failed to run the gapless.sh

[kovimallik]

Hi,

I downloaded the gapless-0.4 and ran the gapless.sh

sh gapless.sh -j 40 -i genome.fasta -t nanopore porechop_output.fastq.gz -o /mnt/project/IPV2/gapless/gapless/final_output_assembly/

But it is showing the following error

gapless.sh: line 162: syntax error near unexpected token (' gapless.sh: line 162: env time -v -o pass${i}/timing/minimap2_extension.txt minimap2 -t $threads -x $mm_ava <(seqtk subseq "${reads}" pass${i}/gapless_extending_reads.lst) <(seqtk subseq "${reads}" pass${i}/gapless_extending_reads.lst) > pass${i}/gapless_extending_reads.paf 2>pass${i}/logs/minimap2_extension.log || rm -f pass${i}/gapless_extending_reads.paf'

It would be great, if you could look into this error and help out.

With thanks, Mallik

[schmeing]

I strongly assume that the crash is caused by the -o /mnt/project/IPV2/gapless/gapless/final_output_assembly/ after the read file specification porechop_output.fastq.gz. sh gapless.sh -j 40 -i genome.fasta -o /mnt/project/IPV2/gapless/gapless/final_output_assembly/ -t nanopore porechop_output.fastq.gz is how you should run it.

Nevertheless, I am verifying that this causes the syntax error you mentioned and there is not another issue on top. Additionally, I will add a warning that you should not put parameters after the file.

[schmeing]

I added an error message, but the order of the options is not the cause of the error you provided. gapless simply ignores the -o option in this case.

[schmeing]

I cannot reproduce this error under ubuntu linux. What system are you using?