Error in Process in calling methylation from aligned bam

[xscapintime]

Hi,

I am running detect command:

python $deepmod2 detect --bam $inp --input raw/ --file_type pod5 --seq_type dna \
	--model bilstm_r9.4.1 --threads 6 --ref $ref --output .

The alignment was done with winnowmap

winnowmap -t 4 -W $kmer -y --eqx -ax map-ont -s 4000 -I 10g $ref $inp | samtools view -u -F 2308 -  | samtools sort -o $out.sorted.bam -@ 4

it raises error in process.py, part of the error looks like this:

Traceback (most recent call last):
  File "/home/usr/apps/miniconda3/envs/deepmod2/lib/python3.11/multiprocessing/process.py", line 314, in _bootstrap
    self.run()
  File "/home/usr/apps/miniconda3/envs/deepmod2/lib/python3.11/multiprocessing/process.py", line 108, in run
    self._target(*self._args, **self._kwargs)
  File "/home/usr/apps/DeepMod2/src/detect.py", line 535, in process
    pos_list_c, pos_list_candidates, read_to_ref_pairs=get_candidates(fq, align_data, aligned_pairs, ref_pos_dict, exp_motif_seq, motif_base, motif_ind, position_based)
                                                       ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/home/usr/apps/DeepMod2/src/detect.py", line 115, in get_candidates
    aligned_pairs_ref_wise=aligned_pairs[aligned_pairs[:,1]!=-1][common_pos-reference_start]
                           ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^
IndexError: index 403 is out of bounds for axis 0 with size 230
Pausing input due to INPUT queue size limit. Signal_qsize=201
Pausing input due to INPUT queue size limit. Signal_qsize=201

It looks like there's something wrong in reading the files. I appreciate any input to solve this. Thanks!!!

[umahsn]

Hi,

Thank you for bringing this to our attention. It seems like the the end coordinate of read mapping to the reference doesnt not match with read length inferred from cigar string.

Can you edit src/detect.py file and replace Line 535?

pos_list_c, pos_list_candidates, read_to_ref_pairs=get_candidates(fq, align_data, aligned_pairs, ref_pos_dict, exp_motif_seq, motif_base, motif_ind, position_based)

with the following lines:

try:
	pos_list_c, pos_list_candidates, read_to_ref_pairs=get_candidates(fq, align_data, aligned_pairs, ref_pos_dict, exp_motif_seq, motif_base, motif_ind, position_based)
except IndexError:
	print('Index Error', read_dict['name'], align_data, read_dict['cigar'], read_dict['flag'])
	sys.exit()

and then run DeepMod2? This will help us figure out what the cigar string and other info for the problematic read looks like.

[xscapintime]

Hi there,

Thanks for your advice!!

