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4.8 years ago
bioguy24
▴
230
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
