rnaSPAdes 3.11 "finished abnormally"

[nologo68]

Hi all,

I'm trying to assemble a transcriptome from pair-end read files (fastq) using rnaSPAdes 3.11. Here is the .bat file I used:

PBS -N rnaspades_metaT

PBS -l walltime=26:00:00

PBS -l nodes=1:ppn=48

PBS -j oe

PBS -m abe

PBS -A PAA0034

set -x

cd $PBS_O_WORKDIR

/usr/bin/time -v python /fs/project/PAS1117/modules/spades/3.11.1/bin/rnaspades.py -k 55 -1 /fs/project/PAS1117/Tara_Euk/upwelling-v2/ERR1719296_1.fastq.gz -2 /fs/project/PAS1117/Tara_Euk/upwelling-v2/ERR1719296_2.fastq.gz -o rnaspades2_out

echo $PBS_JOBID echo $PBS-JOBNAME

*And here is the final lines of the .o file I received:**

== Error == system call for: "['/fs/project/PAS1117/modules/spades/3.11.1/bin/spades', '/fs/project/PAS1117/GuiDH/Amanda_B/RNASPADES/rnaspades2-v1_out/K55/configs/config.info', '/fs/project/PAS1117/GuiDH/Amanda_B/RNASPADES/rnaspades2-v1_out/K55/configs/mda_mode.info', '/fs/project/PAS1117/GuiDH/Amanda_B/RNASPADES/rnaspades2-v1_out/K55/configs/rna_mode.info']" finished abnormally, err code: -6

Do you know what is the problem here?

Thanks!!

[asl]

Please attach params.txt and spades.log file as you were instructed in the error message.

[nologo68]

Sorry where are those attached files?

[asl]

In the output project directory.

[nologo68]

Here is what I got:

Params.txt

OS: Linux-3.10.0-693.25.7.el7.x86_64-x86_64-with-redhat-7.4-Maipo

Output dir: /fs/project/PAS1117/GuiDH/Amanda_B/RNASPADES/rnaspades2_out Mode: read error correction and assembling Debug mode is turned OFF

Dataset parameters: RNA-seq mode Reads: Library number: 1, library type: paired-end orientation: fr left reads: ['/fs/project/PAS1117/Tara_Euk/upwelling-v2/ERR1719296_1.fastq.gz'] right reads: ['/fs/project/PAS1117/Tara_Euk/upwelling-v2/ERR1719296_2.fastq.gz'] interlaced reads: not specified single reads: not specified Read error correction parameters: Iterations: 1 PHRED offset will be auto-detected Corrected reads will be compressed (with gzip) Assembly parameters: k: [55] Repeat resolution is enabled Mismatch careful mode is turned OFF MismatchCorrector will be SKIPPED Coverage cutoff is turned OFF Other parameters: Dir for temp files: /fs/project/PAS1117/GuiDH/Amanda_B/RNASPADES/rnaspades2_out/tmp Threads: 16 Memory limit (in Gb): 250

spades.log

0:00:00.043 4M / 4M INFO General (kmer_splitters.hpp : 74) Memory available for splitting buffers: 5.20825 Gb 0:00:00.043 4M / 4M INFO General (kmer_splitters.hpp : 82) Using cell size of 262144 0:00:02.281 8G / 8G INFO K-mer Splitting (kmer_data.cpp : 96) Processing /fs/project/PAS1117/Tara_Euk/upwelling-v2/ERR1719296_1.fastq.gz 0:00:31.441 8G / 9G INFO K-mer Splitting (kmer_data.cpp : 106) Processed 5703635 reads 0:01:03.833 8G / 9G INFO K-mer Splitting (kmer_data.cpp : 106) Processed 11577069 reads 0:01:31.924 8G / 9G INFO K-mer Splitting (kmer_data.cpp : 106) Processed 16866328 reads 0:02:05.581 8G / 9G INFO K-mer Splitting (kmer_data.cpp : 106) Processed 22516174 reads 0:02:36.490 8G / 9G INFO K-mer Splitting (kmer_data.cpp : 106) Processed 28295098 reads 0:03:10.916 8G / 9G INFO K-mer Splitting (kmer_data.cpp : 106) Processed 33894141 reads 0:03:45.782 8G / 9G INFO K-mer Splitting (kmer_data.cpp : 106) Processed 39671913 reads 0:04:19.761 8G / 9G INFO K-mer Splitting (kmer_data.cpp : 106) Processed 45680726 reads 0:04:50.827 8G / 9G INFO K-mer Splitting (kmer_data.cpp : 106) Processed 51243897 reads 0:05:25.070 8G / 9G INFO K-mer Splitting (kmer_data.cpp : 106) Processed 57204038 reads 0:05:57.139 8G / 9G INFO K-mer Splitting (kmer_data.cpp : 106) Processed 63018736 reads 0:06:32.453 8G / 9G INFO K-mer Splitting (kmer_data.cpp : 106) Processed 68806739 reads 0:13:14.773 8G / 9G INFO K-mer Splitting (kmer_data.cpp : 106) Processed 135597991 reads 0:16:34.365 8G / 9G INFO K-mer Splitting (kmer_data.cpp : 96) Processing /fs/project/PAS1117/Tara_Euk/upwelling-v2/ERR1719296_2.fastq.gz 0:26:52.533 8G / 9G INFO K-mer Splitting (kmer_data.cpp : 106) Processed 273383930 reads 0:33:14.864 8G / 9G INFO K-mer Splitting (kmer_data.cpp : 111) Total 337047498 reads processed 0:33:16.069 64M / 9G INFO General (kmer_index_builder.hpp : 109) Starting k-mer counting. 0:43:40.142 64M / 9G INFO General (kmer_index_builder.hpp : 115) K-mer counting done. There are 3655268028 kmers in total. 0:43:40.142 64M / 9G INFO General (kmer_index_builder.hpp : 121) Merging temporary buckets. 0:46:11.601 64M / 9G INFO K-mer Index Building (kmer_index_builder.hpp : 298) Building perfect hash indices 0:49:09.499 1G / 9G INFO General (kmer_index_builder.hpp : 137) Merging final buckets. 0:49:46.638 1G / 9G INFO K-mer Index Building (kmer_index_builder.hpp : 320) Index built. Total 1694970864 bytes occupied (3.70965 bits per kmer). 0:49:46.639 1G / 9G INFO K-mer Counting (kmer_data.cpp : 357) Arranging kmers in hash map order

[asl]

Please provide the whole files.

[nologo68]

Sorry!! spades.log params.txt

[asl]

I don't see any errors in the attached files. Are you sure they are from the same run and were not truncated?