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jtamames / SqueezeMeta

A complete pipeline for metagenomic analysis
GNU General Public License v3.0
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Sample information problem #750

Closed zhenzhao123 closed 6 months ago

zhenzhao123 commented 7 months ago

I have a touble. when i run the code "SqueezeMeta.pl -m coassembly -p low_salt -s /home/lmb600/work_space/li/raw_data/yandu/sample2 -f ../yandu/ -t 100" . It told me that "Reading configuration from /home/lmb600/work_space/li/raw_data/yandu/low_salt/SqueezeMeta_conf.pl /home/lmb600/work_space/li/raw_data/yandu/low_salt/data/00.low_salt.samples ln: failed to create symbolic link '/home/lmb600/work_space/li/raw_data/yandu/low_salt/data/raw_fastq/9d20ppt3-LEK8542_L1_1.fq.gz': File exists 12 samples found: 9d30ppt1 9d20ppt2 9d25ppt3 9d35ppt1 9d35ppt2 9d25ppt1 9d20ppt1 9d30ppt2 9d35ppt3 9d25ppt2 9d20ppt3 9d30ppt3

Now merging files There must be at least one 'pair1' sequence file in your samples file /home/lmb600/work_space/li/raw_data/yandu/low_salt/data/00.low_salt.samples, and there is none!"

fpusan commented 7 months ago

Can you share the /home/lmb600/work_space/li/raw_data/yandu/sample2 file with us?

zhenzhao123 commented 7 months ago

this file showned that :9d20ppt1 9d20ppt1-LEK8540_L1_1.fq.gz pair1 9d20ppt1 9d20ppt1-LEK8540_L1_2.fq.gz pair2 9d20ppt2 9d20ppt2-LEK8541_L1_1.fq.gz pair1 9d20ppt2 9d20ppt2-LEK8541_L1_2.fq.gz pair2 9d20ppt3 9d20ppt3-LEK8542_L1_1.fq.gz pair1 9d20ppt3 9d20ppt3-LEK8542_L1_1.fq.gz pair2 9d25ppt1 9d25ppt1-LEK8543_L1_1.fq.gz pair1 9d25ppt1 9d25ppt1-LEK8543_L1_2.fq.gz pair2 9d25ppt2 9d25ppt2-LEK8544_L1_1.fq.gz pair1 9d25ppt2 9d25ppt2-LEK8544_L1_2.fq.gz pair2 9d25ppt3 9d25ppt3-LEK8545_L1_1.fq.gz pair1 9d25ppt3 9d25ppt3-LEK8545_L1_2.fq.gz pair2 9d30ppt1 9d30ppt1-LEK8546_L1_1.fq.gz pair1 9d30ppt1 9d30ppt1-LEK8546_L1_2.fq.gz pair2 9d30ppt2 9d30ppt2-LEK8547_L1_1.fq.gz pair1 9d30ppt2 9d30ppt2-LEK8547_L1_2.fq.gz pair2 9d30ppt3 9d30ppt3-LEK8548_L1_1.fq.gz pair1 9d30ppt3 9d30ppt3-LEK8548_L1_2.fq.gz pair2 9d35ppt1 9d35ppt1-LEK8549_L1_1.fq.gz pair1 9d35ppt1 9d35ppt1-LEK8549_L1_2.fq.gz pair2 9d35ppt2 9d35ppt2-LEK8550_L1_1.fq.gz pair1 9d35ppt2 9d35ppt2-LEK8550_L1_2.fq.gz pair2 9d35ppt3 9d35ppt3-LEK8551_L1_1.fq.gz pair1 9d35ppt3 9d35ppt3-LEK8551_L1_2.fq.gz pair2

fpusan commented 7 months ago 
9d20ppt3 9d20ppt3-LEK8542_L1_1.fq.gz pair1
9d20ppt3 9d20ppt3-LEK8542_L1_1.fq.gz pair2

Correct the duplicated filenames here and it should work

zhenzhao123 commented 7 months ago

Thank you , bro !

zhenzhao123 commented 7 months ago

and it told me that : Reading configuration from /home/lmb600/work_space/li/raw_data/yandu/low_salt/SqueezeMeta_conf.pl /home/lmb600/work_space/li/raw_data/yandu/low_salt/data/00.low_salt.samples 12 samples found: 9d30ppt2 9d25ppt3 9d35ppt3 9d30ppt3 9d20ppt2 9d25ppt2 9d20ppt3 9d35ppt1 9d25ppt1 9d30ppt1 9d20ppt1 9d35ppt2

Now merging files There must be at least one 'pair1' sequence file in your samples file /home/lmb600/work_space/li/raw_data/yandu/low_salt/data/00.low_salt.samples, and there is none!

fpusan commented 7 months ago

I would still look like your samples file is malformed, but I see you posted issues requesting help with steps further down the pipeline... would I be right to assume you figured this issue out?

fpusan commented 6 months ago

Closing due to lack of activity, feel free to reopen