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quinlan-lab / STRling

Detect novel (and reference) STR expansions from short-read data
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SIGSEGV: Illegal storage access. (Attempt to read from nil?) #114

Closed christopher-schroeder closed 6 months ago

christopher-schroeder commented 1 year ago

Hey, I get the following error for one of my samples in one of my projects

strling version: 0.5.1
using first reads in fragment_length_distribution calculation as there were not enough
Read 67332 bounds from results/strling/merge/tremor-ataxia-bounds.txt
SIGSEGV: Illegal storage access. (Attempt to read from nil?)

I may help to fix this by providing any information you need!

brentp commented 1 year ago

I am guessing this and your other issue are because you have a very small bam/cram file. If you have extract part from the larger file, I would run with the full file instead. Since that's unlikely, I'll have a look to see what is expecting more reads. Could you also run with the debug binary here and report the output?

christopher-schroeder commented 1 year ago

Thank you for your answer. The cram is 42 gb, a normal > 30x coverage whole genome. I will run the debug tomorrow

brentp commented 1 year ago

can you show the output of samtools flagstat on your cram file?

christopher-schroeder commented 1 year ago

977501933 + 0 in total (QC-passed reads + QC-failed reads) 971524030 + 0 primary 0 + 0 secondary 5977903 + 0 supplementary 91216263 + 0 duplicates 91216263 + 0 primary duplicates 974127477 + 0 mapped (99.65% : N/A) 968149574 + 0 primary mapped (99.65% : N/A) 971524030 + 0 paired in sequencing 485485340 + 0 read1 486038690 + 0 read2 0 + 0 properly paired (0.00% : N/A) 968089186 + 0 with itself and mate mapped 60388 + 0 singletons (0.01% : N/A) 14810476 + 0 with mate mapped to a different chr 11084 + 0 with mate mapped to a different chr (mapQ>=5)

brentp commented 1 year ago

ok. thanks. here is the location of the warning about not enough reads. Does your sample have a very large insert size or something? It is only making these checks:

    if not aln.flag.proper_pair: continue
    if aln.flag.supplementary or aln.flag.secondary: continue
    if aln.isize < 0: continue
    if aln.isize > result.high: continue # result.high == 4096
christopher-schroeder commented 1 year ago

Not that I am aware of. But the 2 errors I posted here, are from 2 different samples from the same trio. I have to contact some cooperation partner to get more information, but maybe they are generated in a special way. The third sample from this trio is ok. I have no problem for more then 1000 samples with strling by now, so maybe something fishy is going on here.

christopher-schroeder commented 1 year ago

Here is the debug log:

strling version: 0.5.1
compiled in debug mode
using first reads in fragment_length_distribution calculation as there were not enough
Read 1999 bounds from results/strling/merge/tremor-ataxia-bounds.reduced.txt
[strling] got 2 treads for locus: (tid: 23, left: 135646175, left_most: 135645361, right: 135646629, right_most: 135646647, center_mass: 135646175, n_left: 0, n_right: 2, n_total: 132, repeat: "AT", name: "", force_report: false) with indexes 97..99
[strling] got 1 treads for locus: (tid: 18, left: 52680577, left_most: 52680005, right: 52680718, right_most: 52681291, center_mass: 52680714, n_left: 2, n_right: 7, n_total: 19, repeat: "AT", name: "", force_report: false) with indexes 64..65
[strling] got 2 treads for locus: (tid: 18, left: 81468142, left_most: 81467312, right: 81468190, right_most: 81468664, center_mass: 81468142, n_left: 0, n_right: 11, n_total: 232, repeat: "AT", name: "", force_report: false) with indexes 79..81
[strling] got 1 treads for locus: (tid: 18, left: 92239733, left_most: 92239090, right: 92239778, right_most: 92240376, center_mass: 92239770, n_left: 5, n_right: 9, n_total: 17, repeat: "AT", name: "", force_report: false) with indexes 79..80
[strling] got 2 treads for locus: (tid: 18, left: 140646237, left_most: 140645446, right: 140646238, right_most: 140646732, center_mass: 140646238, n_left: 0, n_right: 20, n_total: 46, repeat: "AT", name: "", force_report: false) with indexes 114..116
[strling] got 2 treads for locus: (tid: 18, left: 154357598, left_most: 154356962, right: 154357599, right_most: 154358342, center_mass: 154357837, n_left: 2, n_right: 1, n_total: 114, repeat: "AT", name: "", force_report: false) with indexes 125..127
[strling] got 2 treads for locus: (tid: 18, left: 162747474, left_most: 162746811, right: 162747493, right_most: 162748097, center_mass: 162747493, n_left: 6, n_right: 32, n_total: 46, repeat: "AT", name: "", force_report: false) with indexes 139..141
[strling] got 4 treads for locus: (tid: 17, left: 170105374, left_most: 170104738, right: 170105394, right_most: 170106024, center_mass: 170105394, n_left: 2, n_right: 42, n_total: 49, repeat: "AG", name: "", force_report: false) with indexes 28..32
[strling] got 5 treads for locus: (tid: 14, left: 25412763, left_most: 25412120, right: 25412785, right_most: 25413406, center_mass: 25412763, n_left: 25, n_right: 18, n_total: 44, repeat: "AG", name: "", force_report: false) with indexes 0..5
[strling] got 2 treads for locus: (tid: 1, left: 1633549, left_most: 1632896, right: 1633612, right_most: 1634182, center_mass: 1633565, n_left: 15, n_right: 14, n_total: 41, repeat: "ATCT", name: "", force_report: false) with indexes 0..2
[strling] got 2 treads for locus: (tid: 16, left: 39348424, left_most: 39347598, right: 39348483, right_most: 39348884, center_mass: 39348394, n_left: 8, n_right: 3, n_total: 118, repeat: "AAAAG", name: "", force_report: false) with indexes 0..2
[strling] got 2 treads for locus: (tid: 10, left: 32085356, left_most: 32084439, right: 32085357, right_most: 32085725, center_mass: 32085356, n_left: 0, n_right: 0, n_total: 22, repeat: "ATGG", name: "", force_report: false) with indexes 0..2
[strling] got 1 treads for locus: (tid: 11, left: 17214463, left_most: 17213820, right: 17214492, right_most: 17215106, center_mass: 17214492, n_left: 30, n_right: 33, n_total: 64, repeat: "GT", name: "", force_report: false) with indexes 3..4
[strling] got 1 treads for locus: (tid: 15, left: 103099700, left_most: 103099058, right: 103099701, right_most: 103100344, center_mass: 103099701, n_left: 0, n_right: 10, n_total: 14, repeat: "CTTTT", name: "", force_report: false) with indexes 0..1
[strling] got 1 treads for locus: (tid: 1, left: 100314970, left_most: 100314328, right: 100314971, right_most: 100315614, center_mass: 100315028, n_left: 0, n_right: 12, n_total: 39, repeat: "AAGGG", name: "", force_report: false) with indexes 0..1
[strling] got 4 treads for locus: (tid: 20, left: 50570226, left_most: 50569583, right: 50570273, right_most: 50570869, center_mass: 50570273, n_left: 8, n_right: 49, n_total: 58, repeat: "ATTTT", name: "", force_report: false) with indexes 1..5
[strling] got 2 treads for locus: (tid: 8, left: 56792730, left_most: 56791909, right: 56792731, right_most: 56793195, center_mass: 56792821, n_left: 5, n_right: 0, n_total: 440, repeat: "GGT", name: "", force_report: false) with indexes 0..2
[strling] got 1 treads for locus: (tid: 1, left: 8362544, left_most: 8361821, right: 8362545, right_most: 8363205, center_mass: 8362918, n_left: 10, n_right: 4, n_total: 735, repeat: "AT", name: "", force_report: false) with indexes 7..8
[strling] got 3 treads for locus: (tid: 1, left: 32830121, left_most: 32829229, right: 32830141, right_most: 32830515, center_mass: 32830141, n_left: 28, n_right: 47, n_total: 107, repeat: "AT", name: "", force_report: false) with indexes 22..25
[strling] got 2 treads for locus: (tid: 1, left: 83413354, left_most: 83412711, right: 83413368, right_most: 83413997, center_mass: 83413368, n_left: 4, n_right: 28, n_total: 33, repeat: "AT", name: "", force_report: false) with indexes 68..70
[strling] got 4 treads for locus: (tid: 0, left: 154714544, left_most: 154713326, right: 154714545, right_most: 154714707, center_mass: 154714544, n_left: 1, n_right: 0, n_total: 111, repeat: "GT", name: "", force_report: false) with indexes 28..32
[strling] got 6 treads for locus: (tid: 19, left: 4391252, left_most: 4391068, right: 4391253, right_most: 4391331, center_mass: 4391271, n_left: 0, n_right: 8, n_total: 36, repeat: "AAAG", name: "", force_report: false) with indexes 1..7
[strling] got 6 treads for locus: (tid: 15, left: 115360784, left_most: 115360133, right: 115360786, right_most: 115361419, center_mass: 115360784, n_left: 0, n_right: 54, n_total: 61, repeat: "AG", name: "", force_report: false) with indexes 10..16
[strling] got 2 treads for locus: (tid: 1, left: 103810918, left_most: 103810276, right: 103810919, right_most: 103811562, center_mass: 103810919, n_left: 0, n_right: 42, n_total: 44, repeat: "AC", name: "", force_report: false) with indexes 11..13
[strling] got 6 treads for locus: (tid: 18, left: 14449049, left_most: 14448961, right: 14449050, right_most: 14449068, center_mass: 14449050, n_left: 0, n_right: 176, n_total: 177, repeat: "GT", name: "", force_report: false) with indexes 3..9
[strling] got 2 treads for locus: (tid: 3, left: 67184705, left_most: 67183885, right: 67184722, right_most: 67185171, center_mass: 67184705, n_left: 3, n_right: 3, n_total: 29, repeat: "AAG", name: "", force_report: false) with indexes 3..5
[strling] got 6 treads for locus: (tid: 16, left: 20102058, left_most: 20101415, right: 20102092, right_most: 20102701, center_mass: 20102092, n_left: 13, n_right: 46, n_total: 60, repeat: "ATTTT", name: "", force_report: false) with indexes 0..6
[strling] got 2 treads for locus: (tid: 16, left: 146104237, left_most: 146103457, right: 146104279, right_most: 146104743, center_mass: 146104237, n_left: 0, n_right: 11, n_total: 86, repeat: "AG", name: "", force_report: false) with indexes 19..21
[strling] got 1 treads for locus: (tid: 16, left: 33162556, left_most: 33161838, right: 33162557, right_most: 33163124, center_mass: 33162615, n_left: 5, n_right: 0, n_total: 101, repeat: "CTT", name: "", force_report: false) with indexes 0..1
[strling] got 10 treads for locus: (tid: 14, left: 32424574, left_most: 32423886, right: 32424602, right_most: 32425172, center_mass: 32424602, n_left: 6, n_right: 43, n_total: 114, repeat: "CTT", name: "", force_report: false) with indexes 0..10
SIGSEGV: Illegal storage access. (Attempt to read from nil?)
brentp commented 1 year ago

Thanks @christopher-schroeder . can you show the command that you are running? I think something must be odd about these samples but we should be able to give a better error message. Unfortunately, the SIGSEGV still doesn't help us know where it came from. I expect an array or something is empty and we are expecting at least 1 value.

christopher-schroeder commented 1 year ago

I am the one who have to say "thank you"! The command is

./strling_debug call -f resources/genome.dna.homo_sapiens.GRCh38.100.fasta -b results/strling/merge/tremor-ataxia-bounds.reduced.txt -o results/strling/call/tremor-ataxia/AAD-NAN-ROU-560-80 /vol/nano/depienne/ataxia/dna-seq-varlociraptor-central/results/recal/AAD-NAN-ROU-560-80.cram results/strling/extract/AAD-NAN-ROU-560-80.bin 2> logs/strling/call/tremor-ataxia/AAD-NAN-ROU-560-80.log

