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OR- to OR/ rename
Modify label generating scripts to handle the accepted OR/ labeling (instead of OR-)
Segmentation faults
When I run on larger samples, IgSCUEAL seems to kick seq faults about ten percent of the time (~95/1000 jobs, where each job has ten sequences). Logs follow:
[SEND] Sequence 04-A-M_2943612 to MPI node 1
[RECEIVE] Sequence 04-A-M_2943612 from node 1 (9 alignments remaining): V4-34*11,J4*02
[SEND] Sequence 04-A-M_1107136 to MPI node 1
Error:
Master node received an error:Bad binary operator placement in the following context: '<<ERROR HERE>HyPhy Base Object>'
Function call stack
1 : returnAVL={"SEQUENCE_NAME":"04-A-M_1107136","REFERENCE":"Human IgG (heavy chain) with all unique F+ORF alleles, based on IMGT from Dec 2014","BEST_REARRANGEMENT":"V1-18*01,J?","SUPPORT":0.1687626935203052,"SCORE":8047.160355358626,"DELTA_IC":-8047.160355358626,"TERMINATOR":0,"SEQUENCE":"GACCACAGACGCATCCACGAGCACTGTTTACATGGCGCTGCGGAGCCTGAAATCTGACGACACGGCCGTGTATTATAGTTCCCGCGATTTCTCATCTGCCCTCTGGGGCCAGGGA","SISTER_SEQUENCES":{"0":"NODE348","1":"NODE209"},"BRANCH_LENGTHS":{"TO_SISTER":{{5.000000025e-09}{0.0001286543421442442}},"TO_PARENT":{{0.1279953855652854}{4485.903776979053}},"TO_QUERY":{{0.2261950337603474}{0.85454963896991}}},"REARRANGEMENTS":{"V1-18*01,J?":0.1687626935203052,"V1-18*01,J5*02":0.1434141888155421,"V1-18*04,J?":0.07873096170526599,"V1-18*02,J?":0.07253781076073025,"V1-18*02,J5*02":0.0697150539934551,"V1-18*04,J5*02":0.0563133354481517,"V1-18*01,J5*01":0.05389071872010095,"V1-18*01,J4*01":0.03007341541002615,"V1-18*02,J5*01":0.02960649717280993,"V1-18*01,J4*02":0.02787880568984089,"V1-18*03,J5*02":0.02450016610967478,"V1-18*04,J5*01":0.02332684532410361,"V1-18*01,J3*01":0.02164179855076386,"V1-18*01,J6*03":0.01949288284065922,"V1-18*01,J2*01":0.01778238543506694,"V1-18*03,J?":0.01187363571830067,"V1-18*02,J4*01":0.0113027372457437,"V1-18*04,J2*01":0.01120192234741949,"V1-18*04,J4*01":0.01089631135708937,"V1-18*04,J6*03":0.0107443750110703,"V1-18*02,J6*03":0.01019296599363384},"MODELS_TRIED":16200,"EXTRA":{"FW1":"","FW1_AA":"","CDR1":"","CDR1_AA":"","FW2":"","FW2_AA":"","CDR2":"","CDR2_AA":"","FW3":"NNGACCACAGACGCATCCACGAGCACTGTTTACATGGCGCTGCGGAGCCTGAAATCTGACGACACGGCCGTGTATTATTGGTCGACAGGGCTGAGT","FW3_AA":"?TTDASTSTVYMALRSLKSDDTAVYYWSTGLS","CDR3":"TCCCGC","CDR3_AA":"SR","JUNCTION":"","JUNCTION_AA":"","D_ALLELE":<HyPhy Base Object>,"D":<HyPhy Base Object>,"D_AA":<HyPhy Base Object>,"D_SCORE":<HyPhy Base Object>,"D/INV_ALLELE":<HyPhy Base Object>,"D/INV":<HyPhy Base Object>,"D/INV_AA":<HyPhy Base Object>,"D/INV_SCORE":<HyPhy Base Object>,"J":"GATTTCTCATCTGCCCTCTGGGGCCAGGGA","J_AA":"DFSSALWGQG","Mapped