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jtamames / SqueezeMeta

A complete pipeline for metagenomic analysis
GNU General Public License v3.0
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assembly error #718

Closed wittney-m closed 1 year ago

wittney-m commented 1 year ago

Hi,

I have attempted to run SqueezeMeta using this command:

./SqueezeMeta.pl -m coassembly -p PERMAFROST -s /home/wdmays/samples.file -f /home/wdmays/permafrost_files/ --minion -map minimap2-ont --euk -canumem 32

I have attached the output error:

[0mRun started Mon Jul 31 08:38:34 2023 in coassembly mode 5 metagenomes found: Sample611 Sample551 Sample256 Sample492 Sample273

Now creating directories Reading configuration from /home/wdmays/miniconda3/envs/SqueezeMeta/SqueezeMeta/scripts/PERMAFROST/SqueezeMeta_conf.pl [1 seconds]: STEP1 -> RUNNING ASSEMBLY: 01.run_all_assemblies.pl (canu)  Concatenating all samples: PAI33648_pass_barcode01_4bca8ddf_4ac63679_256.fastq.gz PAI33648_pass_barcode04_4bca8ddf_4ac63679_273.fastq.gz PAI33648_pass_barcode02_4bca8ddf_4ac63679_492.fastq.gz PAI33648_pass_barcode03_4bca8ddf_4ac63679_551.fastq.gz PAI33648_pass_barcode05_4bca8ddf_4ac63679_611.fastq.gz pair1: cat /home/wdmays/permafrost_files//PAI33648_pass_barcode01_4bca8ddf_4ac63679_256.fastq.gz /home/wdmays/permafrost_files//PAI33648_pass_barcode04_4bca8ddf_4ac63679_273.fastq.gz /home/wdmays/permafrost_files//PAI33648_pass_barcode02_4bca8ddf_4ac63679_492.fastq.gz /home/wdmays/permafrost_files//PAI33648_pass_barcode03_4bca8ddf_4ac63679_551.fastq.gz /home/wdmays/permafrost_files//PAI33648_pass_barcode05_4bca8ddf_4ac63679_611.fastq.gz > /home/wdmays/miniconda3/envs/SqueezeMeta/SqueezeMeta/scripts/PERMAFROST/data/raw_fastq/par1.fastq.gz Running assembly with canu: perl /home/wdmays/miniconda3/envs/SqueezeMeta/SqueezeMeta/lib/SqueezeMeta/assembly_canu.pl /home/wdmays/miniconda3/envs/SqueezeMeta/SqueezeMeta/scripts/PERMAFROST PERMAFROST /home/wdmays/miniconda3/envs/SqueezeMeta/SqueezeMeta/scripts/PERMAFROST/data/raw_fastq/par1.fastq.gz mv: cannot stat ‘/home/wdmays/miniconda3/envs/SqueezeMeta/SqueezeMeta/scripts/PERMAFROST/data/canu/PERMAFROST.contigs.fasta’: No such file or directory Error running command: /home/wdmays/miniconda3/envs/SqueezeMeta/SqueezeMeta/bin/canu-2.2/bin/canu -p PERMAFROST -d /home/wdmays/miniconda3/envs/SqueezeMeta/SqueezeMeta/scripts/PERMAFROST/data/canu genomeSize=5m corOutCoverage=10000 corMhapSensitivity=high corMinCoverage=0 maxThreads=12 maxMemory=32 -nanopore-raw /home/wdmays/miniconda3/envs/SqueezeMeta/SqueezeMeta/scripts/PERMAFROST/data/raw_fastq/par1.fastq.gz > /home/wdmays/miniconda3/envs/SqueezeMeta/SqueezeMeta/scripts/PERMAFROST/syslog 2>&1;mv /home/wdmays/miniconda3/envs/SqueezeMeta/SqueezeMeta/scripts/PERMAFROST/data/canu/PERMAFROST.contigs.fasta /home/wdmays/miniconda3/envs/SqueezeMeta/SqueezeMeta/scripts/PERMAFROST/data/canu/contigs.fasta at /home/wdmays/miniconda3/envs/SqueezeMeta/SqueezeMeta/lib/SqueezeMeta/assembly_canu.pl line 46. Assembly not present in /home/wdmays/miniconda3/envs/SqueezeMeta/SqueezeMeta/scripts/PERMAFROST/results/01.PERMAFROST.fasta, exiting 31mStopping in STEP1 -> 01.run_all_assemblies.pl. Program finished abnormally 0m31m

I have also attached the syslog to this post. syslog.gz

jtamames commented 1 year ago

Apparently, your dataset is very small for the assembly to work. I would recommend using sqm_longreads.pl to analyze it. Best, J