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Step 1 crashes no matter what we tried #675
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Hi |
2023-04-28 17:06:44 - MEGAHIT v1.2.9 |
Hello |
Hi again. We tried spades but it is extremely slow. We decided to quit the run after it was stuck on Step 1 for 10 days. This is why we tried megahit instead. |
Hi, |
Is this happening also with the test files we provide when downloading the databases? |
My apologies for the delayed response. Yes it was also the case with those test files. You mentioned that you were also having issues with megahit lately. Was this related to my issue and/or have you found the issue? |
Hum, then it is system-related, since we tried megahit using these files and it works fine. Could it be a memory-related problem? |
Hi James,
We have 512 Gb RAM installed. I will try it again with those samples. I am actually not 100% sure if we tried megahit on these test samples before
On 11 May 2023, at 8:39 pm, Javier Tamames ***@***.***> wrote:
Hum, then it is system-related, since we tried megahit using these files and it works fine. Could it be a memory-related problem?
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|
Closing due to lack of activity, feel free to reopen! |
Hello again. There seems to be an issue at step 1. If I understand the error correctly, there is no assembly created in the Results subdirectory and the script cannot continue. We tried different samples, different assembly strategies (c-assembly, seqmerge, and now sequential). We keep getting the same error. Please see screen shot below as well as the logfile attached.
Marco
Thanks for your help!
(SqueezeMeta) marco@marco-HP-Z840-Workstation:~/miniconda3/envs/SqueezeMeta/SqueezeMeta/scripts$ SqueezeMeta.pl -m sequential -s ~/miniconda3/envs/SqueezeMeta/SqueezeMeta/scripts/MC_SGM17Apr23/data/Mulu_DC_biofilms2.samples -f ~/miniconda3/envs/SqueezeMeta/SqueezeMeta/scripts/MC_SGM17Apr23/data/raw_fastq --nopfam --Euk -miniden 50 -t 48 -binners metabat2 -a megahit
SqueezeMeta v1.6.2, March 2023 - (c) J. Tamames, F. Puente-Sánchez CNB-CSIC, Madrid, SPAIN
Please cite: Tamames & Puente-Sanchez, Frontiers in Microbiology 9, 3349 (2019). doi: https://doi.org/10.3389/fmicb.2018.03349
Run started Fri Apr 28 17:05:35 2023 in sequential mode
4 metagenomes found: D3B_Ye D5B_Ac D6B_Gu D3B
--- SAMPLE D3B_Ye ---
Now creating directories
Reading configuration from /home/marco/miniconda3/envs/SqueezeMeta/SqueezeMeta/scripts/D3B_Ye/SqueezeMeta_conf.pl
Running trimmomatic (Bolger et al 2014, Bioinformatics 30(15):2114-20) for quality filtering
Parameters:
[0 seconds]: STEP1 -> RUNNING ASSEMBLY: 01.run_all_assemblies.pl (megahit)
Working for sample D3B_Ye
Preparing files for pair1: cat /home/marco/miniconda3/envs/SqueezeMeta/SqueezeMeta/scripts/MC_SGM17Apr23/data/raw_fastq/D3B_Ye_R1.fastq.gz > /home/marco/miniconda3/envs/SqueezeMeta/SqueezeMeta/scripts/D3B_Ye/data/raw_fastq/par1.fastq.gz
Preparing files for pair2: cat /home/marco/miniconda3/envs/SqueezeMeta/SqueezeMeta/scripts/MC_SGM17Apr23/data/raw_fastq/D3B_Ye_R2.fastq.gz > /home/marco/miniconda3/envs/SqueezeMeta/SqueezeMeta/scripts/D3B_Ye/data/raw_fastq/par2.fastq.gz
Running assembly with megahit: perl /home/marco/miniconda3/envs/SqueezeMeta/SqueezeMeta/lib/SqueezeMeta/assembly_megahit.pl /home/marco/miniconda3/envs/SqueezeMeta/SqueezeMeta/scripts/D3B_Ye D3B_Ye /home/marco/miniconda3/envs/SqueezeMeta/SqueezeMeta/scripts/D3B_Ye/data/raw_fastq/par1.fastq.gz /home/marco/miniconda3/envs/SqueezeMeta/SqueezeMeta/scripts/D3B_Ye/data/raw_fastq/par2.fastq.gz
Error running command: /home/marco/miniconda3/envs/SqueezeMeta/SqueezeMeta/bin/megahit/megahit -1 /home/marco/miniconda3/envs/SqueezeMeta/SqueezeMeta/scripts/D3B_Ye/data/raw_fastq/par1.fastq.gz -2 /home/marco/miniconda3/envs/SqueezeMeta/SqueezeMeta/scripts/D3B_Ye/data/raw_fastq/par2.fastq.gz -t 48 -o /home/marco/miniconda3/envs/SqueezeMeta/SqueezeMeta/scripts/D3B_Ye/data/megahit >> /home/marco/miniconda3/envs/SqueezeMeta/SqueezeMeta/scripts/D3B_Ye/syslog 2>&1 at /home/marco/miniconda3/envs/SqueezeMeta/SqueezeMeta/lib/SqueezeMeta/assembly_megahit.pl line 36.
Assembly not present in /home/marco/miniconda3/envs/SqueezeMeta/SqueezeMeta/scripts/D3B_Ye/results/01.D3B_Ye.fasta, exiting
Stopping in STEP1 -> 01.run_all_assemblies.pl. Program finished abnormally
If you don't know what went wrong or want further advice, please look for similar issues in https://github.com/jtamames/SqueezeMeta/issues
Feel free to open a new issue if you don't find the answer there. Please add a brief description of the problem and upload the /home/marco/miniconda3/envs/SqueezeMeta/SqueezeMeta/scripts/D3B_Ye/syslog file (zip it first)
Died at /home/marco/miniconda3/envs/SqueezeMeta/bin/SqueezeMeta.pl line 941.
syslog.zip
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