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Oshlack / necklace

Combine reference and assembled transcriptomes for RNA-Seq analysis
https://github.com/Oshlack/necklace/wiki
GNU General Public License v3.0
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FAILED at the beginning of pipeline #8

Closed ghost closed 3 years ago

ghost commented 5 years ago

I ran the first command and I got the follow:

WARNING: An illegal reflective access operation has occurred WARNING: Illegal reflective access by org.codehaus.groovy.reflection.CachedClass$3$1 (file:/home/cesarihv7/superTranscriptome/necklace-1.01/tools/bpipe-0.9.9.2/bin/../lib/bpipe.jar) to method java.lang.Object.finalize() WARNING: Please consider reporting this to the maintainers of org.codehaus.groovy.reflection.CachedClass$3$1 WARNING: Use --illegal-access=warn to enable warnings of further illegal reflective access operations WARNING: All illegal access operations will be denied in a future release

| Starting Pipeline at 2019-06-12 00:19 |

========================================= Stage set_input ========================================== ERROR: Expected output file /.fastq.gz could not be found

========================================= Pipeline Failed ==========================================

Expected output file /.fastq.gz could not be found

Use 'bpipe errors' to see output from failed commands.

root@instance-1-lev820:/home/cesarihv7/superTranscriptome/necklace-1.01# exit

nadiadavidson commented 5 years ago

Hi, What command did you run? and what is the contents of your configuration file? It looks like you need to replace " /.fastq.gz" with the path and name of your file. Cheers, Nadia.