search

Dfam-consortium / RepeatMasker

RepeatMasker is a program that screens DNA sequences for interspersed repeats and low complexity DNA sequences.
Other
226 stars 49 forks source link

Aborting with a SIGHUP #139

Closed jingydz closed 2 years ago

jingydz commented 2 years ago

Describe the issue Aborting with a SIGHUP

Reproduction steps time RepeatMasker -parallel 30 -species "Mus musculus" -html -gff -dir repeat/ Mus_musculus_c57bl6nj.C57BL_6NJ_v1.dna.toplevel.fa

Log output RepeatMasker version 4.1.1 Search Engine: NCBI/RMBLAST [ 2.11.0+ ]

Using Master RepeatMasker Database: /xxx/software/RepeatMasker/Libraries/RepeatMaskerLib.h5 Title : Dfam withRBRM Version : 3.2 Date : 2020-07-02 Families : 51,780

Species/Taxa Search: Mus musculus [NCBI Taxonomy ID: 10090] Lineage: root;cellular organisms;Eukaryota;Opisthokonta;Metazoa; Eumetazoa;Bilateria;Deuterostomia;Chordata; Craniata ;Vertebrata ; Gnathostomata ;Teleostomi;Euteleostomi; Sarcopterygii;Dipnotetrapodomorpha;Tetrapoda;Amniota; Mammalia;Theria ;Eutheria;Boreoeutheria; Euarchontoglires;Glires;Rodentia;Myomorpha;Muroidea;Muridae 1281 families in ancestor taxa; 126 lineage-specific families

Building general libraries in: /xxx/software/RepeatMasker/Libraries/CONS-Dfam_withRBRM_3.2/general Building species libraries in: /xxx/software/RepeatMasker/Libraries/CONS-Dfam_withRBRM_3.2/Mus_musculus

analyzing file /xxx/genome/c57bl6nj/Mus_musculus_c57bl6nj.C57BL_6NJ_v1.dna.toplevel.fa

Checking for E. coli insertion elements

Checking for E. coli insertion elements .... identifying Simple Repeats in batch 48361 of 48363 identifying Simple Repeats in batch 48360 of 48363 identifying Simple Repeats in batch 48362 of 48363

Aborting with a SIGHUP

Environment (please include as much of the following information as you can find out):

jebrosen commented 2 years ago

Hi @jingydz, the SIGHUP signal usually indicates that something external asked/suggested the program to quit. Some examples might be if the program was running in a shell or terminal window which was paused or closed, or if the operating system or task scheduler is logging out a user or terminating tasks that have been running for a long time.

Depending on the reason for the SIGHUP, you may be able to prevent this by running RepeatMasker in the background through a tool such as nohup or with a disown command.

jingydz commented 2 years ago

Yes, I did use the nohup command. The 'RepeatMasker.sh' file is time RepeatMasker -parallel 30 -species "Mus musculus" -html -gff -dir repeat/ Mus_musculus_c57bl6nj.C57BL_6NJ_v1.dna.toplevel.fa nohup bash RepeatMasker.sh >RepeatMasker.logfile 2>&1 & Now I wonder if my fasta file name is too long?

jingydz commented 2 years ago

I changed the name of the fasta file to shorten it to C57BL_6nJ.fasta and it worked!

jebrosen commented 2 years ago

I am glad to hear that it worked!

I would be very surprised if the filename was an important difference; we regularly run RepeatMasker with long filenames such as those with no problem. If this or similar does happen again, though, please do re-open or comment on this or a new issue.