Question: STAR-Fusion error while executing and produces some intermediates files
0
9 weeks ago
bioguy24 • 190
Chicago

I have run STAR and am now executing STAR-Fusion on the Chimeric.out.Junction.Out and it executes but I get the below error and no output is produced. I am not sure what the error means, am I missing something? Thank you :).

version

 STAR-2.7.0f
 STAR-Fusion 1.6.0

command

STAR-Fusion-v1.6.0/STAR-Fusion --genome_lib_dir STAR-Fusion-v1.6.0/CTAT/GRCh37_gencode_v19_CTAT_lib_Mar272019.plug-n-play/ctat_genome_lib_build_dir \
         -J /home/win/STAR/Chimeric.out.junction \
         --output_dir /home/win/STAR

error

CMD: ln -sf /home/win/STAR/star-fusion.preliminary/star-fusion.filter.intermediates_dir/star-fusion.post_blast_and_promiscuity_filter /home/win/STAR/star-fusion.preliminary/star-fusion.fusion_candidates.preliminary.filtered
ln: failed to create symbolic link ‘/home/win/STAR/star-fusion.preliminary/star-fusion.fusion_candidates.preliminary.filtered’: Operation not supported
Error, cmd:
ln -sf /home/win/STAR/star-fusion.preliminary/star-fusion.filter.intermediates_dir/star-fusion.post_blast_and_promiscuity_filter /home/win/STAR/star-fusion.preliminary/star-fusion.fusion_candidates.preliminary.filtered
died with ret (256) at /usr/local/bin/STAR-Fusion-v1.6.0/util/../PerlLib/Process_cmd.pm line 19.
Process_cmd::process_cmd('ln -sf /home/win/STAR/star-fusion.preliminary/star-fusion.fil...') called at /usr/local/bin/STAR-Fusion-v1.6.0/util/STAR-Fusion.filter line 282
 Error, cmd: /usr/local/bin/STAR-Fusion-v1.6.0/util/STAR-Fusion.filter  --fusion_preds /home/win/STAR/star-fusion.preliminary/star-fusion.fusion_candidates.preliminary  -J /home/win/STAR/Chimeric.out.junction  --tmpdir /tmp  --min_junction_reads 1  --min_sum_frags 2  --require_LDAS 1  --max_promiscuity 10  --min_pct_dom_promiscuity 20  --min_novel_junction_support 3  --min_alt_pct_junction 10  --aggregate_novel_junction_dist 5  --min_spanning_frags_only 5  --genome_lib_dir /usr/local/bin/STAR-Fusion-v1.6.0/CTAT/GRCh37_gencode_v19_CTAT_lib_Mar272019.plug-n-play/ctat_genome_lib_build_dir  --out_prefix /home/win/STAR/star-fusion.preliminary/star-fusion died with ret 6400 No such file or directory at /usr/local/bin/STAR-Fusion-v1.6.0/PerlLib/Pipeliner.pm line 181.
Pipeliner::run('Pipeliner=HASH(0xf76538)') called at /usr/local/bin/STAR-Fusion-v1.6.0/STAR-Fusion line 678
Star-fusion • 37 views
ADD COMMENTlink 9 weeks ago bioguy24 • 190

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