01.run_assembly.pl. Program finished abnormally

[jahid10]

Run started Mon Nov 28 10:01:59 2022 in coassembly mode Now creating directories Reading configuration from /media/bioinfo/hdd1/Jahid_NGS_metagenomics/rajbari_control_result/SqueezeMeta_conf.pl Reading samples from /media/bioinfo/hdd1/Jahid_NGS_metagenomics/rajbari_control_result/data/00.rajbari_control_result.samples 4 samples found: RC_d0 RC_d10 RC_d5 RC_d14

Now merging files [8 minutes, 58 seconds]: STEP1 -> RUNNING CO-ASSEMBLY: 01.run_assembly.pl (megahit) Running assembly with megahit Error running command: /home/bioinfo/anaconda3/envs/SqueezeMeta/SqueezeMeta/bin/megahit/megahit -1 /media/bioinfo/hdd1/Jahid_NGS_metagenomics/rajbari_control_result/data/raw_fastq/par1.fastq.gz -2 /media/bioinfo/hdd1/Jahid_NGS_metagenomics/rajbari_control_result/data/raw_fastq/par2.fastq.gz -t 12 -o /media/bioinfo/hdd1/Jahid_NGS_metagenomics/rajbari_control_result/data/megahit >> /media/bioinfo/hdd1/Jahid_NGS_metagenomics/rajbari_control_result/syslog 2>&1 at /home/bioinfo/anaconda3/envs/SqueezeMeta/SqueezeMeta/scripts/01.run_assembly.pl line 119. Stopping in STEP1 -> 01.run_assembly.pl. Program finished abnormally syslog.zip megahit-log.zip

Died at /home/bioinfo/anaconda3/envs/SqueezeMeta/bin/SqueezeMeta.pl line 1381.

[jtamames]

Hello Please check your input files. Do both pairs have the same number of reads? Best, J

[fconstancias]

I experienced the same issue which was due to mistake in the pair2 files in the sample_list leading to par2.fastq.gz beeing the same fastq.gz file concatenated several time. Running fastqc on the par*.fastq.gz and the input files helped to resolve the issue.