Hello everyone!
I've been trying to run both CICERO and RNApeg with the refence files provided.
I've aligned my reads with ensembl primary assembly (hg38) FASTA file and GTF file, the most updated version up to january/2021
But then I getting the following error:
[root@tcg gabriel.gama]# docker run -v /home/Análises/Teste1/RNAPEG/trueseq:/results -v /home/gabriel.gama:/data ghcr.io/stjude/rnapeg:latest -b /data/Análises/Teste1/star/all_samples_ensembl_chimericwithinbam/99_FRAS202421989-1a_1.fqAligned.sortedByCoord.out.bam -f /data/references/cicero/reference/Homo_sapiens/GRCh38_no_alt/FASTA/GRCh38_no_alt.fa -r /data/references/cicero/reference/Homo_sapiens/GRCh38_no_alt/mRNA/RefSeq/refFlat.txt set REFGENE to default /data/references/cicero/reference/Homo_sapiens/GRCh38_no_alt/mRNA/RefSeq/refFlat.txt [*] Running junction_extraction_wrapper.pl Tue Nov 30 20:48:45 2021: running: bam_junction.pl -type all -bam /data/Análises/Teste1/star/all_samples_ensembl_chimericwithinbam/99_FRAS202421989-1a_1.fqAligned.sortedByCoord.out.bam -annotate -now -force 1 -out 99_FRAS202421989-1a_1.fqAligned.sortedByCoord.out.bam.junctions.tab -no-config -refflat /data/references/cicero/reference/Homo_sapiens/GRCh38_no_alt/mRNA/RefSeq/refFlat.txt -fasta /data/references/cicero/reference/Homo_sapiens/GRCh38_no_alt/FASTA/GRCh38_no_alt.fa /usr/bin/env java -Xmx5g org.stjude.compbio.rnapeg.SplicedReadReporter -bam /data/Análises/Teste1/star/all_samples_ensembl_chimericwithinbam/99_FRAS202421989-1a_1.fqAligned.sortedByCoord.out.bam -of 99_FRAS202421989-1a_1.fqAligned.sortedByCoord.out.bam.junctions.tab -refflat /data/references/cicero/reference/Homo_sapiens/GRCh38_no_alt/mRNA/RefSeq/refFlat.txt -fasta /data/references/cicero/reference/Homo_sapiens/GRCh38_no_alt/FASTA/GRCh38_no_alt.fa -annotate intron cache: chr16_KI270854v1_alt: 22 chr19_KI270915v1_alt: 93 chr12_GL877875v1_alt: 36 chr21: 2809 chr6_GL000255v2_alt: 1567 chr22: 5237 chrUn_GL000224v1: 2 chr6_KI270801v1_alt: 56 chr20: 6091 chr8_KI270812v1_alt: 1 chr3_KI270780v1_alt: 5 chr11_KI270903v1_alt: 15 chr20_KI270870v1_alt: 29 chr19_GL949753v2_alt: 338 chr3_KI270779v1_alt: 96 chr5_KI270791v1_alt: 43 chr2_KI270767v1_alt: 12 chr22_KI270879v1_alt: 101 chr10: 10500 chr11: 13005 chrX_KI270881v1_alt: 10 chr16_GL383557v1_alt: 11 chr17_KI270909v1_alt: 80 chr12: 13602 chr13: 4738 chr17_JH159148v1_alt: 5 chr12_KI270837v1_alt: 8 chr18: 3804 chr19: 13382 chr6_GL000250v2_alt: 658 chr14: 7276 chr15: 9088 chr16: 10275 chr15_KI270905v1_alt: 508 chr17: 13711 chrUn_KI270753v1: 3 chr7_KI270899v1_alt: 8 chr19_KI270930v1_alt: 103 chr4_GL383527v1_alt: 25 chr17_KI270861v1_alt: 111 chr19_KI270885v1_alt: 93 chr18_KI270911v1_alt: 2 chr5_GL339449v2_alt: 245 chr2_KI270773v1_alt: 5 chrX_KI270880v1_alt: 13 chr19_GL949747v2_alt: 336 chr3_KI270935v1_alt: 108 chr5_KI270796v1_alt: 1 chr9_GL383541v1_alt: 14 chr15_KI270906v1_alt: 28 chrUn_KI270741v1: 4 chr12_GL877876v1_alt: 19 chr8_KI270817v1_alt: 20 chr6_GL000254v2_alt: 1494 chr15_KI270848v1_alt: 88 chr4_KI270786v1_alt: 2 chrUn_GL000213v1: 10 chr19_KI270914v1_alt: 91 chr5_GL949742v1_alt: 12 chr19_KI270884v1_alt: 81 chr17_KI270860v1_alt: 36 chr21_GL383579v2_alt: 4 chr4_KI270896v1_alt: 16 chr8_KI270811v1_alt: 2 chr8_KI270818v1_alt: 1 chr15_GL383555v2_alt: 19 chr20_KI270869v1_alt: 17 chr3_KI270934v1_alt: 74 chr2_KI270774v1_alt: 19 chr11_JH159136v1_alt: 1 chr13_KI270838v1_alt: 23 chr15_KI270849v1_alt: 24 chr22_KI270875v1_alt: 19 chr1_KI270759v1_alt: 12 chr4_KI270925v1_alt: 4 chr12_KI270833v1_alt: 20 chr14_KI270847v1_alt: 244 chr19_KI270919v1_alt: 94 chr11_KI270831v1_alt: 71 chr3_KI270777v1_alt: 20 chr19_KI270866v1_alt: 10 chr2_KI270768v1_alt: 11 chr19_KI270921v1_alt: 149 chr12_GL383550v2_alt: 12 chr19_KI270886v1_alt: 102 chr21_GL383580v2_alt: 9 chr19_GL949746v1_alt: 428 chr17_GL383563v3_alt: 25 chr1_KI270763v1_alt: 79 chr8_KI270816v1_alt: 179 chr5_KI270793v1_alt: 2 chr19_KI270889v1_alt: 93 chr19_GL000209v2_alt: 96 chr3_KI270936v1_alt: 74 chr10_KI270825v1_alt: 31 chr7_GL383534v2_alt: 42 chr19_KI270890v1_alt: 103 chr8_KI270821v1_alt: 85 chr21_KI270873v1_alt: 3 chr6_KI270797v1_alt: 27 chr6_GL000256v2_alt: 1426 chr2_GL383521v1_alt: 1 chr1_GL383520v2_alt: 22 chr19_GL949748v2_alt: 237 chr7_KI270804v1_alt: 8 chr3_KI270781v1_alt: 1 chr15_GL383554v1_alt: 60 chr8_KI270813v1_alt: 28 chr15_KI270727v1_random: 17 chr19_KI270865v1_alt: 31 chr19_KI270917v1_alt: 102 chr19_KI270888v1_alt: 79 chr5_KI270897v1_alt: 158 chr10_GL383546v1_alt: 27 chr19_KI270923v1_alt: 86 chr22_KI270877v1_alt: 14 