEVNULL, shell=True, check=True)
File "/home/iipruser/yes/lib/python3.8/subprocess.py", line 512, in run
raise CalledProcessError(retcode, process.args,
subprocess.CalledProcessError: Command 'cat /media/iipruser/Drive_2/FW_qtlseq_icrisat2/log/bcftools.*.log > /media/iipruser/Drive_2/FW_qtlseq_icrisat2/log/bcftools.log' returned non-zero exit status 2.
pls help me to solve