bridge_lchains assertion error

[tobiasrausch]

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

[adcosta17]

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

[lh3]

Sorry for the late response. This has been fixed on the github HEAD.