I observe a different sized log, when I rerun the command

strling version: 0.5.1
compiled in debug mode
using first reads in fragment_length_distribution calculation as there were not enough
Read 1999 bounds from results/strling/merge/tremor-ataxia-bounds.reduced.txt
[strling] got 2 treads for locus: (tid: 23, left: 135646175, left_most: 135645361, right: 135646629, right_most: 135646647, center_mass: 135646175, n_left: 0, n_right: 2, n_total: 132, repeat: "AT", name: "", force_report: false) with indexes 97..99
[strling] got 1 treads for locus: (tid: 18, left: 52680577, left_most: 52680005, right: 52680718, right_most: 52681291, center_mass: 52680714, n_left: 2, n_right: 7, n_total: 19, repeat: "AT", name: "", force_report: false) with indexes 64..65
[strling] got 2 treads for locus: (tid: 18, left: 81468142, left_most: 81467312, right: 81468190, right_most: 81468664, center_mass: 81468142, n_left: 0, n_right: 11, n_total: 232, repeat: "AT", name: "", force_report: false) with indexes 79..81
[strling] got 1 treads for locus: (tid: 18, left: 92239733, left_most: 92239090, right: 92239778, right_most: 92240376, center_mass: 92239770, n_left: 5, n_right: 9, n_total: 17, repeat: "AT", name: "", force_report: false) with indexes 79..80
[strling] got 2 treads for locus: (tid: 18, left: 140646237, left_most: 140645446, right: 140646238, right_most: 140646732, center_mass: 140646238, n_left: 0, n_right: 20, n_total: 46, repeat: "AT", name: "", force_report: false) with indexes 114..116
[strling] got 2 treads for locus: (tid: 18, left: 154357598, left_most: 154356962, right: 154357599, right_most: 154358342, center_mass: 154357837, n_left: 2, n_right: 1, n_total: 114, repeat: "AT", name: "", force_report: false) with indexes 125..127
[strling] got 2 treads for locus: (tid: 18, left: 162747474, left_most: 162746811, right: 162747493, right_most: 162748097, center_mass: 162747493, n_left: 6, n_right: 32, n_total: 46, repeat: "AT", name: "", force_report: false) with indexes 139..141
[strling] got 4 treads for locus: (tid: 17, left: 170105374, left_most: 170104738, right: 170105394, right_most: 170106024, center_mass: 170105394, n_left: 2, n_right: 42, n_total: 49, repeat: "AG", name: "", force_report: false) with indexes 28..32
[strling] got 5 treads for locus: (tid: 14, left: 25412763, left_most: 25412120, right: 25412785, right_most: 25413406, center_mass: 25412763, n_left: 25, n_right: 18, n_total: 44, repeat: "AG", name: "", force_report: false) with indexes 0..5
[strling] got 2 treads for locus: (tid: 1, left: 1633549, left_most: 1632896, right: 1633612, right_most: 1634182, center_mass: 1633565, n_left: 15, n_right: 14, n_total: 41, repeat: "ATCT", name: "", force_report: false) with indexes 0..2
[strling] got 2 treads for locus: (tid: 16, left: 39348424, left_most: 39347598, right: 39348483, right_most: 39348884, center_mass: 39348394, n_left: 8, n_right: 3, n_total: 118, repeat: "AAAAG", name: "", force_report: false) with indexes 0..2
[strling] got 2 treads for locus: (tid: 10, left: 32085356, left_most: 32084439, right: 32085357, right_most: 32085725, center_mass: 32085356, n_left: 0, n_right: 0, n_total: 22, repeat: "ATGG", name: "", force_report: false) with indexes 0..2
[strling] got 1 treads for locus: (tid: 11, left: 17214463, left_most: 17213820, right: 17214492, right_most: 17215106, center_mass: 17214492, n_left: 30, n_right: 33, n_total: 64, repeat: "GT", name: "", force_report: false) with indexes 3..4
[strling] got 1 treads for locus: (tid: 15, left: 103099700, left_most: 103099058, right: 103099701, right_most: 103100344, center_mass: 103099701, n_left: 0, n_right: 10, n_total: 14, repeat: "CTTTT", name: "", force_report: false) with indexes 0..1
[strling] got 1 treads for locus: (tid: 1, left: 100314970, left_most: 100314328, right: 100314971, right_most: 100315614, center_mass: 100315028, n_left: 0, n_right: 12, n_total: 39, repeat: "AAGGG", name: "", force_report: false) with indexes 0..1
[strling] got 4 treads for locus: (tid: 20, left: 50570226, left_most: 50569583, right: 50570273, right_most: 50570869, center_mass: 50570273, n_left: 8, n_right: 49, n_total: 58, repeat: "ATTTT", name: "", force_report: false) with indexes 1..5
[strling] got 2 treads for locus: (tid: 8, left: 56792730, left_most: 56791909, right: 56792731, right_most: 56793195, center_mass: 56792821, n_left: 5, n_right: 0, n_total: 440, repeat: "GGT", name: "", force_report: false) with indexes 0..2
[strling] got 1 treads for locus: (tid: 1, left: 8362544, left_most: 8361821, right: 8362545, right_most: 8363205, center_mass: 8362918, n_left: 10, n_right: 4, n_total: 735, repeat: "AT", name: "", force_report: false) with indexes 7..8
[strling] got 3 treads for locus: (tid: 1, left: 32830121, left_most: 32829229, right: 32830141, right_most: 32830515, center_mass: 32830141, n_left: 28, n_right: 47, n_total: 107, repeat: "AT", name: "", force_report: false) with indexes 22..25
[strling] got 2 treads for locus: (tid: 1, left: 83413354, left_most: 83412711, right: 83413368, right_most: 83413997, center_mass: 83413368, n_left: 4, n_right: 28, n_total: 33, repeat: "AT", name: "", force_report: false) with indexes 68..70
[strling] got 4 treads for locus: (tid: 0, left: 154714544, left_most: 154713326, right: 154714545, right_most: 154714707, center_mass: 154714544, n_left: 1, n_right: 0, n_total: 111, repeat: "GT", name: "", force_report: false) with indexes 28..32
[strling] got 6 treads for locus: (tid: 19, left: 4391252, left_most: 4391068, right: 4391253, right_most: 4391331, center_mass: 4391271, n_left: 0, n_right: 8, n_total: 36, repeat: "AAAG", name: "", force_report: false) with indexes 1..7
[strling] got 6 treads for locus: (tid: 15, left: 115360784, left_most: 115360133, right: 115360786, right_most: 115361419, center_mass: 115360784, n_left: 0, n_right: 54, n_total: 61, repeat: "AG", name: "", force_report: false) with indexes 10..16
[strling] got 2 treads for locus: (tid: 1, left: 103810918, left_most: 103810276, right: 103810919, right_most: 103811562, center_mass: 103810919, n_left: 0, n_right: 42, n_total: 44, repeat: "AC", name: "", force_report: false) with indexes 11..13
[strling] got 6 treads for locus: (tid: 18, left: 14449049, left_most: 14448961, right: 14449050, right_most: 14449068, center_mass: 14449050, n_left: 0, n_right: 176, n_total: 177, repeat: "GT", name: "", force_report: false) with indexes 3..9
[strling] got 2 treads for locus: (tid: 3, left: 67184705, left_most: 67183885, right: 67184722, right_most: 67185171, center_mass: 67184705, n_left: 3, n_right: 3, n_total: 29, repeat: "AAG", name: "", force_report: false) with indexes 3..5
[strling] got 6 treads for locus: (tid: 16, left: 20102058, left_most: 20101415, right: 20102092, right_most: 20102701, center_mass: 20102092, n_left: 13, n_right: 46, n_total: 60, repeat: "ATTTT", name: "", force_report: false) with indexes 0..6
[strling] got 2 treads for locus: (tid: 16, left: 146104237, left_most: 146103457, right: 146104279, right_most: 146104743, center_mass: 146104237, n_left: 0, n_right: 11, n_total: 86, repeat: "AG", name: "", force_report: false) with indexes 19..21
[strling] got 1 treads for locus: (tid: 16, left: 33162556, left_most: 33161838, right: 33162557, right_most: 33163124, center_mass: 33162615, n_left: 5, n_right: 0, n_total: 101, repeat: "CTT", name: "", force_report: false) with indexes 0..1
[strling] got 10 treads for locus: (tid: 14, left: 32424574, left_most: 32423886, right: 32424602, right_most: 32425172, center_mass: 32424602, n_left: 6, n_right: 43, n_total: 114, repeat: "CTT", name: "", force_report: false) with indexes 0..10
[strling] got 16 treads for locus: (tid: 28, left: 4880, left_most: 3555, right: 4894, right_most: 4920, center_mass: 4880, n_left: 436, n_right: 45, n_total: 545, repeat: "ATTCC", name: "", force_report: false) with indexes 0..16
[strling] got 2 treads for locus: (tid: 18, left: 65278016, left_most: 65277373, right: 65278061, right_most: 65278659, center_mass: 65278061, n_left: 17, n_right: 65, n_total: 87, repeat: "CTTTT", name: "", force_report: false) with indexes 2..4
[strling] got 4 treads for locus: (tid: 1, left: 33028281, left_most: 33027620, right: 33028304, right_most: 33028906, center_mass: 33028275, n_left: 2, n_right: 50, n_total: 55, repeat: "CT", name: "", force_report: false) with indexes 5..9
[strling] got 2 treads for locus: (tid: 1, left: 44765520, left_most: 44764588, right: 44765581, right_most: 44765968, center_mass: 44765581, n_left: 3, n_right: 5, n_total: 605, repeat: "CT", name: "", force_report: false) with indexes 6..8
[strling] got 2 treads for locus: (tid: 1, left: 96415716, left_most: 96414756, right: 96415775, right_most: 96416100, center_mass: 96415775, n_left: 10, n_right: 15, n_total: 889, repeat: "CT", name: "", force_report: false) with indexes 13..15
[strling] got 2 treads for locus: (tid: 16, left: 28124614, left_most: 28123971, right: 28124631, right_most: 28125257, center_mass: 28124614, n_left: 25, n_right: 15, n_total: 54, repeat: "AT", name: "", force_report: false) with indexes 18..20
[strling] got 1 treads for locus: (tid: 16, left: 28987290, left_most: 28986490, right: 28987308, right_most: 28987776, center_mass: 28987290, n_left: 1, n_right: 6, n_total: 43, repeat: "AT", name: "", force_report: false) with indexes 18..19
[strling] got 1 treads for locus: (tid: 16, left: 32734032, left_most: 32733390, right: 32734033, right_most: 32734676, center_mass: 32734033, n_left: 0, n_right: 13, n_total: 17, repeat: "AT", name: "", force_report: false) with indexes 19..20
[strling] got 4 treads for locus: (tid: 16, left: 49039306, left_most: 49038663, right: 49039333, right_most: 49039949, center_mass: 49039306, n_left: 27, n_right: 12, n_total: 45, repeat: "AT", name: "", force_report: false) with indexes 39..43
[strling] got 4 treads for locus: (tid: 16, left: 125073890, left_most: 125073247, right: 125073911, right_most: 125074533, center_mass: 125073911, n_left: 14, n_right: 30, n_total: 47, repeat: "AT", name: "", force_report: false) with indexes 128..132
[strling] got 4 treads for locus: (tid: 16, left: 157940772, left_most: 157940129, right: 157940786, right_most: 157941415, center_mass: 157940786, n_left: 21, n_right: 26, n_total: 49, repeat: "AT", name: "", force_report: false) with indexes 158..162
[strling] got 8 treads for locus: (tid: 10, left: 29016186, left_most: 29015543, right: 29016323, right_most: 29016829, center_mass: 29016186, n_left: 49, n_right: 2, n_total: 53, repeat: "CT", name: "", force_report: false) with indexes 23..31
[strling] got 2 treads for locus: (tid: 6, left: 96280712, left_most: 96280051, right: 96280713, right_most: 96281337, center_mass: 96280798, n_left: 3, n_right: 0, n_total: 34, repeat: "AAG", name: "", force_report: false) with indexes 0..2
[strling] got 2 treads for locus: (tid: 17, left: 10084364, left_most: 10083695, right: 10084403, right_most: 10084981, center_mass: 10084364, n_left: 31, n_right: 2, n_total: 52, repeat: "AT", name: "", force_report: false) with indexes 14..16
[strling] got 2 treads for locus: (tid: 17, left: 16982888, left_most: 16982110, right: 16982929, right_most: 16983396, center_mass: 16982888, n_left: 1, n_right: 9, n_total: 42, repeat: "AT", name: "", force_report: false) with indexes 25..27
[strling] got 1 treads for locus: (tid: 17, left: 43043828, left_most: 43043039, right: 43043829, right_most: 43044325, center_mass: 43043829, n_left: 0, n_right: 2, n_total: 42, repeat: "AT", name: "", force_report: false) with indexes 82..83
[strling] got 1 treads for locus: (tid: 17, left: 85856420, left_most: 85855611, right: 85856421, right_most: 85856897, center_mass: 85856420, n_left: 0, n_right: 1, n_total: 50, repeat: "AT", name: "", force_report: false) with indexes 114..115
[strling] got 1 treads for locus: (tid: 17, left: 143012552, left_most: 143011849, right: 143012575, right_most: 143013135, center_mass: 143012575, n_left: 11, n_right: 26, n_total: 53, repeat: "AT", name: "", force_report: false) with indexes 164..165
[strling] got 6 treads for locus: (tid: 17, left: 160092013, left_most: 160091370, right: 160092026, right_most: 160092656, center_mass: 160092026, n_left: 22, n_right: 27, n_total: 50, repeat: "AT", name: "", force_report: false) with indexes 187..193
[strling] got 2 treads for locus: (tid: 17, left: 172368571, left_most: 172367784, right: 172368572, right_most: 172369070, center_mass: 172368593, n_left: 0, n_right: 2, n_total: 32, repeat: "AT", name: "", force_report: false) with indexes 199..201
[strling] got 1 treads for locus: (tid: 17, left: 85316061, left_most: 85315418, right: 85316120, right_most: 85316704, center_mass: 85316120, n_left: 2, n_right: 54, n_total: 68, repeat: "ATTTT", name: "", force_report: false) with indexes 0..1
[strling] got 2 treads for locus: (tid: 19, left: 2812636, left_most: 2811977, right: 2812697, right_most: 2813263, center_mass: 2812636, n_left: 13, n_right: 5, n_total: 30, repeat: "ACATC", name: "", force_report: false) with indexes 0..2
[strling] got 6 treads for locus: (tid: 16, left: 53885247, left_most: 53885223, right: 53885248, right_most: 53885277, center_mass: 53885247, n_left: 134, n_right: 0, n_total: 137, repeat: "AAG", name: "", force_report: false) with indexes 0..6
[strling] got 1 treads for locus: (tid: 16, left: 65045263, left_most: 65044513, right: 65045264, right_most: 65045799, center_mass: 65045263, n_left: 34, n_right: 1, n_total: 81, repeat: "AAG", name: "", force_report: false) with indexes 0..1
[strling] got 2 treads for locus: (tid: 16, left: 137322710, left_most: 137321926, right: 137322739, right_most: 137323212, center_mass: 137322710, n_left: 64, n_right: 58, n_total: 207, repeat: "AAG", name: "", force_report: false) with indexes 0..2
[strling] got 4 treads for locus: (tid: 16, left: 156014090, left_most: 156013227, right: 156014091, right_most: 156014513, center_mass: 156013987, n_left: 45, n_right: 0, n_total: 156, repeat: "AAG", name: "", force_report: false) with indexes 4..8
[strling] got 14 treads for locus: (tid: 16, left: 179857398, left_most: 179856755, right: 179857422, right_most: 179858041, center_mass: 179857398, n_left: 178, n_right: 91, n_total: 270, repeat: "AAG", name: "", force_report: false) with indexes 4..18
[strling] got 3 treads for locus: (tid: 10, left: 40880762, left_most: 40880120, right: 40880763, right_most: 40881406, center_mass: 40880763, n_left: 0, n_right: 42, n_total: 44, repeat: "AG", name: "", force_report: false) with indexes 7..10
[strling] got 2 treads for locus: (tid: 15, left: 171562605, left_most: 171561679, right: 171562803, right_most: 171562965, center_mass: 171562592, n_left: 9, n_right: 4, n_total: 698, repeat: "CTT", name: "", force_report: false) with indexes 4..6
[strling] got 2 treads for locus: (tid: 15, left: 123348036, left_most: 123347393, right: 123348089, right_most: 123348679, center_mass: 123348036, n_left: 36, n_right: 15, n_total: 52, repeat: "GT", name: "", force_report: false) with indexes 50..52
[strling] got 2 treads for locus: (tid: 16, left: 190111590, left_most: 190110948, right: 190111591, right_most: 190112234, center_mass: 190111591, n_left: 0, n_right: 4, n_total: 8, repeat: "AGGGTT", name: "", force_report: false) with indexes 0..2
[strling] got 2 treads for locus: (tid: 5, left: 104300949, left_most: 104300282, right: 104300989, right_most: 104301568, center_mass: 104300982, n_left: 4, n_right: 4, n_total: 21, repeat: "CCG", name: "", force_report: false) with indexes 0..2
[strling] got 5 treads for locus: (tid: 39, left: 173036, left_most: 172835, right: 173037, right_most: 173147, center_mass: 173036, n_left: 16, n_right: 0, n_total: 17, repeat: "AATGG", name: "", force_report: false) with indexes 0..5
SIGSEGV: Illegal storage access. (Attempt to read from nil?)

