*.auc.threshold.merge.bed not created

[MariaRig]

Hello,
I'm running seacr in the following mode:

        $seacr $input_folder/$sample\_Normalized.sorted.bedgraph \
        $input_folder/$control\_Normalized.sorted.bedgraph \
        non relaxed $sample\_seacr.peaks

And the process doesn't finish and I get the following error because the merged file is not created:

Merging nearby features and eliminating control-enriched features: Fri Nov 19 17:43:58 CET 2021
SEACR_1.3.sh: line 169: noDOX_seacr.peaks.auc.threshold.merge.bed: No such file or directory

This only happens with the non&relaxed combinations. Not with non&stringent, norm&relaxed or norm&stringent, which all work.
Line 169 in SEACR_1.3.sh is :

awk -v value=$mean 'BEGIN{s=1}; {if(s==1){chr=$1; start=$2; stop=$3; auc=$4; max=$5; coord=$6; s++}else{if(chr==$1 && $2 < stop+value){stop=$3; auc=auc+$4; if($5 > max){max=$5; coord=$6}else if($5==max){split(coord,t,"-"); split($6,u,"-"); coord=t[1]"-"u[2]}}else{print chr"\t"start"\t"stop"\t"auc"\t"max"\t"coord; chr=$1; start=$2; stop=$3; auc=$4; max=$5; coord=$6}}}' $password.auc.threshold.bed | bedtools intersect -wa -v -a - -b $password2.auc.threshold.bed > $5.auc.threshold.merge.bed 

I was wondering if it could have to do with the last part, where the -a bed file is not specified and there is just a "-".

Thank you

[mpmeers]

Hi,

This seems like it may be an error that's specific to your input files since I can't replicate it with my internal test files and since there's a non-relaxed specific failure that might indicate some data quality issue. However, the "-a -" is simply passing the output from before the pipe to bedtools, so I don't think that specific error would arise at that line. It's even more odd since line 169 should be writing that file rather than accessing it, so that specific error shouldn't arise until line 176 where the file is renamed. Can you verify that the code you're using is identical to the v1.3 code presented in the master branch? If you're willing to share data I can also give it a try to see if I can identify specific issues.

Mike

[ptsourkas]

I am also getting the same error, except I get it for all parameters (non, norm, relaxed, stringent).

[ptsourkas]

I was able to run it without error by writing changing the directory to which I was writing the output file. Not sure why, but it worked for me.