Hi,
I am trying to reorder the reads in my BAM file to match the ordering contigs
of the reference file and get this error:
ceres@wensleydale /WTCHG_162322_201_tophat/ java -jar
/apps/well/picard-tools/1.111/ReorderSam.jar INPUT=accepted_hits.bam
OUTPUT=ceresC2.bam REFERENCE=../../REFERENCE_SEQUENCES/human_g1k_v37.fasta
[Wed Feb 04 16:41:01 GMT 2015] net.sf.picard.sam.ReorderSam
INPUT=accepted_hits.bam OUTPUT=ceresC2.bam
REFERENCE=../../REFERENCE_SEQUENCES/human_g1k_v37.fasta
ALLOW_INCOMPLETE_DICT_CONCORDANCE=false ALLOW_CONTIG_LENGTH_DISCORDANCE=false
VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5
MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false
[Wed Feb 04 16:41:01 GMT 2015] Executing as ce...@wensleydale.well.ox.ac.uk on
Linux 2.6.32-431.29.2.el6.x86_64 amd64; Java HotSpot(TM) 64-Bit Server VM
1.7.0_51-b13; Picard version: 1.111(1901) IntelDeflater
INFO 2015-02-04 16:41:02 ReorderSam SAM/BAM file
INFO 2015-02-04 16:41:02 ReorderSam SN=%s LN=%d%nchr1249250621
INFO 2015-02-04 16:41:02 ReorderSam SN=%s LN=%d%nchr10135534747
INFO 2015-02-04 16:41:02 ReorderSam SN=%s LN=%d%nchr11135006516
INFO 2015-02-04 16:41:02 ReorderSam SN=%s LN=%d%nchr12133851895
INFO 2015-02-04 16:41:02 ReorderSam SN=%s LN=%d%nchr13115169878
INFO 2015-02-04 16:41:02 ReorderSam SN=%s LN=%d%nchr14107349540
INFO 2015-02-04 16:41:02 ReorderSam SN=%s LN=%d%nchr15102531392
INFO 2015-02-04 16:41:02 ReorderSam SN=%s LN=%d%nchr1690354753
INFO 2015-02-04 16:41:02 ReorderSam SN=%s LN=%d%nchr1781195210
INFO 2015-02-04 16:41:02 ReorderSam SN=%s LN=%d%nchr1878077248
INFO 2015-02-04 16:41:02 ReorderSam SN=%s LN=%d%nchr1959128983
INFO 2015-02-04 16:41:02 ReorderSam SN=%s LN=%d%nchr2243199373
INFO 2015-02-04 16:41:02 ReorderSam SN=%s LN=%d%nchr2063025520
INFO 2015-02-04 16:41:02 ReorderSam SN=%s LN=%d%nchr2148129895
INFO 2015-02-04 16:41:02 ReorderSam SN=%s LN=%d%nchr2251304566
INFO 2015-02-04 16:41:02 ReorderSam SN=%s LN=%d%nchr3198022430
INFO 2015-02-04 16:41:02 ReorderSam SN=%s LN=%d%nchr4191154276
INFO 2015-02-04 16:41:02 ReorderSam SN=%s LN=%d%nchr5180915260
INFO 2015-02-04 16:41:02 ReorderSam SN=%s LN=%d%nchr6171115067
INFO 2015-02-04 16:41:02 ReorderSam SN=%s LN=%d%nchr7159138663
INFO 2015-02-04 16:41:02 ReorderSam SN=%s LN=%d%nchr8146364022
INFO 2015-02-04 16:41:02 ReorderSam SN=%s LN=%d%nchr9141213431
INFO 2015-02-04 16:41:02 ReorderSam SN=%s LN=%d%nchrM16571
INFO 2015-02-04 16:41:02 ReorderSam SN=%s LN=%d%nchrX155270560
INFO 2015-02-04 16:41:02 ReorderSam SN=%s LN=%d%nchrY59373566
INFO 2015-02-04 16:41:02 ReorderSam Reference
INFO 2015-02-04 16:41:02 ReorderSam SN=%s LN=%d%n1249250621
INFO 2015-02-04 16:41:02 ReorderSam SN=%s LN=%d%n2243199373
INFO 2015-02-04 16:41:02 ReorderSam SN=%s LN=%d%n3198022430
INFO 2015-02-04 16:41:02 ReorderSam SN=%s LN=%d%n4191154276
INFO 2015-02-04 16:41:02 ReorderSam SN=%s LN=%d%n5180915260
INFO 2015-02-04 16:41:02 ReorderSam SN=%s LN=%d%n6171115067
INFO 2015-02-04 16:41:02 ReorderSam SN=%s LN=%d%n7159138663
INFO 2015-02-04 16:41:02 ReorderSam SN=%s LN=%d%n8146364022
INFO 2015-02-04 16:41:02 ReorderSam SN=%s LN=%d%n9141213431