So the error is at least partially non-deterministic, which I find very odd.

brentp commented 1 year ago

Can you try the binary attached here? (just download, gunzip, chmod+x) It will likely give the same segfault, but maybe a bit more info.

If this doesn't yield antying useful, it would be helpful to run the extract with debug binary as well.

strling_dbg_dev.gz

christopher-schroeder commented 1 year ago

I've run this 4 times in a row now

./strling_dbg_dev call -f resources/genome.dna.homo_sapiens.GRCh38.100.fasta -b results/strling/merge/tremor-ataxia-bounds.reduced.txt -o results/strling/call/tremor-ataxia/AAD-NAN-ROU-560-80 /vol/nano/depienne/ataxia/dna-seq-varlociraptor-central/results/recal/AAD-NAN-ROU-560-80.cram results/strling/extract/AAD-NAN-ROU-560-80.bin 2> logs/strling/call/tremor-ataxia/AAD-NAN-ROU-560-80.log

strling version: 0.5.1
compiled in debug mode
using first reads in fragment_length_distribution calculation as there were not enough
Read 1999 bounds from results/strling/merge/tremor-ataxia-bounds.reduced.txt
[strling] got 2 treads for locus: (tid: 23, left: 135646175, left_most: 135645361, right: 135646629, right_most: 135646647, center_mass: 135646175, n_left: 0, n_right: 2, n_total: 132, repeat: "AT", name: "", force_report: false) with indexes 97..99
[strling] got 1 treads for locus: (tid: 18, left: 52680577, left_most: 52680005, right: 52680718, right_most: 52681291, center_mass: 52680714, n_left: 2, n_right: 7, n_total: 19, repeat: "AT", name: "", force_report: false) with indexes 64..65
[strling] got 2 treads for locus: (tid: 18, left: 81468142, left_most: 81467312, right: 81468190, right_most: 81468664, center_mass: 81468142, n_left: 0, n_right: 11, n_total: 232, repeat: "AT", name: "", force_report: false) with indexes 79..81
[strling] got 1 treads for locus: (tid: 18, left: 92239733, left_most: 92239090, right: 92239778, right_most: 92240376, center_mass: 92239770, n_left: 5, n_right: 9, n_total: 17, repeat: "AT", name: "", force_report: false) with indexes 79..80
[strling] got 2 treads for locus: (tid: 18, left: 140646237, left_most: 140645446, right: 140646238, right_most: 140646732, center_mass: 140646238, n_left: 0, n_right: 20, n_total: 46, repeat: "AT", name: "", force_report: false) with indexes 114..116
[strling] got 2 treads for locus: (tid: 18, left: 154357598, left_most: 154356962, right: 154357599, right_most: 154358342, center_mass: 154357837, n_left: 2, n_right: 1, n_total: 114, repeat: "AT", name: "", force_report: false) with indexes 125..127
[strling] got 2 treads for locus: (tid: 18, left: 162747474, left_most: 162746811, right: 162747493, right_most: 162748097, center_mass: 162747493, n_left: 6, n_right: 32, n_total: 46, repeat: "AT", name: "", force_report: false) with indexes 139..141
[strling] got 4 treads for locus: (tid: 17, left: 170105374, left_most: 170104738, right: 170105394, right_most: 170106024, center_mass: 170105394, n_left: 2, n_right: 42, n_total: 49, repeat: "AG", name: "", force_report: false) with indexes 28..32
[strling] got 5 treads for locus: (tid: 14, left: 25412763, left_most: 25412120, right: 25412785, right_most: 25413406, center_mass: 25412763, n_left: 25, n_right: 18, n_total: 44, repeat: "AG", name: "", force_report: false) with indexes 0..5
[strling] got 2 treads for locus: (tid: 1, left: 1633549, left_most: 1632896, right: 1633612, right_most: 1634182, center_mass: 1633565, n_left: 15, n_right: 14, n_total: 41, repeat: "ATCT", name: "", force_report: false) with indexes 0..2
[strling] got 2 treads for locus: (tid: 16, left: 39348424, left_most: 39347598, right: 39348483, right_most: 39348884, center_mass: 39348394, n_left: 8, n_right: 3, n_total: 118, repeat: "AAAAG", name: "", force_report: false) with indexes 0..2
[strling] got 2 treads for locus: (tid: 10, left: 32085356, left_most: 32084439, right: 32085357, right_most: 32085725, center_mass: 32085356, n_left: 0, n_right: 0, n_total: 22, repeat: "ATGG", name: "", force_report: false) with indexes 0..2
[strling] got 1 treads for locus: (tid: 11, left: 17214463, left_most: 17213820, right: 17214492, right_most: 17215106, center_mass: 17214492, n_left: 30, n_right: 33, n_total: 64, repeat: "GT", name: "", force_report: false) with indexes 3..4
[strling] got 1 treads for locus: (tid: 15, left: 103099700, left_most: 103099058, right: 103099701, right_most: 103100344, center_mass: 103099701, n_left: 0, n_right: 10, n_total: 14, repeat: "CTTTT", name: "", force_report: false) with indexes 0..1
[strling] got 1 treads for locus: (tid: 1, left: 100314970, left_most: 100314328, right: 100314971, right_most: 100315614, center_mass: 100315028, n_left: 0, n_right: 12, n_total: 39, repeat: "AAGGG", name: "", force_report: false) with indexes 0..1
[strling] got 4 treads for locus: (tid: 20, left: 50570226, left_most: 50569583, right: 50570273, right_most: 50570869, center_mass: 50570273, n_left: 8, n_right: 49, n_total: 58, repeat: "ATTTT", name: "", force_report: false) with indexes 1..5
[strling] got 2 treads for locus: (tid: 8, left: 56792730, left_most: 56791909, right: 56792731, right_most: 56793195, center_mass: 56792821, n_left: 5, n_right: 0, n_total: 440, repeat: "GGT", name: "", force_report: false) with indexes 0..2
[strling] got 1 treads for locus: (tid: 1, left: 8362544, left_most: 8361821, right: 8362545, right_most: 8363205, center_mass: 8362918, n_left: 10, n_right: 4, n_total: 735, repeat: "AT", name: "", force_report: false) with indexes 7..8
[strling] got 3 treads for locus: (tid: 1, left: 32830121, left_most: 32829229, right: 32830141, right_most: 32830515, center_mass: 32830141, n_left: 28, n_right: 47, n_total: 107, repeat: "AT", name: "", force_report: false) with indexes 22..25
[strling] got 2 treads for locus: (tid: 1, left: 83413354, left_most: 83412711, right: 83413368, right_most: 83413997, center_mass: 83413368, n_left: 4, n_right: 28, n_total: 33, repeat: "AT", name: "", force_report: false) with indexes 68..70
fatal.nim(53)            sysFatal
Error: unhandled exception: collect.nim(37, 12) `L.start <= R.start`  [AssertionDefect]
strling version: 0.5.1
compiled in debug mode
using first reads in fragment_length_distribution calculation as there were not enough
Read 1999 bounds from results/strling/merge/tremor-ataxia-bounds.reduced.txt
SIGSEGV: Illegal storage access. (Attempt to read from nil?)
strling version: 0.5.1
compiled in debug mode
using first reads in fragment_length_distribution calculation as there were not enough
Read 1999 bounds from results/strling/merge/tremor-ataxia-bounds.reduced.txt
[strling] got 2 treads for locus: (tid: 23, left: 135646175, left_most: 135645361, right: 135646629, right_most: 135646647, center_mass: 135646175, n_left: 0, n_right: 2, n_total: 132, repeat: "AT", name: "", force_report: false) with indexes 97..99
[strling] got 1 treads for locus: (tid: 18, left: 52680577, left_most: 52680005, right: 52680718, right_most: 52681291, center_mass: 52680714, n_left: 2, n_right: 7, n_total: 19, repeat: "AT", name: "", force_report: false) with indexes 64..65
[strling] got 2 treads for locus: (tid: 18, left: 81468142, left_most: 81467312, right: 81468190, right_most: 81468664, center_mass: 81468142, n_left: 0, n_right: 11, n_total: 232, repeat: "AT", name: "", force_report: false) with indexes 79..81
[strling] got 1 treads for locus: (tid: 18, left: 92239733, left_most: 92239090, right: 92239778, right_most: 92240376, center_mass: 92239770, n_left: 5, n_right: 9, n_total: 17, repeat: "AT", name: "", force_report: false) with indexes 79..80
[strling] got 2 treads for locus: (tid: 18, left: 140646237, left_most: 140645446, right: 140646238, right_most: 140646732, center_mass: 140646238, n_left: 0, n_right: 20, n_total: 46, repeat: "AT", name: "", force_report: false) with indexes 114..116
[strling] got 2 treads for locus: (tid: 18, left: 154357598, left_most: 154356962, right: 154357599, right_most: 154358342, center_mass: 154357837, n_left: 2, n_right: 1, n_total: 114, repeat: "AT", name: "", force_report: false) with indexes 125..127
[strling] got 2 treads for locus: (tid: 18, left: 162747474, left_most: 162746811, right: 162747493, right_most: 162748097, center_mass: 162747493, n_left: 6, n_right: 32, n_total: 46, repeat: "AT", name: "", force_report: false) with indexes 139..141
[strling] got 4 treads for locus: (tid: 17, left: 170105374, left_most: 170104738, right: 170105394, right_most: 170106024, center_mass: 170105394, n_left: 2, n_right: 42, n_total: 49, repeat: "AG", name: "", force_report: false) with indexes 28..32
[strling] got 5 treads for locus: (tid: 14, left: 25412763, left_most: 25412120, right: 25412785, right_most: 25413406, center_mass: 25412763, n_left: 25, n_right: 18, n_total: 44, repeat: "AG", name: "", force_report: false) with indexes 0..5
[strling] got 2 treads for locus: (tid: 1, left: 1633549, left_most: 1632896, right: 1633612, right_most: 1634182, center_mass: 1633565, n_left: 15, n_right: 14, n_total: 41, repeat: "ATCT", name: "", force_report: false) with indexes 0..2
[strling] got 2 treads for locus: (tid: 16, left: 39348424, left_most: 39347598, right: 39348483, right_most: 39348884, center_mass: 39348394, n_left: 8, n_right: 3, n_total: 118, repeat: "AAAAG", name: "", force_report: false) with indexes 0..2
[strling] got 2 treads for locus: (tid: 10, left: 32085356, left_most: 32084439, right: 32085357, right_most: 32085725, center_mass: 32085356, n_left: 0, n_right: 0, n_total: 22, repeat: "ATGG", name: "", force_report: false) with indexes 0..2
[strling] got 1 treads for locus: (tid: 11, left: 17214463, left_most: 17213820, right: 17214492, right_most: 17215106, center_mass: 17214492, n_left: 30, n_right: 33, n_total: 64, repeat: "GT", name: "", force_report: false) with indexes 3..4
[strling] got 1 treads for locus: (tid: 15, left: 103099700, left_most: 103099058, right: 103099701, right_most: 103100344, center_mass: 103099701, n_left: 0, n_right: 10, n_total: 14, repeat: "CTTTT", name: "", force_report: false) with indexes 0..1
[strling] got 1 treads for locus: (tid: 1, left: 100314970, left_most: 100314328, right: 100314971, right_most: 100315614, center_mass: 100315028, n_left: 0, n_right: 12, n_total: 39, repeat: "AAGGG", name: "", force_report: false) with indexes 0..1
[strling] got 4 treads for locus: (tid: 20, left: 50570226, left_most: 50569583, right: 50570273, right_most: 50570869, center_mass: 50570273, n_left: 8, n_right: 49, n_total: 58, repeat: "ATTTT", name: "", force_report: false) with indexes 1..5
[strling] got 2 treads for locus: (tid: 8, left: 56792730, left_most: 56791909, right: 56792731, right_most: 56793195, center_mass: 56792821, n_left: 5, n_right: 0, n_total: 440, repeat: "GGT", name: "", force_report: false) with indexes 0..2
[strling] got 1 treads for locus: (tid: 1, left: 8362544, left_most: 8361821, right: 8362545, right_most: 8363205, center_mass: 8362918, n_left: 10, n_right: 4, n_total: 735, repeat: "AT", name: "", force_report: false) with indexes 7..8
[strling] got 3 treads for locus: (tid: 1, left: 32830121, left_most: 32829229, right: 32830141, right_most: 32830515, center_mass: 32830141, n_left: 28, n_right: 47, n_total: 107, repeat: "AT", name: "", force_report: false) with indexes 22..25
[strling] got 2 treads for locus: (tid: 1, left: 83413354, left_most: 83412711, right: 83413368, right_most: 83413997, center_mass: 83413368, n_left: 4, n_right: 28, n_total: 33, repeat: "AT", name: "", force_report: false) with indexes 68..70
fatal.nim(53)            sysFatal
Error: unhandled exception: collect.nim(37, 12) `L.start <= R.start`  [AssertionDefect]
strling version: 0.5.1
compiled in debug mode
using first reads in fragment_length_distribution calculation as there were not enough
Read 1999 bounds from results/strling/merge/tremor-ataxia-bounds.reduced.txt
[strling] got 2 treads for locus: (tid: 23, left: 135646175, left_most: 135645361, right: 135646629, right_most: 135646647, center_mass: 135646175, n_left: 0, n_right: 2, n_total: 132, repeat: "AT", name: "", force_report: false) with indexes 97..99
[strling] got 1 treads for locus: (tid: 18, left: 52680577, left_most: 52680005, right: 52680718, right_most: 52681291, center_mass: 52680714, n_left: 2, n_right: 7, n_total: 19, repeat: "AT", name: "", force_report: false) with indexes 64..65
[strling] got 2 treads for locus: (tid: 18, left: 81468142, left_most: 81467312, right: 81468190, right_most: 81468664, center_mass: 81468142, n_left: 0, n_right: 11, n_total: 232, repeat: "AT", name: "", force_report: false) with indexes 79..81
[strling] got 1 treads for locus: (tid: 18, left: 92239733, left_most: 92239090, right: 92239778, right_most: 92240376, center_mass: 92239770, n_left: 5, n_right: 9, n_total: 17, repeat: "AT", name: "", force_report: false) with indexes 79..80
[strling] got 2 treads for locus: (tid: 18, left: 140646237, left_most: 140645446, right: 140646238, right_most: 140646732, center_mass: 140646238, n_left: 0, n_right: 20, n_total: 46, repeat: "AT", name: "", force_report: false) with indexes 114..116
[strling] got 2 treads for locus: (tid: 18, left: 154357598, left_most: 154356962, right: 154357599, right_most: 154358342, center_mass: 154357837, n_left: 2, n_right: 1, n_total: 114, repeat: "AT", name: "", force_report: false) with indexes 125..127
[strling] got 2 treads for locus: (tid: 18, left: 162747474, left_most: 162746811, right: 162747493, right_most: 162748097, center_mass: 162747493, n_left: 6, n_right: 32, n_total: 46, repeat: "AT", name: "", force_report: false) with indexes 139..141
[strling] got 4 treads for locus: (tid: 17, left: 170105374, left_most: 170104738, right: 170105394, right_most: 170106024, center_mass: 170105394, n_left: 2, n_right: 42, n_total: 49, repeat: "AG", name: "", force_report: false) with indexes 28..32
[strling] got 5 treads for locus: (tid: 14, left: 25412763, left_most: 25412120, right: 25412785, right_most: 25413406, center_mass: 25412763, n_left: 25, n_right: 18, n_total: 44, repeat: "AG", name: "", force_report: false) with indexes 0..5
[strling] got 2 treads for locus: (tid: 1, left: 1633549, left_most: 1632896, right: 1633612, right_most: 1634182, center_mass: 1633565, n_left: 15, n_right: 14, n_total: 41, repeat: "ATCT", name: "", force_report: false) with indexes 0..2
[strling] got 2 treads for locus: (tid: 16, left: 39348424, left_most: 39347598, right: 39348483, right_most: 39348884, center_mass: 39348394, n_left: 8, n_right: 3, n_total: 118, repeat: "AAAAG", name: "", force_report: false) with indexes 0..2
[strling] got 2 treads for locus: (tid: 10, left: 32085356, left_most: 32084439, right: 32085357, right_most: 32085725, center_mass: 32085356, n_left: 0, n_right: 0, n_total: 22, repeat: "ATGG", name: "", force_report: false) with indexes 0..2
[strling] got 1 treads for locus: (tid: 11, left: 17214463, left_most: 17213820, right: 17214492, right_most: 17215106, center_mass: 17214492, n_left: 30, n_right: 33, n_total: 64, repeat: "GT", name: "", force_report: false) with indexes 3..4
[strling] got 1 treads for locus: (tid: 15, left: 103099700, left_most: 103099058, right: 103099701, right_most: 103100344, center_mass: 103099701, n_left: 0, n_right: 10, n_total: 14, repeat: "CTTTT", name: "", force_report: false) with indexes 0..1
[strling] got 1 treads for locus: (tid: 1, left: 100314970, left_most: 100314328, right: 100314971, right_most: 100315614, center_mass: 100315028, n_left: 0, n_right: 12, n_total: 39, repeat: "AAGGG", name: "", force_report: false) with indexes 0..1
[strling] got 4 treads for locus: (tid: 20, left: 50570226, left_most: 50569583, right: 50570273, right_most: 50570869, center_mass: 50570273, n_left: 8, n_right: 49, n_total: 58, repeat: "ATTTT", name: "", force_report: false) with indexes 1..5
[strling] got 2 treads for locus: (tid: 8, left: 56792730, left_most: 56791909, right: 56792731, right_most: 56793195, center_mass: 56792821, n_left: 5, n_right: 0, n_total: 440, repeat: "GGT", name: "", force_report: false) with indexes 0..2
SIGSEGV: Illegal storage access. (Attempt to read from nil?)

Sometimes its Illegal storage access. (Attempt to read from nil?), sometimes Error: unhandled exception: collect.nim(37, 12) L.start <= R.start [AssertionDefect]

I will perform extract now with strling_dbg_dev now

christopher-schroeder commented 1 year ago

I cannot see any debug information with the strling_dbg_dev. Is that correct?

