s1_bwaAlignment.sh: line 30: [: GATC: integer expression expected

[abhisheksinghnl]

Hi,

I put GATC as my cut site and when I run trhe program I get this message

 bash s1_bwaAlignment.sh "$name" "$ref" "$bwaDir" "$samtoolsDir" "$fastqDir" "$resultsDir/s1" "$bin" "$nCores" "$resultsDir/mHiC.summary_w${resolution}_s1" "$saveFiles" "${cutsite[@]}"
s1_bwaAlignment.sh: line 30: [: GATC: integer expression expected
(We assume the reads length are the same within the same fastq file.)......
Start alignment of read end 1
Step1.1 - BWA alignment
[bwa_aln_core] calculate SA coordinate... 64.42 sec
[bwa_aln_core] write to the disk... 0.07 sec
[bwa_aln_core] 262144 sequences have been processed.
[bwa_aln_core] calculate SA coordinate... 63.31 sec
[bwa_aln_core] write to the disk... 0.07 sec

Could please let me know, what shall I do to fix this, if it is a warning/error.

Thank you

[yezhengSTAT]

So sorry to get it back this late! Somehow GitHub didn't push notification to me. Apologize for the late reply!!

It seems that you missed the 11th parameter which is read length. Give a "25" before "${cutsite[@]}". Besides, please set "cutsite=GATCGATC" which is the sequence at the ligation site.

Thanks for using mHi-C!

Ye