seqprep 150305_D00365_0435_BH2LLNBCXX --suffix '_test1' --verbose --lanes 2
seqprep 150305_NS500422_0094_AH57JTBGXX --verbose --mismatches 1 --suppressAdapterTrimming --suffix '_test1'
Once a run has begun processing, seqprep_seen.txt will be written to the run folder. If you want the cron job to process a run again, delete this file from the run’s primray_data folder.
To see current state of a processing run, look at log.txt in its log folder:
/n/informatics_external/seq/seqprep_log/<run_name>
If you started processing with the seqprep, be sure to add the suffix that you passed to seqprep to the log folder name.
A note on the NextSeq bcl2fastq2 parameter –minimum-trimmed-read-length (which corresponds to seqprep parameter –minTrimmedReadLength): When using the –use-bases-mask option, this option must be manually set to be less than or equal to the minimum read length. Otherwise, bcl2fastq 2.15.0 will N-pad the reads to the default minimum trimmed read length of 32 basepairs.
As a workaround, SeqPrep passes a value of 0 to bcl2fastq2 for the minimum trimmed read length.