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lindenb / jvarkit

Java utilities for Bioinformatics
https://jvarkit.readthedocs.io/
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BUG:[INFO][Launcher]sam2tsv Exited with failure (-1) #233

Closed WXY-Belief closed 1 year ago

WXY-Belief commented 1 year ago

hello, when i run Command-“sam2tsv --reference ${genome_fa} ${i}.sam”，there eixst a bug as follows:

[SEVERE][Sam2Tsv]scan error: java.lang.IllegalArgumentException: No sequence dictionary in the reference. Use picard CreateSequenceDictionary to index the sequence https://broadinstitute.github.io/picard/command-line-overview.html. at com.github.lindenb.jvarkit.util.picard.GenomicSequence.(GenomicSequence.java:141) at com.github.lindenb.jvarkit.tools.sam2tsv.Sam2Tsv.printAln(Sam2Tsv.java:339) at com.github.lindenb.jvarkit.tools.sam2tsv.Sam2Tsv.scan(Sam2Tsv.java:465) at com.github.lindenb.jvarkit.tools.sam2tsv.Sam2Tsv.doWork(Sam2Tsv.java:501) at com.github.lindenb.jvarkit.util.jcommander.Launcher.instanceMain(Launcher.java:1156) at com.github.lindenb.jvarkit.util.jcommander.Launcher.instanceMainWithExit(Launcher.java:1342) at com.github.lindenb.jvarkit.tools.sam2tsv.Sam2Tsv.main(Sam2Tsv.java:525) [SEVERE][Sam2Tsv]No sequence dictionary in the reference. Use picard CreateSequenceDictionary to index the sequence https://broadinstitute.github.io/picard/command-line-overview.html. java.lang.RuntimeException: No sequence dictionary in the reference. Use picard CreateSequenceDictionary to index the sequence https://broadinstitute.github.io/picard/command-line-overview.html. at com.github.lindenb.jvarkit.tools.sam2tsv.Sam2Tsv.scan(Sam2Tsv.java:473) at com.github.lindenb.jvarkit.tools.sam2tsv.Sam2Tsv.doWork(Sam2Tsv.java:501) at com.github.lindenb.jvarkit.util.jcommander.Launcher.instanceMain(Launcher.java:1156) at com.github.lindenb.jvarkit.util.jcommander.Launcher.instanceMainWithExit(Launcher.java:1342) at com.github.lindenb.jvarkit.tools.sam2tsv.Sam2Tsv.main(Sam2Tsv.java:525) Caused by: java.lang.IllegalArgumentException: No sequence dictionary in the reference. Use picard CreateSequenceDictionary to index the sequence https://broadinstitute.github.io/picard/command-line-overview.html. at com.github.lindenb.jvarkit.util.picard.GenomicSequence.(GenomicSequence.java:141) at com.github.lindenb.jvarkit.tools.sam2tsv.Sam2Tsv.printAln(Sam2Tsv.java:339) at com.github.lindenb.jvarkit.tools.sam2tsv.Sam2Tsv.scan(Sam2Tsv.java:465) ... 4 more [INFO][Launcher]sam2tsv Exited with failure (-1)

lindenb commented 1 year ago

There is no sequence dictionary associated to your fasta; Use picard CreateSequenceDictionary to index the sequence https://broadinstitute.github.io/picard/command-line-overview.html