Stopping in STEP10: Error: No input read files were valid

[luciamartinf]

I run SqueezeMeta in a cluster with 200GB reserved memory and 15 cores per node using the following command : SqueezeMeta.pl -m coassembly -p RyC -s /home/lmartin/SRV_RyC/02-trimmomatic/samples_id_SqueezeMeta.txt -f /home/lmartin/SRV_RyC/02-trimmomatic -b 25 -t 15

The program run smoothly until step 10 where I got the error: cp: falta el fichero de destino después de «/home/lmartin/SRV_RyC/08-SqueezeMeta/RyC/temp/RyC.0505-0101.current_1» Pruebe 'cp --help' para más información. stat: No such file or directory Warning: Could not open read file "/home/lmartin/SRV_RyC/08-SqueezeMeta/RyC/temp/RyC.0505-0101.current_1" for reading; skipping... Error: No input read files were valid (ERR): bowtie2-align exited with value 1 stat: No such file or directory Warning: Could not open read file "/home/lmartin/SRV_RyC/08-SqueezeMeta/RyC/temp/RyC.0505-0101.current_1" for reading; skipping... Error: No input read files were valid (ERR): bowtie2-align exited with value 1 An error occurred during mapping! at /home/lmartin/miniconda3/envs/SqueezeMeta/SqueezeMeta/scripts/10.mapsamples.pl line 180. Died at /home/lmartin/miniconda3/envs/SqueezeMeta/bin/SqueezeMeta.pl line 933.

I observed, that in fact, the current_1 file is not in my directory but the current_2 file for the first sample is.

The standard output and errors can be observed with the files: Squeezemeta-40344263_fat01.out.txt Squeezemeta-40344263_fat01.err.txt

Find attached the syslog and SqueezeMeta_conf.pl files: syslog.txt SqueezeMeta_conf.pl.txt

[jtamames]

Ups! I am very sorry, I did not see this issue until now! If this is still unresolved, could you please attach a copy of your samples file /home/lmartin/SRV_RyC/02-trimmomatic/samples_id_SqueezeMeta.txt ? Thanks!

[fpusan]

Closing due to lack of activity, feel free to reopen