Here's the output

2025-03-05 15:07:49.850144: Finished building BAM index.
Index Error 0004203f-95f5-494c-8bcf-bbbb6287d5af (True, True, 'chr3', 36416174, 36418845, 2668) 738=1X47=2D1X14=1X142=1I99=2D1X3=1X15=1D1X2=1D48=1I52=5I6=1I43=1I111=2I126=1D1X42=1X7=1I123=1X162=3D2=1D15=1D1X88=1D6=3I1=1I22=1D20=1D52=1I29=1X72=1D44=1I9=1D22=1D38=2I3=1D15=1D153=1D60=2D1=1X101=1D23=1D27=2I51= 0
Index Error 03b63026-914f-4e9e-b888-36b5d5ef161b (True, False, 'chr7', 25572261, 25606463, 34398) 13=1X2=1X67=2X24=1D2X1=2X1=1X50=4I4=1I6=1X10=1I2=4X32=2I1=1X1=3D87=1D4=1D23=1D50=2I1=1X1=2D26=2D79=1I63=2D50=3D49=2I1X91=3I1X1=1X4=1D38=1I1X67=1D30=2I4=1D40=1X1=1X73=1I45=1I6=3D15=4I72=1D173=2D61=1I122=1X317=2D169=2D79=1X165=1X9=1D2=1X12=2I2=2X13=1I409=1I161=1I710=2D100=1I127=2D40=1I129=1X182=3D36=1I108=2D176=1D21=1X282=1X171=1D8=3D25=1I43=3D1=5D474=1X90=1X131=5I129=1D19=1I57=2X76=3D130=3D149=2D1=1D1=1X2=1X41=1I2=2D1X15=2I1=1I6=1X244=2D106=1X23=2I21=1X24=1X31=2X1=1I2=1I1X5=1D1X1=1X54=1X2=2D14=4I36=2X4=2I3=1X1=1X6=2D7=2D1X1=1D120=3D79=1I3=1X1=1D2X33=1D53=1X69=2X11=1X31=2X1=1D82=1D10=2D61=5D3=1D1X4=1X1=1I3=1X15=1D1=1X21=2D2=1X17=1D14=2I3=1D1=1X28=1I1=3X49=2D1X12=1D1=1D1X39=1D215=1D4=1D11=2I103=2D16=1D40=4I27=1I107=2I16=1X2=2X2=2I145=1D44=1D4=1D14=1D2=1X28=2X36=1X58=3I34=1X17=2X1=1D53=1D45=3D27=1X28=2D189=1I1=1X35=3I1=1D155=1D129=2D84=1D2=2X8=1X23=1X2=1I73=1D37=1D4=1X2=2D65=1X4=1X145=1X40=1X271=1D113=3D32=2I63=1D41=3D3=1D15=6I101=1X114=1X5=2X248=1D94=1D1=3X113=2D94=2D149=1D73=2D3=1I1X22=1I21=1I46=2I43=2D3=1D64=3I328=1X596=1X102=1X108=1X931=1X155=1X375=1X272=1X1=3D123=1D7=1D8=110I9=1I140=1I1X1=1X62=2X56=1D18=1I71=1I8=1D13=1I87=3D10=2I85=1I191=14I46=1I246=1X46=2I250=1D124=1I32=1D122=15I26=2D29=1X1=1X37=1X228=2X8=1D117=1X1=1X1=1X5=2I129=1I282=1D6=2X88=1X107=2I15=1D63=1X209=1X5=1D11=1I15=1I3=1X12=1I14=2D1X48=1X32=5X227=2X20=1X73=2X13=1D1X13=2X17=1X110=1I101=1D1X99=1I2=1X2=1X34=2D6=1D6=2D1X86=1I3=1I4=1I33=1D94=1X5=1X2=3D190=1D28=2I1X2=1I2=1I130=1D67=1D97=3I2=1I2X155=1I92=1D2=1X2=3X7=2I21=1X116=1D70=1X2=2X3=1I201=1I34=1X163=1I31=1I108=3D49=1I227=1X3=1D61=1X9=4D43=1D104=1D15=1D406=1X112=1X27=3I95=4D262=1X87=1X153=2D1=1X2=1X61=1X1=1I2=1I2X136=1D325=4D141=4D32=2X46=1D5=1I12=6I84=1I9=1X173=1I9=1I34=1I42=1D3=1D100=1I27=2X2=154I47=3I1=1D3=1D3=1I92=1I27=1D29=1I97=1D124=1X69=1D15=2D1=2X22=1D11=5I193=1I22=2D72=1D1=1X36=1I87=2D42=1X1=2X1=1X96=1D71=1D2=1X6=1D180=1I43=1I3=1D64=2X2=1D122=1I33=1I1=2D58=1D160