When trying to run a genome assembly with the a5 pipeline I receive an error [a5] error buildings contigs with IDB. I have tried running it over 10 times and no luck
this is the code
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(base) Christinas-MacBook-Air-2:~ christinacelispuga$ cd Desktop/
(base) Christinas-MacBook-Air-2:Desktop christinacelispuga$ mkdir a5lastdemo
(base) Christinas-MacBook-Air-2:Desktop christinacelispuga$ cd a5lastdemo/
(base) Christinas-MacBook-Air-2:a5lastdemo christinacelispuga$ /Users/christinacelispuga/Desktop/a5_miseq_macOS_20160825/bin/a5_pipeline.pl /Users/christinacelispuga/Desktop/a5_miseq_macOS_20160825/example/phiX_p1.fastq /Users/christinacelispuga/Desktop/a5_miseq_macOS_20160825/example/phiX_p2.fastq a5demotest
[a5] Found the following libraries:
raw1:
id=raw1
p1=/Users/christinacelispuga/Desktop/a5_miseq_macOS_20160825/example/phiX_p1.fastq
p2=/Users/christinacelispuga/Desktop/a5_miseq_macOS_20160825/example/phiX_p2.fastq
[a5] Found 1 libraries
[a5] Starting pipeline at step 1
[a5] Cleaning reads with SGA
[a5] Cleaning reads with SGA
cleaning each PE lib
p1 is /Users/christinacelispuga/Desktop/a5_miseq_macOS_20160825/example/phiX_p1.fastq
Cleaning reads
[a5] java -Xmx512m -jar '/Users/christinacelispuga/Desktop/a5_miseq_macOS_20160825/bin'/trimmomatic.jar SE -threads 4 -phred64 a5demotest.s1/phiX_p1.fastq.both.fastq a5demotest.s1/phiX_p1.fastq.trim.fastq ILLUMINACLIP:/Users/christinacelispuga/Desktop/a5_miseq_macOS_20160825/bin/../adapter.fasta:2:30:10 LEADING:3 TRAILING:3 SLIDINGWINDOW:4:15 MINLEN:36
TrimmomaticSE: Started with arguments: -threads 4 -phred64 a5demotest.s1/phiX_p1.fastq.both.fastq a5demotest.s1/phiX_p1.fastq.trim.fastq ILLUMINACLIP:/Users/christinacelispuga/Desktop/a5_miseq_macOS_20160825/bin/../adapter.fasta:2:30:10 LEADING:3 TRAILING:3 SLIDINGWINDOW:4:15 MINLEN:36
Using PrefixPair: 'TACACTCTTTCCCTACACGACGCTCTTCCGATCT' and 'GTGACTGGAGTTCAGACGTGTGCTCTTCCGATCT'
Using PrefixPair: 'TACACTCTTTCCCTACACGACGCTCTTCCGATCT' and 'TCTCGGCATTCCTGCTGAACCGCTCTTCCGATCT'
Using PrefixPair: 'AGATGTGTATAAGAGACAG' and 'AGATGTGTATAAGAGACAG'
Using Long Clipping Sequence: 'AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTA'
Using Long Clipping Sequence: 'CTGTCTCTTATACACATCTCCGAGCCCACGAGAC'
Using Long Clipping Sequence: 'CTGTCTCTTATACACATCTGACGCTGCCGACGA'
Using Long Clipping Sequence: 'TCGTCGGCAGCGTCAGATGTGTATAAGAGACAG'
Using Long Clipping Sequence: 'GCCTCCCTCGCGCCATCAGAGATGTGTATAAGAGACAG'
Using Long Clipping Sequence: 'GCCTTGCCAGCCCGCTCAGAGATGTGTATAAGAGACAG'
Using Long Clipping Sequence: 'TACACTCTTTCCCTACACGACGCTCTTCCGATCT'
Using Long Clipping Sequence: 'AGATCGGAAGAGCGGTTCAGCAGGAATGCCGAGA'
Using Long Clipping Sequence: 'GTGACTGGAGTTCAGACGTGTGCTCTTCCGATCT'
Using Long Clipping Sequence: 'TTTTTTTTTTAATGATACGGCGACCACCGAGATCTACAC'
Using Long Clipping Sequence: 'CTGTCTCTTATACACATCTCTGATGGCGCGAGGGAGGC'
