Spades not showing any output after starting processing read Two #1242
Comments
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Hello Does the problem reproduce with the latest SPAdes 3.15.5? |
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Yes, actually, I tried with it too, but it had the same issue. |
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Hello, I met the same problem! What's the reason and are there any solutions? |
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In this case, I tried all sorts of ideas, like compiling, many times.
But I used a newer version, though it was showing an error, and I read
somewhere that if this comes up many times, check the data file, so
I removed my file from the server and re-uploaded it, and somehow it
worked.
*Shailesh Desai*
*Ph.D. Student*
*Cytogenetic lab, *
*Dept.**, of Zoology, Institute of Science,*
*BHU, Varanasi. *
Cell - (+91) 7698946714
…On Fri, Feb 23, 2024 at 6:50 AM qianguo ***@***.***> wrote:
Hello,
I met the same problem! What's the reason and are there any solutions?
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Hi, I alternatively used the lower version of Spades and that worked. Best |
Description of bug
I am running spades to assemble the genome using short reads. At first, it appeared that everything was working fine. As it started processing read, it completed read 1 and started reading read 2 (reverse), but Spades was not showing any progress after then nor showing any error.
I tried to run three or four times, but its not working.
spades.log
Command line: /home/gyaneshwer.bhu/miniconda3/bin/spades.py -1 /scratch/gyaneshwer.bhu/Frogs/Meg3_read1.fq.gz -2 /scratch/gyaneshwer.bhu/Frogs/Meg3_read2.fq.gz --only-error-correction -o /scratch/gyaneshwer.bhu/Frogs/error_only
System information:
SPAdes version: 3.13.1
Python version: 3.11.5
OS: Linux-3.10.0-957.el7.x86_64-x86_64-with-glibc2.17
Output dir: /scratch/gyaneshwer.bhu/Frogs/error_only
Mode: ONLY read error correction (without 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: ['/scratch/gyaneshwer.bhu/Frogs/Meg3_read1.fq.gz']
right reads: ['/scratch/gyaneshwer.bhu/Frogs/Meg3_read2.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
Other parameters:
Dir for temp files: /scratch/gyaneshwer.bhu/Frogs/error_only/tmp
Threads: 16
Memory limit (in Gb): 187
======= SPAdes pipeline started. Log can be found here: /scratch/gyaneshwer.bhu/Frogs/error_only/spades.log
===== Read error correction started.
== Running read error correction tool: /home/gyaneshwer.bhu/miniconda3/share/spades-3.13.1-0/bin/spades-hammer /scratch/gyaneshwer.bhu/Frogs/error_only/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 9a9d54d
0:00:00.000 4M / 4M INFO General (main.cpp : 76) Loading config from /scratch/gyaneshwer.bhu/Frogs/error_only/corrected/configs/config.info
0:00:00.002 4M / 4M INFO General (main.cpp : 78) Maximum # of threads to use (adjusted due to OMP capabilities): 16
0:00:00.002 4M / 4M INFO General (memory_limit.cpp : 49) Memory limit set to 187 Gb
0:00:00.002 4M / 4M INFO General (main.cpp : 86) Trying to determine PHRED offset
0:00:00.016 4M / 4M INFO General (main.cpp : 92) Determined value is 33
0:00:00.016 4M / 4M INFO General (hammer_tools.cpp : 36) Hamming graph threshold tau=1, k=21, subkmer positions = [ 0 10 ]
0:00:00.016 4M / 4M INFO General (main.cpp : 113) Size of aux. kmer data 24 bytes
=== ITERATION 0 begins ===
0:00:00.017 4M / 4M INFO K-mer Index Building (kmer_index_builder.hpp : 301) Building kmer index
0:00:00.017 4M / 4M INFO General (kmer_index_builder.hpp : 117) Splitting kmer instances into 256 files using 16 threads. This might take a while.
0:00:00.018 4M / 4M INFO General (file_limit.hpp : 32) Open file limit set to 1024
0:00:00.018 4M / 4M INFO General (kmer_splitters.hpp : 89) Memory available for splitting buffers: 3.89575 Gb
0:00:00.018 4M / 4M INFO General (kmer_splitters.hpp : 97) Using cell size of 262144
0:00:01.656 8G / 8G INFO K-mer Splitting (kmer_data.cpp : 97) Processing /scratch/gyaneshwer.bhu/Frogs/Meg3_read1.fq.gz
0:00:19.993 8G / 9G INFO K-mer Splitting (kmer_data.cpp : 107) Processed 3003331 reads
0:00:38.833 8G / 9G INFO K-mer Splitting (kmer_data.cpp : 107) Processed 6143529 reads
0:00:57.565 8G / 9G INFO K-mer Splitting (kmer_data.cpp : 107) Processed 9271848 reads
0:01:16.758 8G / 9G INFO K-mer Splitting (kmer_data.cpp : 107) Processed 12462492 reads
0:01:35.827 8G / 9G INFO K-mer Splitting (kmer_data.cpp : 107) Processed 15645291 reads
0:01:55.233 8G / 9G INFO K-mer Splitting (kmer_data.cpp : 107) Processed 18869508 reads
0:02:14.248 8G / 9G INFO K-mer Splitting (kmer_data.cpp : 107) Processed 22051764 reads
0:02:33.391 8G / 9G INFO K-mer Splitting (kmer_data.cpp : 107) Processed 25241518 reads
0:02:51.826 8G / 9G INFO K-mer Splitting (kmer_data.cpp : 107) Processed 28346928 reads
0:03:10.789 8G / 9G INFO K-mer Splitting (kmer_data.cpp : 107) Processed 31511063 reads
0:03:28.960 8G / 9G INFO K-mer Splitting (kmer_data.cpp : 107) Processed 34576302 reads
0:07:00.235 8G / 9G INFO K-mer Splitting (kmer_data.cpp : 107) Processed 69695310 reads
0:13:42.758 8G / 9G INFO K-mer Splitting (kmer_data.cpp : 107) Processed 136700132 reads
0:27:08.383 8G / 9G INFO K-mer Splitting (kmer_data.cpp : 107) Processed 270403827 reads
0:30:20.391 8G / 9G INFO K-mer Splitting (kmer_data.cpp : 97) Processing /scratch/gyaneshwer.bhu/Frogs/Meg3_read2.fq.gz
0:54:12.222 8G / 9G INFO K-mer Splitting (kmer_data.cpp : 107) Processed 537223303 reads
params.txt
Command line: /home/gyaneshwer.bhu/miniconda3/bin/spades.py -1 /scratch/gyaneshwer.bhu/Frogs/Meg3_read1.fq.gz -2 /scratch/gyaneshwer.bhu/Frogs/Meg3_read2.fq.gz --only-error-correction -o /scratch/gyaneshwer.bhu/Frogs/error_only
System information:
SPAdes version: 3.13.1
Python version: 3.11.5
OS: Linux-3.10.0-957.el7.x86_64-x86_64-with-glibc2.17
Output dir: /scratch/gyaneshwer.bhu/Frogs/error_only
Mode: ONLY read error correction (without 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: ['/scratch/gyaneshwer.bhu/Frogs/Meg3_read1.fq.gz']
right reads: ['/scratch/gyaneshwer.bhu/Frogs/Meg3_read2.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
Other parameters:
Dir for temp files: /scratch/gyaneshwer.bhu/Frogs/error_only/tmp
Threads: 16
Memory limit (in Gb): 187
SPAdes version
SPades 3.13.1
Operating System
linux server
Python Version
Python 3.11.5
Method of SPAdes installation
conda
No errors reported in spades.log
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