Question: Dragen alignment failing/terminating
0
gravatar for Floydian_slip
7 weeks ago by
Floydian_slip130
United States
Floydian_slip130 wrote:

Hi, I am running Dragen on my sample for alignment and it terminates/exits early without any error. I am new to the Dragen alignment world. I was wondering if there is anything in the .out file (copied below) which could hint if its a Dragen issue or a hardware issue? Can anybody advise me on what could be going wrong? I am also copying the small .err file at the end of the message. Thanks!

==================================================================
Writing reference to card memory
==================================================================
Sending 32212254720 bytes to card address 0x0
Sending 1524944896 bytes to card address 0x780000000
Sending 47654656 bytes to card address 0x7dae4d000

==================================================================
DNA Mapper/Aligner Configuration
==================================================================

    config-file:                       /nfs/seqscratch_ssd/ALIGNMENT/BUILD37/DRAGEN/GENOME/sqcudn748499.199027/scripts/sqcudn748499.199027.DragenAlignment.203917..1.conf
    fastq-file1:                       /nfs/tx/in/4928/sqcudn748499/FASTQ/895401-UDN748499-P_L001_R1_1.fastq.gz
    fastq-file2:                       /nfs/tx/in/4928/sqcudn748499/FASTQ/895401-UDN748499-P_L001_R2_1.fastq.gz
    ref-dir:                           /staging/REF/b37_decoy/
    ref-config:                        not alt-aware capable
    alt-aware:                         false
    intermediate-results-dir:          /staging/tmp
    output-directory:                  /nfs/seqscratch_ssd/ALIGNMENT/BUILD37/DRAGEN/GENOME/sqcudn748499.199027/
    output-file-prefix:                sqcudn748499.199027..1

output-format:                     BAM
enable-map-align:                  true
auto-pe-stats-detection:           enabled
pe-stats-continuous-update:        disabled
pe-stats-update-log-only:          disabled
enable-map-align-output:           true
enable-sort:                       true
enable-duplicate-marking:          true
remove-duplicates:                 false
methylation-protocol:              none

==================================================================
Processing reads
==================================================================
LICENSE_MSG|  Requested streams: DNA mapper(x1) unzip(x2) zip(x1)
LICENSE_MSG|   Board AC05142591657, CHIPID=0050F10A097EB01C
LICENSE_MSG|  Requested streams: DNA mapper(x1) unzip(x2) zip(x1)
LICENSE_MSG|   Board AC05142591657, CHIPID=0050F10A097EB01C
LICENSE_MSG|  Allocation:
LICENSE_MSG|   #0: board 0 stream 0, DNA mapper|DBAM loopback|Simple loopback|memory -> DNA mapper
LICENSE_MSG|   #1: board 0 stream 1, DBAM loopback|Simple loopback|unzip|zip -> unzip
LICENSE_MSG|   #2: board 0 stream 2, DBAM loopback|Simple loopback|unzip|zip -> unzip
LICENSE_MSG|   #3: board 0 stream 3, DBAM loopback|Simple loopback|zip -> zip
Opening FASTQ file 895401-UDN748499-P_L001_R1_1.fastq.gz
Opening FASTQ file 895401-UDN748499-P_L001_R2_1.fastq.gz
Dividing sort intermediate data into 1146 partitions for mapped, and an equal number for unmapped, records.
  predicted_output_size :  1006GB
  max_bin_size          :  900MB
  total_system_memory   :  125GB
  total_bin_memory      :  20GB
  sort_buffer_size      :  1024kB
  predicted_num_bins    :  1146
  max_num_bins          :  8192
  num_bins              :  1146
  sort_threads          :  4
  dedup_threads         :  4
  dbam2bam_threads      :  32

Initial paired-end statistics detected for read group 0, based on 91244 high quality pairs for FR orientation
        Quartiles (25 50 75) = 491 602 725
        Mean = 605.864
        Standard deviation = 188.04
        Rescue radius = 446.925
        Effective rescue sigmas = 2.37676
        WARNING: Default rescue sigmas value of 2.5 was overridden by host software!
        The user may wish to set a rescue sigmas value explicitly with --Aligner.rescue-sigmas
        Boundaries for mean and standard deviation: low = 23, high = 1193
        Boundaries for proper pairs: low = 1, high = 1427
        NOTE: DRAGEN's insert estimates include corrections for clipping (so they are not identical to TLEN)
read A00307:69:HJVYTDSXX:1:2550:2844:4163 id = 0x6A9C9E27
read A00307:69:HJVYTDSXX:1:2550:2844:4163 id = 0x6A9C9E27
Closing FASTQ file 895401-UDN748499-P_L001_R1_1.fastq.gz
Closing FASTQ file 895401-UDN748499-P_L001_R2_1.fastq.gz

