EricKutschera
commented
1 year ago The reason for the error is as you posted: die if !exists $chr_seq_len_ref->{$line[2]};
That line is checking the chromosome name from the alignment against the chromosome names from the FASTA file given as -F or --fa. That --fa file might differ from what was used to align the reads. You could try editing that line to die "did not find: $line[2]" if !exists $chr_seq_len_ref->{$line[2]}; and then rerunning to get a better message
I think <IN> line 72 means that the error occured on the 72nd line of a bam file. If you could check that line you may see that the chromosome name is different than what's in --fa
Hello,
I am running into an issue where the thread gets terminated: Thread 1 terminated abnormally:
Died at ESPRESSO_S.pl line 865, <IN> line 72Here is the command I used:
perl ESPRESSO_S.pl -L trial.tsv -F genome.fasta -A genes.gtf -O dRNA_age_outI also checked my sorted BAM file because line 865 of https://github.com/Xinglab/espresso/blob/v1.3.0-beta/src/ESPRESSO_S.pl reads:
die if !exists $chr_seq_len_ref->{$line[2]};. There does not seem to be an issue with my BAM file (example of BAM file below) but the first line does differ from the SAM file provided in the example.c24482d2-30cd-4e1f-9787-3931c1bb6603 16 chr1 3547555 60 98S12M1D34M1D3M1I40M1D14M3I46M1D9M1I6M1I3M2D37M1023N11M2D7M2I58M4D16M1D17M3I48M1D1M1D4M2D6M3I20M3I67M1I10M1D10M1D4M2I41M2005N17M1D1M3D2M1D23M1D35M2I12M1D35M1I30M3I1M1I13M1D22M1I22M3D1M1D6M1D17M1D29M2I13M * 0 0 GAGGAGTTTTAATGGAATGGATGGATGGAATGAATGTGTAATAATGGAATATGTATAAATGGGAATGAAAAACCCTGAAACAGTGTTGCAGTTTCAGGATTCTGTGTGGAACAGATACTTGAACATACCATAGTATTCTCCTCAAACTTCAGGCTTCGTTTATCACAACAGGACACTGCCAACATAGCATTGTTGACAAAGAAAGAGCATCCCTGTGATGAGGGATGTGGCAATCTTCCAGCTGCATTGTCTTTCAATTTAGATTGCAAAGGGACTACTATTGATACCTTTTTGTTTATCTTCACTGTCCTAAGCCTTGGTGATGTTATAGCTGTTATTTTCCAAGAGCTCTCTTTGTCCGCATCAAATTCTCCTTGATTCAGTGAAGATTTTGTTTGTTTCTTATCGTTACTGGTCCACAGCAGCTATGATCAGACCTCACGTAACAAGATCTTTTACATCAGACTTGGTAAGAAGACTGAAAAGATGCAGAGCTGAACAGCTGTGGTGATCCATCACTTACTGACTGCCGCACATCAGTGTCACCGAGCCCGTTTTCGTCCCAGCACAATGGAAAAAGGGCCAGGTAATGATGATTAAGAAACATCATGCATTAAGATGTTTCACAAACTTGCACAGCACCTCAACATGCTGTTTCCCAAATATTGACGTTCAGGAAGCTGTGTTTAGCTATGCCATCAAGCTATAAGCTACGCAGGCATATGAAATCAGATTTGCTCAATTGCATTGGCTAATCATTACTTTGATGAAATCATCAGGACAACAGCATGCAACATTTTCAAGAAGGATATAAAGGTGGGGCTGGGATCAAGAAAGACTAGAACTGACCCAGTGTCCTTTAGAAGGTCTATAACCTTCAGGTCTCAAGACCACAGTGTTCTAAAATAAGAGGCACATCAGTTCCAGCAGA &%&'%$%*'%))$$$&)&$&%$%$$'''&($$%*$$$$$,*$**)((*)%'%$#(&&(('&(%&*&%%,&+-#%%%%(',..)&&%&&&$%%%)''%.)/667)&)&(//./+((6::A+.)%<667%&*/031:7*0+((('()(21')),;@EA3.B69787;65*48.;02513.*.7'>77.'&*()'''+.3)((&9(.+(0:4:89542(,---(0)+&1239::7)/5A4&'::4789AC=0:4416696.17+(&&&&%(%'(953:4613::;5?<103<?:655::;&.,-&,7<8<,110/6486E43'&(''''(*233064-.559=<14:.((4;<<:'H=:41*),,.4574988320+00749512.-*-+*533:<@;8?:::<9B98B94418:><D+8:<97*''-974597582.222'+,***)*&)'%-35?;>78./465&-5745**6(')&+7471+')&)28775'))*/686?<14<53-2.,4:9;BB92.*&3<9=:/<4691/)9<>=?77-346,+/.233'',0=:54A==56*5)971/0),&1(+(239:;7+)2-++)**-7871((36<94>5*26431*%%',==<5:459=605<2-6::'(2'+'(78985<9=A77:21*33<0088<;:788<=0775.1/1,7:7>99021+1<?=;3<751>;>7+*96=7,8<78;88+/(.,6743(($%/3227:9>8<=@B@>:7;9+'(-+144B42'+))*(31)(,-+)3.,,068/42012-1.&)*1/-**)+)1-,()32).')%/4<839<7'7)50)'&&')<0/%')52;9::=24)&,59:0,,-%*%.-1/.''5:5H>8974745512%%*13//0)&&()2021<534-0*'-)*)(';93?>583%$*(% NM:i:86 ms:i:604 AS:i:529 nn:i:0 ts:A:+ tp:A:P cm:i:103 s1:i:498 s2:i:0 de:f:0.0736 MD:Z:6A1A3^C1G32^G0T42^A29T30^T16G1^TA26G21^AA1A0A62^GAAG16^T65^A1^G0T3^AG65T37^G10^A16C0A2A0G40^T1^ATG2^T23^T39G7^G1A18G45T12^G13G0A8T20^GTA1^G6^G0C16^G42 rl:i:28Any help to fix this would be very appreciated!