Read":"---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------NNGACCACAGACGCATCCACGAGCACTGTTTACATGGCGCTGCGGAGCCTGAAATCTGACGACACGGCCGTGTATTATTGGTCGACAGGGCTGAGTTCC---CGC---------GATTTCTCATCTGCCCTCTGGGGCCAGGGA","ALIGNMENT_SPANS":{{0}{0}{0}{0}{0}{321}{330}{369}}},"BREAKPOINTS":{{76}},"BREAKPOINT_SUPPORT":{{0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.01404955757345511,0.01409359126603213,0.007159888877939839,0.04189616111431885,0.05905429497046503,0.06170181950948323,0.06713508169240467,0.1654889321992937,0.2310853891229091,0.3409299640085231,1.123540372970069,2.682209327053691,0.7458619817774067,0.02755255857121293,0.1450060289560257,0.4866524126627346,0.05064460134784571,0.1436209425651628,0.009644212957660374,0.002147411334251959,0.01133581575225164,0.0008842481662898203,0.001130882611333214,0.000998782103531933,0.001192719360368263,0.001146212364101266,0.004786997457793554,0.008433031388062354,0.004144938968578325,0.005808816094464929,0.01378854583722991,0.005163536909114533,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0}},"BRANCH_SUPPORT":{"NODE348":0.2646191754622641,"IGHJ1_01_CRF_01":0.02119906189272637,"NODE323":1.639975749263915e-07,"NODE209":0.2399673301615894,"IGHV1_18_01_CRF_1":0.2361599780965632,"NODE215":0.04416736761646182,"NODE222":0.05620579591911656,"IGHJ4_03_CRF_01":0.01087239844141774,"NODE321":5.845226266121082e-07,"IGHJ2_01_CRF_01":0.03645524926902291,"IGHV1_69_05_CRF_1":7.73929145489338e-08,"NODE223":0.0942071725033531,"NODE217":0.0001507980283316502,"NODE210":0.03698425150899463,"IGHJ6_02_CRF_01":0.0001143649879910973,"IGHJ6_01_CRF_01":0.0001201874267519578,"IGHJ4_02_CRF_01":0.04889930069813665,"NODE213":0.03573366424839848,"IGHV1_18_02_CRF_1":0.2171996236272148,"NODE226":0.03798950451401927,"IGHJ6_04_CRF_01":3.891750612592212e-05,"NODE298":5.019366195444026e-08,"NODE263":5.226418026980619e-08,"IGHV1_69_11_CRF_1":5.6426394062391e-09,"IGHV1_69_07_CRF_1":5.642639894449284e-09,"IGHV1_18_04_CRF_1":0.2144841863311469,"NODE218":0.0001067079974052938,"IGHV1_18_03_CRF_1":0.06753355033212066,"IGHJ5_01_CRF_01":0.02140559030268662,"IGHJ6_03_CRF_01":0.0001470857212962572,"IGHJ3_01_CRF_01":0.003013246881429785,"IGHJ5_02_CRF_01":0.2939438580854014,"IGHJ3_02_CRF_01":0.002288994280585856,"IGHJ4_01_CRF_01":0.01598915200875662,"IGHV1_46_02_CRF_1":2.593138547387373e-07,"NODE331":5.685450136126517e-09,"IGHV1_69_03_CRF_1":2.129486249304418e-08,"IGHV1_69_13_CRF_1":5.6426394062391e-09,"IGHV1_69D_01_CRF_1":5.6426394062391e-09,"IGHV1_69_12_CRF_1":5.6426394062391e-09,"NODE264":4.957367864672318e-08,"NODE273":2.816412020031636e-08,"IGHV1_38_4_01_CRF_1":2.86286733191622e-08,"NODE296":2.79534666414367e-08,"NODE310":2.566421342337107e-07,"IGHV1_46_01_CRF_1":2.544756072700783e-07,"IGHV1_46_03_CRF_1":6.162694363348138e-07,"NODE297":3.594941481501865e-08,"NODE305":3.064921138626917e-08,"NODE274":2.842627980530069e-08,"NODE322":8.865403437273759e-07},"FRAME":0}
-------
2 : ExecuteCommands in string "returnAVL = "+returnValue using basepath /fh/fast/matsen_e/dralph/work/igscueal/A/data/istartstop-0-10000/igs-477/.
-------
3 : mpiNode=ReceiveAJob(0)
-------
4 : SendAJob(seqID)
-------
-----
err----
srun: job 26096285 queued and waiting for resources
srun: job 26096285 has been allocated resources
--------------------------------------------------------------------------
MPI_ABORT was invoked on rank 0 in communicator MPI_COMM_WORLD
with errorcode 1.
NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI processes.
You may or may not see output from other processes, depending on
exactly when Open MPI kills them.