chr19_KI270891v1_alt: 93 chr12_KI270835v1_alt: 52 chr3_GL383526v1_alt: 7 chr19_KI270916v1_alt: 105 chr22_KB663609v1_alt: 32 chr2_KI270770v1_alt: 2 chr8_KI270814v1_alt: 14 chr17_KI270910v1_alt: 26 chr3_KI270937v1_alt: 77 chr2_GL383522v1_alt: 29 chr11_KI270827v1_alt: 1 chr19_GL949752v1_alt: 462 chr19_KI270887v1_alt: 109 chr19_KI270922v1_alt: 104 chr20_KI270871v1_alt: 6 chr9_KI270823v1_alt: 10 chr10_GL383545v1_alt: 4 chr11_KI270832v1_alt: 127 chr7_KI270806v1_alt: 29 chr21_GL383581v2_alt: 22 chr5_KI270792v1_alt: 36 chr6_KI270802v1_alt: 4 chr1_KI270762v1_alt: 103 chr22_KI270878v1_alt: 24 chr7_KI270803v1_alt: 178 chr8_KI270815v1_alt: 4 chr9: 9769 chr19_GL949749v2_alt: 234 chr7: 11845 chr3_KI270783v1_alt: 4 chr8: 8584 chr5: 10980 chr6_KI270799v1_alt: 2 chr6: 12073 chr3: 14739 chr8_KI270900v1_alt: 14 chr4: 9486 chr1: 24620 chr2: 18571 chrUn_GL000220v1: 6 chr5_KI270794v1_alt: 4 chr8_KI270822v1_alt: 82 chr11_KI270830v1_alt: 23 chr6_GL000252v2_alt: 1561 chr21_KI270872v1_alt: 32 chr11_KI270721v1_random: 12 chr3_KI270924v1_alt: 85 chr14_KI270846v1_alt: 11 chr1_GL383519v1_alt: 90 chr5_KI270898v1_alt: 10 chr19_KI270918v1_alt: 72 chr19_KI270932v1_alt: 103 chr19_KI270938v1_alt: 497 chr22_KI270876v1_alt: 24 chr19_GL949750v2_alt: 218 chr12_KI270834v1_alt: 60 chr19_KI270882v1_alt: 118 chr4_KI270790v1_alt: 3 chr15_KI270852v1_alt: 30 chr22_GL383583v2_alt: 8 chr14_GL000194v1_random: 9 chr8_KI270926v1_alt: 14 chr14_KI270845v1_alt: 10 chr16_KI270728v1_random: 34 chr7_KI270808v1_alt: 5 chr19_KI270920v1_alt: 105 chr1_GL383518v1_alt: 52 chr18_KI270863v1_alt: 17 chr11_KI270829v1_alt: 8 chr8_KI270810v1_alt: 3 chr17_GL383566v1_alt: 2 chr6_KI270758v1_alt: 14 chr19_KI270868v1_alt: 25 chrUn_GL000218v1: 4 chr17_GL000258v2_alt: 176 chr6_KI270798v1_alt: 24 chr22_GL383582v2_alt: 31 chr7_KI270809v1_alt: 23 chrY: 1017 chr13_KI270842v1_alt: 2 chr3_KI270782v1_alt: 8 chr1_KI270765v1_alt: 3 chrX: 8331 chr17_KI270907v1_alt: 8 chr19_GL949751v2_alt: 256 chr22_KI270928v1_alt: 41 chr19_KI270867v1_alt: 24 chr2_KI270769v1_alt: 10 chr5_KI270795v1_alt: 8 chrUn_GL000195v1: 6 chr16_GL383556v1_alt: 30 chr19_KI270883v1_alt: 94 chr17_GL383564v2_alt: 38 chr6_GL000251v2_alt: 1657 chr17_KI270908v1_alt: 168 chrUn_GL000219v1: 6 chr4_KI270789v1_alt: 3 chr19_KI270929v1_alt: 96 chr3_KI270895v1_alt: 74 chr19_KI270931v1_alt: 95 chr1_KI270766v1_alt: 25 chr17_KI270862v1_alt: 39 chr2_KI270893v1_alt: 12 chr3_JH636055v2_alt: 10 chr19_GL383576v1_alt: 2 chr16_KI270853v1_alt: 504 chr14_KI270844v1_alt: 39 chr18_GL383572v1_alt: 2 chr3_KI270784v1_alt: 26 chr22_KI270731v1_random: 12 chr8_KI270819v1_alt: 21 chr12_KI270904v1_alt: 32 chr11_KI270927v1_alt: 108 chr13_KI270840v1_alt: 23 chr18_GL383567v1_alt: 7 chr16_KI270856v1_alt: 4 chr9_GL383540v1_alt: 10 chr19_GL383575v2_alt: 9 chr6_GL000253v2_alt: 1227 chr19_KI270933v1_alt: 94 chr15_KI270850v1_alt: 100 chr2_KI270776v1_alt: 20 chr2_GL582966v2_alt: 25 chr12_GL383553v2_alt: 19 chr16_KI270855v1_alt: 97 chrX_KI270913v1_alt: 12 chr17_KI270857v1_alt: 587 chr17_JH159146v1_alt: 47 chr18_GL383571v1_alt: 1 chr19_GL383573v1_alt: 13 chr15_KI270851v1_alt: 87 chr22_KI270734v1_random: 22 chr4_GL000008v2_random: 4 chr17_JH159147v1_alt: 11 chr4_GL000257v2_alt: 49 chr1_KI270713v1_random: 11 chr19_GL383574v1_alt: 11 chr11_KI270902v1_alt: 55 total=266245 flatfile db load: 1062 ms checking BAM/reference compatibility...reference sequence names: [chr9_KI270719v1_random, chrUn_KI270509v1, chr21, chr22, chrUn_GL000224v1, chrUn_KI270317v1, chr2_KI270715v1_random, chr20, chrUn_KI270305v1, chrUn_KI270320v1, chrUn_KI270366v1, chrUn_KI270389v1, chrUn_KI270512v1, chrUn_KI270742v1, chrUn_KI270438v1, chrUn_KI270381v1, chrUn_KI270414v1, chr10, chr14_GL000009v2_random, chr11, chr12, chr13, chr18, chr19, chrUn_KI270316v1, chr14, chr15, chr14_KI270722v1_random, chr16, chr17, chrUn_KI270753v1, chr1_KI270710v1_random, chr22_KI270736v1_random, chrUn_KI270392v1, chrUn_KI270442v1, chrUn_KI270465v1, chrUn_KI270548v1, chr17_KI270729v1_random, chrUn_KI270382v1, chrUn_KI270741v1, chrUn_KI270749v1, chrUn_GL000213v1, chrUn_KI270329v1, chrUn_KI270378v1, chrUn_KI270393v1, chrUn_KI270752v1, chr22_KI270732v1_random, chrUn_KI270507v1, chrUn_KI270424v1, chrUn_GL000226v1, chr1_KI270712v1_random, chrUn_KI270510v1, chrUn_KI270579v1, chrUn_KI270303v1, chrUn_KI270364v1, chrUn_KI270387v1, chr17_KI270730v1_random, chrUn_KI270744v1, chr1_KI270711v1_random, chr9_KI270720v1_random, chr1_KI270708v1_random, chrUn_KI270412v1, chrUn_KI270435v1, chrUn_GL000214v1, chrUn_KI270519v1, chr1_KI270709v1_random, chrUn_KI270337v1, chrUn_KI270522v1, chrUn_KI270375v1, chrUn_KI270755v1, chrUn_KI270583v1, chrUn_KI270390v1, chr15_KI270727v1_random, chr14_KI270724v1_random, chrUn_KI270508v1, chrUn_KI270425v1, chrUn_KI270448v1, chrUn_KI270511v1, chrUn_KI270304v1, chrUn_KI270388v1, chrUn_GL000216v2, chrUn_KI270743v1, chr9_KI270717v1_random, chr22_KI270739v1_random, chrUn_KI270584v1, chrUn_KI270338v1, chrUn_KI270315v1, chrUn_KI270376v1, chrUn_KI270330v1, chrUn_KI270754v1, chrUn_KI270391v1, chrUn_KI270422v1, chrUn_KI270468v1, chr9, chr22_KI270735v1_random, chr7, chr8, chr5, chr6, chr3, chr4, chr1, chrUn_KI270528v1, chr2, chrUn_GL000220v1, chrUn_KI270362v1, chrUn_KI270385v1, chrUn_KI270419v1, chr11_KI270721v1_random, chr1_KI270714v1_random, chrUn_KI270746v1, chr14_KI270723v1_random, chrUn_KI270517v1, chrUn_KI270312v1, chrUn_KI270335v1, chr5_GL000208v1_random, chrUn_KI270589v1, chrUn_KI270396v1, chrUn_KI270373v1, chr14_GL000194v1_random, chrUn_KI270581v1, chr3_GL000221v1_random, chr16_KI270728v1_random, chrUn_KI270423v1, chrUn_KI270757v1, chrUn_KI270529v1, chrEBV, chr9_KI270718v1_random, chrUn_GL000218v1, chrUn_KI270302v1, chrUn_KI270386v1, chrUn_KI270363v1, chrUn_KI270745v1, chrUn_KI270340v1, chrUn_KI270593v1, chrUn_KI270411v1, chrY, chrX, chr2_KI270716v1_random, chrY_KI270740v1_random, chrUn_KI270518v1, chrM, chr1_KI270706v1_random, chrUn_KI270336v1, chr14_KI270725v1_random, chrUn_KI270521v1, chrUn_KI270544v1, chrUn_KI270374v1, chrUn_KI270756v1, chrUn_GL000195v1, chr22_KI270733v1_random, chrUn_KI270582v1, chr22_KI270738v1_random, chrUn_KI270420v1, chrUn_KI270466v1, chrUn_GL000219v1, chrUn_KI270322v1, chrUn_KI270590v1, chrUn_KI270383v1, chrUn_KI270417v1, chrUn_KI270748v1, chr14_GL000225v1_random, chrUn_KI270515v1, chrUn_KI270538v1, chr22_KI270731v1_random, chrUn_KI270587v1, chrUn_KI270310v1, chrUn_KI270379v1, chrUn_KI270333v1, chrUn_KI270394v1, chrUn_KI270371v1, chrUn_KI270751v1, chrUn_KI270467v1, chr1_KI270707v1_random, chrUn_KI270530v1, chr17_GL000205v2_random, chrUn_KI270418v1, chrUn_KI270384v1, chr22_KI270737v1_random, chrUn_KI270591v1, chrUn_KI270747v1, chrUn_KI270516v1, chr22_KI270734v1_random, chr4_GL000008v2_random, chr14_KI270726v1_random, chrUn_KI270539v1, chrUn_KI270311v1, chr1_KI270713v1_random, chrUn_KI270588v1, chrUn_KI270334v1, chrUn_KI270429v1, chrUn_KI270395v1, chrUn_KI270372v1, chrUn_KI270580v1, chrUn_KI270750v1] raw=1 ref_name_bam:1 ref_name_ref:chr1 raw=10 ref_name_bam:10 ref_name_ref:chr10 raw=11 ref_name_bam:11 ref_name_ref:chr11 raw=12 ref_name_bam:12 ref_name_ref:chr12 raw=13 ref_name_bam:13 ref_name_ref:chr13 raw=14 ref_name_bam:14 ref_name_ref:chr14 raw=15 ref_name_bam:15 ref_name_ref:chr15 raw=16 ref_name_bam:16 ref_name_ref:chr16 raw=17 ref_name_bam:17 ref_name_ref:chr17 raw=18 ref_name_bam:18 ref_name_ref:chr18 raw=19 ref_name_bam:19 ref_name_ref:chr19 raw=2 ref_name_bam:2 ref_name_ref:chr2 raw=20 ref_name_bam:20 ref_name_ref:chr20 raw=21 ref_name_bam:21 ref_name_ref:chr21 raw=22 ref_name_bam:22 ref_name_ref:chr22 raw=3 ref_name_bam:3 ref_name_ref:chr3 raw=4 ref_name_bam:4 ref_name_ref:chr4 raw=5 ref_name_bam:5 ref_name_ref:chr5 raw=6 ref_name_bam:6 ref_name_ref:chr6 raw=7 ref_name_bam:7 ref_name_ref:chr7 raw=8 ref_name_bam:8 ref_name_ref:chr8 raw=9 ref_name_bam:9 ref_name_ref:chr9 raw=MT ref_name_bam:MT ref_name_ref:chrM raw=X ref_name_bam:X ref_name_ref:chrX raw=Y ref_name_bam:Y ref_name_ref:chrY raw=KI270728.1 ref_name_bam:KI270728.1 ref_name_ref:null raw=KI270727.1 ref_name_bam:KI270727.1 ref_name_ref:null raw=KI270442.1 ref_name_bam:KI270442.1 ref_name_ref:null raw=KI270729.1 ref_name_bam:KI270729.1 ref_name_ref:null raw=GL000225.1 ref_name_bam:GL000225.1 ref_name_ref:null raw=KI270743.1 ref_name_bam:KI270743.1 ref_name_ref:null raw=GL000008.2 ref_name_bam:GL000008.2 ref_name_ref:null raw=GL000009.2 ref_name_bam:GL000009.2 ref_name_ref:null raw=KI270747.1 ref_name_bam:KI270747.1 ref_name_ref:null raw=KI270722.1 ref_name_bam:KI270722.1 ref_name_ref:null raw=GL000194.1 ref_name_bam:GL000194.1 ref_name_ref:null raw=KI270742.1 ref_name_bam:KI270742.1 ref_name_ref:null raw=GL000205.2 ref_name_bam:GL000205.2 ref_name_ref:null raw=GL000195.1 ref_name_bam:GL000195.1 ref_name_ref:null raw=KI270736.1 ref_name_bam:KI270736.1 ref_name_ref:null raw=KI270733.1 ref_name_bam:KI270733.1 ref_name_ref:null raw=GL000224.1 ref_name_bam:GL000224.1 ref_name_ref:null raw=GL000219.1 ref_name_bam:GL000219.1 ref_name_ref:null raw=KI270719.1 ref_name_bam:KI270719.1 ref_name_ref:null raw=GL000216.2 ref_name_bam:GL000216.2 