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lbcb-sci / graphmap2

GraphMap - A highly sensitive and accurate mapper for long, error-prone reads http://www.nature.com/ncomms/2016/160415/ncomms11307/full/ncomms11307.html https://www.biorxiv.org/content/10.1101/720458v1
MIT License
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Sam file not create it killed #14

Open aman21392 opened 4 years ago

aman21392 commented 4 years ago

/home/aclab/apps/graphmap2/bin/Linux-x64/graphmap2 align -r Homo_sapiens.fa -i /Drive4/graphmap2/Homo_sapiens.fa.gmidx -d combined_T.fastq -o homo.sam

e313594bd264 runi...[19:21:34 BuildIndexes] Loading reference sequences. [19:28:18 SetupIndex_] Loading index from file: '/Drive4/graphmap2/Homo_sapiens.fa.gmidx'. [19:40:42 Index] Memory consumption: [currentRSS = 156693 MB, peakRSS = 217297 MB] [19:40:42 Run] Hits will be thresholded at the percentil value (percentil: 99.000000%, frequency: 1496). [19:40:42 Run] Minimizers will be used. Minimizer window length: 5 [19:40:42 Run] Automatically setting the maximum allowed number of regions: max. 5101, attempt to reduce after 0 [19:40:42 Run] Reference genome is assumed to be linear. [19:40:42 Run] Only one alignment will be reported per mapped read. [19:40:42 ProcessReads] Reads will be loaded in batches of up to 1024 MB in size. [19:40:47 ProcessReads] Batch of 482940 reads (1024 MiB) loaded in 4.71 sec. (93960397030528 bases) [19:40:47 ProcessReads] Memory consumption: [currentRSS = 157878 MB, peakRSS = 217297 MB] [19:40:47 ProcessReads] Using 24 threads. [19:40:47 ProcessReads] [CPU time: 4.72 sec, RSS: 157878 MB] Read: 10/482940 (0.00%) [m: 0, u: 0], length = 229, qname: bed425b1-097a-4528-a5a0-8e9c41d99ffb run...

After than it killed.
I have memory 500gb so its not a problem i think but it killed always i tried many times. Can you please help me what is the problem.

Wardale24 commented 4 years ago

Hello,

I ran into the same issue and can't seem to resolve it:

bin/Linux-x64/graphmap2 align -x rnaseq -r /home/alex/Desktop/Zbf_adult_polyA/Zbf_adult/mapping/Danio_rerio.GRCz11.dna.primary_assembly.fa -d /home/alex/Desktop/Zbf_adult_polyA/Zbf_adult/fastq_trimmed/trimmed_10_50reads.fastq -o alignments.sam [15:55:00 BuildIndexes] Loading reference sequences. [15:55:09 SetupIndex] Building the index for shape: '11110111101111'. [15:55:12 Create] Allocated memory for a list of 686735693 seeds (128 bits each) (0.00001 sec, diff: 2.77950 sec). [15:55:12 Create] Memory consumption: [currentRSS = 3934 MB, peakRSS = 3960 MB] [15:55:12 Create] Collecting seeds. [15:55:12 Create] Minimizer seeds will be used. Minimizer window is 5. [15:55:58 Create] [currentRSS = 14366 MB, peakRSS = 14366 MB] Sequence: 1003/1986, len: 51023478, name: '18'Killed

AW