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yechengxi / DBG2OLC

A genome assembler that reduces the computational time of human genome assembly from 400,000 CPU hours to 2,000 CPU hours, utilizing long erroneous 3GS sequencing reads and short accurate NGS sequencing reads.
GNU General Public License v3.0
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segfault #71

Closed Aphrix closed 3 years ago

Aphrix commented 4 years ago

Hello, I am encountering a segmentation fault. Apparently, everything stopped during the multiple alignment for error correction. Thanks for your help.

error DBG2OLC[45500]: segfault at 28 ip 000055b60cb32140 sp 00007ffc827b5f70 error 4 in DBG2OLC[55b60cb09000+4f000] command DBG2OLC k 17 AdaptiveTH 0.01 KmerCovTh 3 MinOverlap 20 Contigs short-reads-contigs.fa f long-reads.fa RemoveChimera 1 log Loading contigs. 383754216 k-mers in round 1. 344563592 k-mers in round 2. Analyzing reads... File1: /data/Astacus/long-reads-CCS-1000.fa Long reads indexed. Total Kmers: 11659391465 Matching Unique Kmers: 1378134164 Compression time: 22933 secs. Scoring method: 3 Match method: 1 Loading long read index Loading file: ReadsInfoFrom_long-reads-CCS-1000.fa 1420614 bad reads skipped. 1557966 reads loaded. 130191 selected reads. 1557966 reads loaded. Average size: 4 Loaded. 130191 reads. Calculating reads overlaps, round 1 Multiple alignment for error correction.

yechengxi commented 3 years ago

I cannot tell what the error could be from these outputs.