read counts

[zhenzhao123]

Hello, Is there an upper limit on the sample size per assembly, I tried 12 samples, but except for the first sample, the read counts result of all other samples are 0. I don't know why other samples are 0 read counts.
BASE ZHAO

[fpusan]

Hi, Is this happening with a dev version of SqueezeMeta? Can you share your syslog with us?

[zhenzhao123]

syslog.gz

[jtamames]

Hello! Yep, something happened in the mapping step. It maps correctly the first sample, starts the mapping of the second, but it gets interrupted by some reason. Could you run again the step 10, see if it happens again, and paste here the screen output? Simply do: 10.mapsamples.pl low_salt in your /home/lmb600/work_space/li/raw_data/yandu directory Best, J

[zhenzhao123]

Hello!, J. It replied with the following information ： “Working with sample 3: 9d20ppt3 Getting raw reads cp: missing destination file operand after '/home/lmb600/work_space/li/raw_data/yandu/low_salt/temp/low_salt.9d20ppt3.current_1' Try 'cp --help' for more information. Aligning to reference with bowtie stat: No such file or directory Warning: Could not open read file "/home/lmb600/work_space/li/raw_data/yandu/low_salt/temp/low_salt.9d20ppt3.current_1" for reading; skipping... Error: No input read files were valid (ERR): bowtie2-align exited with value 1 An error occurred during mapping with command /home/lmb600/anaconda3/envs/SqueezeMeta/SqueezeMeta/bin/bowtie2/bowtie2 -x /home/lmb600/work_space/li/raw_data/yandu/low_salt/data/low_salt.bowtie -1 /home/lmb600/work_space/li/raw_data/yandu/low_salt/temp/low_salt.9d20ppt3.current_1 -2 /home/lmb600/work_space/li/raw_data/yandu/low_salt/temp/low_salt.9d20ppt3.current_2.gz --quiet -p 80 -S /home/lmb600/work_space/li/raw_data/yandu/low_salt/data/bam/low_salt.9d20ppt3.sam --very-sensitive-local! at /home/lmb600/anaconda3/envs/SqueezeMeta/bin/10.mapsamples.pl line 267.” Thanks！

[jtamames]

Could you please copy your samples file here?

[zhenzhao123]

sample2_back.TXT This is my samples file, please check.

[zhenzhao123]

The terminal print result is : 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

[jtamames]

Hum.. You have duplicated read files. For instance 9d20ppt3-LEK8542_L1_1.fq.gz is listed both as pair1 and pair2 for sample 9d20ppt3. It that correct, or is it a mistake?

[zhenzhao123]

Oh, my God, I didn't see it. I'm so sorry for the trouble!