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bcgsc / tigmint

⛓ Correct misassemblies using linked AND long reads
https://bcgsc.github.io/tigmint/
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tigmint-long error #56

Closed estolle closed 2 years ago

estolle commented 3 years ago

Hi there,

I seem to have problems running tigmint-long (installed via conda) on a draft assembly using my nanopore reads.

I get this weird error about the bed file being malformatted. Since this is not an input from my side, this seems to be a problem introduced by tigmint itself. I am not sure which bed file the error refers to, but the one bed (.cut500.as0.65.nm500.molecule.size2000.bed) file has no such malformatting in it at line 33

contig1006_shasta 0 3935 978453 5 contig1006_shasta 0 4951 125221 8 contig1006_shasta 74 5598 522996 8 contig1006_shasta 92 5686 498725 8 contig1006_shasta 194 5672 394040 7 contig1006_shasta 245 4638 80577 6 contig1006_shasta 254 5649 1035475 7 contig1006_shasta 293 5684 573992 7 contig1006_shasta 349 5718 793715 6 contig1006_shasta 399 5761 343613 9 contig1006_shasta 417 4915 576630 5 contig1006_shasta 428 4905 389381 6 contig1006_shasta 433 4944 414072 5 contig1006_shasta 437 4463 38003 6 contig1006_shasta 451 4952 269440 5 contig1006_shasta 463 4950 75560 5 contig1006_shasta 536 4544 882874 6 contig1006_shasta 543 5544 1040578 7 contig1006_shasta 593 5590 202003 6 contig1006_shasta 672 5688 861879 6 contig1006_shasta 802 5761 641545 7 contig1006_shasta 837 5761 625202 7 contig1006_shasta 843 4891 817031 4 contig1006_shasta 986 4013 839224 4 contig1006_shasta 1231 4722 13220 4 contig1006_shasta 1288 5761 954350 5 contig100_shasta 0 3884 777567 5 contig100_shasta 0 4337 828621 4 contig100_shasta 0 4391 351030 8 contig100_shasta 0 8531 658954 8 contig100_shasta 0 8744 644223 9 contig100_shasta 0 9100 2106 11 contig100_shasta 0 11316 459022 18 contig100_shasta 0 13326 162799 18 contig100_shasta 0 13473 322356 16

Here is the commandline output: samtools faidx draft.fa /home/ek/.conda/envs/tigmint/bin/tigmint-cut -p30 -w1000 -t100 -f Bterter.recalled-dna_r9.4.1_450bps_sup.prowler.filtlong.10kb.Q95.tigmint-long.params.tsv -o draft.Bterter.recalled-dna_r9.4.1_450bps_sup.prowler.filtlong.10kb.Q95.cut500.as0.65.nm500.molecule.size2000.trim100.window1000.spanauto.breaktigs.fa draft.fa draft.Bterter.recalled-dna_r9.4.1_450bps_sup.prowler.filtlong.10kb.Q95.cut500.as0.65.nm500.molecule.size2000.bed Started at: 2021-06-16 19:12:42.185574 Reading contig lengths... Finding breakpoints... Cutting assembly at breakpoints... Error: malformed BED entry at line 33. Start was greater than end. Exiting. DONE! Ended at: 2021-06-16 19:22:20.750825

Any ideas what the problem may be?

Thanks in advance

github-actions[bot] commented 2 years ago

This issue has been automatically marked as stale because it has not had any recent activity. It will be closed if no further activity occurs. Thank you for your interest in Tigmint!