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Thank you to all the Monks! I made the mods suggested by you, GrandFather, and by the Monks before you on this node. For the larger datasets there does not appear to be any difference. I am running one such job, and its been 30 minutes already. As you point out, the problem is likely with my algorithm/logic/approach in EXTRACT and START loops not scaling up well...Any thoughts on improving this scale-up for massive files? Some input file datasets can be found at http://bit.ly/1K69JuQ

The command line syntax would be

perl Length_dstrbtn_seq_extractor.pl Ath167_sORF.facleaned-up_ReMapped_v2-5p-flanking.fa Athaliana_167_TAIR10.cds_primaryTranscriptOnly.facleaned-up

perl Length_dstrbtn_seq_extractor.pl Ath167_sORF.facleaned-up_ReMapped_v2-5p-flanking.fa Athaliana_167_intron_ONLY_FASTextract-intronic-seqs.fasta

perl Length_dstrbtn_seq_extractor.pl Ath167_sORF.facleaned-up_ReMapped_v2-3p-flanking.fa Athaliana_167_TAIR10.cds_primaryTranscriptOnly.facleaned-up

perl Length_dstrbtn_seq_extractor.pl Ath167_sORF.facleaned-up_ReMapped_v2-3p-flanking.fa Athaliana_167_intron_ONLY_FASTextract-intronic-seqs.fasta

There are other datasets, some super small, and one set that is still uploading that is very very large

In reply to Re^2: Speeding up stalled script by Anonymous Monk
in thread Speeding up stalled script by onlyIDleft

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