ElementFinder is throwing an error but I suspect it is simply encountering a normal but perhaps unexpected eventuality. Do I interpret this output correctly to mean that of the 13 tyr captain candidates, none show insertional polymorphism when compared with the reference genome? In this case, why is the program attempting to build a blast directory from an empty candidate element file?
Also, it might help to have some additional blast hit info. For example, were there 0 tyr captains with candidate insertion sites, or were there simply no blast hits between the candidate tyr captains and the reference? No blast input/output files are saved (as far as I can tell) so it's not possible to investigate this manually.
[Mon Aug 5 22:03:37 2024] reading in data..
[Mon Aug 5 22:03:37 2024] parsing upstream regions of 13 candidate tyr captains..
[Mon Aug 5 22:03:37 2024] searching for hits to the upstream regions of 13 candidate tyr captains..
[Mon Aug 5 22:03:37 2024] found 0 tyr captains with candidate insertion sites
[Mon Aug 5 22:03:37 2024] searching for hits to the downstream regions of candidate insertion sites for 0 tyr captains that are also downstream of those captains..
BLAST options error: File elementFinder/elementDB.CD156.fna is empty
[Mon Aug 5 22:03:37 2024] error: could not execute makeblastdb on commandline, exiting..
Inappropriate ioctl for device
ElementFinder is throwing an error but I suspect it is simply encountering a normal but perhaps unexpected eventuality. Do I interpret this output correctly to mean that of the 13 tyr captain candidates, none show insertional polymorphism when compared with the reference genome? In this case, why is the program attempting to build a blast directory from an empty candidate element file?
Also, it might help to have some additional blast hit info. For example, were there 0 tyr captains with candidate insertion sites, or were there simply no blast hits between the candidate tyr captains and the reference? No blast input/output files are saved (as far as I can tell) so it's not possible to investigate this manually.
(base) [farman@mcc-login001 STARFISH]$ singularity run --app starfish100 /share/singularity/images/ccs/conda/amd-conda16-rocky8.sinf starfish insert -T 6 -a ome2assembly.txt -d elementFinder/B71v2sh.fasta -b CD156_SF_starships/CD156.tyr.bed -i tyr -x CD156 -o elementFinder [Mon Aug 5 22:03:37 2024] executing command: starfish insert -T 6 -a ome2assembly.txt -d elementFinder/B71v2sh.fasta -b CD156_SF_starships/CD156.tyr.bed -i tyr -x CD156 -o elementFinder Key parameters: --upstream 0-17000 --downstream 0-14000 --length 2000-700000 --pid 90 --hsp 1000 minDR 4 maxDR 40 maxEmptySiteLength 2000 maxElementLengthFlag 700000 minElementLengthFlag 2000 maxInsertCoverage 0.25 maxFlankCoverage 0.25 blastn -task dc-megablast -evalue 0.0001 -max_target_seqs 1000000 nucmer --mum delta-filt -m -l 1000 -i 90
[Mon Aug 5 22:03:37 2024] reading in data.. [Mon Aug 5 22:03:37 2024] parsing upstream regions of 13 candidate tyr captains.. [Mon Aug 5 22:03:37 2024] searching for hits to the upstream regions of 13 candidate tyr captains.. [Mon Aug 5 22:03:37 2024] found 0 tyr captains with candidate insertion sites [Mon Aug 5 22:03:37 2024] searching for hits to the downstream regions of candidate insertion sites for 0 tyr captains that are also downstream of those captains.. BLAST options error: File elementFinder/elementDB.CD156.fna is empty
[Mon Aug 5 22:03:37 2024] error: could not execute makeblastdb on commandline, exiting.. Inappropriate ioctl for device