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mummer and/or mgaps returned non-zero #11

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shiyi-pan opened this issue Mar 10, 2022 · 0 comments

shiyi-pan commented Mar 10, 2022

Hi, I want to compare to genomes using MUMmer3 and meet an error.

Here is my code:

$MUMMER3/nucmer --maxmatch -c 100 -b 500 -l 50 --prefix Wm82_NN Gmax_275_v2.0.fa NN1138-2.v1.0.fa

Here is my error:

1: PREPARING DATA
2,3: RUNNING mummer AND CREATING CLUSTERS

reading input file "Wm82_NN.ntref" of length 978496462

construct suffix tree for sequence of length 978496462

(maximum reference length is 2305843009213693948)

(maximum query length is 18446744073709551615)

process 9784964 characters per dot

#....................................................................................................

CONSTRUCTIONTIME /gss1/home/hjb20181119/panyongpeng/NN1138-2/sv_detection/MUMmer3.23/mummer Wm82_NN.ntref 423.83

reading input file "/gss1/home/hjb20181119/panyongpeng/N24852/01.SV_detection/Wm82_NN/NN1138-2.v1.0.fa" of length 959747921

matching query-file "/gss1/home/hjb20181119/panyongpeng/N24852/01.SV_detection/Wm82_NN/NN1138-2.v1.0.fa"

against subject-file "Wm82_NN.ntref"

ERROR: mummer and/or mgaps returned non-zero

and the Wm82_NN.mgaps file is 0 byte and no Wm82_NN.delta file.

Could you help me fix it ? Thank you very much.

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