Reads are good but throws error: "Sequence/quality scores do not match" about ngmerge

[jsh58]

Thanks for the question, and for including the dataset.

Unfortunately, I cannot reproduce the error. Here is the command and verbose output:

$ ./NGmerge \
  -1 reads_NC_008261.1.100.101.10_R1.fq.gz \
  -2 reads_NC_008261.1.100.101.10_R2.fq.gz \
  -o merged \
  -t '/' \
  -v
Processing files: reads_NC_008261.1.100.101.10_R1.fq.gz,reads_NC_008261.1.100.101.10_R2.fq.gz
  Fragments (pairs of reads) analyzed: 162830
  Successfully stitched: 126562

As you can see, using -t '/' solves the header issue. I wonder if, when you were dealing with the header issue, you substituted ' ' before every /, thus possibly introducing spaces in some of the quality score strings.

[pjaborges]

Yes, you are correct.
I introduced spaces in the quality score strings when doing the replace.

It worked perfectly!
Thanks

[Kaderi15]

Dear Sir
I got the "Error! @ERR3385738.1.1: not matched in input files" when run NGmerge to merge sequences. Please help me, sir. Sir I have attached my sample sequence files herewith.
Command: $ ./NGmerge -1 CDTC160004_R1.fastq.gz -2 CDTC160004_R2.fastq.gz -t ' ' -o merged -v

CDTC160075_S95_L001_R1_trim.fastq.gz

CDTC160075_S95_L001_R2_trim.fastq.gz

[jsh58]

Please open a New Issue. This is unrelated to #12