query Chr01 block 51435129-51435189 exceeds sequence length 51433939
for 201 cases out of 2882 .psl files. Below is both my LASTZ, mafToPsl and axtChain command:
LASTZ:
lastz Gmax_275_v2.0.softmasked.fa[multiple] Pvulgaris_442_v2.0.softmasked.fa[multiple] --strand=both --notransition --step=20 --nogapped --progress=1 --format=maf > gmaxv2_vs_pvulv2.maf
mafToPsl (This is a loop in a python script after traversing the .maf file collecting non-empty target-query pairs):
# Run command like `mafToPsl Chr01 Chr01 gmaxv2_vs_pvulv2.maf gmaxv2_vs_pvulv2_chr01.psl`
for target_seqname, query_seqname in target_query_pairs: outfile_name = '%s_%s_vs_%s.psl' %(prefix_root, target_seqname, query_seqname) subprocess.run(["mafToPsl", query_seqname, target_seqname, "gmaxv2_vs_pvulv2.maf", outfile_name])
axtChain (with a bash loop):
for i in ../00_mafToPsl/00_psl_files/*.psl do axtChain ${i} ../Gmax_275_v2.0.softmasked.2bit ../Pvulgaris_442_v2.0.softmasked.2bit ./${i%%.psl}.chain -linearGap=loose -psl done
What is wrong?--
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Hello Zeta,
Thank you for using the UCSC Genome Browser and further explaining your issues.
From the axtChain error in the original email:
axtChain sees that the size of the query, Chr01, in the input sequence file is 51,433,939 bp, but then the PSL input has a query range with coordinates greater than this size. So either the size is wrong, or LASTZ's math is going wrong somewhere. The command lines you shared appear to have the correct argument order, i.e., mafToPsl wants the query then target, and the other tools should have the target then query. Please make sure all arguments for target and query are in the correct order for all commands.
Is 51,433,939 indeed the correct length for pvulv2 Chr01? The next thing to look at would be the output of LASTZ; in gmaxv2_vs_pvulv2.maf, is there a MAF block in which pvulv2 Chr01 has coordinates greater than 51,433,939?
I hope this is helpful. If you have any further questions, please reply to gen...@soe.ucsc.edu.
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Jairo Navarro
UCSC Genomics Institute
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