Using Long Clipping Sequence: 'CTGTCTCTTATACACATCTCTGAGCGGGCTGGCAAGGC'
Using Long Clipping Sequence: 'AGATCGGAAGAGCACACGTCTGAACTCCAGTCAC'
Using Long Clipping Sequence: 'TTTTTTTTTTCAAGCAGAAGACGGCATACGA'
Using Long Clipping Sequence: 'GTCTCGTGGGCTCGGAGATGTGTATAAGAGACAG'
Using Long Clipping Sequence: 'TCTCGGCATTCCTGCTGAACCGCTCTTCCGATCT'
ILLUMINACLIP: Using 3 prefix pairs, 16 forward/reverse sequences, 0 forward only sequences, 0 reverse only sequences
Input Reads: 6400 Surviving: 6371 (99.55%) Dropped: 29 (0.45%)
TrimmomaticSE: Completed successfully
[a5] '/Users/christinacelispuga/Desktop/a5_miseq_macOS_20160825/bin'/sga preprocess -q 25 -f 20 -m 35 --pe-mode=0 --phred64 a5demotest.s1/phiX_p1.fastq.trim.fastq > a5demotest.s1/phiX_p1.fastq.both.pp 2> /dev/null
[a5] sga index -d 2097152 -t 1 a5demotest.s1/a5demotest.pp.fastq > a5demotest.s1/index.out 2> a5demotest.s1/index.err
[a5] '/Users/christinacelispuga/Desktop/a5_miseq_macOS_20160825/bin'/sga correct -t 1 -p a5demotest.pp -o a5demotest.s1/phiX_p1.fastq.both.pp.ec.fastq a5demotest.s1/phiX_p1.fastq.both.pp > a5demotest.s1/raw1.correct.out
[timer - sga::correct] wall clock: 1.40s CPU: 1.36s
Running cat a5demotest.s1/phiX_p1.fastq.both.repair.fastq >> a5demotest.s1/a5demotest.ec.fastq
Done merging libraries
[a5_s2] Building contigs from a5demotest.ec.fastq with IDBA
[a5_s2] Building contigs from a5demotest.ec.fastq with IDBA
[a5] a5demotest.s2/a5demotest.ec.fasta has 767171 bytes of FastA sequence data
[a5] '/Users/christinacelispuga/Desktop/a5_miseq_macOS_20160825/bin'/idba_ud --num_threads 4 -r a5demotest.s2/a5demotest.ec.fasta -o a5demotest.s2/a5demotest --mink 35 --maxk 84 --min_pairs 2
sh: line 1: 11039 Killed: 9 '/Users/christinacelispuga/Desktop/a5_miseq_macOS_20160825/bin'/idba_ud --num_threads 4 -r a5demotest.s2/a5demotest.ec.fasta -o a5demotest.s2/a5demotest --mink 35 --maxk 84 --min_pairs 2 > a5demotest.s2/idba.out
[a5] Previous IDBA-UD run failed. Trying again single-threaded.
sh: line 1: 11041 Killed: 9 '/Users/christinacelispuga/Desktop/a5_miseq_macOS_20160825/bin'/idba_ud --num_threads 4 -r a5demotest.s2/a5demotest.ec.fasta -o a5demotest.s2/a5demotest --mink 35 --maxk 84 --min_pairs 2 --num_threads 1 > a5demotest.s2/idba.out
[a5] Error building contigs with IDBA
(base) Christinas-MacBook-Air-2:a5lastdemo christinacelispuga$
Please help
Please use the formatting bar (especially the
code
option) to present your post better. You can use backticks for inline code (`text` becomestext
), or select a chunk of text and use the highlighted button to format it as a code block. I've done it for you this time.Also, this is a question, not a "blog". I don't understand why the "Blog" option was picked at all.
You should also show us what your perl script does exactly. Right now, you're asking us to help you debug a black box that you have full access to.