=1I2=3I1=1X24=2D16=2D59=2I1X1=1D84=1X9=1D13=2I20=1I7=1I34=1X98=2I198=1I1X132=3I72=1D75=1X67=1D1X8=2D135=1D1=1D52=2D215=1D2=2I241=1D88=1D196=1I183=1X10=1X7=1X49=1D90=2D73=2D38=1X48=2I2=1X11=3I269=1I1=1X72=1X24=4I9=2X21=1D14=2D46=2I142=1D170=1X8=3D34=1D81=1D3=8D36=1X133=3D2=1I76=2D17=1D2=1X52=4D44=1D13=1X8=2I3=1D124=10I182=1I3=1X179=1D4=1D2=2I60=1I2=4D80=3D29=1I523=2I1X66=2X1=1D6=1X1=1X164=1D10=1I2=1I1X38=2D23=1D43=1X1=1X3=1D1X87=1D117=1D104=1D20=1I2X32=1D2=1X244=1X1=1X1=1I216=3D185=1X22=2I4=1X33=1I24=1D129=1I56=1X1=1I3=1X1=1X3=1X1=1X1=1X6=1X52=1I16=1D71=4D132=1X11=1D2X3=1I71=1X40=1X146=3I154=2D21=1I26=1X108=1X10=1X8=1I2=3I2=1X104=1X15=1D1=1D7=2X14=1I3=1D34=1X2=1D1=1X6=2D114=1I74=1D45=1D103=1D1X1=1X66=2X9=1I2=1D1=1X63=1X8=1I98=1X12=2D25=4D10=2X1=1X37=3D6=2D20=1D3=1D7=1D116=2I30=1D60=1I8=1D20=3D75=1I9=1X89=3D67=2D28=3X1=3X39=2S 16
Index Error 05f37fcb-5b2c-4fc5-aeea-d6ccbe41e78f (True, False, 'chr1', 133768457, 133802944, 34000) 231=1X56=1X216=1X282=1X41=5I522=1X52=1X101=1X555=2X216=1X282=1X78=1X409=1X127=1X38=1X62=1X555=2X216=1X76=1X205=1X78=1X96=26D362=1X52=1X101=1X75=1X480=1X30=1X134=1X127=1X43=1X15=1X224=1X267=1X137=5I132=1X14=1X86=1X114=1X441=1X30=1X134=1X127=1X43=1X240=1X267=1X141=1X127=1X14=1X86=1X114=1X439=1X69=1X15=1X81=1X101=1X25=1X71=1X212=1X412=1X124=1X38=1X62=1X7=1X109=1I18=1X419=2X165=1X101=1X25=1X284=1X409=1X74=1X52=1X101=1X252=1X224=1X64=1X13=1X79=1X85=1X101=1X25=1X71=1X212=1X412=1X124=1X38=1X62=1X176=1X379=1X267=1X25=1X354=1I340=1X74=1X52=1X101=1X117=1I135=1X224=1X64=1X13=1X79=1X85=1X169=1X29=1X48=1X43=1X119=1X69=26D107=1X123=1X5=1X395=1X112=1X52=1X412=1X294=1X117=1X124=1X101=1X556=1X30=1X5=1X128=1X127=1X552=1X114=1X26=1X127=1X28=1X72=1X114=1X229=1X132=1X78=1X165=1X269=1X210=1X469=1X20=1X80=1X125=1X9=1X8=1X354=1X56=1X3=1X212=1X82=23I177=1X78=1X433=1X50=1X52=1X25=1X12=1X14=1X47=1X722=1X127=1X28=1X255=1X172=468D722=1X127=1X28=1X120=1X544=1X127=1X101=1X114=1X2=1I506=1X97=1X199=1X87=1X124=1X137=1X399=1X101=1X540=1X15=1X165=1X75=1X123=1X204=1X7=1X409=1X127=1X101=1X540=1X15=1X165=1X55=1X348=1X7=1X345=1I64=1X127=1X101=1X540=1X15=1X165=1X55=1X356=1X281=1X3=1X3=2D7=1X2=2X1=1X10=2X1=1X2=1X2=2X1=1X3=4D1X2=1X2=3D8=1X8=1X5=4S 16
