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OPERA-MS - Hybrid Metagenomic Assembler
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Nucmer error #85

Open yutoupai opened 1 year ago

yutoupai commented 1 year ago

Hello OPERA-MS Team,

I received an error which is very similar to issue #72.

Error in during gap_filling. Please see /public/hyrothermalS/ouyangyt/01.data/01.Graduation_Design/03.OPERA_MS_hybrid_assemble/01.CK/intermediate_files/opera_long_read/GAPFILLING/gap_filling.err for details.

Error during tilling generation. Please see /public/hyrothermalS/ouyangyt/01.data/01.Graduation_Design/03.OPERA_MS_hybrid_assemble/01.CK/intermediate_files/opera_long_read/GAPFILLING/TILLING/tilling_1.out and /public/hyrothermalS/ouyangyt/01.data/01.Graduation_Design/03.OPERA_MS_hybrid_assemble/01.CK/intermediate_files/opera_long_read/GAPFILLING/TILLING/tilling_1.err for details.

rm -r /public/hyrothermalS/ouyangyt/01.data/01.Graduation_Design/03.OPERA_MS_hybrid_assemble/01.CK/intermediate_files/opera_long_read/GAPFILLING/TILLING/QUERY /public/hyrothermalS/ouyangyt/01.data/01.Graduation_Design/03.OPERA_MS_hybrid_assemble/01.CK/intermediate_files/opera_long_read/GAPFILLING/TILLING/REF

rm: cannot remove ‘/public/hyrothermalS/ouyangyt/01.data/01.Graduation_Design/03.OPERA_MS_hybrid_assemble/01.CK/intermediate_files/opera_long_read/GAPFILLING/TILLING/QUERY’: No such file or directory rm: cannot remove ‘/public/hyrothermalS/ouyangyt/01.data/01.Graduation_Design/03.OPERA_MS_hybrid_assemble/01.CK/intermediate_files/opera_long_read/GAPFILLING/TILLING/REF’: No such file or directory mkdir /public/hyrothermalS/ouyangyt/01.data/01.Graduation_Design/03.OPERA_MS_hybrid_assemble/01.CK/intermediate_files/opera_long_read/GAPFILLING/TILLING/REF split /public/hyrothermalS/ouyangyt/01.data/01.Graduation_Design/03.OPERA_MS_hybrid_assemble/01.CK/intermediate_files/opera_long_read/GAPFILLING/TILLING/consensus.fa mkdir /public/hyrothermalS/ouyangyt/01.data/01.Graduation_Design/03.OPERA_MS_hybrid_assemble/01.CK/intermediate_files/opera_long_read/GAPFILLING/TILLING/QUERY split /public/hyrothermalS/ouyangyt/01.data/01.Graduation_Design/03.OPERA_MS_hybrid_assemble/01.CK/intermediate_files/megahit_assembly/final.contigs.fa *** run the mummer mapping rm -r /public/hyrothermalS/ouyangyt/01.data/01.Graduation_Design/03.OPERA_MS_hybrid_assemble/01.CK/intermediate_files/opera_long_read/GAPFILLING/mummer rm: cannot remove ‘/public/hyrothermalS/ouyangyt/01.data/01.Graduation_Design/03.OPERA_MS_hybrid_assemble/01.CK/intermediate_files/opera_long_read/GAPFILLING/mummer’: No such file or directory mkdir /public/hyrothermalS/ouyangyt/01.data/01.Graduation_Design/03.OPERA_MS_hybrid_assemble/01.CK/intermediate_files/opera_long_read/GAPFILLING/mummer cat /public/hyrothermalS/ouyangyt/01.data/01.Graduation_Design/03.OPERA_MS_hybrid_assemble/01.CK/intermediate_files/opera_long_read/GAPFILLING/mummer/cmd_delta.txt | xargs -I cmd --max-procs=64 bash -c cmd > /dev/null xargs: bash: exited with status 255; aborting xargs: bash: exited with status 255; aborting Error in during nucmer.

Feel free to inform me if you require additional logs or further details.

Thanks for your help.

jsgounot commented 1 year ago

Hi,

sorry to hear you have an issue with our assembler. Did you try to run one of the command line provided in /public/hyrothermalS/ouyangyt/01.data/01.Graduation_Design/03.OPERA_MS_hybrid_assemble/01.CK/intermediate_files/opera_long_read/GAPFILLING/mummer/cmd_delta.txt?

Regards, JSG