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baoe / AlignGraph

Algorithm for secondary de novo genome assembly guided by closely related references
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Get stuck in bowtie-align #39

Closed FelipeMelis closed 4 years ago

FelipeMelis commented 4 years ago

Hello, I ran this AlignGraph --read1 8111_ALS1279-S13_1_P.fastq --read2 8111_ALS1279-S13_2_P.fastq --contig contigs_scaffolds.fasta --genome GCF_001941865_1.fasta --distanceLow 50 --distanceHigh 1602 --extendedContig extendedContigs.fa --remainingContig remainingContigs.fa --fastMap

And got stuck in bowtie-align. When I killed the process I got this message and an empty extendedContigs.fa file

I'm using a scaffold from ragout and 250pb PE reads from illumina


CHROMOSOME 0: 
(1) Chromosome loaded
(2) Contig alignment loaded

(3) Read alignment loaded
(4) Contigs extended
(5) Contigs scaffolded

FINISHED SUCCESSFULLY for 22288 seconds (22226 seconds for alignment) :-)
FelipeMelis commented 4 years ago

I think it was a problem with my bowtie installation