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kensung-lab / hypo-assembler

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Error while writing to temporary file #18

Closed JianhuaCao closed 2 months ago

JianhuaCao commented 2 months ago

Hi, guys: here, we report a error: log output:

Short read file 1: /data/b/wu/1-data/sg.wu1-2_1.fq.gz Short read file 2: /data/b/wu/1-data/sg.wu1-2_2.fq.gz Long reads: /data/b/wu/1-data/ont.pass.wu2.fa.gz Using 10 threads Using /data/c/_t as temporary directory. Using initial draft: /data/b/wu/2-asm_wu/wu2v2.chr.fa.gz Long read mapping: /data/b/wu/3-ont-to-asm/r2/wu2v2.csrt.bam [STEP 1] Getting solid kmers

Stage 1: 26%Error: Error while writing to temporary file 319 <==== Error here! RESOURCES ([SUK:KMC]: Running KMC done. ): TIME= 133.931 sec; PEAK RSS (so far)= 2071MB; CURRENT RSS (so far)= 2071MB. Failed to open KMC database. <=== what's this DB? [STEP 2] Scanning misjoin ....

Our script: ./run_all.sh -1 $fq1 -2 $fq2 -l $long -t 10 -T $tmp -o $pfix -d $draft -B $bam -s $gsize >$log 2>&1

My question: 1) how to solve this writing error? 2) Failed to open KMC db, what's it?

Thank you in advance.

Cao Huazhong Agricultural University, China.

JianhuaCao commented 2 months ago

Problem solved! Cau's KMC need big mem. The 2.5Gb gsize, say pig assembly, need about 200G mem. default is 12G, not enough.