modifying the path to root of data structure with PC download/install

[figueroakl]

This happened when I moved the directory holding all fastq files to the an external drive. Although I kept providing the absolute path to the new location of my fastq dir within the command it kept shooting out Traceback errors which would show that the original fastq dir location was no longer found. I changed the config file as well and still the same error.

[averagehat]

When you have a chance, please include the config file you used, the command you used to start ngs_mapper, and the error that was output.

[figueroakl]

alright I gotta set up the environment to what didn't work again. Background info: I had all my fastq files stored within my home directory under a folder called ReadsBySample. Once I deleted that folder and tried to set up the location of my files as my external harddrive the Traceback Errors occurred. Regadless, I will upload the info you requested.

[figueroakl]

# Make sure to set this to the absolute path of your NGS Data structure
# Does not need the trailing /
NGSDATA: &NGSDATA /run/media/My\ Passport/ReadsBySample/ 

# Default threads to use for any stage that supports it
THREADS: &THREADS 1

# All scripts by name should be top level items
# Sub items then are the option names(the dest portion of the add_arugment for the script)
# Each option needs to define the default as well as the help message
ngs_filter:
    dropNs:
        default: False
        help: 'Drop all reads that have Ns.'
    indexQualityMin:
        default: 0
        help: 'The index for each associated MiSeq read must be equal or above this value.'
    threads:
        default: *THREADS
        help: 'How many threads to use[Default: %(default)s]'
    platforms:
        choices:
        - MiSeq
        - Sanger
        - Roche454
        - IonTorrent
        default:
        - MiSeq
        - Sanger
        - Roche454
        - IonTorrent
        help: 'List of platforms to include data for[Default: %(default)s]'
trim_reads:
    q:
        default: 20
        help: 'Quality threshold to trim[Default: %(default)s]'
    headcrop:
        default: 0
        help: 'How many bases to crop off the beginning of the reads after quality trimming[Default: %(default)s]'
    outputdir:
        default: trimmed_reads
        help: 'Where to output the resulting files[Default: %(default)s]'
    primerfile:
        default:
        help:  'Primer File'
    primerseed:
        default: 2
        help:   'seed mismatches'
    palindromeclip:
        default: 30
        help: 'palindrome clip threshold'
    simpleclip:
        default: 20
        help: 'simple clip threshold' 
    platforms:
        choices:
        - MiSeq
        - Sanger
        - Roche454
        - IonTorrent
        default:
        - MiSeq
        - Sanger
        - Roche454
        - IonTorrent
        help: 'List of platforms to include data for[Default: %(default)s]'
run_bwa_on_samplename:
    platforms:
        choices:
            - MiSeq
            - Sanger
            - Roche454
            - IonTorrent
        default:
            - MiSeq
            - Sanger
            - Roche454
            - IonTorrent
        help: 'List of platforms to include data for[Default: %(default)s]'
    output:
        default: bwa_mem.bam
        help: 'Where the output bam should be placed[Default: %(default)s]'
    keep_temp:
        default: False
        help: 'Flag to indicate that you want the temporary files kept instead of removing them[Default: %(default)s]'
    threads:
        default: *THREADS
        help: 'How many threads to use for bwa[Default: %(default)s]'
tagreads:
    SM:
        default:
        help: 'Sets the SM tag value inside of each read group. Default is the portion of the filname that preceeds the .bam[Default: %(default)s]'
    CN:
        default:
        help: 'Sets the CN tag inside of each read group to the value specified.[Default: %(default)s]'
base_caller:
    regionstr:
        default:
        help: 'Specify a region string in the format of REFERENCE:START-STOP. See samtools documentation for more information.[Default: %(default)s]'
    minbq:
        default: 30
        help: 'The minimum base quality to be considered high quality[Default: %(default)s]'
    maxd:
        default: 100000
        help: 'The maximum depth to use for the pileup[Default: %(default)s]'
    mind:
        default: 10
        help: 'Minimum depth for base trimming. Below this depth low quality bases will be called N[Default: %(default)s]'
    minth:
        default: 0.95
        help: 'Minimum fraction of all remaining bases after trimming/N calling that will trigger a base to be called[Default: %(default)s]'
    biasth:
        default: 50
        help: 'Minimum base quality threshold to bias towards. Will increase the amount of bases that have >= this value by a factor of what bias is set to[Default: %(default)s]'
    bias:
        default: 10
        help: 'What factor to bias high quality bases by. Must be an integer >= 1[Default: %(default)s]'
    threads:
        default: *THREADS
        help: 'How many threads to use when running base_caller.py[Default: %(default)s]'
miseq_sync:
    ngsdata:
        default: *NGSDATA
        help: 'Path to the root of the NGSData structure [Default: %(default)s]'
roche_sync:
    ngsdata:
        default: *NGSDATA
        help: 'Path to the root of the NGSData structure [Default: %(default)s]'
    midparse:
        # Leave this blank to use the installed version
        default:
        help: 'Path to your MidParse.conf file [Default: %(default)s]'
sanger_sync:
    ngsdata:
        default: *NGSDATA
        help: 'Path to the root of the NGSData structure [Default: %(default)s]'
ion_sync:
    ngsdata:
        default: *NGSDATA
        help: 'Path to the root of the NGSData structure [Default: %(default)s]'
    min_fastq_size:
        default: 1000000
        help: 'Minimum file size to determine if a fastq is a ghost read [Default: %(default)s]'

[figueroakl]

cant drag the config.yaml file in here so teach me the proper etiquette lol I just wanted to keep the integrity of the file so I didn't change the extension from .yaml to anything else, but let me know of any other option you would prefer me to use to post it up

[averagehat]

This looks fine to me.