Can't find sample file

[zhenzhao123]

Hello, dear software developer: I initially SqueezeMeta.pl -m coassembly -p LJCQ1 -s sampletest -f Low_group,Being reminded all the time "Can't find sample file /databack/LJCQ/RNAseq_YD/9day/Low_group/Low_group/9d35ppt1-LEK8549_L1_1.fq.gz for sample9d35ppt1_rep1 in the samples file. Please check". The sample information file is generated by tabs, and I check that the sample sequence name matches the sample information. Search for solution. The code is "SqueezeMeta.pl -m coassembly -p LJCQ1 -s sampletest -f Low_group" Sample file: 9d35ppt1-LEK8549 ../9d35ppt1-LEK8549_L1_1.fq.gz pair1 9d35ppt1-LEK8549 9d35ppt1-LEK8549_L1_2.fq.gz pair2 9d35ppt1-LEK8550 9d35ppt1-LEK8550_L1_1.fq.gz pair1 9d35ppt1-LEK8550 9d35ppt1-LEK8550_L1_2.fq.gz pair2 9d35ppt1-LEK8551 9d35ppt1-LEK8551_L1_1.fq.gz pair1 9d35ppt1-LEK8551 9d35ppt1-LEK8551_L1_2.fq.gz pair2 9d20ppt1-LEK8540 9d20ppt1-LEK8540_L1_1.fq.gz pair1 9d20ppt1-LEK8540 9d20ppt1-LEK8540_L1_2.fq.gz pair2 9d20ppt1-LEK8541 9d20ppt1-LEK8541_L1_1.fq.gz pair1 9d20ppt1-LEK8541 9d20ppt1-LEK8541_L1_2.fq.gz pair2 9d20ppt1-LEK8542 9d20ppt1-LEK8542_L1_1.fq.gz pair1 9d20ppt1-LEK8542 9d20ppt1-LEK8542_L1_2.fq.gz pair2 9d25ppt1-LEK8543 9d25ppt1-LEK8543_L1_1.fq.gz pair1 9d25ppt1-LEK8543 9d25ppt1-LEK8543_L1_2.fq.gz pair2 9d25ppt1-LEK8544 9d25ppt1-LEK8544_L1_1.fq.gz pair1 9d25ppt1-LEK8544 9d25ppt1-LEK8544_L1_2.fq.gz pair2 9d25ppt1-LEK8545 9d25ppt1-LEK8545_L1_1.fq.gz pair1 9d25ppt1-LEK8545 9d25ppt1-LEK8545_L1_2.fq.gz pair2 9d30ppt1-LEK8546 9d30ppt1-LEK8546_L1_1.fq.gz pair1 9d30ppt1-LEK8546 9d30ppt1-LEK8546_L1_2.fq.gz pair2 9d30ppt1-LEK8547 9d30ppt1-LEK8547_L1_1.fq.gz pair1 9d30ppt1-LEK8547 9d30ppt1-LEK8547_L1_2.fq.gz pair2 9d30ppt1-LEK8548 9d30ppt1-LEK8548_L1_1.fq.gz pair1 9d30ppt1-LEK8548 9d30ppt1-LEK8548_L1_2.fq.gz pair2

[fpusan]

Hi! What is the output of ls /databack/LJCQ/RNAseq_YD/9day/Low_group/Low_group/9d35ppt1-LEK8549_L1_1.fq.gz

[fpusan]

Also note that the first line of the sample file looks like

9d35ppt1-LEK8549 ../9d35ppt1-LEK8549_L1_1.fq.gz pair1

I don't think those two dots .. should be there

[zhenzhao123]

Thanks for your suggest. I adjusted the sample information, as shown in the figure below:

When I rerun it, the result is as follows:

Thanks for your attention again! Looking forward to your reply! ------------------ 原始邮件 ------------------ 发件人: "jtamames/SqueezeMeta" @.>; 发送时间: 2023年9月11日(星期一) 下午5:50 @.>; 抄送: "Zhao @.**@.>; 主题: Re: [jtamames/SqueezeMeta] Can't find sample file (Issue #727)