INFO 2015-02-04 16:41:02 ReorderSam SN=%s LN=%d%n10135534747
INFO 2015-02-04 16:41:02 ReorderSam SN=%s LN=%d%n11135006516
INFO 2015-02-04 16:41:02 ReorderSam SN=%s LN=%d%n12133851895
INFO 2015-02-04 16:41:02 ReorderSam SN=%s LN=%d%n13115169878
INFO 2015-02-04 16:41:02 ReorderSam SN=%s LN=%d%n14107349540
INFO 2015-02-04 16:41:02 ReorderSam SN=%s LN=%d%n15102531392
INFO 2015-02-04 16:41:02 ReorderSam SN=%s LN=%d%n1690354753
INFO 2015-02-04 16:41:02 ReorderSam SN=%s LN=%d%n1781195210
INFO 2015-02-04 16:41:02 ReorderSam SN=%s LN=%d%n1878077248
INFO 2015-02-04 16:41:02 ReorderSam SN=%s LN=%d%n1959128983
INFO 2015-02-04 16:41:02 ReorderSam SN=%s LN=%d%n2063025520
INFO 2015-02-04 16:41:02 ReorderSam SN=%s LN=%d%n2148129895
INFO 2015-02-04 16:41:02 ReorderSam SN=%s LN=%d%n2251304566
INFO 2015-02-04 16:41:02 ReorderSam SN=%s LN=%d%nX155270560
INFO 2015-02-04 16:41:02 ReorderSam SN=%s LN=%d%nY59373566
INFO 2015-02-04 16:41:02 ReorderSam SN=%s LN=%d%nMT16569
INFO 2015-02-04 16:41:02 ReorderSam SN=%s LN=%d%nGL000207.14262
INFO 2015-02-04 16:41:02 ReorderSam SN=%s LN=%d%nGL000226.115008
INFO 2015-02-04 16:41:02 ReorderSam SN=%s LN=%d%nGL000229.119913
INFO 2015-02-04 16:41:02 ReorderSam SN=%s LN=%d%nGL000231.127386
INFO 2015-02-04 16:41:02 ReorderSam SN=%s LN=%d%nGL000210.127682
INFO 2015-02-04 16:41:02 ReorderSam SN=%s LN=%d%nGL000239.133824
INFO 2015-02-04 16:41:02 ReorderSam SN=%s LN=%d%nGL000235.134474
INFO 2015-02-04 16:41:02 ReorderSam SN=%s LN=%d%nGL000201.136148
INFO 2015-02-04 16:41:02 ReorderSam SN=%s LN=%d%nGL000247.136422
INFO 2015-02-04 16:41:02 ReorderSam SN=%s LN=%d%nGL000245.136651
INFO 2015-02-04 16:41:02 ReorderSam SN=%s LN=%d%nGL000197.137175
INFO 2015-02-04 16:41:02 ReorderSam SN=%s LN=%d%nGL000203.137498
INFO 2015-02-04 16:41:02 ReorderSam SN=%s LN=%d%nGL000246.138154
INFO 2015-02-04 16:41:02 ReorderSam SN=%s LN=%d%nGL000249.138502
INFO 2015-02-04 16:41:02 ReorderSam SN=%s LN=%d%nGL000196.138914
INFO 2015-02-04 16:41:02 ReorderSam SN=%s LN=%d%nGL000248.139786
INFO 2015-02-04 16:41:02 ReorderSam SN=%s LN=%d%nGL000244.139929
INFO 2015-02-04 16:41:02 ReorderSam SN=%s LN=%d%nGL000238.139939
INFO 2015-02-04 16:41:02 ReorderSam SN=%s LN=%d%nGL000202.140103
INFO 2015-02-04 16:41:02 ReorderSam SN=%s LN=%d%nGL000234.140531
INFO 2015-02-04 16:41:02 ReorderSam SN=%s LN=%d%nGL000232.140652
INFO 2015-02-04 16:41:02 ReorderSam SN=%s LN=%d%nGL000206.141001
INFO 2015-02-04 16:41:02 ReorderSam SN=%s LN=%d%nGL000240.141933
INFO 2015-02-04 16:41:02 ReorderSam SN=%s LN=%d%nGL000236.141934
INFO 2015-02-04 16:41:02 ReorderSam SN=%s LN=%d%nGL000241.142152
INFO 2015-02-04 16:41:02 ReorderSam SN=%s LN=%d%nGL000243.143341
INFO 2015-02-04 16:41:02 ReorderSam SN=%s LN=%d%nGL000242.143523
INFO 2015-02-04 16:41:02 ReorderSam SN=%s LN=%d%nGL000230.143691
INFO 2015-02-04 16:41:02 ReorderSam SN=%s LN=%d%nGL000237.145867
INFO 2015-02-04 16:41:02 ReorderSam SN=%s LN=%d%nGL000233.145941
INFO 2015-02-04 16:41:02 ReorderSam SN=%s LN=%d%nGL000204.181310
INFO 2015-02-04 16:41:02 ReorderSam SN=%s LN=%d%nGL000198.190085
INFO 2015-02-04 16:41:02 ReorderSam SN=%s LN=%d%nGL000208.192689