./strling_dbg_dev extract -f resources/genome.dna.homo_sapiens.GRCh38.100.fasta -g resources/genome.dna.homo_sapiens.GRCh38.100.fasta.str /vol/nano/depienne/ataxia/dna-seq-varlociraptor-central/results/recal/AAD-NAN-ROU-560-80.cram results/strling/extract/AAD-NAN-ROU-560-80.bin 2> logs/strling/extract/AAD-NAN-ROU-560-80.log

strling version: 0.5.1
compiled in debug mode
using first reads in fragment_length_distribution calculation as there were not enough
[strling] using existing file resources/genome.dna.homo_sapiens.GRCh38.100.fasta.str for genome repeats
[strling] got STR repeats from genome into an interval tree
[strling] collecting str-like reads
[strling] extracting chromosome:1
[strling] extracting chromosome:10
[strling] extracting chromosome:11
[strling] extracting chromosome:12
[strling] extracting chromosome:13
[strling] extracting chromosome:14
[strling] extracting chromosome:15
[strling] extracting chromosome:16
[strling] extracting chromosome:17
[strling] extracting chromosome:18
[strling] extracting chromosome:19
[strling] extracting chromosome:2
[strling] extracting chromosome:20
[strling] extracting chromosome:21
[strling] extracting chromosome:22
[strling] extracting chromosome:3
[strling] extracting chromosome:4
[strling] extracting chromosome:5
[strling] extracting chromosome:6
[strling] extracting chromosome:7
[strling] extracting chromosome:8
[strling] extracting chromosome:9
[strling] extracting chromosome:X
[strling] extracting chromosome:Y
[strling] extracting unmapped reads
[strling] writing binary file:results/strling/extract/AAD-NAN-ROU-560-80.bin
[strling] finished extraction
brentp commented 1 year ago

I think that's OK. But it will write the qname to the binfile so it might help us track down later issues.

brentp commented 1 year ago

Can you run the strling call using your bin files that were extracted with the debug build and try this binary? I added more debugging stuff. It's hard to guess where the problem might be so it might not yield much.

strling_dbg_dev2.gz

christopher-schroeder commented 1 year ago

yes, this is the start and end of the log file

./strling_dbg_dev2 call -f resources/genome.dna.homo_sapiens.GRCh38.100.fasta -b results/strling/merge/tremor-ataxia-bounds.reduced.txt -o results/strling/call/tremor-ataxia/AAD-NAN-ROU-560-80 /vol/nano/depienne/ataxia/dna-seq-varlociraptor-central/results/recal/AAD-NAN-ROU-560-80.cram results/strling/extract/AAD-NAN-ROU-560-80.bin 2> logs/strling/call/tremor-ataxia/AAD-NAN-ROU-560-80.log

