salmon quant not working #1
Description
I hope someone can help. I have tried running the following command -
salmon quant -i gencode_v33_index -l A -o GSM4432380 -r SRR11412223.fastq.gz SRR11412224.fastq.gz SRR11412225.fastq.gz SRR11412226.fastq.gz
I get he following error-
Exception : [Error: The index version file gencode_v33_index/versionInfo.json doesn't seem to exist. Please try re-building the salmon index.[2021-11-26 22:03:35.685] [jointLog] [info] Fragment incompatibility prior below threshold. Incompatible fragments will be ignored.
I have looked through the forum and someone advised the issue may be with the Mac M1 I am using. The advice was to build the index on AWS . I used google cloud server. I still get the same error. The confusion is that is I do bash ./run_salmon.sh either on my local drive or on GCP it runs with no error ( so index is okay!) producing only a GSM4432378 but then hangs on the next file and does not continue. Is this a memory issue. I can select an instance on GCP with greater than 4G. Ive tried to leave this running also on my local drive for an entire day and it can't process the run_salmon.sh beyond one GSM accession number. It was mentioned in the video tutorial that the whole script for 12 GSM accession numbers should take an hour?
Im running the script pulled off week 5 as is and built the index on GCP. It does not give an error with the script but cannot complete? I have tried doing each GSM on its own as above but then I get the error? Is the salmon quant code above wrong somewhere ? Appreciate any help on this? Stuck for a while now . I am using salmon docker container. Thank you