ref_name_ref:null raw=KI270712.1 ref_name_bam:KI270712.1 ref_name_ref:null raw=KI270706.1 ref_name_bam:KI270706.1 ref_name_ref:null raw=KI270725.1 ref_name_bam:KI270725.1 ref_name_ref:null raw=KI270744.1 ref_name_bam:KI270744.1 ref_name_ref:null raw=KI270734.1 ref_name_bam:KI270734.1 ref_name_ref:null raw=GL000213.1 ref_name_bam:GL000213.1 ref_name_ref:null raw=GL000220.1 ref_name_bam:GL000220.1 ref_name_ref:null raw=KI270715.1 ref_name_bam:KI270715.1 ref_name_ref:null raw=GL000218.1 ref_name_bam:GL000218.1 ref_name_ref:null raw=KI270749.1 ref_name_bam:KI270749.1 ref_name_ref:null raw=KI270741.1 ref_name_bam:KI270741.1 ref_name_ref:null raw=GL000221.1 ref_name_bam:GL000221.1 ref_name_ref:null raw=KI270716.1 ref_name_bam:KI270716.1 ref_name_ref:null raw=KI270731.1 ref_name_bam:KI270731.1 ref_name_ref:null raw=KI270751.1 ref_name_bam:KI270751.1 ref_name_ref:null raw=KI270750.1 ref_name_bam:KI270750.1 ref_name_ref:null raw=KI270519.1 ref_name_bam:KI270519.1 ref_name_ref:null raw=GL000214.1 ref_name_bam:GL000214.1 ref_name_ref:null raw=KI270708.1 ref_name_bam:KI270708.1 ref_name_ref:null raw=KI270730.1 ref_name_bam:KI270730.1 ref_name_ref:null raw=KI270438.1 ref_name_bam:KI270438.1 ref_name_ref:null raw=KI270737.1 ref_name_bam:KI270737.1 ref_name_ref:null raw=KI270721.1 ref_name_bam:KI270721.1 ref_name_ref:null raw=KI270738.1 ref_name_bam:KI270738.1 ref_name_ref:null raw=KI270748.1 ref_name_bam:KI270748.1 ref_name_ref:null raw=KI270435.1 ref_name_bam:KI270435.1 ref_name_ref:null raw=GL000208.1 ref_name_bam:GL000208.1 ref_name_ref:null raw=KI270538.1 ref_name_bam:KI270538.1 ref_name_ref:null raw=KI270756.1 ref_name_bam:KI270756.1 ref_name_ref:null raw=KI270739.1 ref_name_bam:KI270739.1 ref_name_ref:null raw=KI270757.1 ref_name_bam:KI270757.1 ref_name_ref:null raw=KI270709.1 ref_name_bam:KI270709.1 ref_name_ref:null raw=KI270746.1 ref_name_bam:KI270746.1 ref_name_ref:null raw=KI270753.1 ref_name_bam:KI270753.1 ref_name_ref:null raw=KI270589.1 ref_name_bam:KI270589.1 ref_name_ref:null raw=KI270726.1 ref_name_bam:KI270726.1 ref_name_ref:null raw=KI270735.1 ref_name_bam:KI270735.1 ref_name_ref:null raw=KI270711.1 ref_name_bam:KI270711.1 ref_name_ref:null raw=KI270745.1 ref_name_bam:KI270745.1 ref_name_ref:null raw=KI270714.1 ref_name_bam:KI270714.1 ref_name_ref:null raw=KI270732.1 ref_name_bam:KI270732.1 ref_name_ref:null raw=KI270713.1 ref_name_bam:KI270713.1 ref_name_ref:null raw=KI270754.1 ref_name_bam:KI270754.1 ref_name_ref:null raw=KI270710.1 ref_name_bam:KI270710.1 ref_name_ref:null raw=KI270717.1 ref_name_bam:KI270717.1 ref_name_ref:null raw=KI270724.1 ref_name_bam:KI270724.1 ref_name_ref:null raw=KI270720.1 ref_name_bam:KI270720.1 ref_name_ref:null raw=KI270723.1 ref_name_bam:KI270723.1 ref_name_ref:null raw=KI270718.1 ref_name_bam:KI270718.1 ref_name_ref:null raw=KI270317.1 ref_name_bam:KI270317.1 ref_name_ref:null raw=KI270740.1 ref_name_bam:KI270740.1 ref_name_ref:null raw=KI270755.1 ref_name_bam:KI270755.1 ref_name_ref:null raw=KI270707.1 ref_name_bam:KI270707.1 ref_name_ref:null raw=KI270579.1 ref_name_bam:KI270579.1 ref_name_ref:null raw=KI270752.1 ref_name_bam:KI270752.1 ref_name_ref:null raw=KI270512.1 ref_name_bam:KI270512.1 ref_name_ref:null raw=KI270322.1 ref_name_bam:KI270322.1 ref_name_ref:null raw=GL000226.1 ref_name_bam:GL000226.1 ref_name_ref:null raw=KI270311.1 ref_name_bam:KI270311.1 ref_name_ref:null raw=KI270366.1 ref_name_bam:KI270366.1 ref_name_ref:null raw=KI270511.1 ref_name_bam:KI270511.1 ref_name_ref:null raw=KI270448.1 ref_name_bam:KI270448.1 ref_name_ref:null raw=KI270521.1 ref_name_bam:KI270521.1 ref_name_ref:null raw=KI270581.1 ref_name_bam:KI270581.1 ref_name_ref:null raw=KI270582.1 ref_name_bam:KI270582.1 ref_name_ref:null raw=KI270515.1 ref_name_bam:KI270515.1 ref_name_ref:null raw=KI270588.1 ref_name_bam:KI270588.1 ref_name_ref:null raw=KI270591.1 ref_name_bam:KI270591.1 ref_name_ref:null raw=KI270522.1 ref_name_bam:KI270522.1 ref_name_ref:null raw=KI270507.1 ref_name_bam:KI270507.1 ref_name_ref:null raw=KI270590.1 ref_name_bam:KI270590.1 ref_name_ref:null raw=KI270584.1 ref_name_bam:KI270584.1 ref_name_ref:null raw=KI270320.1 ref_name_bam:KI270320.1 ref_name_ref:null raw=KI270382.1 ref_name_bam:KI270382.1 ref_name_ref:null raw=KI270468.1 ref_name_bam:KI270468.1 ref_name_ref:null raw=KI270467.1 ref_name_bam:KI270467.1 ref_name_ref:null raw=KI270362.1 ref_name_bam:KI270362.1 ref_name_ref:null raw=KI270517.1 ref_name_bam:KI270517.1 ref_name_ref:null raw=KI270593.1 