--------------------------------------------------------------------------
[gizmof86:04550] *** Process received signal ***
[gizmof86:04550] Signal: Segmentation fault (11)
[gizmof86:04550] Signal code: Address not mapped (1)
[gizmof86:04550] Failing at address: 0x31
HYPHYMPI terminated.
Error:
HyPhy killed by signal 15
--------------------------------------------------------------------------
mpirun noticed that process rank 0 with PID 4550 on node gizmof86 exited on signal 11 (Segmentation fault).
--------------------------------------------------------------------------
[gizmof86:04546] 1 more process has sent help message help-mpi-api.txt / mpi-abort
[gizmof86:04546] Set MCA parameter "orte_base_help_aggregate" to 0 to see all help / error messages
srun: error: gizmof86: task 0: Exited with exit code 139
-----
proc 516
out----
Read 10 sequences
[SEND] Sequence 04-A-M_2161043 to MPI node 1
[RECEIVE] Sequence 04-A-M_2161043 from node 1 (9 alignments remaining): V4-34*03,J3*02
[SEND] Sequence 04-A-M_3089759 to MPI node 1
[RECEIVE] Sequence 04-A-M_3089759 from node 1 (8 alignments remaining): Error/ alignment failed
[SEND] Sequence 04-A-M_3291667 to MPI node 1
[RECEIVE] Sequence 04-A-M_3291667 from node 1 (7 alignments remaining): V1-3*01,J3*02
[SEND] Sequence 04-A-M_0222347 to MPI node 1
Error:
Master node received an error:Bad binary operator placement in the following context: '<<ERROR HERE>HyPhy Base Object>'
Function call stack
1 : returnAVL={"SEQUENCE_NAME":"04-A-M_0222347","REFERENCE":"Human IgG (heavy chain) with all unique F+ORF alleles, based on IMGT from Dec 2014","BEST_REARRANGEMENT":"V3-30*01,J4*02","SUPPORT":0.1318769985697806,"SCORE":8970.486911234248,"DELTA_IC":-8970.486911234248,"TERMINATOR":0,"SEQUENCE":"TGAAGGGCCGATTCACCTTCTCCAGAGACAATTCCAAGAAAACGCTGTCCCCGCAAATGGACAGCCTGAGAGTTGAGGACCCCTTTTGGGGGACTCATCGTTGTTAAACTTTGACTATTGGGGCCAGGGA","SISTER_SEQUENCES":{"0":"NODE445","1":"IGHJ4_02_CRF_01"},"BRANCH_LENGTHS":{"TO_SISTER":{{5.000000025e-09}{5.000000025e-09}},"TO_PARENT":{{5.000000025e-09}{0.1441022137585326}},"TO_QUERY":{{0.244364006254017}{1.056723261281907}}},"REARRANGEMENTS":{"V3-30*01,J4*02":0.1318769985697806,"V3,J4*02":0.05959158972785008,"V3-30*07,J4*02":0.04334413364776475,"V3-30-3*03,J4*02":0.04257894983591554,"V3-30*01,J4*01":0.04083935715882302,"V3-30*01,J1*01":0.03468297271933957,"V3-30*14,J4*02":0.03465891864148216,"V3-30*05,J4*02":0.0329914375145054,"V3-30*18,J4*02":0.03096750646788657,"V3/OR16-12*01,J4*02":0.02989218121743175,"V3-30*16,J4*02":0.02813022613848904,"V3-30*11,J4*02":0.0278765885638487,"V3-30*10,J4*02":0.02729311683091139,"V3-30*09,J4*02":0.02587858386162856,"V3-30,J4*02":0.02562609043142575,"V3-30*01,J4*03":0.02410732739740173,"V3-30*17,J4*02":0.0226624577590648,"V3-30*12,J4*02":0.01862398710181084,"V3-33*06,J4*02":0.01861692389660067,"V3-30*03,J4*02":0.01817059358104309,"V3-30*02,J4*02":0.01816533761737234,"V3-30*01,J?":0.01767391190707603,"V3,J4*01":0.0115024134862091,"V?,J4*02":0.01118804517162647,"V3-30*07,J1*01":0.01116205717370535,"V3-30*07,J4*01":0.01101613442150444},"MODELS_TRIED":16021,"EXTRA":{"FW1":"","FW1_AA":"","CDR1":"","CDR1_AA":"","FW2":"","FW2_AA":"","CDR2":"","CDR2_AA":"","FW3":"NTGAAGGGCCGATTCACCTTCTCCAGAGACAATTCCAAGAAAACGCTGTCCCCGCAAATGGACAGCCTGAGAGTTGAGGACNCCCTTTTGGGGGACTCA","FW3_AA":"?KGRFTFSRDNSKKTLSPQMDSLRVED?LLGDS","CDR3":"TCGTTG","CDR3_AA":"SL","JUNCTION":"","JUNCTION_AA":"","D_ALLELE":<HyPhy