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BrendelGroup / SRAssembler

Selective and Recursive local Assembler
GNU General Public License v3.0
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The walking is terminated: No new reads found #28

Closed DongnaMa closed 5 years ago

DongnaMa commented 5 years ago

Hello， I have a question,the data which came from the software ran without errors., but I used my data had errors and showed the walking is terminated: No new reads found！The all_contigs.fasta also was zero. can you helo me?

Thanks Molly

vpbrendel commented 5 years ago

If the examples ran, then you have installed the program correctly. If your read don't give any contigs, then your data do not assemble.

Please use this site for issues with the code only.

DongnaMa commented 5 years ago

Sorry, I have not solved my problem, why my data do not assemble? can you help me again? Thanks

vpbrendel commented 5 years ago

Please do NOT use this site for matters not related to the code.. Ask anyone with a little bit of understanding of using bioinformatics programs to look at what you are doing. We cannot possibly figure this out from the distance. If the examples ran, then you installed the code correctly. Whether or not your read data match your probe is a matter of the data. Your data. So you need to look at this.

AssiaS commented 5 years ago

i'm possibly having the same problem, and it might have something to do with the 'sh: /usr/bin/ls: Argument list too long' error message from the log below:

[2019-08-17 21:22:45] [INFO] Total processors: 1 [2019-08-17 21:22:45] [INFO] We have 1 libraries [2019-08-17 21:22:45] [INFO] library 1: R1_001library [2019-08-17 21:22:45] [INFO] insert size: 200 [2019-08-17 21:22:45] [INFO] left read: ../input_data/BC_6/R1_001.fastq [2019-08-17 21:22:45] [INFO] right read: ../input_data/BC_6/R2_001.fastq [2019-08-17 21:22:45] [INFO] reversed: 0 [2019-08-17 21:22:45] [INFO] Paired-end: 1 [2019-08-17 21:22:45][DOING] Now pre-processing the reads files ... [2019-08-17 21:22:45][DOING] Splitting read library 1 ... sh: /usr/bin/ls: Argument list too long [2019-08-17 21:25:51] [INFO] Library 1 has 0 split files [2019-08-17 21:25:51][DOING] Preprocessing done. [2019-08-17 21:25:51] [INFO] Begin chromosome walking ... [2019-08-17 21:25:51] [INFO] Starting round 1 ... [2019-08-17 21:25:51] [INFO] The walking is terminated: No new reads found. [2019-08-17 21:25:51][DOING] Checking the final contigs assembled in round 1 ... [2019-08-17 21:25:51] [INFO] ... no contigs found in round 1 [2019-08-17 21:25:51] [INFO] Execution time: 186 seconds

twmccart commented 5 years ago

i'm possibly having the same problem, and it might have something to do with the 'sh: /usr/bin/ls: Argument list too long' error message from the log below:

[2019-08-17 21:22:45] [INFO] Total processors: 1 [2019-08-17 21:22:45] [INFO] We have 1 libraries [2019-08-17 21:22:45] [INFO] library 1: R1_001library [2019-08-17 21:22:45] [INFO] insert size: 200 [2019-08-17 21:22:45] [INFO] left read: ../input_data/BC_6/R1_001.fastq [2019-08-17 21:22:45] [INFO] right read: ../input_data/BC_6/R2_001.fastq [2019-08-17 21:22:45] [INFO] reversed: 0 [2019-08-17 21:22:45] [INFO] Paired-end: 1 [2019-08-17 21:22:45][DOING] Now pre-processing the reads files ... [2019-08-17 21:22:45][DOING] Splitting read library 1 ... sh: /usr/bin/ls: Argument list too long [2019-08-17 21:25:51] [INFO] Library 1 has 0 split files [2019-08-17 21:25:51][DOING] Preprocessing done. [2019-08-17 21:25:51] [INFO] Begin chromosome walking ... [2019-08-17 21:25:51] [INFO] Starting round 1 ... [2019-08-17 21:25:51] [INFO] The walking is terminated: No new reads found. [2019-08-17 21:25:51][DOING] Checking the final contigs assembled in round 1 ... [2019-08-17 21:25:51] [INFO] ... no contigs found in round 1 [2019-08-17 21:25:51] [INFO] Execution time: 186 seconds

Could you attach the command you originally ran to launch SRAssembler?