Comments (2)
nh13
commented on September 18, 2024
For reference, other tools handle this a bit more gracefully:
WARNING 2022-11-28 13:40:01 QualityScoreDistribution No valid bases found in input file. No plot will be produced.
WARNING 2022-11-28 13:40:01 MeanQualityByCycle No valid bases found in input file. No plot will be produced.
WARNING 2022-11-28 13:40:01 CollectBaseDistributionByCycle No valid bases found in input file. No plot will be produced.
INFO 2022-11-28 13:40:01 RExecutor Executing R script via command: Rscript /var/folders/wh/hhg8fhpn2w52nxcnjjn548_c0000gn/T/script5121851671603744911.R <redacted>.gc_bias.detail_metrics.txt <redacted>.gc_bias.summary_metrics.txt <redacted>.gc_bias.pdf 100
ERROR 2022-11-28 13:40:02 ProcessExecutor Error in read.table(summaryMetricsFile, header = T, sep = "\t", skip = firstBlankLine2) :
ERROR 2022-11-28 13:40:02 ProcessExecutor no lines available in input
ERROR 2022-11-28 13:40:02 ProcessExecutor Execution halted
WARNING 2022-11-28 13:40:02 CollectInsertSizeMetrics All data categories were discarded because they contained < 0.05 of the total aligned paired data.
WARNING 2022-11-28 13:40:02 CollectInsertSizeMetrics Total mapped pairs in all categories: 0.0
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kachulis
commented on September 18, 2024
Just noticed, this was fixed in #1859
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Related Issues (20)
- Thresholds for AT_DROPOUT and GC_DROPOUT HOT 1
- Exception in thread "main" htsjdk.samtools.SAMException: Cannot read non-existent file HOT 3
- Possible MarkDuplicates bug: no optical duplicates found HOT 2
- SamToFastq writes to /dev/stdout Exception HOT 1
- Order of rows in crosscheck metrics files are non-deterministic HOT 4
- OutOfMemoryError HOT 2
- CollectAlignmentSummaryMetrics fails on some small inputs due to unsafe Histogram methods HOT 1
- Picard new release HOT 6
- SamToFastq HOT 5
- GENOTYPING_ERROR_RATE doesn't do anything in CrosscheckFingerprints HOT 3
- Sum of Which columns in MarkDulicates metrices gives us total reads? HOT 1
- Question about Depth HOT 1
- Sequence dictionaries are not the same size HOT 5
- CONVERT BAM TO U-BAM Error HOT 2
- CollectSamErrorMetrics overlap total bases HOT 1
- BUILD FAILED error HOT 1
- Mark Duplicates - Not Enough Fields Exception HOT 2
- Samtofastq does not retain all the information HOT 5
- Picard build failed HOT 1
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