Base Object>,"D":<HyPhy Base Object>,"D_AA":<HyPhy Base Object>,"D_SCORE":<HyPhy Base Object>,"D/INV_ALLELE":<HyPhy Base Object>,"D/INV":<HyPhy Base Object>,"D/INV_AA":<HyPhy Base Object>,"D/INV_SCORE":<HyPhy Base Object>,"J":"TTAAACTTTGACTATTGGGGCCAGGGA","J_AA":"LNFDYWGQG","Mapped Read":"---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------NTGAAGGGCCGATTCACCTTCTCCAGAGACAATTCCAAGAAAACGCTGTCCCCGCAAATGGACAGCCTGAGAGTTGAGGACNCCCTTTTGGGGGACTCATCG---TTG------------TTAAACTTTGACTATTGGGGCCAGGGA","ALIGNMENT_SPANS":{{0}{0}{0}{0}{0}{306}{315}{354}}},"BREAKPOINTS":{{83}},"BREAKPOINT_SUPPORT":{{0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,1.45085322801466,0.3239677038796874,0.1039743749822445,0.3983229139633723,0.11048868421681,0.1717966130400485,0.2701874641679753,0.07904994863133302,0.030659030254975,0.01109208300837162,0.004470296702856308,0.005923269800824802,0.008388010296701019,0.01219993057775807,0.005064975658881993,0.001847121142520358,0.0009436823877044408,0.001237688870629853,0.001808122429970612,0.0008075902286256045,0.0002609028030346997,0.000182203421367615,0.0005467039958071922,0.002253320622669284,0.009749967964236744,0.1094482394993599,0.07637551933978209,0.04907221015653911,0.03213942740386044,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0}},"BRANCH_SUPPORT":{"IGHV3_30_09_CRF_1":0.0418357377075905,"IGHJ4_02_CRF_01":0.6654178139224658,"IGHV3_30_14_CRF_1":0.04924272726252444,"NODE405":0.001100439026870182,"NODE446":0.05804446820979609,"NODE445":0.1768126677358203,"NODE210":0.000544047685451084,"IGHJ4_01_CRF_01":0.05330462476131995,"NODE223":0.01346021442031723,"NODE443":0.0424260762268793,"NODE215":0.001272415735901916,"IGHJ5_01_CRF_01":0.0003722296893956261,"IGHJ4_03_CRF_01":0.06742210051954192,"IGHJ6_03_CRF_01":2.014643087862353e-05,"IGHJ5_02_CRF_01":0.0005193961156858213,"NODE222":0.02074372542143424,"NODE442":0.04368984874892554,"IGHJ6_02_CRF_01":7.689422072550709e-05,"NODE218":5.531303088728891e-05,"NODE226":0.05963511749538448,"IGHV3_30_03_CRF_1":0.01825697471294562,"IGHJ6_01_CRF_01":8.776227344553492e-05,"IGHJ3_01_CRF_01":8.225318454738479e-05,"NODE213":0.001015617243123346,"IGHJ6_04_CRF_01":3.099794391245247e-05,"IGHV3_30_3_03_CRF_1":0.05678762449951918,"NODE217":2.298467650015281e-05,"NODE432":0.0181675255558069,"NODE209":0.03114668457902806,"NODE477":2.95962246791252e-07,"IGHJ1_01_CRF_01":0.08238852147012608,"IGHJ2_01_CRF_01":0.002281250284622224,"IGHV3_30_16_CRF_1":0.02831671585759509,"IGHJ3_02_CRF_01":9.988889530493847e-05,"IGHV3_30_18_CRF_1":1.04747781641843e-05,"NODE397":0.0004683579052664735,"IGHV3_30_05_CRF_1":0.04801207561819386,"IGHV3_30_07_CRF_1":0.08100821053301585,"IGHV3_30_11_CRF_1":0.03654020227051658,"IGHV3_30_3_01_CRF_1":0.004750306899467009,"IGHV3_33_02_CRF_1":0.001688540822861517,"IGHV3_30_10_CRF_1":0.03755985731665253,"IGHV3_OR16_13_01_CRF_1":4.309566965681246e-06,"IGHV3_30_01_CRF_1":0.07914