ref_name_bam:KI270593.1 ref_name_ref:null raw=KI270528.1 ref_name_bam:KI270528.1 ref_name_ref:null raw=KI270587.1 ref_name_bam:KI270587.1 ref_name_ref:null raw=KI270364.1 ref_name_bam:KI270364.1 ref_name_ref:null raw=KI270371.1 ref_name_bam:KI270371.1 ref_name_ref:null raw=KI270333.1 ref_name_bam:KI270333.1 ref_name_ref:null raw=KI270374.1 ref_name_bam:KI270374.1 ref_name_ref:null raw=KI270411.1 ref_name_bam:KI270411.1 ref_name_ref:null raw=KI270414.1 ref_name_bam:KI270414.1 ref_name_ref:null raw=KI270510.1 ref_name_bam:KI270510.1 ref_name_ref:null raw=KI270390.1 ref_name_bam:KI270390.1 ref_name_ref:null raw=KI270375.1 ref_name_bam:KI270375.1 ref_name_ref:null raw=KI270420.1 ref_name_bam:KI270420.1 ref_name_ref:null raw=KI270509.1 ref_name_bam:KI270509.1 ref_name_ref:null raw=KI270315.1 ref_name_bam:KI270315.1 ref_name_ref:null raw=KI270302.1 ref_name_bam:KI270302.1 ref_name_ref:null raw=KI270518.1 ref_name_bam:KI270518.1 ref_name_ref:null raw=KI270530.1 ref_name_bam:KI270530.1 ref_name_ref:null raw=KI270304.1 ref_name_bam:KI270304.1 ref_name_ref:null raw=KI270418.1 ref_name_bam:KI270418.1 ref_name_ref:null raw=KI270424.1 ref_name_bam:KI270424.1 ref_name_ref:null raw=KI270417.1 ref_name_bam:KI270417.1 ref_name_ref:null raw=KI270508.1 ref_name_bam:KI270508.1 ref_name_ref:null raw=KI270303.1 ref_name_bam:KI270303.1 ref_name_ref:null raw=KI270381.1 ref_name_bam:KI270381.1 ref_name_ref:null raw=KI270529.1 ref_name_bam:KI270529.1 ref_name_ref:null raw=KI270425.1 ref_name_bam:KI270425.1 ref_name_ref:null raw=KI270396.1 ref_name_bam:KI270396.1 ref_name_ref:null raw=KI270363.1 ref_name_bam:KI270363.1 ref_name_ref:null raw=KI270386.1 ref_name_bam:KI270386.1 ref_name_ref:null raw=KI270465.1 ref_name_bam:KI270465.1 ref_name_ref:null raw=KI270383.1 ref_name_bam:KI270383.1 ref_name_ref:null raw=KI270384.1 ref_name_bam:KI270384.1 ref_name_ref:null raw=KI270330.1 ref_name_bam:KI270330.1 ref_name_ref:null raw=KI270372.1 ref_name_bam:KI270372.1 ref_name_ref:null raw=KI270548.1 ref_name_bam:KI270548.1 ref_name_ref:null raw=KI270580.1 ref_name_bam:KI270580.1 ref_name_ref:null raw=KI270387.1 ref_name_bam:KI270387.1 ref_name_ref:null raw=KI270391.1 ref_name_bam:KI270391.1 ref_name_ref:null raw=KI270305.1 ref_name_bam:KI270305.1 ref_name_ref:null raw=KI270373.1 ref_name_bam:KI270373.1 ref_name_ref:null raw=KI270422.1 ref_name_bam:KI270422.1 ref_name_ref:null raw=KI270316.1 ref_name_bam:KI270316.1 ref_name_ref:null raw=KI270340.1 ref_name_bam:KI270340.1 ref_name_ref:null raw=KI270338.1 ref_name_bam:KI270338.1 ref_name_ref:null raw=KI270583.1 ref_name_bam:KI270583.1 ref_name_ref:null raw=KI270334.1 ref_name_bam:KI270334.1 ref_name_ref:null raw=KI270429.1 ref_name_bam:KI270429.1 ref_name_ref:null raw=KI270393.1 ref_name_bam:KI270393.1 ref_name_ref:null raw=KI270516.1 ref_name_bam:KI270516.1 ref_name_ref:null raw=KI270389.1 ref_name_bam:KI270389.1 ref_name_ref:null raw=KI270466.1 ref_name_bam:KI270466.1 ref_name_ref:null raw=KI270388.1 ref_name_bam:KI270388.1 ref_name_ref:null raw=KI270544.1 ref_name_bam:KI270544.1 ref_name_ref:null raw=KI270310.1 ref_name_bam:KI270310.1 ref_name_ref:null raw=KI270412.1 ref_name_bam:KI270412.1 ref_name_ref:null raw=KI270395.1 ref_name_bam:KI270395.1 ref_name_ref:null raw=KI270376.1 ref_name_bam:KI270376.1 ref_name_ref:null raw=KI270337.1 ref_name_bam:KI270337.1 ref_name_ref:null raw=KI270335.1 ref_name_bam:KI270335.1 ref_name_ref:null raw=KI270378.1 ref_name_bam:KI270378.1 ref_name_ref:null raw=KI270379.1 ref_name_bam:KI270379.1 ref_name_ref:null raw=KI270329.1 ref_name_bam:KI270329.1 ref_name_ref:null raw=KI270419.1 ref_name_bam:KI270419.1 ref_name_ref:null raw=KI270336.1 ref_name_bam:KI270336.1 ref_name_ref:null raw=KI270312.1 ref_name_bam:KI270312.1 ref_name_ref:null raw=KI270539.1 ref_name_bam:KI270539.1 ref_name_ref:null raw=KI270385.1 ref_name_bam:KI270385.1 ref_name_ref:null raw=KI270423.1 ref_name_bam:KI270423.1 ref_name_ref:null raw=KI270392.1 ref_name_bam:KI270392.1 ref_name_ref:null raw=KI270394.1 ref_name_bam:KI270394.1 ref_name_ref:null done ERROR: no local reference sequence found for BAM reference name KI270728.1 ERROR: no local reference sequence found for BAM reference name KI270727.1 ERROR: no local reference sequence found for BAM reference name KI270442.1 ERROR: no local reference sequence found for BAM reference name KI270729.1 ERROR: no local reference sequence found for BAM reference name GL000225.1 ERROR: no local reference sequence found for BAM reference name KI270743.1 ERROR: no