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SPAdes Genome Assembler
http://ablab.github.io/spades/
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Spades not showing any output after starting processing read Two #1242

Open Shaileshdesai76 opened 7 months ago

Shaileshdesai76 commented 7 months ago

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 9a9d54db2ff9abaac718155bf74c12ec9464e8ca 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

asl commented 7 months ago

Hello

Does the problem reproduce with the latest SPAdes 3.15.5?

Shaileshdesai76 commented 7 months ago

Yes, actually, I tried with it too, but it had the same issue. Spades.log

QianGuoPKU commented 6 months ago

Hello,

I met the same problem! What's the reason and are there any solutions?

Shaileshdesai76 commented 6 months ago

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?

— Reply to this email directly, view it on GitHub https://github.com/ablab/spades/issues/1242#issuecomment-1960607361, or unsubscribe https://github.com/notifications/unsubscribe-auth/AW543B3EEBCUVGSZUIEOV6TYU7VHJAVCNFSM6AAAAABC7FXJROVHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMYTSNRQGYYDOMZWGE . You are receiving this because you authored the thread.Message ID: @.***>

QianGuoPKU commented 6 months ago

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? — Reply to this email directly, view it on GitHub <#1242 (comment)>, or unsubscribe https://github.com/notifications/unsubscribe-auth/AW543B3EEBCUVGSZUIEOV6TYU7VHJAVCNFSM6AAAAABC7FXJROVHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMYTSNRQGYYDOMZWGE . You are receiving this because you authored the thread.Message ID: @.***>

Hi,

I alternatively used the lower version of Spades and that worked.

Best Qian