tgsgapcloser报错

我使用ont数据填gapfill，将fq转换成fa之后，出现下面的报错：[root@dd575523c318 14:41:32 /work/kangding_ont/06.gapfill_hap1/ONTReads]# INFO : Run tgsgapcloser. from /share/work/biosoft/TGS-GapCloser/TGS-GapCloser_v1.2.1 ;

Version : 1.2.1 ;

Release time : 2022-12-30 .

INFO : Parsing args starting ...

--thread 10

--min_nread 1

--min_match 2000

--scaff ../Chr01A_Chr19A.fa

--reads ../ont.fasta

--output ONTReads

--racon /share/work/biosoft/Racon/latest/build/bin/racon

INFO : Parsing args end .

INFO : Checking basic args & env ...

- Doing error correction by racon with tgs reads.

- TGS reads type is ont . MINIMAP2_PARAM is -x ava-ont MIN_IDY is 0.3 . MIN_MATCH is 2000 .

INFO : Checking basic args & env end.

INFO : Step 1 , run TGSSeqSplit to split scaffolds into scaftigs(contigs).

INFO : Step 1 , done .

INFO : Step 2 , run TGSCandidate ...

- 2.1 , run minmap2 to map contigs against tgs reads.

/share/work/biosoft/TGS-GapCloser/TGS-GapCloser_v1.2.1/tgsgapcloser: line 445: 336 Segmentation fault (core dumped) $MiniMap2 $MINIMAP2_PARAM -t $THREAD $TGS_READS $TMP_INPUT_SCAFTIG > $OUT_PREFIX.sub.paf 2> $OUT_PREFIX.01.log

我之前填另一个物种基因组没有遇到过，我想确认下是什么问题？

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分类：基因组学

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2 个回答

Ti Amo 2025-06-04 13:23

minimap2跑不过去，可能数据太大了爆内存了，可以考虑命令里面加参数--minmap_arg '-f 0.1'，-f的意思是通过移除高频出现的重复性 minimizer，来减少重复序列对计算过程的干扰

上一次报错的$OUT_PREFIX.01.log最后显示的是什么？根据minimap2的报错查看具体问题。-f 0.1如果是空的，那你调小一点试试0.02这种的

陈黑手 2025-06-05 09:42

谢谢老师，但是比对完之后结果是空的，导致ranco报错，我在单独运行ont数据与基因组比对时就没有出现爆内存的问题，并且我的内存是512gb，是不是ont.fa的数据格式有问题？我是通过seqkit转换的

这是我的ont数据内容：

>1d88d7d1-7e1b-441f-9e7b-5772c8a6d99e runid=53c4be9a0b11aaf13ce892d32830ea5e4dda6e0e ch=2823 start_time=2025-05-27T07:55:59.130533+08:00 flow_cell_id=PBE43008 protocol_group_id=20250527-TW808-1 sample_id=TW808-1 parent_read_id=1d88d7d1-7e1b-441f-9e7b-5772c8a6d99e basecall_model_version_id=dna_r10.4.1_e8.2_400bps_fast@v4.3.0