541408135536,"NODE526":0.001024041447440272,"IGHV3_30_13_CRF_1":0.02675418061396495,"NODE417":4.820763147547731e-07,"IGHV3_30_06_CRF_1":3.556473041838075e-05,"NODE494":4.54682205116259e-08,"IGHV3_30_17_CRF_1":0.03425437161251904,"IGHV3_74_02_CRF_1":1.115542163444193e-06,"NODE518":0.001172054801356104,"IGHV3_30_3_02_CRF_1":9.66770734162313e-05,"IGHV3_53_04_CRF_1":0.0004680781504087257,"NODE475":8.094093751063798e-07,"NODE406":0.001013536067927482,"IGHV3_66_01_CRF_1":1.224186327114287e-07,"IGHV3_64_02_CRF_1":1.59175529149771e-06,"IGHV3_NL1_01_CRF_1":3.742390834084115e-07,"NODE383":0.01198324443455625,"NODE391":2.041353442387813e-07,"NODE522":1.538782674320324e-07,"NODE508":9.9981192688366e-05,"IGHV3_23_02_CRF_1":0.0001024471764599964,"NODE425":0.001270728974432172,"NODE433":0.01861692389660067,"IGHV3_74_01_CRF_1":3.315937397687933e-07,"IGHV3_11_05_CRF_1":4.961933676719082e-09,"NODE377":1.096273236672124e-08,"IGHV3_30_02_CRF_1":0.01816533761737234,"NODE416":0.001270729051070364,"NODE394":0.0009764401450062344,"IGHV3_30_12_CRF_1":0.01862470711595869,"NODE382":0.00789518743169971,"IGHV3_23_04_CRF_1":9.9981192688366e-05,"IGHV3_7_03_CRF_1":1.097957851862692e-08,"IGHV3_74_03_CRF_1":3.315937397687933e-07,"NODE233":2.801935368317744e-09,"IGHV3_38_01_CRF_1":8.516398060677478e-09,"NODE411":0.0009322235420425684,"IGHV3_23_01_CRF_1":9.9981192688366e-05,"IGHV3_33_04_CRF_1":0.001270371979061775,"IGHV3_38_03_CRF_1":3.857007339184241e-09,"IGHV3_OR16_12_01_CRF_1":0.02989218121743175,"IGHV3_9_03_CRF_1":2.00687390636967e-08,"NODE356":1.911205514786855e-06,"IGHV3_30_19_CRF_1":1.482465693224328e-06,"IGHV3_33_01_CRF_1":8.0962743485018e-07,"IGHV3_33_03_CRF_1":5.585777342890001e-08,"IGHV3_66_02_CRF_1":3.162075686491005e-07,"IGHV3_64_04_CRF_1":1.23848121005456e-07,"IGHV3_33_05_CRF_1":1.121161272414383e-08,"IGHV3_33_06_CRF_1":5.585618576527674e-08,"IGHV3_30_08_CRF_1":7.512558618149833e-07,"IGHV3_66_03_CRF_1":3.162306775946821e-07,"IGHV3_30_15_CRF_1":7.200188706932809e-07},"FRAME":0}
-------
2 : ExecuteCommands in string "returnAVL = "+returnValue using basepath /fh/fast/matsen_e/dralph/work/igscueal/A/data/istartstop-0-10000/igs-516/.
-------
3 : mpiNode=ReceiveAJob(0)
-------
4 : SendAJob(seqID)
-------
-----
err----
srun: job 26096290 queued and waiting for resources
srun: job 26096290 has been allocated resources
--------------------------------------------------------------------------
MPI_ABORT was invoked on rank 0 in communicator MPI_COMM_WORLD
with errorcode 1.
NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI processes.
You may or may not see output from other processes, depending on
exactly when Open MPI kills them.
--------------------------------------------------------------------------
[gizmof43:25765] *** Process received signal ***
[gizmof43:25765] Signal: Segmentation fault (11)
[gizmof43:25765] Signal code: Address not mapped (1)
[gizmof43:25765] Failing at address: 0x31
HYPHYMPI terminated.
Error:
HyPhy killed by signal 15
--------------------------------------------------------------------------
mpirun noticed that process rank 0 with PID 25765 on node gizmof43 exited on signal 11 (Segmentation fault).
