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bridge_lchains assertion error
Hi,
With the prebuilt GRCh38 pangenome graph I am getting an assertion error.
minigraph -t 1 -cx lr GRCh38-90c.r518.gfa.gz reads.fa
minigraph: gchain1.c:391: bridge_lchains: Assertion
l0->v == l1->v' failed.`
Below is a single read that reproduces the error:
>read
TACTTCGTTCAGTTACGTATTACTAGTTTCACCCACGCTTTGCTGACTGACCAACACACTGAAGCTCCCTTCAAACCCAGAACTTACTGCACTTGCTTCTAAGATGCACCTGAAATTGCTGTTAGAAAAATGAAGCAGAGAAGGAGCTGCACGTGTGGGGGAGGTGAGGGTGAGAAGGAAGGAAAGGCACAATCTGTCACAGTTTCCAAACACATATGCTTCGCGTGGGAATCTGGGGTTGATTCAAAGGCTGAATGGATCTTCAGTTACTGGAAGGCTTGGCCCAAAATATTTCAGTATATGGAGCAGTTCTCTTCCTTCTAGTAGCAAAAGCAGCAACTGAGAGTGACTGGATTTGTGATCCAGAATGGGGACAGTGGGAAAAGTGCAAACCAATTCTCAATGGAGAAAATAGCCAACTGGTCAAGGAACTGTGATGAGATGGCGGGATTCTCCAGGAGGTGCGTGATGTGGCTGAGGTGCCCATCCATCCTGTATGATGATGACCAAACTCGTCCAGGAGCGAGATGTGGCCGGTGCCCATCCATCACTTGAAAACATGATGGTAAACTCGTCAGGAAGTGTGTGATGTGGCCGGTGCCATCCATCCTGTATGACGGTGAACTTGTCCAGGAGCGAGATGTGGCTGGTGCCCATCCATCCCATATGATGTCCAAACTCGTTCAGGAAGTATGCGGCCAGCGCCACATCCATCTGTATGATGGTGAACTTATCCAGGAGCGAGATGTGGCCGGTGCTTACATCTATCCCATATGATTGTAAACTCGTCCAGGAAGTGTGTGATGTGGCCGGTGCCCATCCATCTGTATGACGGTGAACTCGTCCAGGGCAGAGATGTGGCTGGTGCCCATCCATCTCCATATGATGGTAAACTCGTCAGGAAGTGTGTGACGTGGGGAGCGCCCATCCATCCTGTATGATGGTGAACTTGTCCAGGAGCGAGATGTGGCCGGTGCCCATCCATCCCATATGATGGTAAACTCGTCCAGGAAGGTATGCGACGTGGCCCGGCGCCCATCCATCCTGTATGACGGTGAATTTGTCCAGGAGCGAGATGGCCGGTGCCCATCTATCCCATATGATTGTAAACTCGTTCAGGAAGTGTGTGACGTGGCCAGGCCACATCCATCCTGTATGATGGTAAACTTGATGGAGCATAGTTCCGGGAGCAGCTCTCCTGGGTTTAGGAAGTGGGGAGGGTGTGGGGGGTCACAGCCGTTAGTATGATGATCTTATCCGCTGCTTCAATTTCCTTCAGATAAATTTCAATATTTTTGCATTTCTTCTGGTCACAACTCTCATCCATGGACATTTTAGAGGTAACAAGCCCGCTCACATTTCCATAAATCAACATTGTGGCTTTCTGAGTCCGAATCGGACAGGACGTGGGCAGCTGGCGCTGTTGGTCTCCACTCTCACTGGGCTGAGGCGCACTGAACCCAGAAACCAACACTGCATCGCTACAGATTCTCTCTGACCTGGTGCCGAAAGGGCTTCAGCGGATTTCTCCTCTGCCAACGTCCTTCGAAACTCTCTGTAGTACTTTCTATCCGCCAATCAATGAGCCAGCCAGCACATTCCCTGTGATCAATCCATCAATTCCACCCACCAATCAGTGAGCCAGCAGCACTCCCTGTGATCAATCCATCAATTCCACCCACCAATCAGTGAGCCAGCAGCACTCCTGTGATCAATCCATCAATTCCACCCACCAATCAGTGAGCCAGCAGCACTCCCTGAGATCAATCCATCAATTCCACCCACCAATCAGTGAGCCAGCAGCACTCCCTGTGATCAATCCATCAATTCCACCCACCAGTGAGCCAGCAGCACTCCCTGTGATCAATCAAGAAGCTCAATTCCACCCACCAATCAGTGAGCCAGCAGCACTCCCTGTGATCAATCCATCAATTCCACCCACCAATCGTGAGCCAGCAGCACTCCCTGTGATCAATCCATCAATTCCACCCACCAATCAGTGAGCCAGCAGCACTCCCTGTGATCAATCATCAATTCCACCCACCAATCAGTGAGCCAGAAGCACTCTGTGATCAATCCATCAATTGATCAGTCGACCCACCCGCTGGCTACCAGGGGCACCCAGCGCAGCTGCGCTCACAGAGTCAGGGCGGCGGCTCAGACAGAAACGTGGGTGTGCTTGTGTGTGCAGAGTGCACGCTGCAGAGAAACCACGGGGCTGCAGGCCCAGCCTCCAGTAGAGCCTGGAGCCGGCCTGCAGGGAGGACCCCAGGCGGGTGTGGGGACCCACCTTAGGAGGACAGACGCACATGAGGCTACGGGAAACTGTTGTCATGAACCCCAAATGTGTTGTCAATAAGAGCACCGGACTTAACTTTCAATGCTTCTCTTAGCAAAACCAGGGATTTTCCTGCAGCTGCATGAACATTGACCTGTCCGCCTACTCCCGAGCCACAGATCTGGGGAAAGAATGCATGTAGCCTGCTGTGGGTGAATGGAGCTGGGGCAGTGATGAGCTACTTCTTGCCTTTTGTCAGGGGAAAAGGAAGCTGGATAGATTTCTCTTCTCTTCCTTTGAGAATGAGTGAAGAGGGAAGATAAAAGCCAGCAACCAGGGACAGCTGAAAATATGGTTTCAGTAAGAGACAGGCCACAGCGTCTAGGCCCCTAGGACAAGCAGACCTTCCAGGAGGATTTCTAAGGTGGCTGGAGAGAACTCTGCTACCCTTTCCAACAGATGCAAGACACAGCCTCTCTAAAAACAGGAGCAGAAACACACAACACGGAAAAAACAGGGTGTCAGCTGAACCGTTACCAAGTTATGAGCAAAGAGGCTGGAACTGGGAGAGATGAGAAATAACTGTGAGGAAATTAAAACTACAATAGCAGAGTTAAAATTCACATTGAGGCGGCAGAGCAGAACTGACTACAGTTCACAACCGAACCATAAAGCTCTCTTCGAGAATCACGGAAACAAGCACAAAAGATGCTAAAAGAGGGATATTAGAGACGTACGGCACAGGAAAGAGAGACTCGTCCTAAGGATGGGAGAGTTTGGAGAAGAAGCTAGAATGACTAGTAGGAAGAACAGGAAACAGGGATCTGCAGCAATGCCTCGGCTCTCAGGGGGCGCTCAGGGAGGTGCAGGGCAGAAATTAACAACATAGCCGAAGAGGGTGCACTGCAAATGCGTGGAAACAATGGCTTATTCAAGAAACTAGAGTTTACTTGGGGAAGGTCCTAGTTTATCCCTCACTTCACACACATTACAACCACCAGAAATGATCCAGATACATTAACACATTAATGGAACCATAAAAATAACAAATAAAAACTTGTGTTTCACTGATGACAGGATGAGCAAGCACTTTCTAAACATGAGAGCGATTGACAAAATCTTAAAGGAAACGACTGTGCATTTGAATCCACCAGAGCTCAGCCTTTCTGAACTTCAGACAGTACAACAAGCAACGTTAGACACAGACAAGCCTGGCAGAACATTGGCCAAAAGTAAGAGGCAAAAAACAAATATGAAGAAGTACTCGTGAGTCTATTTCAGAGAATTCACACTCCCATAGGAAAGATTCATGAAGAGATTATCCCAGGAAGCAAGACATCAATAATCAAGTATGATAAAATGTTTAAATCTACAATAAATCAAAAACTATAAATTAAACCAATGATAAGATGCTGTCGTTTGCCCTAAATAATTGCATACACTTGACTGAAGTCCTAACCTGGAGTGGCTAAGTGTGATGGATGATGTGAGTTCATGGACTTGCCAGATGCTTATATTTGTTTGATGTTCACATTCATGGATAAGGAATTGAGGTATTTAGAAGAGCTTGCACCATTTCACATAGTAGTTAGATTTCTAGGAGTGTATCCTAAAAACAGTAAGCCACATAGATTGAATGTAGGATATTAATTGCAGCAAGACTTATGATAATGAAATACTAGAAACAAGCTAAATGTTCAACAATAGCACATGGAGTTGAAAAACTTACAGCAGAACCACATAAAGACCAAAGTGTTCCTCAGAAGCATATTTTAAAGACAATTTGATAGAACACATAGGCAATAAGAATAAAGACACACATACATACACACATATACACATCCTAAAAGAATATCAGAATAGTAAGCATTTTCCTGAGTTTTCCACTAAGTCACTGAACTGAAACAAGTATTTGCTTTTAAATAGATTTCTGAATTAATATAGAGAGGTTTATTTCTGTCTTTGATACTGTGTCTGGCCTGGACCATTTTTAATTGCTCAGAGACTTCTAGGTGTGTCATAAATCTCTGTACAACCAATCATTCATCCATCCATCCATCCATCCATCCCCCGACCAAACCCACCCACTTACTCATCCATCTGCCACCCACCTGCCTCTACCACCTATCCTCACCTGCCTGTCCACTCACACCACCTGTCCATCTACCCTTCCATGCATCCCTCCATCCACCCACCCATCCACCCACCACCTGTCCACCCACCCACCCATCCACATCTGCCTTTCCATGTCCCTCCACCCATCCACCCACCCATCCACTCACCACCACCTGTCCACCTGCCTGCCCATCCACCCGTCCACCCTTCCCATGTGTCCCTCCACCCACCCACCCATCCACTCACCACCACCTGTCCACCTGCCCACCCATCCACGCATCTGCCCTTCCATGTGTCCCTCCATCCACCACCCATCCACCCACCTATCCACTCACCACCACCTGTCCACCTGCCCACCCATCCACACATCCGCCCTTCCATGTGTCCCTCCATCTCCACCCCATCCACCCACACCACCTGTCCACCCGCCCACCCATCCACACATCCCGCCCTTCCATGTGTCCCTCCACCCATCCACCCACCCATCCACTCACCACCACCTGTCCACCTGCCCACCCATCCACACATCCCGCCCTTCCGTGTGTCCCTCCACCATCCCACCCACCCATCCACCCACCCATCCACTCACTACCACCTGTCCACCTGCCCACCCATCCACACATCCACCCCTTCCATGTGTCCCTCCACCCATCCACCACCCATCCACTCACCACCACCTGTCCACCCACCTGCCCATCGGCACGTCTCCATCTACCCACCCACCCAGAGAATTGCTCGCTTGTTGTGTGCTGTGGGCCAGGCTCTGAGGTTTATGGACGGCTGGGACATTATTAATGCCCATGGGGGATGTAGTGTCTGATGGAAGAGGTGGTGGAGAGGAGAACTGTTTTGATGCAAGTCCATCCGAGATGGCTCAGAAGGGCACCATGAGAGCCAGGGCCATGTACCACATTCTGTGGAGGTCGACTCCCCAGCACACGCACCCAGGAACACCCTGGGCTTGACAGCCATCTGCTGGGTCATGCCCTCTTGCTCTGTGCCTGAGTCCTTCGCACTCCTGCCGTCTGCAAGGACACGTCCAGCCCCCGCAGGGCTGGGGACTCCCAGCCTCCTCCATGACCCTCACAAGGACACAGTGTAGCCCAGCCTCCTGCAGGGCAGGACTCACATCCTCCTTCACTCCATGACCCTTCCTTGTTGCCGCCACACGTCTGTTGCACCTGTAGACACGGAGCCTTGGACTCAGGGGTGGGTCCCGTGGATCTCACAGCCCTGCTGCCCAGCATAGGACACTTTGCGTGTCAGTGAGTCCTGCTGAGTGGATGGCAAGGAGAAAGCTCCTCTCCACCGTGGCTACTCCAGTTCCTCTCCCCGCAGTGGATGGCACGGAGAAACTCCCTCTCCACTATGCCTACTCCAGTTCCTCTCGTAGTGGATGGCTGCAGGAGAAAGCTCCTCTCCGCCGTGCCCTACTCCAGTTCCTCTCATAGTGGATGGTACGGGAGAAAGCTCCTCTCCACTATGCCTACTCCAGTTCCTCTCATAGTGGATGGCACGGGAGAAAGCTCCTCTCCACTATGCCTACTCCAGTTCCTCCTCATAGTGGATGGTACGGAGAAAGCTCCTCTCCATATGCCTACTCCAGTTCCTCTCATAGTGGATGGCCTTGAGAGAAAGCTCTCTCCACGCCGTGCACTATTCCAGTTCTCTCGTAGTGGATGGCATGGGAGAAAGCTCCTCTCCGCCGTGCCTACTCACGATTCTCTCGTAGTGGATGGCATGGGAGAAAGCTGCTCTCTGCCGTGTACTCCAGTTCCTCTGAGTGGATGGCACGGGAGAAAGCTCCTCTCCCCACCGTGGCCTCGGATTCCTCTCATAGTGGATGGCACGGGAGAAAGCTCCTCTCCACCGTCGCTGCTCCAGTTCCTCTCATAGTGGATGGCACAGGAAGAAGCTCTCTCCACCGTGGCTACTCCAGTTCCTCTCATAGTGGATGGCTGGCATGGAGAAAGCTCTCTCCACCCGTGGCTACTCCAGTTCCTCTCGTAGTGGATGGCACGGGAAAACTCCTCTCCGCCGTGGCTACTCCAGTTCCTCTCGTAGTGGATGGCACGGGAGAAAACTCCTCTCCGCCGTGGCTACTCCAGTTCCTCTCGTAGTGGATGGCACGGGAGAAGCTCCTCTCCGCCGTGGCTGCTCTCAGTTCCTCACCGACAGTAGTGGATGGCACGGGGAGAAGCTCCTCTCCGCCGTGGCTACTCCAGTTCCTCTCGTAGTGGATGGCACGGGAGAAAGCTCCTCTCCATGTGCTTCTCCAGTTCCTCTCGTAGTGGATGGCACGGGAGAAAGCTCCTCCACTGTGGCTACTCAGTTCCTCTCGTAGTGGATGGCATGGGAGAAAGCTCCTCTCCACCCCCGTGGCTACTCCAGTTCCTCTCGTAGTGGATGGCACGGGAAAACTCCCTCTCCGCCGTGGCACTCCGGATTCCTCTAAATGCCTTCCTGAGGTGGCTGGTGTTCTTGTCTTCGTGAAGTTGCCTCTGATTCCATCCTCTAAAAGCCAATGACTTATATTTGGCACAAGACAGATTAACACGTAATTGTTCTTTGCTGAATTGGTATCTGACTGTGTGAGTTGACTGACATGTATAGTCGTATGTGTATCTGAGTGTGTTTGAATGTATGTGCATGACTGTGAGTGCATGTTCATCACTGTCGGTGTGTCACTGTGTCCATATGTGTGGCTGCATGTGAGTGTATGACTGTGTGTCTGTGTGGCTGTGGGAGTGTATGTGGTGGAAGGTGTGTGTGGCGTGTGTTTGTGTTTGTGAGAGAGAGACTGTGTGTGTGTCTGGCTGTGTGTGTGGTTGTGTGACTGTGTGGGAGTGTATGTGAATGTGCATGTGGCTGTGTCTATGTGTCTGTGTCTGTGTGTGTGACTTTGTATTACTCTGTGTGTCTGTGTGTGTGTGTGGGGGTGTGTGTGTGACTGTGTGAGCATGTGGCTATGTGGAGTGCAAGGGCCTGTGTGGGAATGTGTCTGTGTATGACTGTGTGGCTATGTGTAGTGTGTGTGACTGTGTGTGGAATGTGTATGTGCAACTGTGTGGGAGTGCATATTCTGTGTGACTGTGTGACTGTGTGGCTATGTGAAGTGTGTGTGGCTGTGTGTGTGTATGTAACCATGTGTGGCTGTGTGGCCATATGTGACTGTGTGACCAGGTGTGACTGTGTGGCCACGTGTGACTGTGTGACTGTGTGTGACTGTGTGACCGTGTGGAGTGTGTGTGACTGTGTAACCATGTGGTGACTGTGTGGCCATATGTGACTGTGTGACTGTGTGTGACTGCGTGTGACTGTGTACGTGTGACTGTGTGACCACATTTGACTGTGTGGCCGTGTGTGACTGTGTGTGACTGTGTGACTGTGTGTGACTGTGTGACCACATGGAGTGTGTGTGACTGTGTAACTATGTGGAGGTGTGTGGCCATATGTGACTGTGTGACCGCGTGACTGTGTGACTGTGACTGTGTGGCCGTCACTGTTACCACATGTGACTGTGTGGCCCTGTGTGACTGTGTGACCGTGTGTGACTGTGACCGCGTGTGACTGTGTGGCCACGTGTGACTGTGTGACTGTGTGTGACTGTGTAACCGCGTGTGACTGTGTGGCGCGTGTGACTGTGTGACCGTGTGACTGTGTGACTGTGTGGCCACGTGTGACTGTGTGTGACCGCGTGTGACGTGTGGCCGCGTGTGAGCTGTGTGGCCGCGTGTGACTGTGTGACCGCGTGTGACTGTGTGACCGTGTGTGACTGTGTGACTGTGTGTGACTGTGTGACCGCGTGTGACTGTGTGACCGCGTGCGTGTGTGGCCACGTGTGACTGTGTGACTGTGTGACTGTGTGGAGTGGTGTGTGACTGTGTAACCATGTCCAGGCAGGGTGTAGGTGGAGAGGGTACGGGACGGGAGCTGCAGACAACATCCGAGCCGGCTGAAGCCAGAGCAGGCCCCGTGTTGGGGGTGGAGCCCCAGGGTGGTGCTGGATTCTGGACAGTGGATGACCGATGCTGACGCTGGCACCTGATCACTCCTACAGCCGCCACCAGGCAGCATCCAGAGCCCTCAGCGTTTTCACCCCGAGTGGGTTGCTGCTGTACTCAGCAGTCAGGGGGACAGGTTGTTTCTTCCTGAGGTCTCCAGGCCACACAGGACCCTGAGAGGAGCCCCGTCCTCAGACCCCTCCAGGAGCCAGAAGTGTTTCTTCTTGGAGAGGTGAGGGGCTGGGGCGCCCTCTCAGGCAGTGCAGGAGAAGCACCGGCGGGGGCTGGAGCCACACCTCACCGCCTGCCTGCCCCTCCTCCTCAGCGTCCTGCAGGGCAACCTGCAGATTCACAGCAGCCGCTGCCTGGCCTGGGAGCTCTGCAGTGCCTTCTGCTGGAAGTGCCAGCCGTGTCCGCCCTGCACTCGCTCCCAGCACAGGGCAGAGGCGGTCGCAGAGCTGCATGATCTACTTTAAGTTCTGTGAAAGTCCTTCTGCAGTAACAGTTCATGCGCTGGCCACGATGGCAGCAAGGGCAGCTTTAAGTTAATTCAGGCTGTTTGGAACAGGCTATGGGGTCTTAAGCTTCTTCACCCGCCTTCACTCCCCACACGCTCCCTGTCACTGGCTGAACATCGGTGAAGAGACCAAAACTGTGAACGAGGACATTATCCTAAAGTGCAGAGCCCCACATGGTGGGAAGAGCTCAAATGCTCACCTAACAGGTCGGCCTTCCTTTTCCACAAGTGGTTTTTCAAACTTACCCGTGGTGTACGTGGCTTTAAGTGAAACTTGGTGAAGGATCCTCCCCCTTCCCCACCCCACCCATGGTGATGATTTTGAAAAGCTCCCCCAAGGAACCCTAAATTAGTCTTAAACACACACACAAATCTATCTGAGGCAGGGAAGCTGCCCATTAAGGGCCAGTAATTACCCGAGGCTGCTGGGGTGCCTGCCTGGAAGGGCCCCACCACGGGGCCTTTATTGCTTCCTGGCCTGGCGGACTCTGAGGCTCATGCATTATTCAGGAGCACGTGGGACAATAAGGAAAGCCTTCATAGAAAGAAGCAAAGCTGGGGGTAAATAAAGGTTGTGAGAAACACTACTATTTTCTACATTTATGAAAATATTGCAGCGTTCAGGGTGCTGAGGACGTCCTCTCTGGTTATCAGGAGAACACCTGGATTCTGCGCTTTCCTTCCTGCGGGCCTGCAGCCTGCAGAGGCCCTGAGACAGCATACAGTACCCCGGGACTGTGTCTTTTTCCTCCTCCTCTCCCTTTCTCTCCCCTTAATGCAAAGCTTTGTCAAGCTAATACTTTAAAGCAATACGCTTAA
Thanks for your help!
Best, Tobias
I am also getting the same assertion error from minigraph:
minigraph: gchain1.c:391: bridge_lchains: Assertion
l0->v == l1->v' failed`
I am getting the same error aligning a large fastq to a custom graph, generated with mingraph using the graph generation mode. not the pre-built graph mentioned above.
Looking at gchain1.c in the bridge_lchains
method, the comment on line 392, just after the assertion states that "this part is made redundant by resolve_overlap()". Does this make the assertion redundant as well?
Thanks, Alister
Sorry for the late response. This has been fixed on the github HEAD.