I have been trying to run ABruijn but I get an error related to BLASR. <div class=

It worked. Thanks. <div class="snippet-clipboard-content notranslate position-rela

BLASR error about flye HOT 3 CLOSED

fenderglass commented on August 27, 2024

BLASR error

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Comments (3)

mikolmogorov commented on August 27, 2024

Hi,

Thank you for your feedback!

Yes, it looks like PacBio have recently changed BLASR command line interface a bit. I'll try to fix that shortly.

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mikolmogorov commented on August 27, 2024

It should be fixed now, please try the latest master branch.

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StefanoLonardi commented on August 27, 2024

It worked. Thanks.

(myenv) stelo@H4:~/ABruijn$ ./abruijn.py reads.fa out_dir 50
[20:50:28] INFO: Running ABruijn
[20:50:28] INFO: Assembling reads
[20:50:50] INFO: Counting kmers (1/2):
0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100%
[20:51:03] INFO: Counting kmers (2/2):
0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100%
[20:51:42] INFO: Building kmer index
0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100%
[20:52:40] INFO: Finding overlaps:
0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100%
[20:54:00] INFO: Extending reads
[20:54:01] INFO: Assembled 5 contigs
[20:54:01] INFO: Generating contig sequences
[20:58:55] INFO: Polishing genome (1/2)
[20:58:55] INFO: Running BLASR
[21:10:26] INFO: Chosen 'pacbio' polishing profile
[21:10:26] INFO: Separating draft genome into bubbles
[21:12:55] INFO: Correcting bubbles
0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100%
[22:52:29] INFO: Polishing genome (2/2)
[22:52:29] INFO: Running BLASR
[23:07:05] INFO: Separating draft genome into bubbles
[23:10:24] INFO: Correcting bubbles
0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100%
[23:30:45] INFO: Done! Your assembly is in file: /24-2/home/stelo/ABruijn/out_dir/polished_2.fasta

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