tgsgapcloser: line 645: 81794 Aborted (core dumped)

[Ssmile333]

tgsgapcloser: line 645: 81794 Aborted (core dumped) $GapCloser --ont_reads_a $FINAL_READS --contig2ont_paf $OUT_PREFIX.fill.paf --min_match=$MIN_MATCH --min_idy=$MIN_IDY --prefix $OUT_PREFIX > $OUT_PREFIX.fill.log 2>&1

Running tgsgapcloser gives the above error, but my paf file is only 3.3G and the memory seems to be sufficient, is there any way to fix it?Thanks

free -h total used free shared buff/cache available Mem: 3.0T 85G 172G 140M 2.7T 2.9T Swap: 15G 417M 15G

[cchd0001]

Hi,

Yes. the GapCloser step normally doesn't need a huge memory.

Could you please provide the content of the xxx.fill.log file?

Best wishes Lidong Guo

[Ssmile333]

Thanks. The follow content is the xxx.fill.log tgsgapcloser --prefix Chr1_01 --contig2ont_paf Chr1_01.fill.paf --ont_reads_a test.correctedReads.fasta.gz --min_match 300 --min_idy 0.300000 TGSGapCloser INFO CST 2023/6/24 23:51:21 : TGSGapCloser start now ... TGSGapCloser INFO CST 2023/6/24 23:51:21 : LoadONTReads start now ... TGSGapCloser INFO CST 2023/6/24 23:53:9 : LoadONTReads finish. used wall clock : 108 seconds, cpu time : 107.945145 seconds TGSGapCloser INFO CST 2023/6/24 23:53:9 : LoadPAF start now ... TGSGapCloser INFO CST 2023/6/24 23:55:40 : >the read2contig freq is 1 64584 2 106835 3 80429 4 30148 5 6157 6 860 7 93 8 2

TGSGapCloser INFO CST 2023/6/24 23:55:40 : >the contig2read_num_freq freq is 423 1 4322 1 4600 1 5391 1 8429 1 17218 1 24517 1 136462 1 220125 1 255258 1

TGSGapCloser INFO CST 2023/6/24 23:55:40 : >the contig2a_read_freq freq is 1 201289 2 124551 3 87303 4 62601 5 46350 6 35754 7 26883 8 20534 9 15672 10 11884 11 9324 12 7200 13 5723 14 4452 15 3450 16 2662 17 2087 18 1735 19 1303 20 1088 21 890 22 718 23 529 24 451 25 368 26 294 27 253 28 229 29 178 30 143 31 128 32 100 33 95 34 72 35 56 36 42 37 58 38 45 39 39 40 34 41 21 42 18 43 11 44 24 45 12 46 9 47 13 48 10 49 9 50 11 51 3 52 2 53 4 54 2 55 4 56 3 57 1 58 3 59 1 60 1 61 3 62 1 63 2 64 1 67 2 71 1 72 2 73 2 93 1 99 1

TGSGapCloser INFO CST 2023/6/24 23:55:40 : LoadPAF finish. used wall clock : 151 seconds, cpu time : 151.139252 seconds TGSGapCloser INFO CST 2023/6/24 23:55:40 : LoadScaffInfo start now ... TGSGapCloser INFO CST 2023/6/24 23:55:41 : LoadScaffInfo finish. used wall clock : 1 seconds, cpu time : 0.301835 seconds TGSGapCloser INFO CST 2023/6/24 23:55:41 : ParseAllGap start now ... overlap check c1=1 and Try c2=2 -35219 overlap check c1=1 and Try c2=2 -35158 overlap check c1=1 and Try c2=2 -35226 overlap check c1=1 and Try c2=2 -43100 overlap check c1=1 and Try c2=2 -35077 overlap check c1=1 and Try c2=2 -35246 overlap check c1=1 and Try c2=2 -35101 overlap check c1=2 and Try c2=3 -3046 overlap check c1=2 and Try c2=3 -7904 overlap check c1=4 and Try c2=5 -79 79 500 64 0.810127 1 accept this overlap stack smashing detected : terminated

Best wishes

[cchd0001]

Hi

This is the first time I've seen this bug. It seems unlikely to find problems by simply reading the source code.

Could you please provide a small piece of data that can trigger this issue for me to debug?

Best wishes Lidong Guo

[Ssmile333]

Hello!  I can provide a small piece of data, but how do I send it to you when the ont data is still 6 gigabytes compressed? Is it possible to request an alternative contact Best wishes

------------------ 原始邮件 ------------------ 发件人: "BGI-Qingdao/TGS-GapCloser" @.>; 发送时间: 2023年6月25日(星期天) 下午2:41 @.>; @.**@.>; 主题: Re: [BGI-Qingdao/TGS-GapCloser] tgsgapcloser: line 645: 81794 Aborted (core dumped) (Issue #64)

Hi

This is the first time I've seen this bug. It seems unlikely to find problems by simply reading the source code.

Could you please provide a small piece of data that can trigger this issue for me to debug?

Best wishes Lidong Guo

— Reply to this email directly, view it on GitHub, or unsubscribe. You are receiving this because you authored the thread.Message ID: @.***>

[cchd0001]

Please upload the data to some cloud server and email me the download link . My email : guolidong@genomics.cn