Phyluce CRITICAL issues - Expected assembly files were not found in output.

[jb23590]

Dear all,

I hope you can help. Following from SPAdes assembly using Phyluce-1.7.1 with the following:

phyluce_assembly_assemblo_spades \ --conf Plate1Assembly.conf \ --output Plate1Spades \ --cores 12 \

Within output files there are no contigs.fasta or scaffolds.fasta files. I do get a contigs directory at the same level of the other output files (as expected) however the symlink files within, when clicked, return the error: No such file or directory. Error code: 2

Looking at the log file below I can see a CRITICAL error for each input. I include inputs for the first 5 or so files but this was consistent for all 95 files. This has never happened before so any help is very appreciated.

2024-11-16 19:06:26,142 - phyluce_assembly_assemblo_spades - INFO - =========== Starting phyluce_assembly_assemblo_spades =========== 2024-11-16 19:06:26,144 - phyluce_assembly_assemblo_spades - INFO - Version: 1.7.1 2024-11-16 19:06:26,144 - phyluce_assembly_assemblo_spades - INFO - Commit: None 2024-11-16 19:06:26,144 - phyluce_assembly_assemblo_spades - INFO - Argument --config: /home/jb23590/Plate1/Plate1Assembly.conf 2024-11-16 19:06:26,144 - phyluce_assembly_assemblo_spades - INFO - Argument --cores: 12 2024-11-16 19:06:26,144 - phyluce_assembly_assemblo_spades - INFO - Argument --dir: None 2024-11-16 19:06:26,144 - phyluce_assembly_assemblo_spades - INFO - Argument --log_path: None 2024-11-16 19:06:26,145 - phyluce_assembly_assemblo_spades - INFO - Argument --memory: 8 2024-11-16 19:06:26,145 - phyluce_assembly_assemblo_spades - INFO - Argument --no_clean: False 2024-11-16 19:06:26,145 - phyluce_assembly_assemblo_spades - INFO - Argument --output: /home/jb23590/Plate1/Plate1Spades 2024-11-16 19:06:26,145 - phyluce_assembly_assemblo_spades - INFO - Argument --subfolder: 2024-11-16 19:06:26,145 - phyluce_assembly_assemblo_spades - INFO - Argument --verbosity: INFO 2024-11-16 19:06:26,145 - phyluce_assembly_assemblo_spades - INFO - Getting input filenames and creating output directories 2024-11-16 19:06:26,675 - phyluce_assembly_assemblo_spades - INFO - --------------------- Processing BH_BTHA_01 --------------------- 2024-11-16 19:06:26,682 - phyluce_assembly_assemblo_spades - INFO - Finding fastq/fasta files 2024-11-16 19:06:26,689 - phyluce_assembly_assemblo_spades - INFO - File type is fastq 2024-11-16 19:06:26,690 - phyluce_assembly_assemblo_spades - INFO - Running SPAdes for PE data 2024-11-16 19:11:21,989 - phyluce_assembly_assemblo_spades - INFO - Removing extraneous assembly files 2024-11-16 19:11:21,991 - phyluce_assembly_assemblo_spades - CRITICAL - Expected assembly files were not found in output. 2024-11-16 19:11:21,992 - phyluce_assembly_assemblo_spades - INFO - Symlinking assembled contigs into /home/jb23590/Plate1/Plate1Spades/contigs 2024-11-16 19:11:21,992 - phyluce_assembly_assemblo_spades - INFO - --------------------- Processing BH_BTHA_02 --------------------- 2024-11-16 19:11:21,993 - phyluce_assembly_assemblo_spades - INFO - Finding fastq/fasta files 2024-11-16 19:11:21,997 - phyluce_assembly_assemblo_spades - INFO - File type is fastq 2024-11-16 19:11:21,997 - phyluce_assembly_assemblo_spades - INFO - Running SPAdes for PE data 2024-11-16 19:20:51,254 - phyluce_assembly_assemblo_spades - INFO - Removing extraneous assembly files 2024-11-16 19:20:51,255 - phyluce_assembly_assemblo_spades - CRITICAL - Expected assembly files were not found in output. 2024-11-16 19:20:51,256 - phyluce_assembly_assemblo_spades - INFO - Symlinking assembled contigs into /home/jb23590/Plate1/Plate1Spades/contigs 2024-11-16 19:20:51,257 - phyluce_assembly_assemblo_spades - INFO - --------------------- Processing BH_BTHA_04 --------------------- 2024-11-16 19:20:51,297 - phyluce_assembly_assemblo_spades - INFO - Finding fastq/fasta files 2024-11-16 19:20:51,302 - phyluce_assembly_assemblo_spades - INFO - File type is fastq 2024-11-16 19:20:51,302 - phyluce_assembly_assemblo_spades - INFO - Running SPAdes for PE data 2024-11-16 19:39:27,320 - phyluce_assembly_assemblo_spades - INFO - Removing extraneous assembly files 2024-11-16 19:39:27,321 - phyluce_assembly_assemblo_spades - CRITICAL - Expected assembly files were not found in output. 2024-11-16 19:39:27,321 - phyluce_assembly_assemblo_spades - INFO - Symlinking assembled contigs into /home/jb23590/Plate1/Plate1Spades/contigs 2024-11-16 19:39:27,322 - phyluce_assembly_assemblo_spades - INFO - --------------------- Processing BH_BTHA_05 --------------------- 2024-11-16 19:39:27,323 - phyluce_assembly_assemblo_spades - INFO - Finding fastq/fasta files 2024-11-16 19:39:27,406 - phyluce_assembly_assemblo_spades - INFO - File type is fastq 2024-11-16 19:39:27,407 - phyluce_assembly_assemblo_spades - INFO - Running SPAdes for PE data 2024-11-16 19:53:35,449 - phyluce_assembly_assemblo_spades - INFO - Removing extraneous assembly files 2024-11-16 19:53:35,450 - phyluce_assembly_assemblo_spades - CRITICAL - Expected assembly files were not found in output. 2024-11-16 19:53:35,451 - phyluce_assembly_assemblo_spades - INFO - Symlinking assembled contigs into /home/jb23590/Plate1/Plate1Spades/contigs

Thank you, J

[asl]

Please attach spades.log and params.txt files.

[jb23590]

Attached here for one sample , thank you params.txt spades.log

[asl]

The log reads:

  0:09:27.010   409M / 4G    ERROR  K-mer Counting           (kmer_data.cpp             : 348)   The reads contain too many k-mers to fit into available memory. You need approx. 17.0655GB of free RAM to assemble your dataset

So, you're running out of RAM

[jb23590]

Thank you,

I will contact our cluster operator and see if this can be resolved