Finished - processed 2292024624 reads (1146012312 pairs)
LICENSE_MSG|  Requested streams: DNA mapper(x1) zip(x3)
LICENSE_MSG|   Board AC05142591657, CHIPID=0050F10A097EB01C
LICENSE_MSG|  Requested streams: DNA mapper(x1) zip(x3)
LICENSE_MSG|   Board AC05142591657, CHIPID=0050F10A097EB01C
LICENSE_MSG|  Allocation:
LICENSE_MSG|   #0: board 0 stream 0, DNA mapper|DBAM loopback|Simple loopback|memory -> DNA mapper
LICENSE_MSG|   #1: board 0 stream 1, DBAM loopback|Simple loopback|unzip|zip -> zip
LICENSE_MSG|   #2: board 0 stream 2, DBAM loopback|Simple loopback|unzip|zip -> zip
LICENSE_MSG|   #3: board 0 stream 3, DBAM loopback|Simple loopback|zip -> zip

==================================================================
Sorting
==================================================================
Paired-end statistics were based on initial reads for read group 0, based on 91244 high quality pairs for FR orientation
Paired-end statistics were based on initial reads for read group 0, based on 91244 high quality pairs for FR orientation
        Quartiles (25 50 75) = 491 602 725
        Mean = 605.864
        Standard deviation = 188.04
        Rescue radius = 446.925
        Effective rescue sigmas = 2.37676
        WARNING: Default rescue sigmas value of 2.5 was overridden by host software!
        The user may wish to set a rescue sigmas value explicitly with --Aligner.rescue-sigmas
        Boundaries for mean and standard deviation: low = 23, high = 1193
        Boundaries for proper pairs: low = 1, high = 1427
        NOTE: DRAGEN's insert estimates include corrections for clipping (so they are not identical to TLEN)
LICENSE_MSG| ***********************************************************
LICENSE_MSG| Licenses status:
LICENSE_MSG|   Genome          : used 600669.5/725000 Gbases since 2019-Sep-01 (600669488161648 bases, 82.9%)
LICENSE_MSG|

==================================================================
DRAGEN METRICS
==================================================================

MAPPING/ALIGNING SUMMARY               Total input reads                                       2292024624
MAPPING/ALIGNING SUMMARY               Number of duplicate reads (marked)                      34763650       1.52
MAPPING/ALIGNING SUMMARY               Number of unique reads                                  2257260974     98.48
MAPPING/ALIGNING SUMMARY               Reads with mate sequenced                               2292024624     100.00
MAPPING/ALIGNING SUMMARY               Reads without mate sequenced                            0              0.00
MAPPING/ALIGNING SUMMARY               QC-failed reads                                         0              0.00
MAPPING/ALIGNING SUMMARY               Mapped reads                                            2263601179     98.76
MAPPING/ALIGNING SUMMARY               Number of unique & mapped reads (excl. dups)            2228837529     97.24
MAPPING/ALIGNING SUMMARY               Unmapped reads                                          28423445       1.24
MAPPING/ALIGNING SUMMARY               Singleton reads (itself mapped; mate unmapped)          7736139        0.34
MAPPING/ALIGNING SUMMARY               Paired reads (itself & mate mapped)                     2255865040     98.42
MAPPING/ALIGNING SUMMARY               Properly paired reads                                   2217096062     96.73
MAPPING/ALIGNING SUMMARY               Not properly paired reads (discordant)                  38768978       1.69
MAPPING/ALIGNING SUMMARY               Reads with MAPQ [40:inf)                                2095632883     91.43
MAPPING/ALIGNING SUMMARY               Reads with MAPQ [30:40)                                 9595781        0.42
MAPPING/ALIGNING SUMMARY               Reads with MAPQ [20:30)                                 24156035       1.05
MAPPING/ALIGNING SUMMARY               Reads with MAPQ [10:20)                                 32443054       1.42
MAPPING/ALIGNING SUMMARY               Reads with MAPQ [ 0:10)                                 101773426      4.44
MAPPING/ALIGNING SUMMARY               Total alignments                                        2267967248
MAPPING/ALIGNING SUMMARY               Secondary alignments                                    0
MAPPING/ALIGNING SUMMARY               Supplementary (chimeric) alignments                     4366069
MAPPING/ALIGNING SUMMARY               Estimated read length                                   148.92
MAPPING/ALIGNING SUMMARY               Bases in reference genome                               3137454505
MAPPING/ALIGNING SUMMARY               Bases in target bed [% of genome]                       NA
MAPPING/ALIGNING SUMMARY               Average sequenced coverage over genome                  108.79
MAPPING/ALIGNING SUMMARY               Average alignment coverage over genome                  NA
MAPPING/ALIGNING SUMMARY               PCT of genome with coverage [40x:inf)                   NA
MAPPING/ALIGNING SUMMARY               PCT of genome with coverage [30x:40x)                   NA
MAPPING/ALIGNING SUMMARY               PCT of genome with coverage [20x:30x)                   NA
MAPPING/ALIGNING SUMMARY               PCT of genome with coverage [10x:20x)                   NA
MAPPING/ALIGNING SUMMARY               PCT of genome with coverage [ 5x:10x)                   NA
MAPPING/ALIGNING SUMMARY               PCT of genome with coverage [ 2x: 5x)                   NA
MAPPING/ALIGNING SUMMARY               PCT of genome with coverage [ 1x: 2x)                   NA
MAPPING/ALIGNING SUMMARY               PCT of genome with coverage [ 0x: 1x)                   NA
MAPPING/ALIGNING SUMMARY               DRAGEN mapping rate [mil. reads/second]                 0.83