strling version: 0.5.1
compiled in debug mode
using first reads in fragment_length_distribution calculation as there were not enough
Read 1999 bounds from results/strling/merge/tremor-ataxia-bounds.reduced.txt
[strling] bounds:(tid: 0, left: 17191859, left_most: 17191089, right: 17191860, right_most: 17192375, center_mass: 17191859, n_left: 0, n_right: 0, n_total: 0, repeat: "CTT", name: "", force_report: true)
[strling] bounds:(tid: 0, left: 74060232, left_most: 74059589, right: 74060233, right_most: 74060875, center_mass: 74060232, n_left: 0, n_right: 0, n_total: 0, repeat: "CTT", name: "", force_report: true)
[strling] bounds:(tid: 0, left: 77888009, left_most: 77887169, right: 77888010, right_most: 77888455, center_mass: 77888010, n_left: 0, n_right: 0, n_total: 0, repeat: "CTT", name: "", force_report: true)
[strling] bounds:(tid: 0, left: 100527042, left_most: 100526274, right: 100527043, right_most: 100527560, center_mass: 100527042, n_left: 0, n_right: 0, n_total: 0, repeat: "CTT", name: "", force_report: true)
[strling] bounds:(tid: 0, left: 101657949, left_most: 101657161, right: 101657950, right_most: 101658447, center_mass: 101657949, n_left: 0, n_right: 0, n_total: 0, repeat: "CTT", name: "", force_report: true)
[strling] bounds:(tid: 0, left: 113437816, left_most: 113437004, right: 113437817, right_most: 113438290, center_mass: 113437816, n_left: 0, n_right: 0, n_total: 0, repeat: "CTT", name: "", force_report: true)
[strling] bounds:(tid: 0, left: 151867607, left_most: 151866802, right: 151867608, right_most: 151868088, center_mass: 151867608, n_left: 0, n_right: 0, n_total: 0, repeat: "CTT", name: "", force_report: true)
[strling] bounds:(tid: 0, left: 156928351, left_most: 156927591, right: 156928407, right_most: 156928877, center_mass: 156928383, n_left: 0, n_right: 0, n_total: 0, repeat: "CTT", name: "", force_report: true)
[strling] bounds:(tid: 0, left: 187043556, left_most: 187042723, right: 187043557, right_most: 187044009, center_mass: 187043556, n_left: 0, n_right: 0, n_total: 0, repeat: "CTT", name: "", force_report: true)
[strling] bounds:(tid: 0, left: 214679710, left_most: 214678838, right: 214679711, right_most: 214680124, center_mass: 214679710, n_left: 0, n_right: 0, n_total: 0, repeat: "CTT", name: "", force_report: true)
[strling] bounds:(tid: 0, left: 228466611, left_most: 228465969, right: 228466612, right_most: 228467255, center_mass: 228466612, n_left: 0, n_right: 0, n_total: 0, repeat: "CTT", name: "", force_report: true)
[strling] bounds:(tid: 0, left: 233339267, left_most: 233338530, right: 233339268, right_most: 233339816, center_mass: 233339267, n_left: 0, n_right: 0, n_total: 0, repeat: "CTT", name: "", force_report: true)
[strling] bounds:(tid: 0, left: 239662893, left_most: 239662250, right: 239662894, right_most: 239663536, center_mass: 239662893, n_left: 0, n_right: 0, n_total: 0, repeat: "CTT", name: "", force_report: true)
[strling] bounds:(tid: 5, left: 24406161, left_most: 24405518, right: 24406162, right_most: 24406804, center_mass: 24406161, n_left: 0, n_right: 0, n_total: 0, repeat: "AAAAT", name: "", force_report: true)
[strling] bounds:(tid: 8, left: 18201790, left_most: 18201137, right: 18201791, right_most: 18202423, center_mass: 18201790, n_left: 0, n_right: 0, n_total: 0, repeat: "AGAT", name: "", force_report: true)
[strling] bounds:(tid: 8, left: 70092535, left_most: 70091830, right: 70092536, right_most: 70093116, center_mass: 70092535, n_left: 0, n_right: 0, n_total: 0, repeat: "AGAT", name: "", force_report: true)
[strling] bounds:(tid: 18, left: 3550299, left_most: 3549562, right: 3550300, right_most: 3550848, center_mass: 3550299, n_left: 0, n_right: 0, n_total: 0, repeat: "CTT", name: "", force_report: true)
[strling] bounds:(tid: 18, left: 15853505, left_most: 15852794, right: 15853506, right_most: 15854080, center_mass: 15853505, n_left: 0, n_right: 0, n_total: 0, repeat: "CTT", name: "", force_report: true)
[strling] bounds:(tid: 18, left: 24029597, left_most: 24028586, right: 24029616, right_most: 24029953, center_mass: 24029597, n_left: 0, n_right: 0, n_total: 0, repeat: "CTT", name: "", force_report: true)
[strling] bounds:(tid: 18, left: 29568440, left_most: 29567719, right: 29568473, right_most: 29569005, center_mass: 29568440, n_left: 0, n_right: 0, n_total: 0, repeat: "CTT", name: "", force_report: true)
[strling] bounds:(tid: 18, left: 46744378, left_most: 46743553, right: 46744452, right_most: 46744839, center_mass: 46744378, n_left: 0, n_right: 0, n_total: 0, repeat: "CTT", name: "", force_report: true)
[strling] bounds:(tid: 18, left: 103205304, left_most: 103204919, right: 103205323, right_most: 103205329, center_mass: 103205270, n_left: 0, n_right: 0, n_total: 0, repeat: "CTT", name: "", force_report: true)
[strling] bounds:(tid: 18, left: 103205355, left_most: 103205330, right: 103205356, right_most: 103205767, center_mass: 103205403, n_left: 0, n_right: 0, n_total: 0, repeat: "CTT", name: "", force_report: true)
[strling] bounds:(tid: 18, left: 109916011, left_most: 109915221, right: 109916027, right_most: 109916507, center_mass: 109916011, n_left: 0, n_right: 0, n_total: 0, repeat: "CTT", name: "", force_report: true)
[strling] bounds:(tid: 18, left: 113273274, left_most: 113272484, right: 113273275, right_most: 113273770, center_mass: 113273274, n_left: 0, n_right: 0, n_total: 0, repeat: "CTT", name: "", force_report: true)
[strling] bounds:(tid: 18, left: 153963171, left_most: 153962475, right: 153963172, right_most: 153963761, center_mass: 153963175, n_left: 0, n_right: 0, n_total: 0, repeat: "CTT", name: "", force_report: true)
[strling] bounds:(tid: 18, left: 156897218, left_most: 156896575, right: 156897266, right_most: 156897861, center_mass: 156897262, n_left: 0, n_right: 0, n_total: 0, repeat: "CTT", name: "", force_report: true)
[strling] bounds:(tid: 0, left: 39664514, left_most: 39663818, right: 39664515, right_most: 39665104, center_mass: 39664515, n_left: 0, n_right: 0, n_total: 0, repeat: "CCTCT", name: "", force_report: true)
[strling] bounds:(tid: 10, left: 1164870, left_most: 1164022, right: 1164993, right_most: 1165308, center_mass: 1164870, n_left: 0, n_right: 0, n_total: 0, repeat: "AGG", name: "", force_report: true)
[strling] bounds:(tid: 8, left: 17808425, left_most: 17807735, right: 17808426, right_most: 17809021, center_mass: 17808425, n_left: 0, n_right: 0, n_total: 0, repeat: "ATTTT", name: "", force_report: true)
[strling] bounds:(tid: 11, left: 44013440, left_most: 44012787, right: 44013441, right_most: 44014073, center_mass: 44013440, n_left: 0, n_right: 0, n_total: 0, repeat: "ATTTT", name: "", force_report: true)
[strling] bounds:(tid: 11, left: 212864363, left_most: 212863720, right: 212864364, right_most: 212865006, center_mass: 212864433, n_left: 0, n_right: 0, n_total: 0, repeat: "ATTTT", name: "", force_report: true)
[strling] bounds:(tid: 10, left: 17463972, left_most: 17463211, right: 17463973, right_most: 17464497, center_mass: 17463972, n_left: 0, n_right: 0, n_total: 0, repeat: "AAGGAG", name: "", force_report: true)
[strling] bounds:(tid: 15, left: 113260752, left_most: 113259924, right: 113260753, right_most: 113261210, center_mass: 113260753, n_left: 0, n_right: 0, n_total: 0, repeat: "AACAG", name: "", force_report: true)
[strling] bounds:(tid: 23, left: 3037006, left_most: 3036132, right: 3037007, right_most: 3037418, center_mass: 3037006, n_left: 0, n_right: 0, n_total: 0, repeat: "AT", name: "", force_report: true)
[strling] bounds:(tid: 23, left: 3341520, left_most: 3340798, right: 3341521, right_most: 3342084, center_mass: 3341520, n_left: 0, n_right: 0, n_total: 0, repeat: "AT", name: "", force_report: true)
[strling] bounds:(tid: 23, left: 4227175, left_most: 4226470, right: 4227176, right_most: 4227756, center_mass: 4227175, n_left: 0, n_right: 0, n_total: 0, repeat: "AT", name: "", force_report: true)
[strling] bounds:(tid: 23, left: 8181985, left_most: 8181294, right: 8181986, right_most: 8182580, center_mass: 8181985, n_left: 0, n_right: 0, n_total: 0, repeat: "AT", name: "", force_report: true)
[strling] bounds:(tid: 23, left: 8427529, left_most: 8426740, right: 8427530, right_most: 8428026, center_mass: 8427529, n_left: 0, n_right: 0, n_total: 0, repeat: "AT", name: "", force_report: true)
[strling] bounds:(tid: 23, left: 8483737, left_most: 8482940, right: 8483738, right_most: 8484226, center_mass: 8483737, n_left: 0, n_right: 0, n_total: 0, repeat: "AT", name: "", force_report: true)
[strling] bounds:(tid: 23, left: 9021370, left_most: 9020650, right: 9021371, right_most: 9021936, center_mass: 9021370, n_left: 0, n_right: 0, n_total: 0, repeat: "AT", name: "", force_report: true)
[strling] bounds:(tid: 23, left: 25939945, left_most: 25939193, right: 25939946, right_most: 25940479, center_mass: 25939945, n_left: 0, n_right: 0, n_total: 0, repeat: "AT", name: "", force_report: true)
[strling] bounds:(tid: 23, left: 27403048, left_most: 27402239, right: 27403245, right_most: 27403525, center_mass: 27403048, n_left: 0, n_right: 0, n_total: 0, repeat: "AT", name: "", force_report: true)
[strling] bounds:(tid: 23, left: 27606382, left_most: 27605726, right: 27606382, right_most: 27607012, center_mass: 27606382, n_left: 0, n_right: 0, n_total: 0, repeat: "AT", name: "", force_report: true)
[strling] bounds:(tid: 23, left: 30018500, left_most: 30017688, right: 30018501, right_most: 30018974, center_mass: 30018500, n_left: 0, n_right: 0, n_total: 0, repeat: "AT", name: "", force_report: true)
[strling] bounds:(tid: 23, left: 35433314, left_most: 35432628, right: 35433315, right_most: 35433914, center_mass: 35433314, n_left: 0, n_right: 0, n_total: 0, repeat: "AT", name: "", force_report: true)
