no tbl file in my output files

[jingydz]

What do you want to know? In my output files, there is no tbl file. command:time RepeatMasker -parallel 30 -species murinae -html -gff Mus_musculus_c57bl6nj.C57BL_6NJ_v1.dna.toplevel.fa

• Have you installed RepBase RepeatMasker Edition for RepeatMasker? yes

the files I got: Mus_musculus_c57bl6nj.C57BL_6NJ_v1.dna.toplevel.fa Mus_musculus_c57bl6nj.C57BL_6NJ_v1.dna.toplevel.fa_batch-266.tmp.simple1
Mus_musculus_c57bl6nj.C57BL_6NJ_v1.dna.toplevel.fa_batch-266.masked Mus_musculus_c57bl6nj.C57BL_6NJ_v1.dna.toplevel.fa.cat.all.gz
ncResults-1638589868-3390060.out ncResults-1638589868-3390060.err

the logfile: RepeatMasker version 4.1.1 Search Engine: NCBI/RMBLAST [ 2.11.0+ ]

Using Master RepeatMasker Database: /xxx/software/RepeatMasker/Libraries/RepeatMaskerLib.h5 Title : Dfam Version : 3.2 Date : 2020-07-02 Families : 6,953

Species/Taxa Search: Murinae [NCBI Taxonomy ID: 39107] Lineage: root;cellular organisms;Eukaryota;Opisthokonta;Metazoa; Eumetazoa;Bilateria;Deuterostomia;Chordata; Craniata ;Vertebrata ; Gnathostomata ;Teleostomi;Euteleostomi; Sarcopterygii;Dipnotetrapodomorpha;Tetrapoda;Amniota; Mammalia;Theria ;Eutheria;Boreoeutheria 1030 families in ancestor taxa; 363 lineage-specific families

analyzing file Mus_musculus_c57bl6nj.C57BL_6NJ_v1.dna.toplevel.fa

Checking for E. coli insertion elements

Checking for E. coli insertion elements ... Generating output... ........................................................................................................................... masking done

[jebrosen]

Hi,

These files (_batch*, ncResults-*) are usually found in the RM_* temporary directories. The main output files .masked, .out, .tbl should usually be found next to the original input sequence file. These can be changed to a different output directory with the -dir option.

[jingydz]

Yes, I didn't add the -dir argument the first time I tried to run it. But I can't find the output file in the current directory where I ran the command, so I can't find where the output file is.

[jebrosen]

The output files are not necessarily written to the current directory, but to the directory of the input file. Although, according to your command those are the same. If the files could be mistakenly placed somewhere else, a full filesystem search may help: find startDirectory/ -name Mus_musculus_c57bl6nj.C57BL_6NJ_v1.dna.toplevel.fa.out.

If the files were written to the wrong directory, we should definitely find and fix that problem! RepeatMasker does try to detect and warn if it cannot write files, but perhaps something else is wrong.