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sagnikbanerjee15 / Finder

A fully automated gene annotator from RNA-Seq expression data
MIT License
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Finder generates no files and fails #75

Open ereyred opened 1 year ago

ereyred commented 1 year ago

Hello, I'm running Finder from local installation, not Docker. I'm running with PE RNAseq.fq but no protein file. It makes the necessary output directories and protein dummy file in temp but no other output and it gives me the following error:

_Status: Downloaded newer image for sagnikbanerjee15/finder:1.1.0 docker.io/sagnikbanerjee15/finder:1.1.0 done Traceback (most recent call last): File "/softwares/FINDER/Finder/finder", line 688, in main() File "/softwares/FINDER/Finder/finder", line 637, in main readMetaDataFile( options, logger_proxy, logging_mutex ) File "/softwares/FINDER/Finder/scripts/fileReadWriteOperations.py", line 138, in readMetaDataFile small_rnasamples[condition][Run] = {"bioproject":BioProject, KeyError: ''

The progress.log out put is: _2023-03-19 23:53:40,489 - finder - INFO - Running command - perl /Finder_v1.1.0/gmes_linux_64//change_path_in_perl_scripts.pl "/usr/bin/env perl" 2023-03-19 23:53:40,916 - finder - INFO - Software paths have been set 2023-03-19 23:53:41,498 - finder - INFO - Generating STAR index 2023-03-19 23:53:41,909 - finder - INFO - Running cmd - STAR --runThreadN 20 --runMode genomeGenerate --genomeDir /Finder_v1.1.0/output/indices/star_index_without_transcriptome --genomeFastaFiles /Finder_v1.1.0/output/Genome.fasta.masked --genomeChrBinNbits 18 --genomeSAindexNbases 11.740410536216816 --outFileNamePrefix /Finder_v1.1.0/output/alignments/indexGenome > /Finder_v1.1.0/output/indices/star_index_without_transcriptome.output 2> /Finder_v1.1.0/output/indices/star_index_without_transcriptome.error 2023-03-19 23:53:56,972 - finder - INFO - STAR index generation complete 2023-03-19 23:53:56,973 - finder - INFO - Generating OLego index 2023-03-19 23:53:56,974 - finder - INFO - Running cmd - olegoindex -p /Finder_v1.1.0/output/indices/olego_index /Finder_v1.1.0/Genome.fasta.masked > /Finder_v1.1.0/output/indices_olego_index.output 2> /Finder_v1.1.0/output/indices_olegoindex.error 2023-03-19 23:54:59,284 - finder - INFO - OLego index built 2023-03-19 23:54:59,286 - finder - INFO - Adding dummy file since no protein evidence was provided 2023-03-19 23:54:59,286 - finder - INFO - validateCommandLineArguments execution successful

My metadata file looks like this: BioProject SRA Accession Tissues Description Date Read Length (bp) Ended RNA Seq process Location Name S1_8 na PE 1 1 /dir/Finder_v1.1.0/

Thanks for your help! E

sagnikbanerjee15 commented 1 year ago

Hello @ereyred,

Thank you for your interest in finder. We are aware of the issues in the previous version but we have decided to move forward with new improvements. As of now, we do not have any plans of fixing the issues in the previous version since they will be taken cared of in the new version.

Thank you.