Stopping in STEP10 -> 10.mapsamples.pl. Program finished abnormally

[diegorojasa]

Hola!

Estoy corriendo SqueezeMeta en una computadora virtual (Linux vm-minibiotatech 5.15.0-1054-azure #62~20.04.1-Ubuntu SMP Wed Jan 17 12:22:56 UTC 2024 x86_64 x86_64 x86_64 GNU/Linux). Luego de correr test_install.pl dice 'All checks successful'. Al llegar al paso 10, el primer par lo analiza bien, pero en el segundo arroja el sgte. error:

No se cual pueda ser el error, ya que queda espacio tanto en RAM como en el disco duro.

Adjunto el syslog.

Ahora lo estoy corriendo con bwa en vez de bowtie, actualizo apenas llegue al paso 10.

De antemano, muchas gracias!!

syslog.zip

[fpusan]

What's the output of running /home/admin_mbt/anaconda3/envs/SqueezeMeta/SqueezeMeta/bin/bowtie2/bowtie2 -x /home/admin_mbt/Desktop/shotgun/genomas2/intento2/data/intento2.bowtie -1 /home/admin_mbt/Desktop/shotgun/genomas2/intento2/temp/intento2.GM2353_2_2_L3.current_1 -2 /home/admin_mbt/Desktop/shotgun/genomas2/intento2/temp/intento2.GM2353_2_2_L3.current_2 -p 12 -S /home/admin_mbt/Desktop/shotgun/genomas2/intento2/data/bam/intento2.GM2353_2_2_L3.sam --very-sensitive-local ?

[diegorojasa]

Pude correr el código sin ningún problema con bwa!

Al correr el código que me indicas, da este resultado:

Error, fewer reads in file specified with -1 than in file specified with -2 terminate called after throwing an instance of 'int' Aborted (core dumped) (ERR): bowtie2-align exited with value 134

[fpusan]

Can you check whether the input fastq files are properly paired for the sample that is failing?

[diegorojasa]

they were correctly named on the test.samples file but i was looking at the files themselves and found that one was not the same size as the other. I I deleted and uploaded again and now they are the same size. Most probably there was an error while copying/pasting the files from my computer to the VM :( I'm gonna try the run again

[fpusan]

Closing due to lack of activity, feel free to reopen