Dear List Using samtools V1.1 for a SAM to BAM sorting leads to a "pretty_header" where information in Google is scarce. So I have no clue, what this error is about. The same step does not show problems using samtools V0.1.19. The command lines describing input, error and possible output are shown below. The error shows up in a later step of samtools sort, leaving behind a list of intermediate BAM files.
Thanks and best regards, Axel Appendix: #ll try5 -rw-rw---- 1 user group 13G Jan 21 16:15 try5 #samtools-1.1 view -H try5 @PG ID:bwa PN:bwa VN:0.7.10-r789 CL:bwa samse -n 2 input.fa - input.fastq @HD VN:1.3 SO:coordinate @SQ SN:chr22 LN:51304566 #samtools-1.1 view try5 | head -n2 HWI-BRUNOP16X_0001:2:2:16141:26794#0 4 * 0 0 * * 0 0 GTTAAATACAAACTTTCATTTGGTGATGCACGGCACCAATGCTTTGCATATACCTTGCTGCAAAGAACAGGTTAA TTTTTSSKJFSSPTT\GUHUSSTTSSTPTTMSTTTSSSTTTTTTSb]bbRSSKTTTTKTT``b[bBBBBBBBBBB HWI-BRUNOP16X_0001:2:2:16241:26798#0 4 * 0 0 * * 0 0 GTACACTTCATTCTCTAGGGCTGCAGGGTACAAAAAGCCAATTTCAGAAGTAAGTGGACAAGGCAGAGAAGAAAA gfggggggggggggggggggggggggggfggggggffgggggggggggggfgggfgggggggggggfghggggg] #cat try5 | samtools-1.1 sort - result_1.1 [bam_sort_core] merging from 30 files... [pretty_header] invalid header #ll result_1.1.* -rw-rw---- 1 user group 143M Jan 21 16:44 result_1.1.0000.bam ... -rw-rw---- 1 user group 15M Jan 21 16:52 result_1.1.0029.bam #cat try5 | samtools-0.1.19 sort - result_0.1.19 [bam_header_read] EOF marker is absent. The input is probably truncated. [bam_sort_core] merging from 30 files... #ll result_0.1.19.bam -rw-rw---- 1 user group 3.6G Jan 21 17:14 result_0.1.19.bam #samtools-0.1.19 view -H result_0.1.19.bam @HD VN:1.3 SO:coordinate @PG ID:bwa PN:bwa VN:0.7.10-r789 CL:bwa samse -n 2 /project/altsplice/projekte/rna-seq-analysis/dev/bwa/jctnReference_fastRun/synthJctnReference_ens72synthJctnSize90bp.fa - /scratch/local2/user/rna-seq-analysis_bwa/FCA_s_2_hg19_un.fastq @HD VN:1.3 SO:coordinate @SQ SN:chr22 LN:51304566 #samtools-0.1.19 view result_0.1.19.bam | head -n2 HWI-BRUNOP16X_0001:2:4:2964:191394#0 0 chr22 16100613 25 36M627N39M * 0 0 CCTATGAATTGAATGTGTTACTATCGCTTTCACATCCTGAAGCATTAGAGCATGTGGGGAATGCACAAAAATTGA BBBBBBB_Y`bdgggggggggggggggggggggggggggggggggggggggggggggggggggffgggggggggg XT:A:U NM:i:4 X0:i:1 X1:i:0 XM:i:4 XO:i:0 XG:i:0 MD:Z:0A24C11G17T19 HWI-BRUNOP16X_0001:2:23:17206:48524#0 0 chr22 16100613 37 36M627N39M * 0 0 ACTATGAATTGAATGTGTTACTATCGCTTTCACATCCTGAAGCATTAGAGCATGTGGGGAATGCACAAAAATTGA U]b]OX]\MXTTSORP`^XU`RY^VbbWWb^\^^QR`b^b\\\YY\b^[bTSSSS^bW^\TTSPNSSSSTTTTPT XT:A:U NM:i:3 X0:i:1 X1:i:0 XM:i:3 XO:i:0 XG:i:0 MD:Z:25C11G17T19 # ------------------------------------------------------------------------------ New Year. New Location. New Benefits. New Data Center in Ashburn, VA. GigeNET is offering a free month of service with a new server in Ashburn. Choose from 2 high performing configs, both with 100TB of bandwidth. Higher redundancy.Lower latency.Increased capacity.Completely compliant. http://p.sf.net/sfu/gigenet _______________________________________________ Samtools-help mailing list Samtools-help@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/samtools-help
