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SJTU-CGM / HUPAN

Human pan-genome analysis pipeline
http://cgm.sjtu.edu.cn/hupan/
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Error in hupan alignContig #12

Open Kennyluo4 opened 3 years ago

Kennyluo4 commented 3 years ago

Hello, I have a trouble running the alignment step to reference genome. I run the HUPAN using :hupan alignContig ~/ziliang/assembly_sga_result1/data ~/aligned_result1 ~/software/MUMmer3.23 ~/genome/R570/single_tiling_path_assembly.fa and I got the error no: 400

Processing samples:
Process sample CoC671_L4_179179 ...
1: PREPARING DATA
2,3: RUNNING mummer AND CREATING CLUSTERS
# reading input file /public/home/sugarcane_gx1/ziliang/aligned_result_test/data/CoC671_L4_179179/CoC671_L4_179179.ntref of length 410230280
# construct suffix tree for sequence of length 410230280
# (maximum reference length is 536870908)
# (maximum query length is 4294967295)
# process 4102302 characters per dot
#............................................................................................ERROR: mummer and/or mgaps returned non-zero
ERROR: Could not parse delta file, /public/home/sugarcane_gx1/ziliang/aligned_result_test/data/CoC671_L4_179179/CoC671_L4_179179.delta
error no: 400

The assembly seems successful, and here is a look of the assembled contig:

>contig-73684063 150 0
TGTTTCCCTGGTATGACTCCGTGGAAGCCCCCGATGCTAGGTTGGAGGCGCGCTCTCTCGACCCCCAGAAGGTCGAGGGTCTAGGAGTAGATGATGTTGAGGCTGCTTCCGCCATCCATGAGCACCTTGGTGAGGCGTGTGTTGGCGATG
>contig-550123 466 0
CTAGCTAGGCTACACAGCAACCAGTAAAGAGATCCAAACAACTACAATCTTGCCTAGCCTGGCGAGACAATTCACCACTGACACGTGAAAACTAAGACCCTGTTTAGTTCCTAAAATTTTGTAAATTTTTTCAAGATTCTCCGTCACATCGAATTTTTGGACACATGCATGAAACATTAAATATAGATAAAAAATAAAACTAATTACACAGTTTAGACAAAATTCACGAGACAAATCTTTTAAGTCTAATTAAGCCATGATTGGACACTAATTATTAAATAACAACGAAAGTGCTACAATACCATTTTCAAAAAAAAATTTCGCGAACTAGACCAGGCCTAAAACTCGTCCAGACAGGCGCGAGCTGTCTCACCCAAATAAATATAAATTAAACAAGCTTTGCTCTTGCTCGTATCTTCTCGTTCGGTAAGGTAAACCGTAAGCGTGCCAAGCGGAGGAACAAAAG
>contig-4870773 150 0

It might be the issue with mummer, but I wonder if you can provide any suggestion. Can I use other tools to align the contigs and integrate it into HUPAN pipeline? Thanks Ziliang