local reference sequence found for BAM reference name GL000008.2 ERROR: no local reference sequence found for BAM reference name GL000009.2 ERROR: no local reference sequence found for BAM reference name KI270747.1 ERROR: no local reference sequence found for BAM reference name KI270722.1 ERROR: no local reference sequence found for BAM reference name GL000194.1 ERROR: no local reference sequence found for BAM reference name KI270742.1 ERROR: no local reference sequence found for BAM reference name GL000205.2 ERROR: no local reference sequence found for BAM reference name GL000195.1 ERROR: no local reference sequence found for BAM reference name KI270736.1 ERROR: no local reference sequence found for BAM reference name KI270733.1 ERROR: no local reference sequence found for BAM reference name GL000224.1 ERROR: no local reference sequence found for BAM reference name GL000219.1 ERROR: no local reference sequence found for BAM reference name KI270719.1 ERROR: no local reference sequence found for BAM reference name GL000216.2 ERROR: no local reference sequence found for BAM reference name KI270712.1 ERROR: no local reference sequence found for BAM reference name KI270706.1 ERROR: no local reference sequence found for BAM reference name KI270725.1 ERROR: no local reference sequence found for BAM reference name KI270744.1 ERROR: no local reference sequence found for BAM reference name KI270734.1 ERROR: no local reference sequence found for BAM reference name GL000213.1 ERROR: no local reference sequence found for BAM reference name GL000220.1 ERROR: no local reference sequence found for BAM reference name KI270715.1 ERROR: no local reference sequence found for BAM reference name GL000218.1 ERROR: no local reference sequence found for BAM reference name KI270749.1 ERROR: no local reference sequence found for BAM reference name KI270741.1 ERROR: no local reference sequence found for BAM reference name GL000221.1 ERROR: no local reference sequence found for BAM reference name KI270716.1 ERROR: no local reference sequence found for BAM reference name KI270731.1 ERROR: no local reference sequence found for BAM reference name KI270751.1 ERROR: no local reference sequence found for BAM reference name KI270750.1 ERROR: no local reference sequence found for BAM reference name KI270519.1 ERROR: no local reference sequence found for BAM reference name GL000214.1 ERROR: no local reference sequence found for BAM reference name KI270708.1 ERROR: no local reference sequence found for BAM reference name KI270730.1 ERROR: no local reference sequence found for BAM reference name KI270438.1 ERROR: no local reference sequence found for BAM reference name KI270737.1 ERROR: no local reference sequence found for BAM reference name KI270721.1 ERROR: no local reference sequence found for BAM reference name KI270738.1 ERROR: no local reference sequence found for BAM reference name KI270748.1 ERROR: no local reference sequence found for BAM reference name KI270435.1 ERROR: no local reference sequence found for BAM reference name GL000208.1 ERROR: no local reference sequence found for BAM reference name KI270538.1 ERROR: no local reference sequence found for BAM reference name KI270756.1 ERROR: no local reference sequence found for BAM reference name KI270739.1 ERROR: no local reference sequence found for BAM reference name KI270757.1 ERROR: no local reference sequence found for BAM reference name KI270709.1 ERROR: no local reference sequence found for BAM reference name KI270746.1 ERROR: no local reference sequence found for BAM reference name KI270753.1 ERROR: no local reference sequence found for BAM reference name KI270589.1 ERROR: no local reference sequence found for BAM reference name KI270726.1 ERROR: no local reference sequence found for BAM reference name KI270735.1 ERROR: no local reference sequence found for BAM reference name KI270711.1 ERROR: no local reference sequence found for BAM reference name KI270745.1 ERROR: no local reference sequence found for BAM reference name KI270714.1 ERROR: no local reference sequence found for BAM reference name KI270732.1 ERROR: no local reference sequence found for BAM reference name KI270713.1 ERROR: no local reference sequence found for BAM reference name KI270754.1 ERROR: no local reference sequence found for BAM reference name KI270710.1 ERROR: no local reference sequence found for BAM reference name KI270717.1 ERROR: no local reference sequence found for BAM reference name KI270724.1 