alignGraph failed with error: INCONSISTENT PE FILES!

[wul88]

Hi, Bao,

I used the following command to run alignGraph:
AlignGraph --read1 Oka_S2_R1_002trim.fa
--read2 Oka_S2_R2_002trim.fa
--contig soap_contig.fa --genome oka_HiC_23chromOnly.fa
--distanceLow 150 --distanceHigh 1150
--extendedContig extendedContig.fa
--remainingContig remainingContig.fa --kMer 17
-insertVariation 100

I am also getting the error, INCONSISTENT PE FILES! But the input paired-end files contain the same number of sequences (checked with bioawk -cfastx 'END{print NR}' input_file). The input PE files were trimmed by bbMap quality trim module (using command bbduk.sh -Xmx1g ...)

I wondered what could be wrong here? Can AlignGraph work on un-trimmed PE data? or AlignGraph prefer data trimmed by trimmomatic?

Thank you for your advice!
Lan

[peanut-buddy]

Hello,
I'm getting the same error. I trimmed my files with Trim Galore. Were you able to resolve your issue?
Thank you!