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vice87 / gam-ngs

Genomic Assemblies Merger for NGS
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segmentation fault during gam-merge #21

Closed jvollme closed 9 years ago

jvollme commented 9 years ago

Hi, I'm running GAM-NGS on a machine with 80Gb RAM 32 cores and OS=ubuntu 14.04. gam-create seems to function fine but gam-merge aborts with an "segmentation fault". However the assemblies I want to merge are rather small and work with normalized reads (therefor the libaries are rather small also) I've tried to check memory consumption during gam-merge, in order to find out if my RAM is insufficient, but could not see any increase in RAM usage during gam-merge (gam-merge seems to about the second i start the process).

What could be the problem?

heres the output: /usr/local/tools/gam-ngs/bin/gam-merge --master-bam master.PE.bams.txt --slave-bam slave.PE.bams.txt --blocks-file Blocks_sc3_sc2.blocks --master-fasta /home/john/projects/sc3_pm_1230/results/assemblies/150105/Optimized_spades_corrCLRasCLR_withreference/comparison6_K21-77_normC20K20/contigs.fasta --slave-fasta /home/john/projects/sc2_pm_1230/results/assemblies/150105/Optimized_spades_corrCLRasCLR_withreference/comparison7_K21-77_normC5K20/contigs.fasta --min-block-size 10 --threads 16 --output merged_sc3_sc2 [main] Loading blocks [main] Loaded blocks = 323 [main] Loading BAMs data [bam] Master PE-alignments file master.PE.bams.txt successfully opened: contigs.fasta_readssc3_vs_sc3_bt2_result.sorted.bam inserts size = 182.283 +/- 54.8718 coverage = 29.083 contigs.fasta_readssc2_vs_sc3_bt2_result.sorted.bam inserts size = 254.28 +/- 90.4223 coverage = 19.6787 [bam] Slave PE-alignments file slave.PE.bams.txt successfully opened: contigs.fasta_readssc3_vs_sc2_bt2_result.sorted.bam inserts size = 182.283 +/- 54.8718 coverage = 29.083 contigs.fasta_readssc2_vs_sc2_bt2_result.sorted.bam inserts size = 254.28 +/- 90.4223 coverage = 19.6787 [main] Loading contigs data...done. Master Assembly: sequences = 367 total length = 899682 Slave Assembly: sequences = 367 total length = 899682 [main] Retrieving contigs without blocks...done. [main] Filtering blocks by coverage [main] Remaining blocks = 323 [main] Retrieving contigs with no blocks after coverage filtering...done. [main] Partitioning blocks [main] Loading contig sequences master sequences loaded = 367 zsh: segmentation fault /usr/local/tools/gam-ngs/bin/gam-merge --master-bam master.PE.bams.txt

jvollme commented 9 years ago

I forgot to specify: I'm using GAM-NGS v1.1b

jvollme commented 9 years ago

Found the error: A simple mix up with the input data (GAM-NGS runs fine).