ERROR: no local reference sequence found for BAM reference name KI270720.1 ERROR: no local reference sequence found for BAM reference name KI270723.1 ERROR: no local reference sequence found for BAM reference name KI270718.1 ERROR: no local reference sequence found for BAM reference name KI270317.1 ERROR: no local reference sequence found for BAM reference name KI270740.1 ERROR: no local reference sequence found for BAM reference name KI270755.1 ERROR: no local reference sequence found for BAM reference name KI270707.1 ERROR: no local reference sequence found for BAM reference name KI270579.1 ERROR: no local reference sequence found for BAM reference name KI270752.1 ERROR: no local reference sequence found for BAM reference name KI270512.1 ERROR: no local reference sequence found for BAM reference name KI270322.1 ERROR: no local reference sequence found for BAM reference name GL000226.1 ERROR: no local reference sequence found for BAM reference name KI270311.1 ERROR: no local reference sequence found for BAM reference name KI270366.1 ERROR: no local reference sequence found for BAM reference name KI270511.1 ERROR: no local reference sequence found for BAM reference name KI270448.1 ERROR: no local reference sequence found for BAM reference name KI270521.1 ERROR: no local reference sequence found for BAM reference name KI270581.1 ERROR: no local reference sequence found for BAM reference name KI270582.1 ERROR: no local reference sequence found for BAM reference name KI270515.1 ERROR: no local reference sequence found for BAM reference name KI270588.1 ERROR: no local reference sequence found for BAM reference name KI270591.1 ERROR: no local reference sequence found for BAM reference name KI270522.1 ERROR: no local reference sequence found for BAM reference name KI270507.1 ERROR: no local reference sequence found for BAM reference name KI270590.1 ERROR: no local reference sequence found for BAM reference name KI270584.1 ERROR: no local reference sequence found for BAM reference name KI270320.1 ERROR: no local reference sequence found for BAM reference name KI270382.1 ERROR: no local reference sequence found for BAM reference name KI270468.1 ERROR: no local reference sequence found for BAM reference name KI270467.1 ERROR: no local reference sequence found for BAM reference name KI270362.1 ERROR: no local reference sequence found for BAM reference name KI270517.1 ERROR: no local reference sequence found for BAM reference name KI270593.1 ERROR: no local reference sequence found for BAM reference name KI270528.1 ERROR: no local reference sequence found for BAM reference name KI270587.1 ERROR: no local reference sequence found for BAM reference name KI270364.1 ERROR: no local reference sequence found for BAM reference name KI270371.1 ERROR: no local reference sequence found for BAM reference name KI270333.1 ERROR: no local reference sequence found for BAM reference name KI270374.1 ERROR: no local reference sequence found for BAM reference name KI270411.1 ERROR: no local reference sequence found for BAM reference name KI270414.1 ERROR: no local reference sequence found for BAM reference name KI270510.1 ERROR: no local reference sequence found for BAM reference name KI270390.1 ERROR: no local reference sequence found for BAM reference name KI270375.1 ERROR: no local reference sequence found for BAM reference name KI270420.1 ERROR: no local reference sequence found for BAM reference name KI270509.1 ERROR: no local reference sequence found for BAM reference name KI270315.1 ERROR: no local reference sequence found for BAM reference name KI270302.1 ERROR: no local reference sequence found for BAM reference name KI270518.1 ERROR: no local reference sequence found for BAM reference name KI270530.1 ERROR: no local reference sequence found for BAM reference name KI270304.1 ERROR: no local reference sequence found for BAM reference name KI270418.1 ERROR: no local reference sequence found for BAM reference name KI270424.1 ERROR: no local reference sequence found for BAM reference name KI270417.1 ERROR: no local reference sequence found for BAM reference name KI270508.1 ERROR: no local reference sequence found for BAM reference name KI270303.1 ERROR: no local reference sequence found for BAM reference name KI270381.1 ERROR: no local reference sequence found for BAM reference name KI270529.1 ERROR: no local reference sequence found for BAM reference name KI270425.1 ERROR: no local reference sequence found for BAM reference name