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Spades assembly failed error code 255 #152
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I have exactly the same error. |
Hello sleyn, Its because my read pairs don't match. I figured it out. #install fastq-pair head -1051 FRIDec16A_C10_decon_R1.fastq >test_R1.fastq fastq_pair test_R1.fastq test_R2.fastq |
Thanks! |
sleyn, make sure to remove the phiX. Even when they say isn't on the lane it is. Cheers |
Thanks! Will try it. |
Hi Rick, Thanks in advance, JoJo |
hmm, odd. See if the counts match. If that doesn't work try this --no_correct parameter. |
Can I run rnaspade.py in 8gb ram, 1tb hard disk |
Hello,
I have tried this a couple of times and spades (in unicycler) failed to produce an assembly.
Error log:
== Running assembler: K27
0:00:00.000 4M / 4M INFO General (main.cpp : 74) Loaded config from /data/friesen/testdrive/agro-dir/spades_assembly/assembly/K27/configs/config.info
0:00:00.000 4M / 4M INFO General (memory_limit.cpp : 49) Memory limit set to 250 Gb
0:00:00.000 4M / 4M INFO General (main.cpp : 87) Starting SPAdes, built from refs/heads/spades_3.13.0, git revision 8ea46659e9b2aca35444a808db550ac333006f8b
0:00:00.000 4M / 4M INFO General (main.cpp : 88) Maximum k-mer length: 128
0:00:00.000 4M / 4M INFO General (main.cpp : 89) Assembling dataset (/data/friesen/testdrive/agro-dir/spades_assembly/assembly/dataset.info) with K=27
0:00:00.000 4M / 4M INFO General (main.cpp : 90) Maximum # of threads to use (adjusted due to OMP capabilities): 1
0:00:00.000 4M / 4M INFO General (launch.hpp : 51) SPAdes started
0:00:00.000 4M / 4M INFO General (launch.hpp : 58) Starting from stage: construction
0:00:00.000 4M / 4M INFO General (launch.hpp : 65) Two-step RR enabled: 0
0:00:00.000 4M / 4M INFO StageManager (stage.cpp : 132) STAGE == de Bruijn graph construction
0:00:00.008 4M / 4M INFO General (read_converter.hpp : 77) Converting reads to binary format for library #0 (takes a while)
0:00:00.008 4M / 4M INFO General (read_converter.hpp : 78) Converting paired reads
0:00:00.401 80M / 132M INFO General (binary_converter.hpp : 93) 16384 reads processed
0:00:00.606 92M / 132M INFO General (binary_converter.hpp : 93) 32768 reads processed
0:00:01.021 120M / 132M INFO General (binary_converter.hpp : 93) 65536 reads processed
0:00:02.071 184M / 184M INFO General (binary_converter.hpp : 93) 131072 reads processed
0:00:04.251 320M / 320M INFO General (binary_converter.hpp : 93) 262144 reads processed
0:00:06.537 464M / 464M ERROR General (paired_readers.hpp : 56) The number of right read-pairs is larger than the number of left read-pairs
0:00:06.537 464M / 464M ERROR General (paired_readers.hpp : 60) Unequal number of read-pairs detected in the following files: /data/friesen/testdrive/agro-dir/spades_assem
bly/corrected_1.fastq.gz /data/friesen/testdrive/agro-dir/spades_assembly/corrected_2.fastq.gz
== Error == system call for: "['/home/richard.white3/SPAdes-3.13.0-Linux/bin/spades-core', '/data/friesen/testdrive/agro-dir/spades_assembly/assembly/K27/configs/config.info']" finished abnormally, err c
ode: 255
In case you have troubles running SPAdes, you can write to spades.support@cab.spbu.ru
or report an issue on our GitHub repository github.com/ablab/spades
Please provide us with params.txt and spades.log files from the output directory.
I have checked the inputs prior to error correction and it had the same number of reads.
I tried to check the corrected reads but it formats them weird so I can 't check with fastqc.
uk.ac.babraham.FastQC.Sequence.SequenceFormatException: Midline 'AAAAAAAADDDDDDDDGGGGGFHIHFHHHHHHHHHHHHIHHHHHHHIIHHHHHHHHHHHHHHHFGGEGEDEGEGCEGGEDGGGG?DG?GGGGGGGGGGGGGGGGGGGGGGGGGDGGGGGGGDGGGGGGGGGGGGGGGGGGGEGGGAGDGGEGGGGGGGGGGGGGGGGGAGGEGGGGGCEGGGGGGEEGGGGGGGGGGGGGGDGGGEEGGGGGGGGGGGGGGGGDA>DGGGGGAGGGGGDGGGG' didn't start with '+'
at uk.ac.babraham.FastQC.Sequence.FastQFile.readNext(FastQFile.java:172)
at uk.ac.babraham.FastQC.Sequence.FastQFile.next(FastQFile.java:125)
at uk.ac.babraham.FastQC.Analysis.AnalysisRunner.run(AnalysisRunner.java:76)
at java.lang.Thread.run(Thread.java:748)
Failed to process file corrected_2.fastq.gz
uk.ac.babraham.FastQC.Sequence.SequenceFormatException: ID line didn't start with '@'
at uk.ac.babraham.FastQC.Sequence.FastQFile.readNext(FastQFile.java:158)
at uk.ac.babraham.FastQC.Sequence.FastQFile.next(FastQFile.java:125)
at uk.ac.babraham.FastQC.Analysis.AnalysisRunner.run(AnalysisRunner.java:76)
at java.lang.Thread.run(Thread.java:748)
I found this error code for spades
https://www.biostars.org/p/311603/
Which states use a Try setting --phred-offset 33 or 64 manually and re-run. If you have recent sequence data then the offset will be 33 for sure.
I can't put the --phred-offset flag in for spades for some reason.
help?
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