INFO 2015-02-04 16:41:02 ReorderSam SN=%s LN=%d%nGL000191.1106433
INFO 2015-02-04 16:41:02 ReorderSam SN=%s LN=%d%nGL000227.1128374
INFO 2015-02-04 16:41:02 ReorderSam SN=%s LN=%d%nGL000228.1129120
INFO 2015-02-04 16:41:02 ReorderSam SN=%s LN=%d%nGL000214.1137718
INFO 2015-02-04 16:41:02 ReorderSam SN=%s LN=%d%nGL000221.1155397
INFO 2015-02-04 16:41:02 ReorderSam SN=%s LN=%d%nGL000209.1159169
INFO 2015-02-04 16:41:02 ReorderSam SN=%s LN=%d%nGL000218.1161147
INFO 2015-02-04 16:41:02 ReorderSam SN=%s LN=%d%nGL000220.1161802
INFO 2015-02-04 16:41:02 ReorderSam SN=%s LN=%d%nGL000213.1164239
INFO 2015-02-04 16:41:02 ReorderSam SN=%s LN=%d%nGL000211.1166566
INFO 2015-02-04 16:41:02 ReorderSam SN=%s LN=%d%nGL000199.1169874
INFO 2015-02-04 16:41:02 ReorderSam SN=%s LN=%d%nGL000217.1172149
INFO 2015-02-04 16:41:02 ReorderSam SN=%s LN=%d%nGL000216.1172294
INFO 2015-02-04 16:41:02 ReorderSam SN=%s LN=%d%nGL000215.1172545
INFO 2015-02-04 16:41:02 ReorderSam SN=%s LN=%d%nGL000205.1174588
INFO 2015-02-04 16:41:02 ReorderSam SN=%s LN=%d%nGL000219.1179198
INFO 2015-02-04 16:41:02 ReorderSam SN=%s LN=%d%nGL000224.1179693
INFO 2015-02-04 16:41:02 ReorderSam SN=%s LN=%d%nGL000223.1180455
INFO 2015-02-04 16:41:02 ReorderSam SN=%s LN=%d%nGL000195.1182896
INFO 2015-02-04 16:41:02 ReorderSam SN=%s LN=%d%nGL000212.1186858
INFO 2015-02-04 16:41:02 ReorderSam SN=%s LN=%d%nGL000222.1186861
INFO 2015-02-04 16:41:02 ReorderSam SN=%s LN=%d%nGL000200.1187035
INFO 2015-02-04 16:41:02 ReorderSam SN=%s LN=%d%nGL000193.1189789
INFO 2015-02-04 16:41:02 ReorderSam SN=%s LN=%d%nGL000194.1191469
INFO 2015-02-04 16:41:02 ReorderSam SN=%s LN=%d%nGL000225.1211173
INFO 2015-02-04 16:41:02 ReorderSam SN=%s LN=%d%nGL000192.1547496
INFO 2015-02-04 16:41:02 ReorderSam Reordering SAM/BAM file:
[Wed Feb 04 16:41:02 GMT 2015] net.sf.picard.sam.ReorderSam done. Elapsed time:
0,00 minutes.
Runtime.totalMemory()=2058354688
To get help, see http://picard.sourceforge.net/index.shtml#GettingHelp
Exception in thread "main" net.sf.picard.PicardException: New reference
sequence does not contain a matching contig for chr1
at
net.sf.picard.sam.ReorderSam.buildSequenceDictionaryMap(ReorderSam.java:217)
at net.sf.picard.sam.ReorderSam.doWork(ReorderSam.java:98)
at
net.sf.picard.cmdline.CommandLineProgram.instanceMain(CommandLineProgram.java:179)
at
net.sf.picard.cmdline.CommandLineProgram.instanceMainWithExit(CommandLineProgram.java:120)
at net.sf.picard.sam.ReorderSam.main(ReorderSam.java:77)
Which is very confusing because I know my bam file contains chromosome 1
samtools view -H accepted_hits.bam
@HD VN:1.0 SO:coordinate
@SQ SN:chr1 LN:249250621
And the reference sequence has been downloaded from 1KG as is, plus the .fai
contains the exactly same contig as the bam
less ../../REFERENCE_SEQUENCES/human_g1k_v37.fasta.fai
1 249250621 52 60 61
2 243199373 253404903 60 61
Any clues so as to how to solve this?
Many thanks
Ceres
Dr. Ceres Fernandez-Rozadilla
Molecular and Population Genetics
Wellcome Trust Centre for Human Genetics, University of Oxford
Roosevelt Drive, Oxford
OX3 7BN
+44 01865 287580
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