ablab
Spades binary install fails to run --test
I just downloaded v3.13.1 of spades using:
wget http://cab.spbu.ru/files/release3.13.1/SPAdes-3.13.1-Linux.tar.gz tar zxvf SPAdes-3.13.1-Linux.tar.gz
and then I added the path to .../SPAdes-3.13.1-linux/bin to $PATH. Then I ran:
spades.py --test
and I got this output:
Command line: /gscmnt/gc2732/mitrevalab/TOOLS/SOFTWARE/SPADES/SPAdes-3.13.1-Linux/bin/spades.py --test
System information: SPAdes version: 3.13.1 Python version: 2.7.12 OS: Linux-3.19.0-73-generic-x86_64-with-Ubuntu-16.04-xenial
Output dir: /gscuser/jmartin/spades_test Mode: read error correction and assembling Debug mode is turned OFF
Dataset parameters: Multi-cell mode (you should set '--sc' flag if input data was obtained with MDA (single-cell) technology or --meta flag if processing metagenomic dataset) Reads: Library number: 1, library type: paired-end orientation: fr left reads: ['/gscmnt/gc2732/mitrevalab/TOOLS_Mitreva/SOFTWARE/SPADES/SPAdes-3.13.1-Linux/share/spades/test_dataset/ecoli_1K_1.fq.gz'] right reads: ['/gscmnt/gc2732/mitrevalab/TOOLS_Mitreva/SOFTWARE/SPADES/SPAdes-3.13.1-Linux/share/spades/test_dataset/ecoli_1K_2.fq.gz'] interlaced reads: not specified single reads: not specified merged reads: not specified Read error correction parameters: Iterations: 1 PHRED offset will be auto-detected Corrected reads will be compressed Assembly parameters: k: automatic selection based on read length 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: /gscuser/jmartin/spades_test/tmp Threads: 16 Memory limit (in Gb): 250
======= SPAdes pipeline started. Log can be found here: /gscuser/jmartin/spades_test/spades.log
===== Read error correction started.
== Running read error correction tool: /gscmnt/gc2732/mitrevalab/TOOLS_Mitreva/SOFTWARE/SPADES/SPAdes-3.13.1-Linux/bin/spades-hammer /gscuser/jmartin/spades_test/corrected/configs/config.info
0:00:00.000 4M / 4M INFO General (main.cpp : 75) Starting BayesHammer, built from refs/heads/spades_3.13.1, git revision 9a9d54db2ff9abaac718155bf74c12ec9464e8ca 0:00:00.000 4M / 4M INFO General (main.cpp : 76) Loading config from /gscuser/jmartin/spades_test/corrected/configs/config.info 0:00:00.001 4M / 4M INFO General (main.cpp : 78) Maximum # of threads to use (adjusted due to OMP capabilities): 16 0:00:00.001 4M / 4M INFO General (memory_limit.cpp : 49) Memory limit set to 250 Gb 0:00:00.001 4M / 4M INFO General (main.cpp : 86) Trying to determine PHRED offset 0:00:00.001 4M / 4M INFO General (main.cpp : 92) Determined value is 33 0:00:00.001 4M / 4M INFO General (hammer_tools.cpp : 36) Hamming graph threshold tau=1, k=21, subkmer positions = [ 0 10 ] 0:00:00.001 4M / 4M INFO General (main.cpp : 113) Size of aux. kmer data 24 bytes === ITERATION 0 begins === 0:00:00.005 4M / 4M INFO K-mer Index Building (kmer_index_builder.hpp : 301) Building kmer index 0:00:00.005 4M / 4M INFO General (kmer_index_builder.hpp : 117) Splitting kmer instances into 256 files using 16 threads. This might take a while. 0:00:00.007 4M / 4M INFO General (file_limit.hpp : 32) Open file limit set to 524288 0:00:00.007 4M / 4M INFO General (kmer_splitters.hpp : 89) Memory available for splitting buffers: 5.20825 Gb 0:00:00.007 4M / 4M INFO General (kmer_splitters.hpp : 97) Using cell size of 262144
== Error == system call for: "['/gscmnt/gc2732/mitrevalab/TOOLS_Mitreva/SOFTWARE/SPADES/SPAdes-3.13.1-Linux/bin/spades-hammer', '/gscuser/jmartin/spades_test/corrected/configs/config.info']" finished abnormally, err code: -7
In case you have troubles running SPAdes, you can write to [email protected] 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.
Here are the spades.log & params.txt generated by my attempt to run this test. Can someone help me figure out what's going on?
The unix df -kT command says its a GPFS mount. I am running the command on a remote server inside a docker container, and I am able to see and have permissions for the resources mentioned in the error message. The disk allocation appears to have ample free space (~50Tb).
I get a little fuzzy on the specifics of the running docker container, but I think it should be running as me (my user) which should have permission for everything.
I have recently, successfully used SPADES v3.11.1 on small bacterial assemblies. I was having trouble with assembling this large (~1Gb) genome so I thought I would try the latest version of spades but I can't seem to get the v3.13.1 binary to work.
The container its operating within is using python v2.7.12
Well, it's like an issue with GPFS, we saw lots of such problems in the past...