[strling] bounds:(tid: 23, left: 35600852, left_most: 35599985, right: 35600853, right_most: 35601271, center_mass: 35600852, n_left: 0, n_right: 0, n_total: 0, repeat: "AT", name: "", force_report: true)
[strling] bounds:(tid: 23, left: 37286380, left_most: 37285225, right: 37286381, right_most: 37286550, center_mass: 37286380, n_left: 0, n_right: 0, n_total: 0, repeat: "AT", name: "", force_report: true)
[strling] bounds:(tid: 23, left: 40139480, left_most: 40138703, right: 40139498, right_most: 40139989, center_mass: 40139480, n_left: 0, n_right: 0, n_total: 0, repeat: "AT", name: "", force_report: true)
[strling] bounds:(tid: 23, left: 47667749, left_most: 47666963, right: 47667750, right_most: 47668249, center_mass: 47667749, n_left: 0, n_right: 0, n_total: 0, repeat: "AT", name: "", force_report: true)
[strling] bounds:(tid: 23, left: 50795072, left_most: 50794391, right: 50795073, right_most: 50795677, center_mass: 50795072, n_left: 0, n_right: 0, n_total: 0, repeat: "AT", name: "", force_report: true)
[strling] bounds:(tid: 23, left: 50882058, left_most: 50881431, right: 50882059, right_most: 50882717, center_mass: 50882140, n_left: 0, n_right: 0, n_total: 0, repeat: "AT", name: "", force_report: true)
[strling] bounds:(tid: 23, left: 51691863, left_most: 51691205, right: 51691864, right_most: 51692491, center_mass: 51691863, n_left: 0, n_right: 0, n_total: 0, repeat: "AT", name: "", force_report: true)
[strling] bounds:(tid: 23, left: 52580748, left_most: 52579968, right: 52580749, right_most: 52581254, center_mass: 52580748, n_left: 0, n_right: 0, n_total: 0, repeat: "AT", name: "", force_report: true)
[strling] bounds:(tid: 23, left: 53749321, left_most: 53748567, right: 53749322, right_most: 53749853, center_mass: 53749321, n_left: 0, n_right: 0, n_total: 0, repeat: "AT", name: "", force_report: true)
[strling] bounds:(tid: 23, left: 54910819, left_most: 54910069, right: 54910820, right_most: 54911355, center_mass: 54910819, n_left: 0, n_right: 0, n_total: 0, repeat: "AT", name: "", force_report: true)
[strling] bounds:(tid: 23, left: 57697132, left_most: 57696303, right: 57697133, right_most: 57697589, center_mass: 57697132, n_left: 0, n_right: 0, n_total: 0, repeat: "AT", name: "", force_report: true)
[strling] bounds:(tid: 23, left: 57698121, left_most: 57697193, right: 57698122, right_most: 57698569, center_mass: 57698121, n_left: 0, n_right: 0, n_total: 0, repeat: "AT", name: "", force_report: true)
[strling] bounds:(tid: 23, left: 63250076, left_most: 63249316, right: 63250077, right_most: 63250602, center_mass: 63250076, n_left: 0, n_right: 0, n_total: 0, repeat: "AT", name: "", force_report: true)
[strling] bounds:(tid: 23, left: 64838713, left_most: 64837901, right: 64838714, right_most: 64839187, center_mass: 64838713, n_left: 0, n_right: 0, n_total: 0, repeat: "AT", name: "", force_report: true)
[strling] bounds:(tid: 23, left: 64893289, left_most: 64892581, right: 64893328, right_most: 64893867, center_mass: 64893481, n_left: 0, n_right: 0, n_total: 0, repeat: "AT", name: "", force_report: true)
[strling] bounds:(tid: 23, left: 66036828, left_most: 66036097, right: 66036829, right_most: 66037483, center_mass: 66036914, n_left: 0, n_right: 0, n_total: 0, repeat: "AT", name: "", force_report: true)
[strling] bounds:(tid: 23, left: 67415429, left_most: 67414730, right: 67415430, right_most: 67416059, center_mass: 67415621, n_left: 0, n_right: 0, n_total: 0, repeat: "AT", name: "", force_report: true)
[strling] bounds:(tid: 23, left: 68592810, left_most: 68591974, right: 68592811, right_most: 68593347, center_mass: 68592810, n_left: 0, n_right: 0, n_total: 0, repeat: "AT", name: "", force_report: true)
[strling] bounds:(tid: 23, left: 70917420, left_most: 70916688, right: 70917421, right_most: 70917974, center_mass: 70917420, n_left: 0, n_right: 0, n_total: 0, repeat: "AT", name: "", force_report: true)
[strling] bounds:(tid: 23, left: 72171611, left_most: 72170918, right: 72171612, right_most: 72172204, center_mass: 72171611, n_left: 0, n_right: 0, n_total: 0, repeat: "AT", name: "", force_report: true)
[strling] bounds:(tid: 23, left: 74796200, left_most: 74795396, right: 74796201, right_most: 74796682, center_mass: 74796200, n_left: 0, n_right: 0, n_total: 0, repeat: "AT", name: "", force_report: true)
[strling] bounds:(tid: 23, left: 78269114, left_most: 78268354, right: 78269115, right_most: 78269640, center_mass: 78269114, n_left: 0, n_right: 0, n_total: 0, repeat: "AT", name: "", force_report: true)
[strling] bounds:(tid: 23, left: 78926699, left_most: 78925800, right: 78926700, right_most: 78927086, center_mass: 78926699, n_left: 0, n_right: 0, n_total: 0, repeat: "AT", name: "", force_report: true)
[strling] bounds:(tid: 23, left: 80193791, left_most: 80193039, right: 80193792, right_most: 80194325, center_mass: 80193791, n_left: 0, n_right: 0, n_total: 0, repeat: "AT", name: "", force_report: true)
[strling] bounds:(tid: 23, left: 80461218, left_most: 80460394, right: 80461259, right_most: 80461680, center_mass: 80461218, n_left: 0, n_right: 0, n_total: 0, repeat: "AT", name: "", force_report: true)
[strling] bounds:(tid: 23, left: 82073063, left_most: 82072329, right: 82073064, right_most: 82073615, center_mass: 82073063, n_left: 0, n_right: 0, n_total: 0, repeat: "AT", name: "", force_report: true)
[strling] bounds:(tid: 23, left: 83878363, left_most: 83877592, right: 83878364, right_most: 83878878, center_mass: 83878363, n_left: 0, n_right: 0, n_total: 0, repeat: "AT", name: "", force_report: true)
[strling] bounds:(tid: 23, left: 84191758, left_most: 84190819, right: 84191759, right_most: 84192135, center_mass: 84191758, n_left: 0, n_right: 0, n_total: 0, repeat: "AT", name: "", force_report: true)
[strling] bounds:(tid: 23, left: 85745870, left_most: 85745027, right: 85745871, right_most: 85746313, center_mass: 85745870, n_left: 0, n_right: 0, n_total: 0, repeat: "AT", name: "", force_report: true)
[strling] bounds:(tid: 23, left: 85911165, left_most: 85910362, right: 85911166, right_most: 85911648, center_mass: 85911165, n_left: 0, n_right: 0, n_total: 0, repeat: "AT", name: "", force_report: true)
[strling] bounds:(tid: 23, left: 87024993, left_most: 87024081, right: 87024994, right_most: 87025367, center_mass: 87024993, n_left: 0, n_right: 0, n_total: 0, repeat: "AT", name: "", force_report: true)
[strling] bounds:(tid: 23, left: 87717070, left_most: 87716290, right: 87717103, right_most: 87717576, center_mass: 87717070, n_left: 0, n_right: 0, n_total: 0, repeat: "AT", name: "", force_report: true)
[strling] bounds:(tid: 23, left: 87792066, left_most: 87791206, right: 87792082, right_most: 87792492, center_mass: 87792066, n_left: 0, n_right: 0, n_total: 0, repeat: "AT", name: "", force_report: true)
[strling] bounds:(tid: 23, left: 88905880, left_most: 88905159, right: 88905881, right_most: 88906445, center_mass: 88905880, n_left: 0, n_right: 0, n_total: 0, repeat: "AT", name: "", force_report: true)
[strling] bounds:(tid: 23, left: 90226105, left_most: 90224959, right: 90226106, right_most: 90226340, center_mass: 90226105, n_left: 0, n_right: 0, n_total: 0, repeat: "AT", name: "", force_report: true)
[strling] bounds:(tid: 23, left: 94143548, left_most: 94142905, right: 94143588, right_most: 94144191, center_mass: 94143588, n_left: 0, n_right: 0, n_total: 0, repeat: "AT", name: "", force_report: true)
[strling] bounds:(tid: 23, left: 96082538, left_most: 96081769, right: 96082600, right_most: 96083055, center_mass: 96082600, n_left: 0, n_right: 0, n_total: 0, repeat: "AT", name: "", force_report: true)
[strling] bounds:(tid: 23, left: 97185306, left_most: 97184631, right: 97185307, right_most: 97185917, center_mass: 97185448, n_left: 0, n_right: 0, n_total: 0, repeat: "AT", name: "", force_report: true)
[strling] bounds:(tid: 23, left: 98413718, left_most: 98412950, right: 98413719, right_most: 98414236, center_mass: 98413718, n_left: 0, n_right: 0, n_total: 0, repeat: "AT", name: "", force_report: true)
[strling] bounds:(tid: 23, left: 98654269, left_most: 98653474, right: 98654312, right_most: 98654760, center_mass: 98654269, n_left: 0, n_right: 0, n_total: 0, repeat: "AT", name: "", force_report: true)
[strling] bounds:(tid: 23, left: 104585327, left_most: 104584570, right: 104585328, right_most: 104585856, center_mass: 104585327, n_left: 0, n_right: 0, n_total: 0, repeat: "AT", name: "", force_report: true)
[strling] bounds:(tid: 23, left: 105307574, left_most: 105306820, right: 105307575, right_most: 105308106, center_mass: 105307574, n_left: 0, n_right: 0, n_total: 0, repeat: "AT", name: "", force_report: true)
[strling] bounds:(tid: 23, left: 105540873, left_most: 105540036, right: 105540874, right_most: 105541322, center_mass: 105540873, n_left: 0, n_right: 0, n_total: 0, repeat: "AT", name: "", force_report: true)
[strling] bounds:(tid: 23, left: 106308082, left_most: 106307284, right: 106308083, right_most: 106308570, center_mass: 106308082, n_left: 0, n_right: 0, n_total: 0, repeat: "AT", name: "", force_report: true)
[strling] bounds:(tid: 23, left: 106309216, left_most: 106308494, right: 106309217, right_most: 106309780, center_mass: 106309256, n_left: 0, n_right: 0, n_total: 0, repeat: "AT", name: "", force_report: true)
[strling] bounds:(tid: 23, left: 107152135, left_most: 107151355, right: 107152136, right_most: 107152641, center_mass: 107152135, n_left: 0, n_right: 0, n_total: 0, repeat: "AT", name: "", force_report: true)
[strling] bounds:(tid: 23, left: 107782291, left_most: 107781496, right: 107782292, right_most: 107782800, center_mass: 107782291, n_left: 0, n_right: 0, n_total: 0, repeat: "AT", name: "", force_report: true)
[strling] bounds:(tid: 23, left: 111668314, left_most: 111667632, right: 111668315, right_most: 111668918, center_mass: 111668314, n_left: 0, n_right: 0, n_total: 0, repeat: "AT", name: "", force_report: true)
