make.contigs stops before command is completed

Commands in mothur
1

Hello there,

I am using make.contigs for ~400 fastq files from Illumina HiSeq sequencing. Somehow it stops after 72 files. Here the last lines in the logfile:


>>>>> Processing file pair 7-050112-1-3_1.fastq - 7-050112-1-3_2.fastq (files 72 of 394) <<<<< ILLUMINA_281_C27D3ACXX_6_2107_13613_38480 is in your forward fastq file and not in your reverse file, please remove it using the remove.seqs command before proceeding. ILLUMINA_281_C27D3ACXX_6_2205_14092_39924 is in your forward fastq file and not in your reverse file, please remove it using the remove.seqs command before proceeding. ILLUMINA_281_C27D3ACXX_6_2303_6649_15780 is in your forward fastq file and not in your reverse file, please remove it using the remove.seqs command before proceeding.
I've run make.contigs many times before and it's never given this issue. ANy ideas? I checked both the oligos and the file files and they both look fine compared to other files I used without issues before. Any ideas are more than welcome, I've run this 3 times with the same problem, stopping at the same file.

Thanks,

Claire

2

It sounds like there are some missing reads that file. Have you tried running the command without that sample in the files file, and running that sample alone after removing the problem reads? You can always use the merge.files command to combine your results later.