--------------------------------------------------------------------------
[gizmof43:25761] 1 more process has sent help message help-mpi-api.txt / mpi-abort
[gizmof43:25761] Set MCA parameter "orte_base_help_aggregate" to 0 to see all help / error messages
srun: error: gizmof43: task 0: Exited with exit code 139
-----
proc 538
out----
Read 10 sequences
[SEND] Sequence 04-A-M_3178587 to MPI node 1
[RECEIVE] Sequence 04-A-M_3178587 from node 1 (9 alignments remaining): V3/OR16-13*01,J4*02
[SEND] Sequence 04-A-M_2506680 to MPI node 1
[RECEIVE] Sequence 04-A-M_2506680 from node 1 (8 alignments remaining): V4-30-4*01,J3*02
[SEND] Sequence 04-A-M_4342144 to MPI node 1
[RECEIVE] Sequence 04-A-M_4342144 from node 1 (7 alignments remaining): V3-30*07,J4*02
[SEND] Sequence 04-A-M_3635145 to MPI node 1
[RECEIVE] Sequence 04-A-M_3635145 from node 1 (6 alignments remaining): V3-30*18,J2*01
[SEND] Sequence 04-A-M_2785297 to MPI node 1
[RECEIVE] Sequence 04-A-M_2785297 from node 1 (5 alignments remaining): Error/ alignment failed
[SEND] Sequence 04-A-M_1469223 to MPI node 1
Error:
Master node received an error:Bad binary operator placement in the following context: '<<ERROR HERE>HyPhy Base Object>'
Function call stack
1 : returnAVL={"SEQUENCE_NAME":"04-A-M_1469223","REFERENCE":"Human IgG (heavy chain) with all unique F+ORF alleles, based on IMGT from Dec 2014","BEST_REARRANGEMENT":"V3-30*18,J4*02","SUPPORT":0.3378138701142167,"SCORE":7927.979199338595,"DELTA_IC":-7927.979199338595,"TERMINATOR":0,"SEQUENCE":"CTCCAGAGACAATTCCAAGAGCACACTATATTTGCAAATGAACAGCCTGAGACCTGAGGACACGGCTGTGTATTACCGTGCGAAAACCGTATTTGACTACTGGGGCCAGGGA","SISTER_SEQUENCES":{"0":"IGHV3_30_18_CRF_1","1":"IGHJ4_02_CRF_01"},"BRANCH_LENGTHS":{"TO_SISTER":{{5.000000025e-09}{5.000000025e-09}},"TO_PARENT":{{4.961990153036845e-10}{0.1073009080021175}},"TO_QUERY":{{0.1860012726121573}{5.000000025e-09}}},"REARRANGEMENTS":{"V3-30*18,J4*02":0.3378138701142167,"V3-33*06,J4*02":0.2152630412953875,"V3-30-3*02,J4*02":0.2152624041370635,"V3-30*02,J4*02":0.1293265895035895,"V3-30*13,J4*02":0.01293759429003399,"V3-30*17,J4*02":0.01276951294822532,"V3-30-3*02,J1*01":0.01123691227049751},"MODELS_TRIED":9614,"EXTRA":{"FW1":"","FW1_AA":"","CDR1":"","CDR1_AA":"","FW2":"","FW2_AA":"","CDR2":"","CDR2_AA":"","FW3":"NNCTCCAGAGACAATTCCAAGAGCACACTATATTTGCAAATGAACAGCCTGAGACCTGAGGACACGGCTGTGTATTACCGT","FW3_AA":"?SRDNSKSTLYLQMNSLRPEDTAVYYR","CDR3":"GCGAAA","CDR3_AA":"AK","JUNCTION":"","JUNCTION_AA":"","D_ALLELE":<HyPhy Base Object>,"D":<HyPhy Base Object>,"D_AA":<HyPhy Base Object>,"D_SCORE":<HyPhy Base Object>,"D/INV_ALLELE":<HyPhy Base Object>,"D/INV":<HyPhy Base Object>,"D/INV_AA":<HyPhy Base Object>,"D/INV_SCORE":<HyPhy Base Object>,"J":"GCTTCGGGAGGTGGGAACACCGTATTTGACTACTGGGGCCAGGGA","J_AA":"ASGGGNTVFDYWGQG","Mapped