annadalmolin / circfusion Goto Github PK

Greetings,

sorry to bother you, but we created all the necessary input configuration files (here in attachment), and then we ran circfusion via docker, but we have different problems. The first is:

!!!!! WARNING: --genomeSAindexNbases 10 is too large for the genome size=74580, which may cause seg-fault at the mapping step. Re-run genome generation with recommended --genomeSAindexNbases 7

how to adjust or specify this parameter?

after the index is built succesfully:

Mar 20 12:21:41 ... starting to sort Suffix Array. This may take a long time... Mar 20 12:21:42 ... sorting Suffix Array chunks and saving them to disk... Mar 20 12:21:45 ... loading chunks from disk, packing SA... Mar 20 12:21:46 ... finished generating suffix array Mar 20 12:21:46 ... generating Suffix Array index Mar 20 12:21:46 ... completed Suffix Array index Mar 20 12:21:46 ... writing Genome to disk ... Mar 20 12:21:47 ... writing Suffix Array to disk ... Mar 20 12:21:47 ... writing SAindex to disk Mar 20 12:21:47 ..... finished successfully

we get:

^\ :"^_l .N/scripts/script_find_fusions_Star_part2.sh: line 150: 651 Quit (core dumped) /tools/STAR-2.7.5c/source/STAR --runThreadN $THR --genomeDir /data/reference/genome_reference --readFilesCommand $UNCOMPRESSION_COMMAND --readFilesIn $FILE1 $FILE2 --outFilterMultimapNmax $OUTFILTERMULTIMAPNMAX --outFilterMatchNmin $OUTFILTERMATCHNMIN --outFilterMismatchNmax $OUTFILTERMISMATCHNMAX --outFilterMismatchNoverReadLmax $OUTFILTERMISMATCHNOVERREADLMAX --outSAMprimaryFlag AllBestScore --outSAMtype BAM SortedByCoordinate --outReadsUnmapped Fastx --alignTranscriptsPerReadNmax 20000 --alignSJstitchMismatchNmax $ALIGNSJSTITCHMISMATCHNMAX 2> "$SAMPLE"_alignment.err > "$SAMPLE"_alignment.log [bam_header_read] EOF marker is absent. The input is probably truncated. [bam_header_read] invalid BAM binary header (this is not a BAM file). /scripts/script_find_fusions_Star_part2.sh: line 153: 679 Segmentation fault (core dumped) samtools rmdup -s Aligned.sortedByCoord.out.bam Aligned.sortedByCoord.out_rmdup.bam open: No such file or directory [bam_index_build2] fail to open the BAM file. Failed to open BAM file Aligned.sortedByCoord.out_rmdup.bam

after this, the program loads several R packages and the program tells us:

`output file: script_detected_fusions.knit.md

/usr/bin/pandoc +RTS -K512m -RTS script_detected_fusions.knit.md --to html4 --from markdown+autolink_bare_uris+tex_math_single_backslash --output /data/graphical_output/GLC1DM/script_detected_fusions.html --self-contained --standalone --section-divs --template /usr/local/lib/R/site-library/prettydoc/resources/templates/hpstr.html --highlight-style pygments --mathjax --variable 'mathjax-url=https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML' --css /data/graphical_output/GLC1DM/script_detected_fusions_files/style.css 

Output created: script_detected_fusions.html
Warning message:
package(s) not installed when version(s) same as current; use `force = TRUE` to
  re-install: 'grid' 
> 
>`

but all the output files are empty.
How can are we doing incorrectly or how can we solve these issues?
Thanks so much in advance.

nl

sample_list.txt
[translocation_list.txt](https://github.com/annadalmolin/CircFusion/files/11016195/trans
[params_fusions.txt](https://github.com/annadalmolin/CircFusion/
path_file.txt
files/11016198/params_fusions.txt)
location_list.txt)
params_Star.txt

I tried running the test dataset offline (no internet access on the compute nodes I use) using a Singularity sandbox.
Everything went fine, until the final plotting steps using R.
It looks like the R script tries to access the internet:
Bioconductor version cannot be validated; no internet connection?

I got away with it by running R inside the Singularity image, and installing all dependencies from CRAN.
I then commented out lines 32, 49, 52, 53, 54 from the /scripts/script_detected_fusions.Rmd file, from within the Singularity sandbox image. This allowed the R script to work offline.

Any idea for a more "elegant" solution ?
Thanks for developing CircFusion.

Hi, we want to use CircFusion on a set of cancer-samples and installed it from the docker image, however we get an error
/scripts/pipeline_fusions.sh: line 70: /tools/STAR-2.7.5c/source/STAR: Permission denied
it looks like the pipeline can't access the STAR installation.
Help would be much appreciated.
Thank you!