opened
nalinigans
username_0
This is a placeholder to hold issues we are seeing with logging currently and collect ideas on how to improve logging.
Improve Logging in GenomicsDB
issue
created
nalinigans
username_0
Issue 1: Seen from gatk GenomicsDBImport ...
```
Command: ./gatk GenomicsDBImport --genomicsdb-workspace-path ws -L LG02 --sample-name-map /nfs3/nalini/gatk-issues/vcfs.sample.map
Using GATK wrapper script /nfs/home/nalini/gatk/build/install/gatk/bin/gatk
Running:
    /nfs/home/nalini/gatk/build/install/gatk/bin/gatk GenomicsDBImport --genomicsdb-workspace-path ws -L LG02 --sample-name-map /nfs3/nalini/gatk-issues/vcfs.sample.map
11:06:44.271 INFO  NativeLibraryLoader - Loading libgkl_compression.so from jar:file:/nfs/home/nalini/gatk/build/install/gatk/lib/gkl-0.8.6.jar!/com/intel/gkl/native/libgkl_compression.so
Jul 24, 2019 11:06:45 AM shaded.cloud_nio.com.google.auth.oauth2.ComputeEngineCredentials runningOnComputeEngine
INFO: Failed to detect whether we are running on Google Compute Engine.
11:06:45.940 INFO  GenomicsDBImport - ------------------------------------------------------------
11:06:45.940 INFO  GenomicsDBImport - The Genome Analysis Toolkit (GATK) v4.1.2.0-40-gb11abd1-SNAPSHOT
11:06:45.940 INFO  GenomicsDBImport - For support and documentation go to https://software.broadinstitute.org/gatk/
11:06:45.941 INFO  GenomicsDBImport - Executing as nalini@oda-compute-0-6.oda-internal.com on Linux v3.10.0-957.10.1.el7.x86_64 amd64
11:06:45.942 INFO  GenomicsDBImport - Java runtime: OpenJDK 64-Bit Server VM v1.8.0_212-b04
11:06:45.942 INFO  GenomicsDBImport - Start Date/Time: July 24, 2019 11:06:44 AM PDT
11:06:45.942 INFO  GenomicsDBImport - ------------------------------------------------------------
11:06:45.942 INFO  GenomicsDBImport - ------------------------------------------------------------
11:06:45.942 INFO  GenomicsDBImport - HTSJDK Version: 2.19.0
11:06:45.942 INFO  GenomicsDBImport - Picard Version: 2.19.0
11:06:45.943 INFO  GenomicsDBImport - HTSJDK Defaults.COMPRESSION_LEVEL : 2
11:06:45.943 INFO  GenomicsDBImport - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
11:06:45.943 INFO  GenomicsDBImport - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
11:06:45.943 INFO  GenomicsDBImport - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
11:06:45.943 INFO  GenomicsDBImport - Deflater: IntelDeflater
11:06:45.943 INFO  GenomicsDBImport - Inflater: IntelInflater
11:06:45.943 INFO  GenomicsDBImport - GCS max retries/reopens: 20
11:06:45.943 INFO  GenomicsDBImport - Requester pays: disabled
11:06:45.943 INFO  GenomicsDBImport - Initializing engine
11:06:46.248 INFO  IntervalArgumentCollection - Processing 24054406 bp from intervals
11:06:46.250 INFO  GenomicsDBImport - Done initializing engine
11:06:46.534 INFO  GenomicsDBImport - Vid Map JSON file will be written to /nfs/home/nalini/gatk/ws/vidmap.json
11:06:46.534 INFO  GenomicsDBImport - Callset Map JSON file will be written to /nfs/home/nalini/gatk/ws/callset.json
11:06:46.534 INFO  GenomicsDBImport - Complete VCF Header will be written to /nfs/home/nalini/gatk/ws/vcfheader.vcf
11:06:46.534 INFO  GenomicsDBImport - Importing to array - /nfs/home/nalini/gatk/ws/genomicsdb_array
11:06:46.534 INFO  ProgressMeter - Starting traversal
11:06:46.534 INFO  ProgressMeter -        Current Locus  Elapsed Minutes     Batches Processed   Batches/Minute
11:06:47.770 INFO  GenomicsDBImport - Importing batch 1 with 12 samples
terminate called after throwing an instance of 'File2TileDBBinaryException'
  what():  File2TileDBBinaryException : read_one_line_fully && "Buffer did not have space to hold a line fully - increase buffer size"
```
comment