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genepi / mtdna-server-2

mtDNA-Server 2: A web-service and Nextflow pipeline for mitochondrial genomes
MIT License
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ERROR ~ Unable to parse config file: '/media/manish/Data/Jyoti_Mridha_AIC/Program/mtdna-server-2-2.1.14/nextflow.config' #26

Open Jyoti-Mridha opened 2 months ago

Jyoti-Mridha commented 2 months ago

Hi, I am trying to run mtdna server by installing it offline, however i am using nextflow first time. i am able to install the process but encountered with the error:

ERROR ~ Unable to parse config file: '/media/manish/Data/Jyoti_Mridha_AIC/Program/mtdna-server-2-2.1.14/nextflow.config'

Compile failed for sources FixedSetSources[name='/groovy/script/ScriptCD8527BD770404BAF3BD56A125C65898/_nf_config_96d941a1']. Cause: org.codehaus.groovy.control.MultipleCompilationErrorsException: startup failed: /groovy/script/ScriptCD8527BD770404BAF3BD56A125C65898/_nf_config_96d941a1: 15: Number ending with underscores is invalid @ line 15, column 87 @ line 15, column 87. idha_AIC/Nanopore_Sequencing/1_FINAL_NAN ^

1 error

-- Check '.nextflow.log' file for details

=>> The command which i am using is : sudo nextflow run genepi/mtdna-server-2 -r v2.1.14 -c nextflow.config -profile docker

=>> However i only made the changes in nextflow.config file, and the changes which i made is below: project = barcode17 output = /media/manish/Data/Jyoti_Mridha_AIC/Nanopore_Sequencing/1_FINAL_NANOPORE/Batch1_3runs/1_minimap2_freebayes_Final/Direct_minimap/Structural_Variants/mtdna/ project_date = "18-09-2024" files = /media/manish/Data/Jyoti_Mridha_AIC/Nanopore_Sequencing/1_FINAL_NANOPORE/Batch1_Barcode_Aug_reanalysed/Bam/barcode17_sorted.bam reference = "rcrs" mode = "mutserve" detection_limit = 0.01
mapQ = 20 baseQ = 20 alignQ = 30 coverage_estimation = "on" max_samples = 0 subsampling = "off" subsampling_coverage = 2000

*** Any suggestion how to tackle the issue will be great help. Thank you in advance

lukfor commented 2 months ago

Hi, please make sure to set the value of project, output and files under quotes.

For example, for the project, you can set it as:

project= "barcode17"
output = "/media/manish/Data/Jyoti_Mridha_AIC/Nanopore_Sequencing/1_FINAL_NANOPORE/Batch1_3runs/1_minimap2_freebayes_Final/Direct_minimap/Structural_Variants/mtdna/"
project_date = "18-09-2024"
files = "/media/manish/Data/Jyoti_Mridha_AIC/Nanopore_Sequencing/1_FINAL_NANOPORE/Batch1_Barcode_Aug_reanalysed/Bam/barcode17_sorted.bam"
Jyoti-Mridha commented 2 months ago

Hi, Thanks a lot, now I am able to generate the results.

My major focus is to extract CNV. I have tried on both Fusion and mutect2 mode but the positions of all the variants is at a single point checked on "variants.annotated.txt", though if it is any INDELs. Generally it could be better to get "start" & "End" positions so that it will be helpful for better predicting the point of start and end point of any insertion/deletions. some of the important factors are mainly considerable while checking for any INDELs are: start_pos, end_pos, SVLEN, SVTYPE, CytoBand, Frameshift, exon count, GeneCC_disease, ACMG_class, population databases info, nearest_left_gene, nearest_right_gene, etc which i am not able to identify using Mitoverse Platform. Or I may mistakenly not be able to get this information if such conditions then please help me out. Orelse can you please let me know if i can get raw vcf instead of Mitoverse annotated file by using Mitoverse platform.