Index Error 07668a03-51b9-41cc-b668-1744444a6768 (True, False, 'chr12', 122121442, 122131446, 9974) 12=1D52=1X9=3D103=1D118=1X53=1D5=2D45=1X45=1X14=2I1=1I20=1X41=1X343=4I42=1D25=4D3=1I22=1I119=1X59=1D217=1D22=1I61=1X122=1D128=1X1=3D6=2I48=1D124=3I59=2I3=4D65=2D60=1D114=2I33=1D7=1I227=3I35=1D179=1I72=2I2X237=2X17=4I44=1D32=1D9=2I1X79=1D124=1D143=1X3=1D61=1I162=1X1=2I1=1X2=1I5=4X4=2D1X1=1X7=1X129=1I247=1D328=1D3=1D81=1I4=2I12=1I35=1D104=1D10=2D3=2I235=3I1=1D10=1D19=1D54=1I25=1D209=1X216=1D59=1D2X187=2D74=1D15=2D37=2X1=1X141=1D21=1I31=1X2=1X26=1X5=1X104=1I12=1X10=1X4=1X95=1D151=2D65=35I129=1D110=1X141=1D1=1D29=1D131=2D2=1X270=1I178=1I27=2D70=1X99=2D23=1I39=3D1=1X6=1D1=1X5=1I22=1D1X6=1X1=1D2X3=1X1=1D1=1X1=1X1=1I3=1D3=3I2=1X3=4D4=1I65=1I19=1X1=1I1X1=3D2=2X1=1D11=1X1=1X4=4I8=2D29=2X1=1X2=1I1=2X10=1X1=2D7=1X42=1I143=2X1=2D1=1D3=1D1=2D2X1=1X5=1D1=1X4=1X1=1X27=6I13=1I1X4=1X6=2X5=1X1=1D1=2X7=1I3=1D1=1X2=2X11=2I1X1=1X1=1X2=2I3=1X4=1D2=1I2=1X36=2X8=1X2=1X4=1I1=1X2=3D3=2D4=3D5=1X2=2D6=1D4=1I9=1X1=1X3=1D16=1X4=1D2=2I3=1I1=4D19=3I63=3X21=3D377=1X19=2I57=1X16=1X221=2D11=6D5=1X1=1I1X7=5D55=1X25=1I5=1D58=1D4=1D86=2D1X3=1D2=1X1=2X9=1X1=1D1X7=1I1=1X39=1I20=1D34=1D8=1I1X7=1X14=1I6=1D1=1X4=1D3=1D1=2X1=3D11=1I2X46=1D7=1X8=1I1X4=1D17=1D2=2D2=1X19=1D5=1X5=1D1=1X6=2I1=3D7=1D2X7=1D13=1D1=3D5=2D2=2I1X8=2D1=1X18= 16
Index Error 03d32c68-fd61-4b17-a202-06c1399f2273 (True, True, 'chr13', 19537780, 19545953, 8100) 71=1I7=3D127=3I76=1D1X1=2X8=1X21=1I20=1X8=1D3=3I1X2=1X13=1D2=1X2=1I4=2I2=1X28=2D50=1D109=1I1=1X3=1X75=1D114=1D91=1D9=1I53=1D64=1X58=1I21=1X34=3X116=2D13=1I107=1X9=1D1=1X47=1X6=1X69=1D7=1X6=1D39=2X51=1X1=3I347=1D16=1D91=2D194=1D1=1D1X21=1X41=1D49=1X4=1D80=1D110=1X29=1I40=1X14=1D8=1I243=1X75=1I37=1X300=1D45=1X128=1X53=1X7=1D332=1I56=4D1=1X2=1D7=1X1=1I1X53=1X1=2X4=1D1=2D23=1I2X1=1I35=1X1=2D6=1I97=1X1=3X37=1D1=2I30=1D38=1D4=2D91=2D10=1D2=1D1X59=4I94=2D22=2D2=1X60=2X11=1X8=1I3=1D1X42=2D1X41=3D133=1X17=1D5=2D34=2I24=1X11=2X27=1D1=2X2=1X1=1X1=1X2=1X72=2I35=1I3=1D1=2X22=1I31=1X43=1D9=1X2=1X1=1I1X9=3D28=1D50=1I2X4=2X4=1X21=1X15=1D28=1D3=3I1=1D9=1I9=3D16=1D1X48=3D8=2D4=2X5=1X1=3D1=1X3=1D132=3D1X1=1I1X8=2D33=1X74=1D29=1D5=1I2X1=1X6=4D1X34=2D3=1D92=4D4=2D1=2X4=1D40=2D25=3X88=1X24=1D33=1I152=1I89=2D178=1I15=1D52=2D48=1D7=1D8=1I24=1I1=1X15=2D282=1D99=3D14=3D1=1I113=2D474=1D17=1D43=4I8=1D1=1D1X19=2D126=1D57=1I60=3S 0
Pausing input due to INPUT queue size limit. Signal_qsize=201
Pausing input due to INPUT queue size limit. Signal_qsize=201
Pausing input due to INPUT queue size limit. Signal_qsize=201
Pausing input due to INPUT queue size limit. Signal_qsize=201
Pausing input due to INPUT queue size limit. Signal_qsize=201