ATGTTATGTTACATCTACTGGACTCAGTTTTATCCAAGGGCTGGGACTCTAAGGGTACAACTAGCATTTATAGTGAAACACTTTCACATTTTGGTGCGCCGCTTCATCGGTGAGAACTCATCGATAGAAATTACCTTGAATTAGAAGTATAACACTAAGAAATGAAATTAATACAATACTAAATATCTCTCGTTGAGGAAAATACCATATGGTATATCTTTATTAATCACATCAAAGAACTTATCAAGCAAAGGTTATAAATTCAAGGGGAGAATGATTTATTTCAATATTCCCTGAACAATAGAGAAAAGCCAATGAACATCATCAACAAGTTTACCATTTCAAAACAAGTAACTAAAATATTTCTGCCCCTTTAAAAGGTTTGGACCTGGTTTAGAAGGACCTAATATAATCTTCAAAACCATTTGTTTACAAAAGAATGCATGTTTTTAAAGCTGTCATCTAAAACTTCCTAGCATATTTCTATGAATGATAACCAAATAGACAGAAGTGACATACGTTTTTCATAGGTACTATATCACACCAAACTTAATAGAACGTTTTCCAATGGAGAATGATGAGAGCATATGCTTTTGTTACCTTTCAGTTAGTGCTTATTTTCCATCCATCTCGTTTATAAGGTTGAGGGTGTAAATTAGTTTAAGTACATTTGTTCACCATATAGATAATACAATATAATTTAACCCACTATGATGGTCACTTCATCATGACTGTTTCTATTTGCATTGTAGCGGTGTATAAATCCTGCGAAGACCTAAGTTTCTCACTCTTGTAGTGACAACATGCAAGTTTCTTGGTCTTCAGGAGACAGCCTAATGAGACATAAGTGATTCATCTTCTTGATCTCATTAGTTCAGCAAGTAGTCTTCGTTGTCGGCTATCTCTTTCTCTATGATGACAAACAATTTTGTGATTTTAGACAATCAAAAGTGAATATTGTCCATGACTCTCAAATAACCTTCAGAATCACTCTATAAATAGAACTGTCCGTCATATGCTTTAGAATCAGTTACTGATTTATTTCTTCTAGAGCCTTAAAAATAAAATATCCATATATCTTAGTACTCTTTGAGAATAGAATTTCTCCCCTAATTGAAAGACTCTCCTTAAATGATTTTCCAGACTAGTCTTTAATCCTTTTCTACTGCTTCTCCATATTCAAAACACAAGTTTTCCTTCTGAATGTCCAAATCCTGTGTGAATATCCTGTTTCAAAGCCAAAATTCTGATGATAATTTTTTTATACCTCATTCAATCTCAATGCTTCTCACGATCATATTTCGAAAATTGGTGGGCAGGCTTCATTCATTAGTATTGTACAATACCCGATATGATTGTGTAAATAAATTAATCTCCTTGAAAGTGCTCAATACACCATACCACAACATCATATTTACATATCCATAAGTTTCTCAGTTATATCGATTATTTACATATTCATAAGTTTGCATTATCTCTCATAAGTTTGCATTATATTGGTAGAAAAATTTACATATTGCTACCATTACAAAGTTAATTCAAAATAAAAAGAAGATAGTTTACATCTTAATACATTCATTCATCCAAAATATAGTCATAACTGGGAACATGAAGATACATAGTTTTTCCGATATTATGGACTTGAGGCAAGATTTCCACTATACACCTTGTTATATAACAATACATACAACAATACAAATATCAATACAAGAGATCTGTAGCCAATGAGAAACATGACGAAAGATAAATTGAAGTAACATTGTCATTACTTTCCGTTTATATAACCTAATGTGTGTGAATATCCTTCCCATTACTCTTCCATATATGATGTGTATGTATCCCTTATTATTTCATCAATTACAAAAGTCCATTATAATATTAAACCTGGTCATACCATCTTCGGTTCCCATCACTTTAGATATCGTTAACCGAAGCATCCGTTAATGCTCATCTTGGTCATCCTTAAGACACCATTAGTCGAAACTAATCATCAAACACAGCCGACCATACCTTCTGGACGTCATTAGCCGAAGCTTAAGTTATAATGCTCATCCCTAGTTGATTGAACTTCTAGGACTGTTACGTTAGCCAAAGACTAATCATAATGCTCATCATGACAATTCTTCTAGACGCATTCACCAAAGGTTTCATCATCAAAAAACAACCCGGCCATCCTTCTGGGTGCCATTAGCCGAATCTAATCATAATGCTCATCCCCGACCATCATTCTAGGACGTCATTAGTCAAAGCTAAGATAATCAGAACACAGTCTGGCCATCCTTCTAGTGCCATGAGCCGAAGCTAATCATAATACTCAGTTTAAATATCAATGAATAGTTTTCATCTTGGTTCAGCACAATAATAGATCTTCGTAATGAATTCACTTAAGAAAGAATTAACATTATGCTAGAAAGGATGAAATCACCGCCTATCTTCTTTCGTTGTAATATCCTCGTCCAATCAAAGGTCCGAATACCTGATTGTACCATTTGACATATCAAATGATCATCATTAGCATATTCGCATCTAGCAATCACATAAACCATTACCATACATATCCCAAGAATACACATGTTTCACATTCAAGATGTTCTTACATATAATTCAATCGTACAATAAAATCATTATATGAAGACATTTCTCTTTATTTTGAACGTGGGTCACTCACGTGTGCATAATGTTTGATTCCTAGTTTTGTATCATGAATTAGATTAGATCTATGATGAAATCGTCACAATAATTGAACATTTCTAGAAGATGAGTTGTCAAACAAAGACTCGGGTCGCTGTTTATAATAAAAAATCATCAACAAACCATACGATCCATAACACATAATAACCTATGAAGACTGACACATCGGTGACATGAAAATCATGACGGAAGACTTGGTCGTTGGTAACACAAGAATCAGTCAGTGACAACTGACTCGGTTGACGCCATAGAACTAAAAATTCGTCG

tgsgapcloser报错

2 个回答

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