theislab / bartseq-pipeline Goto Github PK

Hello,

Thank you for your prompt reply for the other issue I opened. I couldn't solve my problem but I realised it might be connected with those commands that are not exist for MacOS. "cp -T" command in "rule seqs_universal" and "rule seqs_by_lib"; "cut" command in "rule map_reads". The error I get is:

cut: illegal option -- - usage: cut -b list [-n] [file ...] cut -c list [file ...] cut -f list [-s] [-w | -d delim] [file ...]

and it is a similar error for the "cp -T" command.

Therefore, I altered them as below:

cp -T:
shell: 'cp -R {input:q} {output:q}'

cut:
I installed gcutils and altered the "cut" command as "gcut". It did not work.
Then I tried:
cut -f 3,10 --output-delimiter='\t' > {output.map:q}
it also did not work.

(By the way, it was the same with "zcat". I installed coreutils and used "gzcat" and it works.)

Now my error is the same as the one before and it says: "(ERR): hisat2-align died with signal 13 (PIPE)".

Unfortunately, I am not experienced, and I could not understand the solution you referred before. I don't know how to run the code on bash without giving the input files. And, I tried --printshellcmds tag, but it didn't show anything new; or I couldn't apply it correctly. I have a feeling that it is because of the inoperative "cut" command instead of a RAM issue.

As a note: I use Macbook Pro M1 2020 and I assume it has enough RAM power to run this. I tried "snakemake --cores" all but did not work.

Thank you very much for your time.
Best regards,
Merve

Hello!

I am a master's student at the Charité Berlin. I am using the BART-Seq technique for my master's thesis project but I get some errors through the pipeline. Could you please help me?

Kind regards,
Merve

Error in rule map_reads:
    jobid: 10
    output: process/4-mapped/R1_001_S0_R1.tsv, process/4-mapped/R1_001_S0_R1_summary.txt
    shell:
        
		hisat2 			--threads 2 			--reorder 			-k 1 			-3 34 			-x process/1-index/amplicons/R1_001_S0 			--new-summary --summary-file process/4-mapped/R1_001_S0_R1_summary.txt 			-q -U process/3-tagged/R1_001_S0_R1.fastq.gz | 			grep -v "^@" - | 		cut -f3,10 --output-delimiter='	' > process/4-mapped/R1_001_S0_R1.tsv
		
        (one of the commands exited with non-zero exit code; note that snakemake uses bash strict mode!)