I checked the first read in my bam file,

0004203f-95f5-494c-8bcf-bbbb6287d5af	0	chr3	36416175	60	738=1X47=2D1X14=1X142=1I99=2D1X3=1X15=1D1X2=1D48=1I52=5I6=1I43=1I111=2I126=1D1X42=1X7=1I123=1X162=3D2=1D15=1D1X88=1D6=3I1=1I22=1D20=1D52=1I29=1X72=1D44=1I9=1D22=1D38=2I3=1D15=1D153=1D60=2D1=1X101=1D23=1D27=2I51=	*	0	0	TTGGTCTTTGATGATGGTGACATACAGATGGGGCTTTGGAGTGGATGTCCTTTCTGTTTGTTAGTTTTCCTTTTAACACTCAGGACCCTCAGCTGCAGGTCTGTTGGAGTTTGCTAGAGGTCCACTCCAGACCCTGTTTGCCTAGGTATCAGCAGTGGAGGCTGCAGAACAGCGAATATTGCTGAACAGCAAATGTTGCTGTCTGATCATTCCTCTGGAGGTTTCATCTCACAGGGGTGCCCAGCCGTGTGAGGTGTCAGTCTGCCCCTACTGGGGAGTGCCTCCCAGATAGGCTACTCGGTGATCAGGGACCCACTTGAGGAGGCAGTCTGTCGGTTCTCGGATCTCAAGCTGCGTACTGGGAGAACCACTACTCTCTTCAAAGCTGTCAGACAGGGACATTTAAGTCTGCAGAGGTTTCTGCTGCCTTTTTTTCAGCTATGCCCTGCCCCCAGAGGTGGAGTCTACAGAGGCAGGCAGGCCTCCTTGAGCTGCGGTGGGCTCCACCCATTCCAGCTTCCCAGCCACTATGTTTACCTACTCAAGCCTCAGCAATGGCAGGCGCCCCTCCCCCAGCCTCGTTGCCACCTTGCAGTTCAATCTCAGACTGCTGTGCTAGCAATGAGCAAGGCTCCGTGGGCGTGGGATATAATCTCCTGGTGTGCTGTTTGCTAAGACCATTGGAAAAGCACAGTATTGGGGTGGGAGTGACCCAGTTTTCCAGGTGCCATCTGTCACGGCTTTGCTTGGCTATGAAAGGGAATTCCCTGACCCCCTGCTTCGGCTTCGTTGGTGCACTGCGCCCACTGTCCGGCACCCACTGTCTGACAAGCCCCAGTGAGAGGAACCCGGTACCTCAGTTGGAAATGCAGAAATCACCCATCTTCTGCGTCGCTCACGTTGGGAGCTGTAGATTGGAGCTGTTCCTATTTGGCCATCTTGGAGACCGCCCTAGATATTTAACTCAACTGTAAATTTGTGTGTGACACAAGGAGAAGAAGGAATCCAATTTGTCCTAAACCATTCTGATATTCACAAAATTCTGTGCGCTCACCCATCTGTTTTGATTCTATGTTTACATTCAATTCCATTGATATATATGGTTGTATATGGTATTTTTATAAATATCTATTTATTAAAAATAAGTATCATGTATTTTTAACATTCTTAAACTGTGGCTTTTCTAGTATGTCTTAAAATCTAGTTGGGCTATTACTCTCTTTCGCTCCTCTTTCTAAATAGGACGTTGGCTCTTTATTCTGGTTCCTTTATTCTGTAATATAATTTTTATTGCAGATGTTAATTTGTTCAGTATCCTTTGGGAATTACTTTTAATTTTTTTATAGTAACTTGGAAAGAATTGACTTACTAAAAATGTTAGTCAGGCCAAGCATGGTGGCTCATGCCTATAATCTTAGCTACTCTGGAAGCTGGTGTGGGAGGATCACTTGAGCCCAGGACTTGAGACCAGCCTGGGAAACATAGTGAGACATGGTATCTCCAAAAATTTTCTTAAAAATTAGCCAACCATGGTGGCACATGCCTGTAGTCCCAGCTACTTAGGAGGCTGAGGTGGGAGGATTGCTTGAGCCCATGAGTTTGAGGCTTCAGTGAGCCATGAGCTTGCCACTGCACTCTAGTATATCATTCATAAACATGGTATACCTTCCTATTATTCAGGTCTCTTTATATACACTTTAATAAAACATTTTAATCATCTGCACAAAGTTATCCTTGCTGCTATTCAGTCCTTCTCTTGGGCTCTTTATATCAAGTCTTGTATTTTTTATGCCCATCATCTGTGGTTCCCTGTGAAAGGTGCTTATTCTTGCATCATGCCTCTGACATTGCCCCTTAATTCTTTAGGATATGTATTATGCATATATTAAGTTTATATTCTATTCTGGCCAATCTTTATTTGTCTTCTCTATGCCATGTTATTTTTCCTGAGGGCTATATTCCCTGGGAGTATTTGCTGCCTTGGCTGGTAATTTGTATGTGGTCAGGGAAGCAAAAAGCACAAGCCATTGAGCATGTCCCTTACTCTTATTTGAGGAGTGAGTAATGCACCAAAGAGCAGGCTTCCTCTGGTACTGTTACCTGGATTCAACCACTCCTGTTTATAACCCCCATCACCCAACCAAGTAATGCTGCTTTTCTAGGAAACTTCCTGCATTTTCACATTAGGCACTTTTTTTGGCCAGGGAGAACTTTGGGGCAGGTCTTTGGCCCCTCTCCTGATATATCTGCCCCCATGGCACCAGGCATCCAAAGATTCTCTGCGGCCCCACAGCCTCCAGTGTGCCCCAAACTGGCATTGCTGCATAAATGCTCTGCATGGACAAGAGTGTAGGAGGCAATGAACTTCCTAAAGCCATGTAGGAGAGGGAAGGGCCCTCCTTAAACATGATACCCTGTGTATGCCATGGTGCTCAGCTCTCTTCTAAGTTTAAGATGTTTTTCTTATAAATGGAACCCAAAGGCCTAGTAGTGTCTCTCTTTTCCTGTGTCCTTGGAGCCTTCAACCTTCTTCCTGTCTATGTAGCACATCCAGGAATGGATTCAGGGAATCAGCATAGTTTATGTTCCTCTTCTTACAGTCCAGTGTACTTATACGCACACACAAACACTCACACAAACACACACACACGTATATAAATTTTTCTAT	33446JNBEC??@>=@?@@?;43435B=?6752++*)&&''(*-39<=?B77<6:=>>?<8:CCAFIISICC>67=<;::<.--8=>?BCBBDCAEAC<?ADCBB>BGDACBA=A@>@C>6=:>@>?A@D?CACCBCCDBBC>****+=?A@@?>55556A@DBC@CDFCFEB=98889?>=;<;;<?>?AABA;98:;?B@A@@@?=9999:DC:<?AA>75<@??=??@<333377556645644666:,,,,47=ADEH>::=97/17;?=?:?;955777@D9=::9:9>@=9987955556;<>?@=?=>@GOGIC?DDE?=<786:;:0///0:=/////<<=555;A<::44556DEGBE?CAFB88889@@CDFDK@?@@=B58>9?ABBBD?>>>7=:8=B@EIFEFNDHHEDCCGB;;;;;E@CBB80/001???>9<42@GFMDDFHAPBA@===>CEGD>10--,.36<BACAB@ADD@@?888;;>DGHINIB<975200)''.26>AB>>><98644689=>A?C:?FEDDB@DBBAA@?:;@ED77533459;DEC@E@?=:5???:99::97678:ECDCDA77767>>@?>B@AA?@A@ABCBFD??@A@>=>;=?B@?>==<9;<::;:<@ABCABEGCAB?A?>>>88989BB>CAD<<<88988>ADIJB<=<<<=;777788;??CB@?<=63369::058<=>>79?66657@?=<==;864458:<>?>=321-,/436<=:??>;=<@<=779?CHE;744(%%$$%23;;=7:9650000.8===A744465:>B@BC?@666991//,+)&&&')+...--.:7999:?>:BBCA??@@AI=ACECDENCFACAB:::8421213567:;;;8700001<=<;@@>=8++)&&',029?;>KIFC9999=@??F@@88****+343379::99:51////)**76665///-,0453:;@>=<=>?C>=>>;;>@>>?<?<<<<@=8;<:77<===>?@A666666=@==667=>9:643''''(2&'',.9:<<=:8*+&%%%%044@AD7;;;;:<ABFCB??>>??@?@?=>>>>><<<=;==<=>?=>>37>=>?>?@?>=>?@AB@@?ACD>@C?>@?=545<<>>AECEC@>=;0//'&$$$%%'))**+*/9<<<=>=>=>?@BCB@<>>>=><=>=>=>>?=?<;7441+)()))+33;?;9::BA8777455668???>?A?@@CBBBAA>>ACBBACABCABCCB@ABAAABE:9999;>=<<=>=>?A=8;=79:;:::AAA@7893----,.:;==<:=?>:>9:<>>=>9999:>>@B<=><>AA@>AA?>>>>AEA;;:9553&&&&)4:>A@B@??@@BCAAADDFJCFHBCCHDFA@>@@BA@?@=<@@?@<<<;;AJGILSEICB@DC@@=??D;:9<<7////22689;<CAEEIHCB=====CBFDB?>=<;;<=<>33=<::;;=A;;999=146;?@@D?>===@CDC@A@?