I am trying to use picard merge bam, after I sort the alignments and unaligned reads wrt queryname using picard. I merge them with SORT_ORDER=queryname
Then I get the following error:
Exception merging bam alignment - attempting to sort aligned reads and try again: Aligned record iterator (GM12878_CTCF_sequence_B1_T1_solid:222_1008_1366) is behind the unmapped reads (GM12878_CTCF_sequence_B1_T1_solid:222_1008_1366/1)
....
Exception in thread "main" java.lang.IllegalStateException: Aligned record iterator (GM12878_CTCF_sequence_B1_T1_solid:222_1008_1366) is behind the unmapped reads (GM12878_CTCF_sequence_B1_T1_solid:222_1008_1366/1)
However, when I look at the input files, they are in the same order :
samtools view unmapped/GM12878_CTCF.clean.sorted.bam | grep -n -B 5 -A 5 -m 1 222_1008_1366 | cut -f 1-5
211-GM12878_CTCF_sequence_B1_T1_solid:222_1008_1148/1 4 * 0 0
212-GM12878_CTCF_sequence_B1_T1_solid:222_1008_1184/1 4 * 0 0
213-GM12878_CTCF_sequence_B1_T1_solid:222_1008_13/1 4 * 0 0
214-GM12878_CTCF_sequence_B1_T1_solid:222_1008_1301/1 4 * 0 0
215-GM12878_CTCF_sequence_B1_T1_solid:222_1008_1344/1 4 * 0 0
216:GM12878_CTCF_sequence_B1_T1_solid:222_1008_1366/1 4 * 0 0
217-GM12878_CTCF_sequence_B1_T1_solid:222_1008_1482/1 4 * 0 0
218-GM12878_CTCF_sequence_B1_T1_solid:222_1008_1492/1 4 * 0 0
219-GM12878_CTCF_sequence_B1_T1_solid:222_1008_1498/1 4 * 0 0
220-GM12878_CTCF_sequence_B1_T1_solid:222_1008_1556/1 4 * 0 0
221-GM12878_CTCF_sequence_B1_T1_solid:222_1008_18/1 4 * 0 0
samtools view alignments/GM12878_CTCF.clean.sorted.bam | grep -n -B 5 -A 5 -m 1 222_1008_1366 | cut -f 1-5
211-GM12878_CTCF_sequence_B1_T1_solid:222_1008_1148 4 * 0 0
212-GM12878_CTCF_sequence_B1_T1_solid:222_1008_1184 4 * 0 0
213-GM12878_CTCF_sequence_B1_T1_solid:222_1008_13 4 * 0 0
214-GM12878_CTCF_sequence_B1_T1_solid:222_1008_1301 4 * 0 0
215-GM12878_CTCF_sequence_B1_T1_solid:222_1008_1344 4 * 0 0
216:GM12878_CTCF_sequence_B1_T1_solid:222_1008_1366 0 chr7 105529114 0
217-GM12878_CTCF_sequence_B1_T1_solid:222_1008_1482 4 * 0 0
218-GM12878_CTCF_sequence_B1_T1_solid:222_1008_1492 4 * 0 0
219-GM12878_CTCF_sequence_B1_T1_solid:222_1008_1498 4 * 0 0
220-GM12878_CTCF_sequence_B1_T1_solid:222_1008_1556 4 * 0 0
221-GM12878_CTCF_sequence_B1_T1_solid:222_1008_18 4 * 0 0
I could not understand the reason for this error. Can you help?