Hello all,
I am a new user here and am getting an error when trying to remove duplicates from my paired end aligned BAM file. I was wondering if anyone else has experienced this error. The message is:
Error Details
Execution resulted in the following messages:
Fatal error: Exit code 1 ()
Tool generated the following standard error:
Picked up JAVA_OPTIONS: -Djava.io.tmpdir=/galaxy-repl/main/jobdir/023/605/23605043/job_tmp -Xmx7g -Xms256m
09:37:48.810 INFO NativeLibraryLoader - Loading libgkl_compression.so from jar:file:/cvmfs/main.galaxyproject.org/deps/conda/pkgs/picard-2.18.2-py36_0/share/picard-2.18.2-0/picard.jar!/com/intel/gkl/native/libgkl_compression.so
Ignoring SAM validation error: ERROR: File /galaxy-repl/main/jobdir/023/605/23605043/working/Map_with_BWA-MEM_on_data_391_and_data_390__mapped_reads_in_BAM_format, Error parsing SAM header. @RG line missing SM tag. Line:
@RG ID:Trim_Galore__on_data_162_and_data_161__trimmed_reads_pair
record #1: NB501108:24:HVNJKAFXX:2:21105:17581:1341 147 chr10 26765330 0 51M23S = 26765334 -47 TGTACCTCTGCACTGCTGTCTGTGTGACAGAGCAAGACCCTGTCTCAAAAACACAAAAAGTAGCCGGGCGCGGT AEA/E//E/A<////E/AEAA//EEEAEEEEEE//EAE/E/E/EA/E/<//EE///E//A////EEEAEAAAAA MC:Z:48S31M MD:Z:2C3A7C1A34 RG:Z:Trim_Galore__on_data_162_and_data_161__trimmed_reads_pair NM:i:4 AS:i:34 XS:i:37
record #2: NB501108:24:HVNJKAFXX:2:21105:17581:1341 99 chr10 26765334 0 48S31M = 26765330 47 GGATCGCTAGAGCCAGGGAGGTGGAGGTTGCAGAGCGCCTTGACTGTTCCACTGCACTCCAGTCAGGGTGACAGAGCAA A/AAAEEE/EEEEEEE/E/E/EEEEE6EEEEEA/E/A//EA////EE/EEEEEEEEEAAE//EE/E/EE/EAEE/EAEE MC:Z:51M23S MD:Z:16T1T12 RG:Z:Trim_Galore__on_data_162_and_data_161__trimmed_reads_pair_ NM:i:2 AS:i:21 XS:i:31
Exception in thread “main” picard.PicardException: Found a samRecordWithOrdinal with sufficiently large clipping that we may have
missed including it in an early duplicate marking iteration. Please increase the minimum distance to at least 116bp
to ensure it is considered (was 100).
Record was: NB501108:24:HVNJKAFXX:2:21105:17581:1341 147 chr10 26765330 0 51M23S = 26765334 -47 TGTACCTCTGCACTGCTGTCTGTGTGACAGAGCAAGACCCTGTCTCAAAAACACAAAAAGTAGCCGGGCGCGGT AEA/E//E/A<////E/AEAA//EEEAEEEEEE//EAE/E/E/EA/E/<//EE///E//A////EEEAEAAAAA MC:Z:48S31M MD:Z:2C3A7C1A34 RG:Z:Trim_Galore__on_data_162_and_data_161__trimmed_reads_pair_ NM:i:4 AS:i:34 XS:i:37
at picard.sam.markduplicates.MarkDuplicatesWithMateCigarIterator.checkForMinimumDistanceFailure(MarkDuplicatesWithMateCigarIterator.java:332)
at picard.sam.markduplicates.MarkDuplicatesWithMateCigarIterator.markDuplicatesAndGetTheNextAvailable(MarkDuplicatesWithMateCigarIterator.java:421)
at picard.sam.markduplicates.MarkDuplicatesWithMateCigarIterator.next(MarkDuplicatesWithMateCigarIterator.java:219)
at picard.sam.markduplicates.MarkDuplicatesWithMateCigarIterator.next(MarkDuplicatesWithMateCigarIterator.java:47)
at picard.sam.markduplicates.MarkDuplicatesWithMateCigar.doWork(MarkDuplicatesWithMateCigar.java:168)
at picard.cmdline.CommandLineProgram.instanceMain(CommandLineProgram.java:282)
at picard.cmdline.PicardCommandLine.instanceMain(PicardCommandLine.java:98)
at picard.cmdline.PicardCommandLine.main(PicardCommandLine.java:108)
Galaxy job runner generated the following standard error:
[W::bam_hdr_read] EOF marker is absent. The input is probably truncated
[E::bgzf_read] Read block operation failed with error 4 after 14 of 171 bytes