Hello Sandrine,

The sequence identifiers are a mismatch between the bam file and the custom reference genome.
https://wiki.galaxyproject.org/Support#Reference_genomes

I'll reply with more detail to your bug report about the same issue.

Best,

Jen
Galaxy team

On 2/10/14 6:09 AM, Sandrine Imbeaud wrote:
Hi,


I am using the "Depth of coverage on BAM files" tool from the NGS: GATK Tools but encounter problem. While part of the BAM files proceed successfully, some BAM files end proceeding with a systematic error (see below). The entire BAM file dataset was generated with the same deepseq analysis pipeline (MiSeq Reporter, PCR amplicon Workflow) => alignemnent is done on Hs. hg19 and manifest is focused on specific regions.

Does someone know how to solve this problem?

Also, the chromosome X and Y appear to be exclude from the calculation. Is there any settings to select in order to include both sexual chromosomes? Is it expected?

Kind Regards
/ Sandrine
--
Sandrine Imbeaud
INSERM, UMR U-674, IUH
Université Paris Descartes
        
Génomique Fonctionnelle des tumeurs solides
27 rue Juliette Dodu
F75010 Paris, France
TEL: +33 (0)1 53 72 51 98
FAX: +33 (0)1 53 72 51 92
MOBILE: +33 (0)6 12 69 80 29
http://www.inserm-u674.net/
Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/tmp
[Mon Feb 10 07:08:03 CST 2014] net.sf.picard.sam.CreateSequenceDictionary REFERENCE=/tmp/tmp-gatk-hPNp7B/gatk_input.fasta OUTPUT=/tmp/tmp-gatk-hPNp7B/dict1033574942916796988.tmp TRUNCATE_NAMES_AT_WHITESPACE=true NUM_SEQUENCES=2147483647 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false [Mon Feb 10 07:08:03 CST 2014] Executing as g2m...@roundup49.tacc.utexas.edu on Linux 2.6.32-431.1.2.0.1.el6.x86_64 amd64; Java HotSpot(TM) 64-Bit Server VM 1.7.0_40-b43; Picard version: 1.58(1057) [Mon Feb 10 07:08:04 CST 2014] net.sf.picard.sam.CreateSequenceDictionary done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=2025324544
##### ERROR ------------------------------------------------------------------------------------------
##### ERROR A USER ERROR has occurred (version 1.4-18-g80a4ce0):
##### ERROR The invalid arguments or inputs must be corrected before the GATK can proceed
##### ERROR Please do not post this error to the GATK forum
##### ERROR
##### ERROR See the documentation (rerun with -h) for this tool to view allowable command-line arguments. ##### ERROR Visit our wiki for extensive documentation http://www.broadinstitute.org/gsa/wiki ##### ERROR Visit our forum to view answers to commonly asked questions http://getsatisfaction.com/gsa
##### ERROR
##### ERROR MESSAGE: Input files reads and reference have incompatible contigs: No overlapping contigs found. ##### ERROR reads contigs = [chrM, chr1, chr2, chr3, chr4, chr5, chr6, chr7, chr8, chr9, chr10, chr11, chr12, chr13, chr14, chr15, chr16, chr17, chr18, chr19, chr20, chr21, chr22, chrX, chrY] ##### ERROR reference contigs = [c1_27022371-27108741, c1_65310990-65312594, c1_103341958-103574198, c1_115256193-115258963, c11_533546-534529, c11_108093339-108239879, c12_25379959-25398502, c12_46123245-46302016, c12_49412540-49449288, c12_70910587-71031382, c12_121416337-121440487, c13_77618564-77901349, c16_337220-402825, c16_2097254-2138873, c17_7571510-7591038, c17_40474813-40500706, c19_10596592-10614570, c2_21224182-21267085, c2_178098515-178099162, c20_57484200-57484647, c3_41240709-41282027, c3_41265294-41266864, c3_47057688-47205620, c3_178928002-178948337, c4_74269729-74287296, c4_185308648-185395907, c5_1253083-1294978, c5_1294819-1295755, c5_55251637-55260189, c5_71402848-71505569, c6_36644019-36655290, c7_135242597-135333692, c7_140452856-140453348, c9_21967531-21994664, c9_135766517-135820181] ##### ERROR ------------------------------------------------------------------------------------------ mv: cannot stat `/galaxy-repl/main/files/007/581/dataset_7581988.dat.sample_summary': No such file or directory





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