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pangenome / pggb

the pangenome graph builder
https://doi.org/10.1038/s41592-024-02430-3
MIT License
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ValueError: too many values to unpack (expected 13) #257

Closed ld9866 closed 1 year ago

ld9866 commented 1 year ago

Dear developer We are using“ https://pggb.readthedocs.io/en/latest/rst/tutorials/sequence_partitioning.html# ”When analyzing our data with the examples provided, we found that paf2net Py cannot run normally, so we cannot perform subsequent analysis. We also performed the same operation on the test data provided by pggb, whether it is DRB1-3123.fa.gz.f38ac34.alignments.wfmash.paf or our own dye donor file, and the error is reported as follows: Could you help us? Thank you!

Code： python3 /shell/pggb-master/scripts/paf2net.py -p DRB1-3123.fa.gz.f38ac34.alignments.wfmash.paf Result： Traceback (most recent call last): File "/home/lidong/shell/pggb-master/scripts/paf2net.py", line 18, in name1, , , , , name2, , , , , alignlen, , est_identity = line.strip().split('\t') ValueError: too many values to unpack (expected 13)

AndreaGuarracino commented 1 year ago

@ld9866, see #256, it could be related. Check the first lines of the DRB1-3123.fa.gz.f38ac34.alignments.wfmash.paf file and please let me know.

ld9866 commented 1 year ago

Hello, l upload the first line here: Look forward to receiving your reply!

gi|568815529:3998044-4011446 13403 0 13403 + gi|568815567:3779003-3792415 13413 0 13413 13402 13413 31 gi:f:99.9851 bi:f:99.918 md:f:99.9926 wt:i:13 pt:i:8 aa:i:1 ap:i:1 cg:Z:4896=10D6889=1X1617=

DRB1-3123.fa.gz.f38ac34.alignments.wfmash.zip

AndreaGuarracino commented 1 year ago

Hi @ld9866, the problem is that you are using the output of wfmash without adding -m as indicated in the tutorial here. However, I have just updated the paf2net script to support also this kind of PAF file, to avoid other users getting the same problem in the future. Therefore, you can either follow carefully the tutorial or update your paf2net script!