Good Afternoon,
I am trying to run the denovo pipeline by hand but cannot input my popmap file successfully.
I have tried making serval different files, typing by hand and checking for hidden characters but keep getting the same error:
Error: Failed to parse command line: '/mnt/scratch2/GROUP-sbipao/sbijf6/work/7_denovo/popMap3.txt' is seen as a positional argument. Expected no positional arguments.
Could you please help troubleshoot?
Thanks,
Jodie
The part of my script is as follows:
.......
threads=20
workDir=/mnt/scratch2/GROUP-sbipao/sbijf6/work/7_denovo
process_radtagsDir=/mnt/scratch2/GROUP-sbipao/sbijf6/work/6_extract_birdreads/FASTQ_extracted_birds
log=${workDir}/log_denovo.txt
popMap=${workDir}/popMap3.txt
.........
cstacks -P ${denovoDir} -M ${popMap} -n 2 -p ${threads}
#echo "Step 2_3) sstacks: Match sets of stacks (ie putative loci) from ustacks against the catalog produced by cstacks " >> $log
## -P directory containing files generated by ustacks and cstacks; -M population map; -p threads; -o output directory
sstacks -P ${denovoDir} -M ${popMap} -p ${threads}
#echo "Step 2_4) tsv2bam: Transpose data so that it is orientated by locus instead of by sample; pull in the set of paired-end reads that are associated with each single-end locus that was assembled de novo " >> $log
tsv2bam -P ${denovoDir} -M ${popMap} -R ${process_radtagsDir} -t 8
My popMap fiile is:
8221952 Kirkijiev
8221958 Kirkijiev
8146878 Hojmosejev
8146879 Hojmosejev
8146880 Hojmosejev
8146873 Hojmosejev
8146883 Hojmosejev
8146884 Hojmosejev
8146886 Hojmosejev
8146888 Hojmosejev
8146889 Hojmosejev
........ ect