Also note that the first line of the sample file looks like

9d35ppt1-LEK8549 ../9d35ppt1-LEK8549_L1_1.fq.gz pair1

I don't think those two dots .. should be there

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[fpusan]

Can't see the info

[zhenzhao123]

The sample file is : LEK8549 9d35ppt1-LEK8549_L1_1.fq.gz     pair1 LEK8549 9d35ppt1-LEK8549_L1_2.fq.gz     pair2 LEK8550 9d35ppt1-LEK8550_L1_1.fq.gz     pair1 LEK8550 9d35ppt1-LEK8550_L1_2.fq.gz     pair2 LEK8551 9d35ppt1-LEK8551_L1_1.fq.gz     pair1 LEK8551 9d35ppt1-LEK8551_L1_2.fq.gz     pair2 LEK8540 9d20ppt1-LEK8540_L1_1.fq.gz     pair1 LEK8540 9d20ppt1-LEK8540_L1_2.fq.gz     pair2 LEK8541 9d20ppt1-LEK8541_L1_1.fq.gz     pair1 LEK8541 9d20ppt1-LEK8541_L1_2.fq.gz     pair2 LEK8542 9d20ppt1-LEK8542_L1_1.fq.gz     pair1 LEK8542 9d20ppt1-LEK8542_L1_2.fq.gz     pair2 LEK8543 9d25ppt1-LEK8543_L1_1.fq.gz     pair1 LEK8543 9d25ppt1-LEK8543_L1_2.fq.gz     pair2 LEK8544 9d25ppt1-LEK8544_L1_1.fq.gz     pair1 LEK8544 9d25ppt1-LEK8544_L1_2.fq.gz     pair2 LEK8545 9d25ppt1-LEK8545_L1_1.fq.gz     pair1 LEK8545 9d25ppt1-LEK8545_L1_2.fq.gz     pair2 LEK8546 9d30ppt1-LEK8546_L1_1.fq.gz     pair1 LEK8546 9d30ppt1-LEK8546_L1_2.fq.gz     pair2 LEK8547 9d30ppt1-LEK8547_L1_1.fq.gz     pair1 LEK8547 9d30ppt1-LEK8547_L1_2.fq.gz     pair2 LEK8548 9d30ppt1-LEK8548_L1_1.fq.gz     pair1 LEK8548 9d30ppt1-LEK8548_L1_2.fq.gz     pair2

and the new code is "SqueezeMeta.pl -m coassembly -p LJCQ1 -s sampletest  -f Low_group" . the result is "Can't find sample file /databack/LJCQ/RNAseq_YD/9day/Low_group/Low_group/9d35ppt1-LEK8549_L1_1.fq.gz for sample LEK8549 in the samples file. Please check".   

------------------ 原始邮件 ------------------ 发件人: "jtamames/SqueezeMeta" @.>; 发送时间: 2023年9月11日(星期一) 晚上6:04 @.>; 抄送: "Zhao @.**@.>; 主题: Re: [jtamames/SqueezeMeta] Can't find sample file (Issue #727)

Can't see the info

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[jtamames]

Indeed I think the problem is in the format of the samples file. There seems to be weird characters in it. Also remember that you must put there just the name of the files, not the paths specifying its location (that is done via the -f option) Best,

[zhenzhao123]

Thank you for your reply.

I looked at usage and found that -f is fastq/fastareadfiles'directory.

Besides, the format of the sample file is delimited by delimiters and I'm not sure how to modify it again to make it feasible.

------------------ 原始邮件 ------------------ 发件人: "jtamames/SqueezeMeta" @.>; 发送时间: 2023年9月11日(星期一) 晚上6:12 @.>; 抄送: "Zhao @.**@.>; 主题: Re: [jtamames/SqueezeMeta] Can't find sample file (Issue #727)

Indeed I think the problem is in the format of the samples file. There seems to be weird characters in it. Also remember that you must put there just the name of the files, not the paths specifying its location (that is done via the -f option) Best,

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[fpusan]

What is the output of ls /databack/LJCQ/RNAseq_YD/9day/Low_group/Low_group/? Also as javier said you need to make sure that your file is tab separated

[fpusan]

Closing due to lack of activity, feel free to reopen