Source: fastqc Version: 0.11.7+dfsg-1 Severity: normal User: [email protected] Usertags: regression
With the upload of version 0.11.7+dfsg-1 of fastqc, the autopkgtest¹ started to fail with the error copied below. As I have zero experience with java, I don't know what to make of this error. Could you please investigate? Paul ¹ https://ci.debian.net/packages/f/fastqc/unstable/amd64/autopkgtest [14:03:24]: test run-unit-test: [----------------------- Started analysis of example.fastq Analysis complete for example.fastq Archive: example_fastqc.zip creating: example_fastqc/ creating: example_fastqc/Icons/ creating: example_fastqc/Images/ inflating: example_fastqc/Icons/fastqc_icon.png inflating: example_fastqc/Icons/warning.png inflating: example_fastqc/Icons/error.png inflating: example_fastqc/Icons/tick.png inflating: example_fastqc/summary.txt inflating: example_fastqc/Images/per_base_quality.png inflating: example_fastqc/Images/per_tile_quality.png inflating: example_fastqc/Images/per_sequence_quality.png inflating: example_fastqc/Images/per_base_sequence_content.png inflating: example_fastqc/Images/per_sequence_gc_content.png inflating: example_fastqc/Images/per_base_n_content.png inflating: example_fastqc/Images/sequence_length_distribution.png inflating: example_fastqc/Images/duplication_levels.png inflating: example_fastqc/Images/adapter_content.png inflating: example_fastqc/fastqc_report.html inflating: example_fastqc/fastqc_data.txt inflating: example_fastqc/fastqc.fo PASS Basic Statistics example.fastq WARN Per base sequence quality example.fastq PASS Per tile sequence quality example.fastq PASS Per sequence quality scores example.fastq WARN Per base sequence content example.fastq WARN Per sequence GC content example.fastq PASS Per base N content example.fastq PASS Sequence Length Distribution example.fastq PASS Sequence Duplication Levels example.fastq WARN Overrepresented sequences example.fastq PASS Adapter Content example.fastq Failed to process toy.sam htsjdk.samtools.util.RuntimeIOException: java.io.IOException: Stream closed at htsjdk.samtools.SamReaderFactory$SamReaderFactoryImpl.open(SamReaderFactory.java:373) at uk.ac.babraham.FastQC.Sequence.BAMFile.<init>(BAMFile.java:64) at uk.ac.babraham.FastQC.Sequence.SequenceFactory.getSequenceFile(SequenceFactory.java:100) at uk.ac.babraham.FastQC.Sequence.SequenceFactory.getSequenceFile(SequenceFactory.java:62) at uk.ac.babraham.FastQC.Analysis.OfflineRunner.processFile(OfflineRunner.java:152) at uk.ac.babraham.FastQC.Analysis.OfflineRunner.<init>(OfflineRunner.java:121) at uk.ac.babraham.FastQC.FastQCApplication.main(FastQCApplication.java:316) Caused by: java.io.IOException: Stream closed at java.base/java.io.BufferedInputStream.getInIfOpen(BufferedInputStream.java:159) at java.base/java.io.BufferedInputStream.fill(BufferedInputStream.java:246) at java.base/java.io.BufferedInputStream.read1(BufferedInputStream.java:286) at java.base/java.io.BufferedInputStream.read(BufferedInputStream.java:345) at htsjdk.samtools.util.BlockCompressedInputStream.readBytes(BlockCompressedInputStream.java:436) at htsjdk.samtools.util.BlockCompressedInputStream.isValidFile(BlockCompressedInputStream.java:351) at htsjdk.samtools.SamStreams.isBAMFile(SamStreams.java:51) at htsjdk.samtools.SamReaderFactory$SamReaderFactoryImpl.open(SamReaderFactory.java:313) ... 6 more autopkgtest [14:03:29]: test run-unit-test: -----------------------]
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