MAPPING/ALIGNING PER RG       .1       Total reads in RG                                       2292024624     100.00
MAPPING/ALIGNING PER RG       .1       Number of duplicate reads (marked)                      34763650       1.52
MAPPING/ALIGNING PER RG       .1       Number of unique reads                                  2257260974     98.48
MAPPING/ALIGNING PER RG       .1       Reads with mate sequenced                               2292024624     100.00
MAPPING/ALIGNING PER RG       .1       Reads without mate sequenced                            0              0.00
MAPPING/ALIGNING PER RG       .1       QC-failed reads                                         0              0.00
MAPPING/ALIGNING PER RG       .1       Mapped reads                                            2263601179     98.76
MAPPING/ALIGNING PER RG       .1       Number of unique & mapped reads (excl. dups)            2228837529     97.24
MAPPING/ALIGNING PER RG       .1       Unmapped reads                                          28423445       1.24
MAPPING/ALIGNING PER RG       .1       Singleton reads (itself mapped; mate unmapped)          7736139        0.34
MAPPING/ALIGNING PER RG       .1       Paired reads (itself & mate mapped)                     2255865040     98.42
MAPPING/ALIGNING PER RG       .1       Properly paired reads                                   2217096062     96.73
MAPPING/ALIGNING PER RG       .1       Not properly paired reads (discordant)                  38768978       1.69
MAPPING/ALIGNING PER RG       .1       Reads with MAPQ [40:inf)                                2095632883     91.43
MAPPING/ALIGNING PER RG       .1       Reads with MAPQ [30:40)                                 9595781        0.42
MAPPING/ALIGNING PER RG       .1       Reads with MAPQ [20:30)                                 24156035       1.05
MAPPING/ALIGNING PER RG       .1       Reads with MAPQ [10:20)                                 32443054       1.42
MAPPING/ALIGNING PER RG       .1       Reads with MAPQ [ 0:10)                                 101773426      4.44
MAPPING/ALIGNING PER RG       .1       Total alignments                                        2267967248
MAPPING/ALIGNING PER RG       .1       Secondary alignments                                    0
MAPPING/ALIGNING PER RG       .1       Supplementary (chimeric) alignments                     4366069
MAPPING/ALIGNING PER RG       .1       Estimated read length                                   148.92
MAPPING/ALIGNING PER RG       .1       Average sequenced coverage over genome                  108.79
MAPPING/ALIGNING PER RG       .1       Insert length: mean                                     605.86
MAPPING/ALIGNING PER RG       .1       Insert length: standard deviation                       188.04

RUN TIME                               Time loading reference                                  00:01:00.333   60.33
RUN TIME                               Time aligning reads                                     00:45:37.964   2737.96
RUN TIME                               Time sorting and marking duplicates                     00:13:48.195   828.20
RUN TIME                               Time saving map/align output                            00:13:52.870   832.87
RUN TIME                               Total runtime                                           01:02:20.192   3740.19
==================================================================

The .err file content:

Spilling sort intermediate results to disk
Partitioning complete.  Lowest evicted: 36
dragen alignment • 126 views
ADD COMMENTlink written 7 weeks ago by Floydian_slip130
1

This might be something to resolve with the Edico/Illumina engineers directly.

ADD REPLYlink written 7 weeks ago by cschu1811.9k
Please log in to add an answer.

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