KI270396.1 ERROR: no local reference sequence found for BAM reference name KI270363.1 ERROR: no local reference sequence found for BAM reference name KI270386.1 ERROR: no local reference sequence found for BAM reference name KI270465.1 ERROR: no local reference sequence found for BAM reference name KI270383.1 ERROR: no local reference sequence found for BAM reference name KI270384.1 ERROR: no local reference sequence found for BAM reference name KI270330.1 ERROR: no local reference sequence found for BAM reference name KI270372.1 ERROR: no local reference sequence found for BAM reference name KI270548.1 ERROR: no local reference sequence found for BAM reference name KI270580.1 ERROR: no local reference sequence found for BAM reference name KI270387.1 ERROR: no local reference sequence found for BAM reference name KI270391.1 ERROR: no local reference sequence found for BAM reference name KI270305.1 ERROR: no local reference sequence found for BAM reference name KI270373.1 ERROR: no local reference sequence found for BAM reference name KI270422.1 ERROR: no local reference sequence found for BAM reference name KI270316.1 ERROR: no local reference sequence found for BAM reference name KI270340.1 ERROR: no local reference sequence found for BAM reference name KI270338.1 ERROR: no local reference sequence found for BAM reference name KI270583.1 ERROR: no local reference sequence found for BAM reference name KI270334.1 ERROR: no local reference sequence found for BAM reference name KI270429.1 ERROR: no local reference sequence found for BAM reference name KI270393.1 ERROR: no local reference sequence found for BAM reference name KI270516.1 ERROR: no local reference sequence found for BAM reference name KI270389.1 ERROR: no local reference sequence found for BAM reference name KI270466.1 ERROR: no local reference sequence found for BAM reference name KI270388.1 ERROR: no local reference sequence found for BAM reference name KI270544.1 ERROR: no local reference sequence found for BAM reference name KI270310.1 ERROR: no local reference sequence found for BAM reference name KI270412.1 ERROR: no local reference sequence found for BAM reference name KI270395.1 ERROR: no local reference sequence found for BAM reference name KI270376.1 ERROR: no local reference sequence found for BAM reference name KI270337.1 ERROR: no local reference sequence found for BAM reference name KI270335.1 ERROR: no local reference sequence found for BAM reference name KI270378.1 ERROR: no local reference sequence found for BAM reference name KI270379.1 ERROR: no local reference sequence found for BAM reference name KI270329.1 ERROR: no local reference sequence found for BAM reference name KI270419.1 ERROR: no local reference sequence found for BAM reference name KI270336.1 ERROR: no local reference sequence found for BAM reference name KI270312.1 ERROR: no local reference sequence found for BAM reference name KI270539.1 ERROR: no local reference sequence found for BAM reference name KI270385.1 ERROR: no local reference sequence found for BAM reference name KI270423.1 ERROR: no local reference sequence found for BAM reference name KI270392.1 ERROR: no local reference sequence found for BAM reference name KI270394.1 ERROR: java.io.IOException: BAM header not fully compatible with specified reference sequence java.io.IOException: BAM header not fully compatible with specified reference sequence at org.stjude.compbio.rnapeg.SplicedReadReporter.report(SplicedReadReporter.java:241) at org.stjude.compbio.rnapeg.SplicedReadReporter.main(SplicedReadReporter.java:765) Uncaught exception from user code: where is 99_FRAS202421989-1a_1.fqAligned.sortedByCoord.out.bam.junctions.tab at /RNApeg/src/bin/junction_extraction_wrapper.pl line 339. main::run_cmd("bam_junction.pl -type all -bam /data/An\x{c3}\x{a1}lises/Teste1/star/all_samples_ensembl_chimericwithinbam/99_FRAS202421989-1a_1.fqAligned.sortedByCoord.out.bam -annotate -now -force 1 -out 99_FRAS202421989-1a_1.fqAligned.sortedByCoord.out.bam.junctions.tab -no-config -refflat /data/references/cicero/reference/Homo_sapiens/GRCh38_no_alt/mRNA/RefSeq/refFlat.txt -fasta /data/references/cicero/reference/Homo_sapiens/GRCh38_no_alt/FASTA/GRCh38_no_alt.fa", "99_FRAS202421989-1a_1.fqAligned.sortedByCoord.out.bam.junctions.tab") called at /RNApeg/src/bin/junction_extraction_wrapper.pl line 217
How can I correct the BAM header or remove the chromossomes/patches that are not present in the reference provided by CICERO?