yyoshiaki
commented
2 years ago Thank you for trying VIRTUS. Can you let me see your inputs and commands?
Open sunnyyakima opened 2 years ago
yyoshiaki
commented
2 years ago Thank you for trying VIRTUS. Can you let me see your inputs and commands?
Hi,
I am trying virtus first time, got an error, could you help to figure it out? salmon quant -i /var/lib/cwl/stg6e961d4d-2bda-4856-afe4-02b076648d2c/salmon_index_human -l A -1 /var/lib/cwl/stg0 97f1658-65e2-4fec-87cd-aba471ac1e4e/SRR11858782.1_1.fastp.fastq -2 /var/lib/cwl/stg095da09f-34ee-441a-a49e-d3f8dab1e5 3b/SRR11858782.1_2.fastp.fastq -p 30 -o /scratch/yu_liu/CAR_T/SRR11858782 --gcBias --validateMappings Version Info: Could not resolve upgrade information in the alotted time. Check for upgrades manually at https://combine-lab.github.io/salmon
salmon (mapping-based) v1.1.0
[ program ] => salmon
[ command ] => quant
[ index ] => { /var/lib/cwl/stg6e961d4d-2bda-4856-afe4-02b076648d2c/salmon_index_human }
[ libType ] => { A }
[ mates1 ] => { /var/lib/cwl/stg097f1658-65e2-4fec-87cd-aba471ac1e4e/SRR11858782.1_1.fastp.fastq }
[ mates2 ] => { /var/lib/cwl/stg095da09f-34ee-441a-a49e-d3f8dab1e53b/SRR11858782.1_2.fastp.fastq }
[ threads ] => { 30 }
[ output ] => { /scratch/yu_liu/CAR_T/SRR11858782 }
[ gcBias ] => { }
[ validateMappings ] => { }
Exception : [boost::filesystem::create_directories: Read-only file system: "/scratch/yu_liu/CAR_T"] salmon quant was invoked improperly. For usage information, try salmon quant --help Exiting. INFO [job salmon_quant_human] Max memory used: 0MiB ERROR [job salmon_quant_human] Job error: ("Error collecting output for parameter 'output_quantdir': ../../../../work/yu_liu/software/virtus/VIRTUS/tool/salmon -cwl/salmon-quant.cwl:63:7: glob patterns must not start with '/'", {}) WARNING [job salmon_quant_human] completed permanentFail ERROR [step salmon_quant_human] Output is missing expected field file:///work/yu_liu/software/virtus/VIR TUS/bin/VIRTUS.PE.cwl#VIRTUS.PE/salmon_quant_human/output_quantdir WARNING [step salmon_quant_human] completed permanentFail INFO [workflow ] completed permanentFail { "Log.out_human": null, "Log.progress.out_human": null, "SJ.out.tab_human": null, "aligned_bam_human": null, "output_unmapped": null, "output_fq2": null, "output_fq1": null, "SJ.out.tab_virus": null, "Log.progress.out_virus": null, "Log.out_virus": null, "aligned_virus": null, "mappingstats_virus": null, "mappingstats_human": null, "output_quantdir_human": null, "output": null, "output_1": null } WARNING Final process status is permanentFail
I applied chmod 777 for all the dirs from /scratch to /CAR_T
still get the same error.