Entering edit mode
4.6 years ago
Floydian_slip
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170
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
This might be something to resolve with the Edico/Illumina engineers directly.
Strange, for me it looks like the alignment ran through successfully, e.g.
MAPPING/ALIGNING SUMMARY Number of unique & mapped reads (excl. dups) 2228837529 97.24
This can depend on the reference genome as well as the sample that is processed. We used the DRAGEN for wheat genomics (reference sizes between 12 and 17Gbp) and that didn't work 100% in the beginning. We had a massive number of exome capture samples and some of those would cause problems. In the case of the reference, the size was definitely an issue, but also the high repetitive fraction potentially caused trouble. As for the samples, I never found out why certain samples had problems (sometimes it also seemed that the DRAGEN was "exhausted" after processing 100s of samples.)