[PRE-CHECK] I am checking availability of the required lpsolve JNI libs. [PRE-CHECK] * successfully loaded lpsolve JNI (version 5.5,release 0,build 14) Scanning annotation file Checking GTF *[WARN] Unsorted in line 52 - chr/strand JH375168.1 + already read. [INFO] Sorting /users/cn/pprieto/projects/chicken/data/merging/total/pc_only.gtf sorting GTF file OK (00:00:12) scanning OK (00:00:03) [INFO] 15345 loci, 16354 transcripts, 179594 exons. OK (00:00:03) Scanning mapping file OK (00:00:40) [WARN] Skipped 177848 lines. [INFO] 16222259 mapped reads, 17955910 mappings: R-factor 1.1068686 [INFO] 12864401 entire, 5091509 split mappings (28.355618%) [INFO] Read descriptor seems OK OK (00:00:40) [INFO] Annotation and mapping input checked [HEHO] We are set, so let's go! [ANNOTATION_FILE] /users/cn/pprieto/projects/chicken/data/merging/total/pc_only.gtf [MAPPING_FILE] /users/rg/dkedra/seqOUT/G.gallus/Jul2013_mappings/gsnap20130720/paired/0780N0013_AGTCAA_L001_r12.Ggal71.gsnap0819.sorted.bam [READ_DESCRIPTOR] {ID}/{MATE}[1,2] [SORT_IN_RAM] true [TMP_DIR] /tmp [STDOUT_FILE] /users/cn/pprieto/projects/chicken/data/quantifications/input.o [INFO] mate pairing information considered [PROFILE] Loading profile [PROFILE] Scanning the input and getting the attributes. profiling [ERROR] Error while iterating loci: net.sf.samtools.SAMException: Value for tag XT is not a Character: class java.lang.String at net.sf.samtools.SAMRecord.getCharacterAttribute(SAMRecord.java:975) at barna.model.sam.SAMMapping.(SAMMapping.java:51) at barna.model.sam.SAMMapping.(SAMMapping.java:60) at barna.io.sam.SAMMappingIterator.init(SAMMappingIterator.java:86) at barna.io.sam.SAMMappingIterator.(SAMMappingIterator.java:70) at barna.io.sam.SAMReader.read(SAMReader.java:227) at barna.flux.capacitor.profile.BiasProfiler.profile(BiasProfiler.java:205) at barna.flux.capacitor.profile.BiasProfiler.call(BiasProfiler.java:101) at barna.flux.capacitor.reconstruction.FluxCapacitor.getProfile(FluxCapacitor.java:2196) at barna.flux.capacitor.reconstruction.FluxCapacitor.call(FluxCapacitor.java:1878) at barna.flux.capacitor.reconstruction.FluxCapacitor.call(FluxCapacitor.java:74) at barna.commons.launcher.Flux.main(Flux.java:197) java.lang.RuntimeException: net.sf.samtools.SAMException: Value for tag XT is not a Character: class java.lang.String at barna.flux.capacitor.profile.BiasProfiler.profile(BiasProfiler.java:252) at barna.flux.capacitor.profile.BiasProfiler.call(BiasProfiler.java:101) at barna.flux.capacitor.reconstruction.FluxCapacitor.getProfile(FluxCapacitor.java:2196) at barna.flux.capacitor.reconstruction.FluxCapacitor.call(FluxCapacitor.java:1878) at barna.flux.capacitor.reconstruction.FluxCapacitor.call(FluxCapacitor.java:74) at barna.commons.launcher.Flux.main(Flux.java:197) Caused by: net.sf.samtools.SAMException: Value for tag XT is not a Character: class java.lang.String at net.sf.samtools.SAMRecord.getCharacterAttribute(SAMRecord.java:975) at barna.model.sam.SAMMapping.(SAMMapping.java:51) at barna.model.sam.SAMMapping.(SAMMapping.java:60) at barna.io.sam.SAMMappingIterator.init(SAMMappingIterator.java:86) at barna.io.sam.SAMMappingIterator.(SAMMappingIterator.java:70) at barna.io.sam.SAMReader.read(SAMReader.java:227) at barna.flux.capacitor.profile.BiasProfiler.profile(BiasProfiler.java:205) ... 5 more [FATAL] Error occured during scanning net.sf.samtools.SAMException: Value for tag XT is not a Character: class java.lang.String first round finished .. took 0 sec. 0 single transcript loci 17955910 mappings in file 0 mappings fall in single transcript loci 0 mappings in annotation-mapped pairs 0,0 min/max read length [SOLVE] Deconvolving reads of overlapping transcripts. decomposing [ERROR] Error while iterating loci: net.sf.samtools.SAMException: Value for tag XT is not a Character: class java.lang.String at net.sf.samtools.SAMRecord.getCharacterAttribute(SAMRecord.java:975) at barna.model.sam.SAMMapping.(SAMMapping.java:51) at barna.model.sam.SAMMapping.(SAMMapping.java:60) at barna.io.sam.SAMMappingIterator.init(SAMMappingIterator.java:86) at barna.io.sam.SAMMappingIterator.(SAMMappingIterator.java:70) at barna.io.sam.SAMReader.read(SAMReader.java:227) at barna.flux.capacitor.reconstruction.FluxCapacitor.explore(FluxCapacitor.java:2625) at barna.flux.capacitor.reconstruction.FluxCapacitor.call(FluxCapacitor.java:1886) at barna.flux.capacitor.reconstruction.FluxCapacitor.call(FluxCapacitor.java:74) at barna.commons.launcher.Flux.main(Flux.java:197) [ERROR] net.sf.samtools.SAMException: Value for tag XT is not a Character: class java.lang.String java.lang.RuntimeException: net.sf.samtools.SAMException: Value for tag XT is not a Character: class java.lang.String at barna.flux.capacitor.reconstruction.FluxCapacitor.explore(FluxCapacitor.java:2680) at barna.flux.capacitor.reconstruction.FluxCapacitor.call(FluxCapacitor.java:1886) at barna.flux.capacitor.reconstruction.FluxCapacitor.call(FluxCapacitor.java:74) at barna.commons.launcher.Flux.main(Flux.java:197) Caused by: net.sf.samtools.SAMException: Value for tag XT is not a Character: class java.lang.String at net.sf.samtools.SAMRecord.getCharacterAttribute(SAMRecord.java:975) at barna.model.sam.SAMMapping.(SAMMapping.java:51) at barna.model.sam.SAMMapping.(SAMMapping.java:60) at barna.io.sam.SAMMappingIterator.init(SAMMappingIterator.java:86) at barna.io.sam.SAMMappingIterator.(SAMMappingIterator.java:70) at barna.io.sam.SAMReader.read(SAMReader.java:227) at barna.flux.capacitor.reconstruction.FluxCapacitor.explore(FluxCapacitor.java:2625) ... 3 more