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jtamames / SqueezeMeta

A complete pipeline for metagenomic analysis
GNU General Public License v3.0
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01.run_all_assemblies.pl. Program finished abnormally #752

Closed zhenzhao123 closed 9 months ago

zhenzhao123 commented 10 months ago

Hi, when i run this code, the software reply me: code: "SqueezeMeta.pl -m coassembly -p salt -s ../yandu/sample2_back -f ../yandu/ -t 100" error: " Concatenating all samples: 9d20ppt1-LEK8540_L1_1.fq.gz 9d20ppt1-LEK8540_L1_2.fq.gz 9d20ppt2-LEK8541_L1_1.fq.gz 9d20ppt2-LEK8541_L1_2.fq.gz 9d20ppt3-LEK8542_L1_1.fq.gz 9d20ppt3-LEK8542_L1_1.fq.gz 9d25ppt1-LEK8543_L1_1.fq.gz 9d25ppt1-LEK8543_L1_2.fq.gz 9d25ppt2-LEK8544_L1_1.fq.gz 9d25ppt2-LEK8544_L1_2.fq.gz 9d25ppt3-LEK8545_L1_1.fq.gz 9d25ppt3-LEK8545_L1_2.fq.gz 9d30ppt1-LEK8546_L1_1.fq.gz 9d30ppt1-LEK8546_L1_2.fq.gz 9d30ppt2-LEK8547_L1_1.fq.gz 9d30ppt2-LEK8547_L1_2.fq.gz 9d30ppt3-LEK8548_L1_1.fq.gz 9d30ppt3-LEK8548_L1_2.fq.gz 9d35ppt1-LEK8549_L1_1.fq.gz 9d35ppt1-LEK8549_L1_2.fq.gz 9d35ppt2-LEK8550_L1_1.fq.gz 9d35ppt2-LEK8550_L1_2.fq.gz 9d35ppt3-LEK8551_L1_1.fq.gz 9d35ppt3-LEK8551_L1_2.fq.gz pair1: cat /home/lmb600/work_space/li/raw_data/yandu/9d20ppt1-LEK8540_L1_1.fq.gz /home/lmb600/work_space/li/raw_data/yandu/9d20ppt2-LEK8541_L1_1.fq.gz /home/lmb600/work_space/li/raw_data/yandu/9d20ppt3-LEK8542_L1_1.fq.gz /home/lmb600/work_space/li/raw_data/yandu/9d25ppt1-LEK8543_L1_1.fq.gz /home/lmb600/work_space/li/raw_data/yandu/9d25ppt2-LEK8544_L1_1.fq.gz /home/lmb600/work_space/li/raw_data/yandu/9d25ppt3-LEK8545_L1_1.fq.gz /home/lmb600/work_space/li/raw_data/yandu/9d30ppt1-LEK8546_L1_1.fq.gz /home/lmb600/work_space/li/raw_data/yandu/9d30ppt2-LEK8547_L1_1.fq.gz /home/lmb600/work_space/li/raw_data/yandu/9d30ppt3-LEK8548_L1_1.fq.gz /home/lmb600/work_space/li/raw_data/yandu/9d35ppt1-LEK8549_L1_1.fq.gz /home/lmb600/work_space/li/raw_data/yandu/9d35ppt2-LEK8550_L1_1.fq.gz /home/lmb600/work_space/li/raw_data/yandu/9d35ppt3-LEK8551_L1_1.fq.gz > /home/lmb600/work_space/li/raw_data/yandu/salt/data/raw_fastq/par1.fastq.gz pair2: cat /home/lmb600/work_space/li/raw_data/yandu/9d20ppt1-LEK8540_L1_2.fq.gz /home/lmb600/work_space/li/raw_data/yandu/9d20ppt2-LEK8541_L1_2.fq.gz /home/lmb600/work_space/li/raw_data/yandu/9d20ppt3-LEK8542_L1_1.fq.gz /home/lmb600/work_space/li/raw_data/yandu/9d25ppt1-LEK8543_L1_2.fq.gz /home/lmb600/work_space/li/raw_data/yandu/9d25ppt2-LEK8544_L1_2.fq.gz /home/lmb600/work_space/li/raw_data/yandu/9d25ppt3-LEK8545_L1_2.fq.gz /home/lmb600/work_space/li/raw_data/yandu/9d30ppt1-LEK8546_L1_2.fq.gz /home/lmb600/work_space/li/raw_data/yandu/9d30ppt2-LEK8547_L1_2.fq.gz /home/lmb600/work_space/li/raw_data/yandu/9d30ppt3-LEK8548_L1_2.fq.gz /home/lmb600/work_space/li/raw_data/yandu/9d35ppt1-LEK8549_L1_2.fq.gz /home/lmb600/work_space/li/raw_data/yandu/9d35ppt2-LEK8550_L1_2.fq.gz /home/lmb600/work_space/li/raw_data/yandu/9d35ppt3-LEK8551_L1_2.fq.gz > /home/lmb600/work_space/li/raw_data/yandu/salt/data/raw_fastq/par2.fastq.gz Running assembly with megahit: perl /home/lmb600/anaconda3/envs/SqueezeMeta/SqueezeMeta/lib/SqueezeMeta/assembly_megahit.pl /home/lmb600/work_space/li/raw_data/yandu/salt salt /home/lmb600/work_space/li/raw_data/yandu/salt/data/raw_fastq/par1.fastq.gz /home/lmb600/work_space/li/raw_data/yandu/salt/data/raw_fastq/par2.fastq.gz Error running command: /home/lmb600/anaconda3/envs/SqueezeMeta/SqueezeMeta/bin/megahit/megahit -1 /home/lmb600/work_space/li/raw_data/yandu/salt/data/raw_fastq/par1.fastq.gz -2 /home/lmb600/work_space/li/raw_data/yandu/salt/data/raw_fastq/par2.fastq.gz -t 100 -o /home/lmb600/work_space/li/raw_data/yandu/salt/data/megahit >> /home/lmb600/work_space/li/raw_data/yandu/salt/syslog 2>&1 at /home/lmb600/anaconda3/envs/SqueezeMeta/SqueezeMeta/lib/SqueezeMeta/assembly_megahit.pl line 36. Assembly not present in /home/lmb600/work_space/li/raw_data/yandu/salt/results/01.salt.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/lmb600/work_space/li/raw_data/yandu/salt/syslog file (zip it first) Died at /home/lmb600/anaconda3/envs/SqueezeMeta/bin/SqueezeMeta.pl line 941. " syslog.gz and then how to solve this problem? thanks!

fpusan commented 10 months ago

Hello, From the syslog the error in megahit is gzip: /home/lmb600/work_space/li/raw_data/yandu/salt/data/raw_fastq/par2.fastq.gz: invalid compressed data--crc error One or several of your pair2 input fastq.gz files appear to be corrupted or not properly formatted. Please check.

zhenzhao123 commented 10 months ago

Thanks, I 'll check it.

fpusan commented 9 months ago

Closing due to lack of activity, feel free to reopen