robin test on provided dataset ROBIN_test_set_A #120
Description
hi ,
we are testing robin pipeline on a Virtual machine (4 threads , 8 Go RAM), on the dataset provided in the issue #97,
https://github.com/LooseLab/ROBIN_test_set_A
we have robin version 0.1.7
The issue is that the pipeline is running for three days, but i still have no classification of CNS tumors neither with strugeon or nanoDX, how long sould it take for the pipeline to complete a classification ?
robin -w ROBIN_test_set_A/test_data_set/
--reference GCA_000001405.15_GRCh38_no_alt_analysis_set.fna
--bed_file MNP-flex-methylationepic-v-1-0-b5-manifest-file-MGMT-complete.sorted.bed
--threads 4
/classifiers_benchmark/robin/
--log-file /classifiers_benchmark/robin/analysis.log
--log-level INFO
we also run sturgeon on the same datas, and we obtain a different classification, with halfless probes found in your dataet:
could you please have a look to the code and tell me if im missing somthing?
`
#samtools merge -@ 10 -o robintot.bam -c -b testmergebamrobin.tsv
#samtools index robintot.bam
#modkit adjust-mods --convert h m robintot.bam robintot_adjustmods.bam
#modkit extract full robintot_adjustmods.bam robintot_adjustmods_extractfull.txt
#sturgeon inputtobed -i robintot_adjustmods_extractfull.txt -o /testSturgeon/ -s modkit
#sturgeon predict -i merged_probes_methyl_calls.bed -o /testSturgeon/ --model-files /models_sturgeon/general.zip --plot-results
`
thank you for your help