ChIA-PET2 ERROR: The input file is neither a BAM file nor a SAM file.

Question

[bioinfo89]

Hi All,

I am using ChIA-PET2 tool to process the data. I am subsampling reads (0.1 to 0.9) using seqtk and running the ChIA-PET pipeline and I get the following error:

ERROR: The input file is neither a BAM file nor a SAM file.

I checked the sam files they appear to be fine (using Picard ValidateSamFile). I am not sure what exactly is causing this error in the pipeline. It was running fine before. Any help would be great to resolve this.

Thanks!

[Ram]

Please show us the exact commands you're using.

[bioinfo89]

 seqtk sample -s100 SRR_1.fastq 0.1 >R1_1_sub0.1.fastq
 seqtk sample -s100 SRR_2.fastq 0.1 >R2_2_sub0.1.fastq

 ####Running ChIA-PET2 :

ChIA-PET2-0.9.3/bin/ChIA-PET2 -t 10 -g hg19.fa -b hg19.chrom.sizes -f R1_1_sub0.1.fastq.gz -r R2_2_sub0.1.fastq.gz -m 1 -A CGCGATATCTTATCTGACT -B GTCAGATAAGATATCGCGT -e 2 -k 2 -l 12 -C 1 -o 0.1 -n ChIAPETV2_0.1

[ATpoint]

seqtk output is .fastq, you feed .fastq.gz into the tool, is that true, did you compress them? Maybe a wrong suffix here?

[bioinfo89]

Yes I did compress it. But the output works fine.