>>=>?A322----/7=C@=CB?33333CCEBCDAABABBDGB:;77;??@<@CAA=<<<=D@@@A;BF@A@BCGB@??>>?>====;<>>>?@?@??.+'&&''+,-566<<<;988776788843334=@55::1/46568:<==??C9>=:;>><<=?ACBDCGDA@?@@DDC@@A>>@@@???@><>?@A@>>>?>@@@@@?@@?@?==>=?@ABB@=::::<:;;<<>?311238::;>>?@AA897550//00212-)'$$$%'**+07:<6//+++*+2,+,-:866677<===>>>>???:77678;55525;<>>?6,***+5==>=666445557>>;;9;?ABBBBBBA@A@@@B:5//,)()*)&&&'))).=?>??A>=>>>>??>==>=?@A8:<;;<@@>8=??>@@@>@5?@@<=<==<@@?@?@?@A>==;<;;;<?AB>====>??@ABBB<<><;8;<BB88:9::..../;BA@@?@?BB<4362222299;<=:650((((,-.054567:;<<<2@==<;;=>>>=>==>:832101489<ACBBDEDB8883355:((;;:<>A??@A?A@<9;=>??=<=:;55:99:@?=<<;966)(())))))*/7((9;;<@AF>B7544311//.002150/28>==>88;=@CDBA387(((*9=?@??<;<<:14:66.--2<;8887788:<>@??>>>??===BD<;;967>0977>>><;:889:<BB@>>=>>>,++/=<@A??==??>>>;<<;;22/--.''++-168==?A@>?==>>?77899954323755==>===?>>?<=>?;<<<;=;;;<>?@>?:8:99<4<=??:77988499:<=;;;<;=<<<=<======>>=@@B@ABBCD@@CA>=;;;>@>@@>?643,+))&%$')38<?=?@>@A@@88;<;;;;<<;<>???:><>>@@B>=<<116-----)(((+<>;79::;<;;<<==<=</////;<===>>>87778?@>==>?=876,7:<;,,,,)****)'''')')))>@@@@@?><>-,,.,,*)(***)+.//10649=:;===77778@@76667@>@??@::76667:;;:;;;>451,+	NM:i:59	ms:i:4994	AS:i:4994	nn:i:0	tp:A:P	cm:i:84	s1:i:1023	s2:i:122	de:f:0.0168	rl:i:30	qs:f:16.8583	du:f:5.10375	ns:i:20415	ts:i:805	mx:i:2	ch:i:2548	st:Z:2022-07-27T05:23:13.300+00:00	rn:i:16	fn:Z:MS367_01.pod5	sm:f:83.338	sd:f:15.1737	sv:Z:med_mad	dx:i:0	MN:i:2668	MM:Z:C+h?,35,17,14,7,1,3,37,24,11,15,0,18,12,1,2,5,13,10,0,2,8,18,24,5,221,81,14;C+m?,35,17,14,7,1,3,37,24,11,15,0,18,12,1,2,5,13,10,0,2,8,18,24,5,221,81,14;	ML:B:C,60,1,16,184,81,133,3,241,7,218,213,8,104,7,33,255,1,21,66,2,133,59,197,252,9,4,2,194,254,239,70,174,122,252,14,248,7,42,247,134,233,222,0,253,24,21,252,121,196,0,1,246,251,253	NM:i:59	ms:i:5008	AS:i:4994	nn:i:0	de:f:0.0167973	tp:A:P	cm:i:316	s1:i:2056	s2:i:171	MD:Z:738A47^CA0C14A241^AC0A3A15^C0G2^G386^C0A42T130G162^CCA2^C15^A0T88^C29^T20^C81G72^C53^C22^T41^A15^C153^A60^CC1A101^G23^A78	rl:i:700

Read length:

cat problematicread_withdeepmod.sam | paste - - - - | cut -f 10 | wc
      1       1    2669

I'd appreciate if you have any idea to solve this.

Thank you so much!!

[umahsn]

Hi, this issue should be fixed now. I forgot to check for "=" operation when parsing the cigar string. Thanks for bringing this to our attention.