Analysis stuck for over two days!

[Jokendo-collab]

I only have 12 samples which I started working on two days ago. The program is stuck and I am not if this is normal. Can someone confirm this?

SqueezeMeta v1.5.1, Jan 2022 - (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 Sat Aug 13 18:44:23 2022 in coassembly mode Now creating directories Reading configuration from /cbio/users/javanokendo/sarsCovProject/art_variantAnalysis/tmp_metagenomics/analysis_results/SqueezeMeta_conf.pl Reading samples from /cbio/users/javanokendo/sarsCovProject/art_variantAnalysis/tmp_metagenomics/analysis_results/data/00.analysis_results.samples 12 samples found: SRR12670008 SRR12670013 SRR12670011 SRR12670006 SRR12670016 SRR12670012 SRR12670015 SRR12670007 SRR12670010 SRR12670017 SRR12670009 SRR12670014

Now merging files [4 minutes, 14 seconds]: STEP1 -> RUNNING CO-ASSEMBLY: 01.run_assembly.pl (spades) Running assembly with spades

[fpusan]

It might be normal, depending on how many cores you are using. As long as spades is progressing (even if it does so slowly) I wouldn't worry. You can check the progress in the syslog file inside the project directory. Also internal spades logs can be found in the data/spades directory inside the project directory. Alternatively you can use megahit as the assembler, since it is less resource intensive...