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LANL-Bioinformatics / MeGAMerge

MeGAMerge (A tool to merge assembled contigs, long reads from metagenomic sequencing runs)
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Fail with status: 137 #7

Open jnarayan81 opened 7 years ago

jnarayan81 commented 7 years ago

This use to be fine on my UBUNTU, but now it fail with status: 137. I tested it on 9MB data with 256GB RAM but killed :( ... I notice, it consume all RAM and perhaps ask for more.

urbe@urbo214b[MeGAMerge] perl MeGAMerge-1.1vimal.pl corrected_MIRA_SPACES_all allCorrected.fa -d -force [] COMMAND perl MeGAMerge-1.1vimal.pl corrected_MIRA_SPACES_all allCorrected.fa -d -force The Merged FASTA will be stored in corrected_MIRA_SPACES_all/MergedContigs.fasta Reading allCorrected.fa Running Newbler assembly with 566 sequences runAssembly -force -large -rip -mi 98 -ml 80 -pairt -cpu 40 -a 0 -o corrected_MIRA_SPACES_all/newbler corrected_MIRA_SPACES_all/newblerIn.fasta Created assembly project directory corrected_MIRA_SPACES_all/newbler 1 read file successfully added. newblerIn.fasta (Fasta dataset) Assembly computation starting at: Tue May 23 16:25:54 2017 (v2.9 (20130529_1641)) Indexing newblerIn.fasta... Warning: No quality scores file found. -> 566 reads, 257471 bases. Setting up long overlap detection... -> 565 of 565, 530 reads to align Building a tree for 5108 seeds... Computing long overlap alignments...

4 sequences marked as repeats, 4 in alignments, removing from 5 chords... -> 565 of 565 Setting up overlap detection... -> 565 of 565, 556 reads to align Starting seed building... -> 565 of 565 Building a tree for 20289 seeds... Computing alignments...

5 sequences marked as repeats, 1 in alignments, removing from 3 chords... -> 565 of 565 Checkpointing... Detangling alignments... -> Level 4, Phase 9, Round 1... Checkpointing... Building contigs/scaffolds... -> 4 large contigs, 10 all contigs Computing signals... -> 7429 of 7429...
Generating output... -> 7429 of 7429...
Assembly computation succeeded at: Tue May 23 16:25:56 2017 517 newbler singletons sequences Checking 454PairAlign.txt Unique Newbler Singletons (>=0 bp): 503 opening corrected_MIRA_SPACES_all/minimus.fasta for writing opening corrected_MIRA_SPACES_all/largefile.fasta for reading opening corrected_MIRA_SPACES_all/newbler/All.fasta for reading Running Minimus2 with 568 sequences Max ID: 1707 minimus2 -D CONSERR=0.06 -D MINID=98 -D OVERLAP=80 corrected_MIRA_SPACES_all/minimus.fasta The log file is: corrected_MIRA_SPACES_all/minimus.fasta.runAmos.log Doing step 10: Building AMOS bank & Dumping reads Doing step 11 Doing step 12 Doing step 13 Doing step 20: Getting overlaps Doing step 21 Doing step 22 Doing step 23: Converting overlaps Doing step 24: Loading overlaps to the bank Doing step 25 Doing step 30: Running contigger Doing step 31 Doing step 40: Running consensus Doing step 41 Command: /home/urbe/Tools/amos-3.1.0/bin/make-consensus -B -e 0.06 -b corrected_MIRA_SPACES_all/minimus.fasta.bnk -w 15 exited with status: 137 minimus2 -D CONSERR=0.06 -D MINID=98 -D OVERLAP=80 corrected_MIRA_SPACES_all/minimus.fasta failed: Died at MeGAMerge-1.1vimal.pl line 283.