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Test dataset does not work, spades-hammer fails #1272
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Just an update. I changed the Spades version to 3.15.3 and now it is python error from PyYaml module (known issue in PyYaml v3).
It seems Spades uses internal PyYaml instead of the one available in system python. Which version would be working stable in Python 3.10? |
OK. I tried to build 3.15.5 and after building it seems to be working fine. You probably would like to state which system the pre-built binaries are compiled for and which ones are supported. |
Description of bug
I have an error on Spades 3.15.5 downloaded and installed as Binary from here (GitHub Releases). It is the same issue as reported in #1267. Unfortunately, it is marked as "outdated" and "wsl", but there is a second comment on the latest version and not in wsl with the same error. Hence, creating the new issue as tags are confusing.
It is run in Docker based on Ubuntu 22.04 image (run under normal user, not root):
Python 3.10.12
spades.log
Command line: /tools/SPAdes-3.15.5-Linux/bin/spades.py --test
System information:
SPAdes version: 3.15.5
Python version: 3.10.12
OS: Linux-5.15.0-102-generic-x86_64-with-glibc2.35
Output dir: /home/user1/2024-04-12-assembly/spades_test
Mode: read error correction and assembling
Debug mode is turned OFF
Dataset parameters:
Standard mode
For multi-cell/isolate data we recommend to use '--isolate' option; for single-cell MDA data use '--sc'; for metagenomic data use '--meta'; for RNA-Seq use '--rna'.
Reads:
Library number: 1, library type: paired-end
orientation: fr
left reads: ['/tools/SPAdes-3.15.5-Linux/share/spades/test_dataset/ecoli_1K_1.fq.gz']
right reads: ['/tools/SPAdes-3.15.5-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: /home/user1/2024-04-12-assembly/spades_test/tmp
Threads: 16
Memory limit (in Gb): 62
======= SPAdes pipeline started. Log can be found here: /home/user1/2024-04-12-assembly/spades_test/spades.log
/tools/SPAdes-3.15.5-Linux/share/spades/test_dataset/ecoli_1K_1.fq.gz: max reads length: 100
/tools/SPAdes-3.15.5-Linux/share/spades/test_dataset/ecoli_1K_2.fq.gz: max reads length: 100
Reads length: 100
===== Before start started.
===== Read error correction started.
===== Read error correction started.
== Running: /tools/SPAdes-3.15.5-Linux/bin/spades-hammer /home/user1/2024-04-12-assembly/spades_test/corrected/configs/config.info
0:00:00.000 1M / 18M INFO General (main.cpp : 75) Starting BayesHammer, built from refs/heads/spades_3.15.5, git revision e757b82
0:00:00.003 1M / 18M INFO General (main.cpp : 76) Loading config from /home/user1/2024-04-12-assembly/spades_test/corrected/configs/config.info
0:00:00.008 1M / 18M INFO General (main.cpp : 78) Maximum # of threads to use (adjusted due to OMP capabilities): 16
0:00:00.010 1M / 18M INFO General (memory_limit.cpp : 54) Memory limit set to 62 Gb
0:00:00.010 1M / 18M INFO General (main.cpp : 86) Trying to determine PHRED offset
0:00:00.011 1M / 18M INFO General (main.cpp : 92) Determined value is 33
0:00:00.011 1M / 18M INFO General (hammer_tools.cpp : 38) Hamming graph threshold tau=1, k=21, subkmer positions = [ 0 10 ]
0:00:00.011 1M / 18M INFO General (main.cpp : 113) Size of aux. kmer data 24 bytes
=== ITERATION 0 begins ===
0:00:00.011 1M / 18M INFO General (kmer_index_builder.hpp : 243) Splitting kmer instances into 16 files using 16 threads. This might take a while.
The program was terminated by segmentation fault
=== Stack Trace ===
/tools/SPAdes-3.15.5-Linux/bin/spades-hammer() [0x421e29]
/tools/SPAdes-3.15.5-Linux/bin/spades-hammer() [0x423956]
/lib/x86_64-linux-gnu/libc.so.6(+0x42520) [0x7f3a4127f520]
/tools/SPAdes-3.15.5-Linux/bin/spades-hammer() [0x4847d4]
/tools/SPAdes-3.15.5-Linux/bin/spades-hammer(cfree+0x85) [0x484a15]
/tools/SPAdes-3.15.5-Linux/bin/spades-hammer() [0x494ffe]
/tools/SPAdes-3.15.5-Linux/bin/spades-hammer() [0x495c65]
/tools/SPAdes-3.15.5-Linux/bin/spades-hammer() [0x460f67]
/tools/SPAdes-3.15.5-Linux/bin/spades-hammer() [0x450515]
/tools/SPAdes-3.15.5-Linux/bin/spades-hammer() [0x461d47]
/tools/SPAdes-3.15.5-Linux/bin/spades-hammer() [0x457100]
/tools/SPAdes-3.15.5-Linux/bin/spades-hammer() [0x416300]
/lib/x86_64-linux-gnu/libc.so.6(+0x29d90) [0x7f3a41266d90]
/lib/x86_64-linux-gnu/libc.so.6(__libc_start_main+0x80) [0x7f3a41266e40]
/tools/SPAdes-3.15.5-Linux/bin/spades-hammer() [0x420681]
== Error == system call for: "['/tools/SPAdes-3.15.5-Linux/bin/spades-hammer', '/home/user1/2024-04-12-assembly/spades_test/corrected/configs/config.info']" finished abnormally, OS return value: -11
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.
SPAdes log can be found here: /home/user1/2024-04-12-assembly/spades_test/spades.log
Thank you for using SPAdes!
params.txt
Command line: /tools/SPAdes-3.15.5-Linux/bin/spades.py --test
System information:
SPAdes version: 3.15.5
Python version: 3.10.12
OS: Linux-5.15.0-102-generic-x86_64-with-glibc2.35
Output dir: /home/user1/2024-04-12-assembly/spades_test
Mode: read error correction and assembling
Debug mode is turned OFF
Dataset parameters:
Standard mode
For multi-cell/isolate data we recommend to use '--isolate' option; for single-cell MDA data use '--sc'; for metagenomic data use '--meta'; for RNA-Seq use '--rna'.
Reads:
Library number: 1, library type: paired-end
orientation: fr
left reads: ['/tools/SPAdes-3.15.5-Linux/share/spades/test_dataset/ecoli_1K_1.fq.gz']
right reads: ['/tools/SPAdes-3.15.5-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: /home/user1/2024-04-12-assembly/spades_test/tmp
Threads: 16
Memory limit (in Gb): 62
SPAdes version
v3.15.5
Operating System
Ubuntu 22.04
Python Version
3.10.12
Method of SPAdes installation
Binaries from GitHub Releases
No errors reported in spades.log
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