Nucmer error

[yutoupai]

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]

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