Read":"---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------NNCTCCAGAGACAATTCCAAGAGCACACTATATTTGCAAATGAACAGCCTGAGACCTGAGGACACGGCTGTGTATTACCGTGCG---AAA------------GCTTCGGGAGGTGGGAACACCGTATTTGACTACTGGGGCCAGGGA","ALIGNMENT_SPANS":{{0}{0}{0}{0}{0}{306}{315}{372}}},"BREAKPOINTS":{{92}},"BREAKPOINT_SUPPORT":{{0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,1.076030555379751e-06,2.748992949263751e-06,3.542874186142279e-06,8.574521508178401e-06,1.107386759693333e-05,1.457579276727761e-05,3.809427152299367e-05,2.540461640592983e-05,6.385152141580877e-05,4.318166786413456e-05,0.0001177740077341401,7.538640803196779e-05,0.0001031297162404811,2.850717842642918e-05,7.663173680207677e-05,0.0001054168498051063,7.216205985238165e-05,9.996250425526663e-05,0.0003145036359217945,0.0002083748042786132,0.001149788010279971,0.001520386594143639,0.002054445954448222,0.002495628285802151,0.003858233064940489,0.006409060360584689,0.04525769831388146,1.999999861086513,0.7014918190327262,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0}},"BRANCH_SUPPORT":{"NODE508":3.555938886890516e-05,"IGHJ4_02_CRF_01":0.9628740568170007,"NODE433":0.2242167321390007,"NODE223":0.002685706420816987,"NODE437":0.008113169872696585,"IGHJ4_03_CRF_01":0.008215342349966036,"IGHV3_30_02_CRF_1":0.000176291911696993,"NODE383":0.0005686456701152556,"IGHJ4_01_CRF_01":0.002894013467423028,"IGHV3_33_01_CRF_1":0.0005689884508633321,"NODE215":1.582369972794782e-06,"NODE210":3.788888520726455e-06,"IGHJ5_01_CRF_01":2.70151130072692e-05,"IGHV3_53_01_CRF_1":1.181844566460966e-06,"NODE407":6.035556745458032e-07,"IGHV3_30_13_CRF_1":0.01391621172373319,"NODE209":1.282602746812234e-06,"IGHJ1_01_CRF_01":0.01942310938868808,"NODE476":1.722382282253248e-08,"IGHJ5_02_CRF_01":3.609154099443355e-05,"IGHV3_33_05_CRF_1":0.008537757576121231,"NODE213":1.003969897716897e-06,"IGHV3_30_17_CRF_1":0.01304435374238977,"IGHV3_30_3_02_CRF_1":0.2355561668375718,"NODE226":0.002735924785503192,"IGHV3_23_02_CRF_1":3.983220988030587e-05,"IGHV3_30_12_CRF_1":0.0001024977387329176,"IGHV3_30_06_CRF_1":0.008520144438959659,"NODE222":0.001099985786557851,"IGHJ3_01_CRF_01":1.523054651330249e-07,"IGHV3_21_01_CRF_1":1.932315804810481e-07,"IGHV3_66_03_CRF_1":0.0002183533571122063,"IGHV3_OR16_9_01_CRF_1":2.987646761832251e-08,"IGHV3_23_01_CRF_1":3.540890441595655e-05,"IGHV3_30_03_CRF_1":0.00509837317984531,"IGHV3_30_01_CRF_1":0.0007393497971517163,"IGHV3_21_04_CRF_1":3.193895064766043e-07,"IGHV3_30_05_CRF_1":0.00742237166643112,"IGHV3_30_11_CRF_1":1.201802970644892e-06,"IGHV3_33_02_CRF_1":4.698009041882146e-07,"IGHV3_30_16_CRF_1":7.271222772340245e-05,"IGHV3_30_10_CRF_1":1.117942078066154e-07,"IGHV3_30_19_CRF_1":7.817251479831898e-06,"IGHV3_30_09_CRF_1":8.707519697085026e-07,"IGHJ3_02_CRF_01":2.378211124279575e-07,"IGHJ2_01_CRF_01":7.063723262195003e-07,"IGHV3_21_03_CRF_1":1.932318969466501e-07,"NODE450":1.014435056703202e-05,"IGHV3_35_01_CRF_1":5.120239943432175e-07,"IGHV3_30_08_CRF_1":7.162329079420878e-06,"IGHV3_30_15_CRF_1":1.073823669689719e-06,"IGHV3_66_02_CRF_1":1.759262137442652e-08,"IGHV3_30_07_CRF_1":1.118004895223714e-07,"NODE358":0.0003682858501004715,"NODE442":0.1239159933667703,"NODE443":0.00101827035297441,"IGHV3_30_18_CRF_1":0.2185075482744162,"NODE430":0.1291510368609973,"NODE391":2.244314512750805e-05,"NODE397":2.029053521263485e-08,"IGHV3_OR16_12_01_CRF_1":1.848966376538812e-08,"IGHV3_33_04_CRF_1":4.180952474339489e-07,"IGHV3_38_3_01_CRF_1":1.321251096329132e-07,"IGHV3_64_04_CRF_1":8.579373117887829e-07,"IGHV3_NL1_01_CRF_1":2.270296576541295e-08},"FRAME":0}
-------
2 : ExecuteCommands in string "returnAVL = "+returnValue using basepath /fh/fast/matsen_e/dralph/work/igscueal/A/data/istartstop-0-10000/igs-538/.