[strling] bounds:(tid: 23, left: 114387158, left_most: 114386109, right: 114387159, right_most: 114387495, center_mass: 114387245, n_left: 0, n_right: 0, n_total: 0, repeat: "AT", name: "", force_report: true)
[strling] bounds:(tid: 23, left: 114387550, left_most: 114386862, right: 114387551, right_most: 114388148, center_mass: 114387550, n_left: 0, n_right: 0, n_total: 0, repeat: "AT", name: "", force_report: true)
[strling] bounds:(tid: 23, left: 114459201, left_most: 114458358, right: 114459202, right_most: 114459644, center_mass: 114459201, n_left: 0, n_right: 0, n_total: 0, repeat: "AT", name: "", force_report: true)
[strling] bounds:(tid: 23, left: 116863865, left_most: 116863090, right: 116863866, right_most: 116864376, center_mass: 116863865, n_left: 0, n_right: 0, n_total: 0, repeat: "AT", name: "", force_report: true)
[strling] bounds:(tid: 23, left: 120296885, left_most: 120295977, right: 120296886, right_most: 120297270, center_mass: 120296885, n_left: 0, n_right: 0, n_total: 0, repeat: "AT", name: "", force_report: true)
[strling] bounds:(tid: 23, left: 124350313, left_most: 124349574, right: 124350314, right_most: 124350860, center_mass: 124350313, n_left: 0, n_right: 0, n_total: 0, repeat: "AT", name: "", force_report: true)
[strling] bounds:(tid: 23, left: 126035804, left_most: 126035098, right: 126035805, right_most: 126036384, center_mass: 126035804, n_left: 0, n_right: 0, n_total: 0, repeat: "AT", name: "", force_report: true)
[strling] bounds:(tid: 23, left: 126944903, left_most: 126944006, right: 126944904, right_most: 126945292, center_mass: 126944993, n_left: 0, n_right: 0, n_total: 0, repeat: "AT", name: "", force_report: true)
[strling] bounds:(tid: 23, left: 132396755, left_most: 132395974, right: 132396756, right_most: 132397260, center_mass: 132396755, n_left: 0, n_right: 0, n_total: 0, repeat: "AT", name: "", force_report: true)
[strling] got 2 treads for locus: (tid: 23, left: 135646175, left_most: 135645361, right: 135646629, right_most: 135646647, center_mass: 135646175, n_left: 0, n_right: 2, n_total: 132, repeat: "AT", name: "", force_report: false) with indexes 97..99
[strling] bounds:(tid: 23, left: 135646175, left_most: 135645361, right: 135646629, right_most: 135646647, center_mass: 135646175, n_left: 0, n_right: 2, n_total: 2, repeat: "AT", name: "", force_report: true)
[strling] bounds:(tid: 23, left: 137315448, left_most: 137314784, right: 137315449, right_most: 137316070, center_mass: 137315448, n_left: 0, n_right: 0, n_total: 0, repeat: "AT", name: "", force_report: true)
[strling] bounds:(tid: 23, left: 139503667, left_most: 139502363, right: 139503668, right_most: 139503746, center_mass: 139503667, n_left: 0, n_right: 0, n_total: 0, repeat: "AT", name: "", force_report: true)
[strling] bounds:(tid: 23, left: 142125976, left_most: 142125188, right: 142126003, right_most: 142126474, center_mass: 142125976, n_left: 0, n_right: 0, n_total: 0, repeat: "AT", name: "", force_report: true)
[strling] bounds:(tid: 23, left: 142129946, left_most: 142129303, right: 142129976, right_most: 142130589, center_mass: 142129946, n_left: 0, n_right: 0, n_total: 0, repeat: "AT", name: "", force_report: true)
[strling] bounds:(tid: 23, left: 143214100, left_most: 143213261, right: 143214101, right_most: 143214547, center_mass: 143214100, n_left: 0, n_right: 0, n_total: 0, repeat: "AT", name: "", force_report: true)
[strling] bounds:(tid: 23, left: 145918063, left_most: 145917251, right: 145918064, right_most: 145918537, center_mass: 145918063, n_left: 0, n_right: 0, n_total: 0, repeat: "AT", name: "", force_report: true)
[strling] bounds:(tid: 23, left: 147349051, left_most: 147348328, right: 147349052, right_most: 147349614, center_mass: 147349051, n_left: 0, n_right: 0, n_total: 0, repeat: "AT", name: "", force_report: true)
[strling] bounds:(tid: 23, left: 148196256, left_most: 148195273, right: 148196257, right_most: 148196559, center_mass: 148196199, n_left: 0, n_right: 0, n_total: 0, repeat: "AT", name: "", force_report: true)
[strling] bounds:(tid: 23, left: 149418487, left_most: 149417794, right: 149418561, right_most: 149419080, center_mass: 149418565, n_left: 0, n_right: 0, n_total: 0, repeat: "AT", name: "", force_report: true)
[strling] bounds:(tid: 23, left: 150001065, left_most: 149999935, right: 150001148, right_most: 150001314, center_mass: 150001065, n_left: 0, n_right: 0, n_total: 0, repeat: "AT", name: "", force_report: true)
[strling] bounds:(tid: 23, left: 151373714, left_most: 151372924, right: 151373715, right_most: 151374210, center_mass: 151373714, n_left: 0, n_right: 0, n_total: 0, repeat: "AT", name: "", force_report: true)
[strling] bounds:(tid: 23, left: 152998660, left_most: 152997853, right: 152998661, right_most: 152999139, center_mass: 152998660, n_left: 0, n_right: 0, n_total: 0, repeat: "AT", name: "", force_report: true)
[strling] bounds:(tid: 13, left: 7925351, left_most: 7924708, right: 7925352, right_most: 7926060, center_mass: 7925351, n_left: 0, n_right: 0, n_total: 0, repeat: "ATTCC", name: "", force_report: true)
[strling] bounds:(tid: 13, left: 10679872, left_most: 10679192, right: 10679873, right_most: 10680478, center_mass: 10679872, n_left: 0, n_right: 0, n_total: 0, repeat: "ATTCC", name: "", force_report: true)
[strling] bounds:(tid: 13, left: 10692855, left_most: 10691826, right: 10692856, right_most: 10693194, center_mass: 10692855, n_left: 0, n_right: 0, n_total: 0, repeat: "ATTCC", name: "", force_report: true)
[strling] bounds:(tid: 0, left: 7863083, left_most: 7862268, right: 7863084, right_most: 7863554, center_mass: 7863083, n_left: 0, n_right: 0, n_total: 0, repeat: "ATTGT", name: "", force_report: true)
[strling] bounds:(tid: 0, left: 63863764, left_most: 63863096, right: 63863765, right_most: 63864382, center_mass: 63863764, n_left: 0, n_right: 0, n_total: 0, repeat: "ATTGT", name: "", force_report: true)
[strling] bounds:(tid: 16, left: 2020802, left_most: 2019838, right: 2020803, right_most: 2021124, center_mass: 2020802, n_left: 0, n_right: 0, n_total: 0, repeat: "CTTT", name: "", force_report: true)
[strling] bounds:(tid: 16, left: 2852193, left_most: 2851425, right: 2852194, right_most: 2852711, center_mass: 2852193, n_left: 0, n_right: 0, n_total: 0, repeat: "CTTT", name: "", force_report: true)
[strling] bounds:(tid: 16, left: 4263813, left_most: 4263004, right: 4263814, right_most: 4264290, center_mass: 4263861, n_left: 0, n_right: 0, n_total: 0, repeat: "CTTT", name: "", force_report: true)
[strling] bounds:(tid: 16, left: 7093510, left_most: 7092793, right: 7093511, right_most: 7094079, center_mass: 7093510, n_left: 0, n_right: 0, n_total: 0, repeat: "CTTT", name: "", force_report: true)
[strling] bounds:(tid: 16, left: 8919089, left_most: 8918271, right: 8919090, right_most: 8919557, center_mass: 8919089, n_left: 0, n_right: 0, n_total: 0, repeat: "CTTT", name: "", force_report: true)
[strling] bounds:(tid: 16, left: 10787339, left_most: 10786696, right: 10787340, right_most: 10787982, center_mass: 10787339, n_left: 0, n_right: 0, n_total: 0, repeat: "CTTT", name: "", force_report: true)
[strling] bounds:(tid: 16, left: 11191874, left_most: 11191081, right: 11191929, right_most: 11192367, center_mass: 11191874, n_left: 0, n_right: 0, n_total: 0, repeat: "CTTT", name: "", force_report: true)
[strling] bounds:(tid: 16, left: 13739143, left_most: 13738421, right: 13739144, right_most: 13739707, center_mass: 13739143, n_left: 0, n_right: 0, n_total: 0, repeat: "CTTT", name: "", force_report: true)
[strling] bounds:(tid: 16, left: 14204702, left_most: 14204030, right: 14204813, right_most: 14205316, center_mass: 14204702, n_left: 0, n_right: 0, n_total: 0, repeat: "CTTT", name: "", force_report: true)
[strling] bounds:(tid: 16, left: 18704714, left_most: 18703958, right: 18704715, right_most: 18705244, center_mass: 18704714, n_left: 0, n_right: 0, n_total: 0, repeat: "CTTT", name: "", force_report: true)
[strling] bounds:(tid: 16, left: 25517043, left_most: 25516279, right: 25517044, right_most: 25517565, center_mass: 25517043, n_left: 0, n_right: 0, n_total: 0, repeat: "CTTT", name: "", force_report: true)
[strling] bounds:(tid: 16, left: 25553476, left_most: 25552614, right: 25553548, right_most: 25553900, center_mass: 25553476, n_left: 0, n_right: 0, n_total: 0, repeat: "CTTT", name: "", force_report: true)
[strling] bounds:(tid: 16, left: 27416782, left_most: 27416140, right: 27416783, right_most: 27417426, center_mass: 27416784, n_left: 0, n_right: 0, n_total: 0, repeat: "CTTT", name: "", force_report: true)
[strling] bounds:(tid: 16, left: 29458065, left_most: 29457242, right: 29458066, right_most: 29458528, center_mass: 29458065, n_left: 0, n_right: 0, n_total: 0, repeat: "CTTT", name: "", force_report: true)
[strling] bounds:(tid: 16, left: 30045051, left_most: 30044408, right: 30045120, right_most: 30045694, center_mass: 30045120, n_left: 0, n_right: 0, n_total: 0, repeat: "CTTT", name: "", force_report: true)
[strling] bounds:(tid: 16, left: 31593299, left_most: 31592508, right: 31593300, right_most: 31593794, center_mass: 31593299, n_left: 0, n_right: 0, n_total: 0, repeat: "CTTT", name: "", force_report: true)
[strling] bounds:(tid: 16, left: 31749447, left_most: 31748783, right: 31749448, right_most: 31750069, center_mass: 31749510, n_left: 0, n_right: 0, n_total: 0, repeat: "CTTT", name: "", force_report: true)
[strling] bounds:(tid: 16, left: 32917996, left_most: 32917228, right: 32917997, right_most: 32918514, center_mass: 32917996, n_left: 0, n_right: 0, n_total: 0, repeat: "CTTT", name: "", force_report: true)
[strling] bounds:(tid: 16, left: 33760048, left_most: 33759389, right: 33760049, right_most: 33760675, center_mass: 33760048, n_left: 0, n_right: 0, n_total: 0, repeat: "CTTT", name: "", force_report: true)
