Seqanswers Leaderboard Ad

Collapse

Announcement

Collapse
No announcement yet.
X
 
  • Filter
  • Time
  • Show
Clear All
new posts

  • Picard CheckIlluminaDirectory: BaseCalls file format not found

    Hi,

    I recently used the MiSeq for a 2 x 76 paired-end sequencing run.

    I moved the 'L001' directory from BaseSpace to our cluster (with Picard 2.1.0; java 1.8.0_77)
    The 'L001' directory contains the sub-directories named 'C1.1', 'C2.1',..., 'C158.1', each containing the '.bcl' and '.stats' files.

    I then run the following command:
    Code:
    java -jar picard.jar CheckIlluminaDirectory \
    B=L001/ \
    RS=76T6B76T \
    L=1 \
    DATA_TYPES=BaseCalls
    It returns:
    Code:
    picard.illumina.CheckIlluminaDirectory BASECALLS_DIR=/home/user/L001 DATA_TYPES=[BaseCalls] READ_STRUCTURE=76T6B76T LANES=[1]    FAKE_FILES=false LINK_LOCS=false VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json
    
    
    INFO     CheckIlluminaDirectory  Checking lanes(1 in basecalls directory (/home/user/L001)
    
    INFO    CheckIlluminaDirectory  Expected cycles: 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67, 68, 69, 70, 71, 72, 73, 74, 75, 76, 77, 78, 79, 80, 81, 82, 83, 84, 85, 86, 87, 88, 89, 90, 91, 92, 93, 94, 95, 96, 97, 98, 99, 100, 101, 102, 103, 104, 105, 106, 107, 108, 109, 110, 111, 112, 113, 114, 115, 116, 117, 118, 119, 120, 121, 122, 123, 124, 125, 126, 127, 128, 129, 130, 131, 132, 133, 134, 135, 136, 137, 138, 139, 140, 141, 142, 143, 144, 145, 146, 147, 148, 149, 150, 151, 152, 153, 154, 155, 156, 157, 158
    
    INFO    CheckIlluminaDirectory  Checking lane 1
    
    INFO    CheckIlluminaDirectory  Expected tiles: 1101, 1102, 1103, 1104, 1105, 1106, 1107, 1108, 1109, 1110, 1111, 1112, 1113, 1114, 1115, 1116, 1117, 1118, 1119, 2101, 2102, 2103, 2104, 2105, 2106, 2107, 2108, 2109, 2110, 2111, 2112, 2113, 2114, 2115, 2116, 2117, 2118, 2119
    
    INFO    CheckIlluminaDirectory  [B][COLOR="Red"]Could not find a format with available files for the following data types: BaseCalls[/COLOR][/B]
    INFO    CheckIlluminaDirectory  Lane 1 FAILED  Total Errors: 1
    INFO    CheckIlluminaDirectory  FAILED! There were 1 in the following lanes: 1
    
    picard.illumina.CheckIlluminaDirectory done. Elapsed time: 0.00 minutes.
    
    Runtime.totalMemory()=995098624
    
    To get help, see http://broadinstitute.github.io/picard/index.html#GettingHelp
    Is this program intended to be ran directly on BaseSpace in order to respect the directory tree with all the sequencing metrics files?

  • #2
    Looking at picard command line overview the entire BaseCalls directory is required (https://broadinstitute.github.io/pic...-overview.html).

    Comment


    • #3
      You are right GenoMax !

      The program needs to look in the 'BaseCalls' directory.
      Plus, the tree architecture needs to be conserved since it will call some files from 'InterOp' dir as well.

      Comment

      Latest Articles

      Collapse

      • seqadmin
        Current Approaches to Protein Sequencing
        by seqadmin


        Proteins are often described as the workhorses of the cell, and identifying their sequences is key to understanding their role in biological processes and disease. Currently, the most common technique used to determine protein sequences is mass spectrometry. While still a valuable tool, mass spectrometry faces several limitations and requires a highly experienced scientist familiar with the equipment to operate it. Additionally, other proteomic methods, like affinity assays, are constrained...
        04-04-2024, 04:25 PM
      • seqadmin
        Strategies for Sequencing Challenging Samples
        by seqadmin


        Despite advancements in sequencing platforms and related sample preparation technologies, certain sample types continue to present significant challenges that can compromise sequencing results. Pedro Echave, Senior Manager of the Global Business Segment at Revvity, explained that the success of a sequencing experiment ultimately depends on the amount and integrity of the nucleic acid template (RNA or DNA) obtained from a sample. “The better the quality of the nucleic acid isolated...
        03-22-2024, 06:39 AM

      ad_right_rmr

      Collapse

      News

      Collapse

      Topics Statistics Last Post
      Started by seqadmin, 04-04-2024, 09:00 AM
      0 responses
      34 views
      0 likes
      Last Post seqadmin  
      Started by seqadmin, 04-04-2024, 08:48 AM
      0 responses
      28 views
      0 likes
      Last Post seqadmin  
      Started by seqadmin, 04-01-2024, 06:45 AM
      0 responses
      45 views
      0 likes
      Last Post seqadmin  
      Started by seqadmin, 03-27-2024, 06:37 PM
      0 responses
      32 views
      0 likes
      Last Post seqadmin  
      Working...
      X