[strling] bounds:(tid: 16, left: 34797223, left_most: 34796564, right: 34797224, right_most: 34797850, center_mass: 34797223, n_left: 0, n_right: 0, n_total: 0, repeat: "CTTT", name: "", force_report: true)
[strling] bounds:(tid: 16, left: 57514497, left_most: 57513678, right: 57514498, right_most: 57514964, center_mass: 57514497, n_left: 0, n_right: 0, n_total: 0, repeat: "CTTT", name: "", force_report: true)
[strling] bounds:(tid: 16, left: 57586665, left_most: 57586010, right: 57586666, right_most: 57587296, center_mass: 57586665, n_left: 0, n_right: 0, n_total: 0, repeat: "CTTT", name: "", force_report: true)
[strling] bounds:(tid: 16, left: 61432587, left_most: 61431944, right: 61432588, right_most: 61433230, center_mass: 61432587, n_left: 0, n_right: 0, n_total: 0, repeat: "CTTT", name: "", force_report: true)
[strling] bounds:(tid: 16, left: 63448351, left_most: 63447588, right: 63448352, right_most: 63448874, center_mass: 63448351, n_left: 0, n_right: 0, n_total: 0, repeat: "CTTT", name: "", force_report: true)
[strling] bounds:(tid: 16, left: 64832475, left_most: 64831589, right: 64832476, right_most: 64832875, center_mass: 64832475, n_left: 0, n_right: 0, n_total: 0, repeat: "CTTT", name: "", force_report: true)
[strling] bounds:(tid: 16, left: 65150918, left_most: 65150098, right: 65150919, right_most: 65151384, center_mass: 65150918, n_left: 0, n_right: 0, n_total: 0, repeat: "CTTT", name: "", force_report: true)
[strling] bounds:(tid: 16, left: 69370196, left_most: 69369562, right: 69370197, right_most: 69370848, center_mass: 69370208, n_left: 0, n_right: 0, n_total: 0, repeat: "CTTT", name: "", force_report: true)
[strling] bounds:(tid: 16, left: 73484433, left_most: 73483790, right: 73484434, right_most: 73485076, center_mass: 73484433, n_left: 0, n_right: 0, n_total: 0, repeat: "CTTT", name: "", force_report: true)
[strling] bounds:(tid: 16, left: 83521147, left_most: 83520402, right: 83521167, right_most: 83521688, center_mass: 83521147, n_left: 0, n_right: 0, n_total: 0, repeat: "CTTT", name: "", force_report: true)
[strling] bounds:(tid: 16, left: 87927855, left_most: 87927043, right: 87927856, right_most: 87928329, center_mass: 87927855, n_left: 0, n_right: 0, n_total: 0, repeat: "CTTT", name: "", force_report: true)
[strling] bounds:(tid: 16, left: 95026098, left_most: 95025467, right: 95026099, right_most: 95026753, center_mass: 95026110, n_left: 0, n_right: 0, n_total: 0, repeat: "CTTT", name: "", force_report: true)
[strling] bounds:(tid: 16, left: 96593081, left_most: 96592438, right: 96593082, right_most: 96593724, center_mass: 96593081, n_left: 0, n_right: 0, n_total: 0, repeat: "CTTT", name: "", force_report: true)
[strling] bounds:(tid: 16, left: 103577252, left_most: 103576382, right: 103577253, right_most: 103577668, center_mass: 103577252, n_left: 0, n_right: 0, n_total: 0, repeat: "CTTT", name: "", force_report: true)
[strling] bounds:(tid: 16, left: 109850422, left_most: 109849779, right: 109850423, right_most: 109851065, center_mass: 109850422, n_left: 0, n_right: 0, n_total: 0, repeat: "CTTT", name: "", force_report: true)
[strling] bounds:(tid: 16, left: 113443920, left_most: 113443277, right: 113443921, right_most: 113444563, center_mass: 113443995, n_left: 0, n_right: 0, n_total: 0, repeat: "CTTT", name: "", force_report: true)
[strling] bounds:(tid: 16, left: 120551729, left_most: 120551086, right: 120551778, right_most: 120552372, center_mass: 120551778, n_left: 0, n_right: 0, n_total: 0, repeat: "CTTT", name: "", force_report: true)
[strling] bounds:(tid: 16, left: 128372856, left_most: 128372214, right: 128372857, right_most: 128373500, center_mass: 128372857, n_left: 0, n_right: 0, n_total: 0, repeat: "CTTT", name: "", force_report: true)
[strling] bounds:(tid: 16, left: 131841350, left_most: 131840703, right: 131841351, right_most: 131841989, center_mass: 131841350, n_left: 0, n_right: 0, n_total: 0, repeat: "CTTT", name: "", force_report: true)
[strling] bounds:(tid: 16, left: 133581591, left_most: 133580830, right: 133581640, right_most: 133582116, center_mass: 133581591, n_left: 0, n_right: 0, n_total: 0, repeat: "CTTT", name: "", force_report: true)
[strling] bounds:(tid: 16, left: 133709436, left_most: 133708549, right: 133709437, right_most: 133709835, center_mass: 133709436, n_left: 0, n_right: 0, n_total: 0, repeat: "CTTT", name: "", force_report: true)
[strling] bounds:(tid: 16, left: 135671742, left_most: 135670999, right: 135671743, right_most: 135672285, center_mass: 135671742, n_left: 0, n_right: 0, n_total: 0, repeat: "CTTT", name: "", force_report: true)
[strling] bounds:(tid: 16, left: 139579091, left_most: 139578344, right: 139579092, right_most: 139579630, center_mass: 139579091, n_left: 0, n_right: 0, n_total: 0, repeat: "CTTT", name: "", force_report: true)
[strling] bounds:(tid: 16, left: 141358462, left_most: 141357677, right: 141358463, right_most: 141358963, center_mass: 141358462, n_left: 0, n_right: 0, n_total: 0, repeat: "CTTT", name: "", force_report: true)
[strling] bounds:(tid: 16, left: 141580065, left_most: 141579202, right: 141580127, right_most: 141580488, center_mass: 141580065, n_left: 0, n_right: 0, n_total: 0, repeat: "CTTT", name: "", force_report: true)
[strling] bounds:(tid: 16, left: 146061373, left_most: 146060671, right: 146061374, right_most: 146061957, center_mass: 146061373, n_left: 0, n_right: 0, n_total: 0, repeat: "CTTT", name: "", force_report: true)
[strling] bounds:(tid: 16, left: 146172141, left_most: 146171385, right: 146172142, right_most: 146172671, center_mass: 146172141, n_left: 0, n_right: 0, n_total: 0, repeat: "CTTT", name: "", force_report: true)
[strling] bounds:(tid: 16, left: 148755206, left_most: 148754475, right: 148755207, right_most: 148755761, center_mass: 148755206, n_left: 0, n_right: 0, n_total: 0, repeat: "CTTT", name: "", force_report: true)
[strling] bounds:(tid: 16, left: 148785285, left_most: 148784642, right: 148785286, right_most: 148785928, center_mass: 148785286, n_left: 0, n_right: 0, n_total: 0, repeat: "CTTT", name: "", force_report: true)
[strling] bounds:(tid: 16, left: 157612089, left_most: 157611446, right: 157612090, right_most: 157612732, center_mass: 157612089, n_left: 0, n_right: 0, n_total: 0, repeat: "CTTT", name: "", force_report: true)
[strling] bounds:(tid: 16, left: 159198309, left_most: 159197666, right: 159198310, right_most: 159198952, center_mass: 159198309, n_left: 0, n_right: 0, n_total: 0, repeat: "CTTT", name: "", force_report: true)
[strling] bounds:(tid: 16, left: 161783680, left_most: 161782930, right: 161783681, right_most: 161784216, center_mass: 161783680, n_left: 0, n_right: 0, n_total: 0, repeat: "CTTT", name: "", force_report: true)
[strling] bounds:(tid: 16, left: 165779314, left_most: 165778671, right: 165779315, right_most: 165779957, center_mass: 165779314, n_left: 0, n_right: 0, n_total: 0, repeat: "CTTT", name: "", force_report: true)
[strling] bounds:(tid: 16, left: 178959875, left_most: 178959232, right: 178959876, right_most: 178960518, center_mass: 178959875, n_left: 0, n_right: 0, n_total: 0, repeat: "CTTT", name: "", force_report: true)
[strling] bounds:(tid: 16, left: 180245014, left_most: 180244008, right: 180245015, right_most: 180245365, center_mass: 180245014, n_left: 0, n_right: 0, n_total: 0, repeat: "CTTT", name: "", force_report: true)
[strling] bounds:(tid: 16, left: 184113907, left_most: 184113246, right: 184113908, right_most: 184114532, center_mass: 184113907, n_left: 0, n_right: 0, n_total: 0, repeat: "CTTT", name: "", force_report: true)
[strling] bounds:(tid: 16, left: 184131205, left_most: 184130547, right: 184131206, right_most: 184131833, center_mass: 184131205, n_left: 0, n_right: 0, n_total: 0, repeat: "CTTT", name: "", force_report: true)
[strling] bounds:(tid: 16, left: 186299807, left_most: 186298960, right: 186299808, right_most: 186300246, center_mass: 186299807, n_left: 0, n_right: 0, n_total: 0, repeat: "CTTT", name: "", force_report: true)
[strling] bounds:(tid: 11, left: 227918126, left_most: 227917480, right: 227918127, right_most: 227918766, center_mass: 227918149, n_left: 0, n_right: 0, n_total: 0, repeat: "ATCC", name: "", force_report: true)
[strling] bounds:(tid: 18, left: 501300, left_most: 500332, right: 501301, right_most: 501718, center_mass: 501300, n_left: 0, n_right: 0, n_total: 0, repeat: "AT", name: "", force_report: true)
[strling] bounds:(tid: 18, left: 1652542, left_most: 1651702, right: 1652543, right_most: 1652988, center_mass: 1652542, n_left: 0, n_right: 0, n_total: 0, repeat: "AT", name: "", force_report: true)
SIGSEGV: Illegal storage access. (Attempt to read from nil?)
christopher-schroeder commented 1 year ago

Well... I found my mistake. The configuration for this sample and the other sample (the other issue here) was wrong. I accidentally map R1.fastq.gz + R1.fastq.gz instead of R1.fastq.gz + R2.fastq.gz I am preprocessing both samples now. Since the two are the only samples that doesn't work with strling and are the only samples that are incorrectly configured that way, I am sure it will solve the problem. I highly appreciate your help Brend and I am sorry for the work. Best Christo

brentp commented 1 year ago

@christopher-schroeder , thanks for letting us know. I would hope that STRling would give a more helpful error message here, but haven't been able to find the location of the segfault.

hdashnow commented 1 year ago

All the insert sizes would be 0. Could look at uses of the insert size estimate later in the code? If wanting to deal with this exact problem, simply reporting the tiny insert size would be helpful if it happens again.

hdashnow commented 6 months ago

Closing for now. Feel free to reopen if this comes up again.