-------
3 : mpiNode=ReceiveAJob(0)
-------
4 : SendAJob(seqID)
-------
-----
err----
srun: job 26096293 queued and waiting for resources
srun: job 26096293 has been allocated resources
--------------------------------------------------------------------------
MPI_ABORT was invoked on rank 0 in communicator MPI_COMM_WORLD
with errorcode 1.
NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI processes.
You may or may not see output from other processes, depending on
exactly when Open MPI kills them.
--------------------------------------------------------------------------
[gizmof43:25803] *** Process received signal ***
[gizmof43:25803] Signal: Segmentation fault (11)
[gizmof43:25803] Signal code: Address not mapped (1)
[gizmof43:25803] Failing at address: 0x31
HYPHYMPI terminated.
Error:
HyPhy killed by signal 15
--------------------------------------------------------------------------
mpirun noticed that process rank 0 with PID 25803 on node gizmof43 exited on signal 11 (Segmentation fault).
--------------------------------------------------------------------------
[gizmof43:25797] 1 more process has sent help message help-mpi-api.txt / mpi-abort
[gizmof43:25797] Set MCA parameter "orte_base_help_aggregate" to 0 to see all help / error messages
srun: error: gizmof43: task 0: Exited with exit code 139
-----
proc 567
out----
Read 10 sequences
[SEND] Sequence 04-A-M_2218609 to MPI node 1
[RECEIVE] Sequence 04-A-M_2218609 from node 1 (9 alignments remaining): V4-30-2*04,J4*02
[SEND] Sequence 04-A-M_2776497 to MPI node 1
[RECEIVE] Sequence 04-A-M_2776497 from node 1 (8 alignments remaining): V3-9*01,J5*01
[SEND] Sequence 04-A-M_0704231 to MPI node 1
Error:
Master node received an error:Bad binary operator placement in the following context: '<<ERROR HERE>HyPhy Base Object>'
Function call stack
1 : returnAVL={"SEQUENCE_NAME":"04-A-M_0704231","REFERENCE":"Human IgG (heavy chain) with all unique F+ORF alleles, based on IMGT from Dec 2014","BEST_REARRANGEMENT":"V3-74*02,J5*02","SUPPORT":0.2237602737093812,"SCORE":8810.557207400598,"DELTA_IC":-8810.557207400598,"TERMINATOR":0,"SEQUENCE":"GGGCCGATTCACCATCTCCAGGGACAACGCCAAGAACACGCTGTATCTGCAAATGAACAGTCGGAGAGCCGACGCCACGGCTCTCCAGTTCGTATCAAGGAATTGGCTTCATTTTTGGGGCCAGGGA","SISTER_SEQUENCES":{"0":"NODE418","1":"IGHJ5_02_CRF_01"},"BRANCH_LENGTHS":{"TO_SISTER":{{5.000000025e-09}{0.0715855535074412}},"TO_PARENT":{{0.08700002006736011}{0.1267496625856585}},"TO_QUERY":{{0.1180370649855118}{0.988171615254068}}},"REARRANGEMENTS":{"V3-74*02,J5*02":0.2237602737093812,"V3-74*02,J5*01":0.2111168893622409,"V3-74*01,J5*01":0.1325379685020027,"V3/OR16-13*01,J5*02":0.1283132612908074,"V3-74*01,J5*02":0.1214005658395974,"V3/OR16-13*01,J5*01":0.09518954993552102,"V3-74*03,J5*02":0.03131190471035731,"V3-74*02,J?":0.01028342087418143},"MODELS_TRIED":14769,"EXTRA":{"FW1":"","FW1_AA":"","CDR1":"","CDR1_AA":"","FW2":"","FW2_AA":"","CDR2":"","CDR2_AA":"","FW3":"NNGGGCCGATTCACCATCTCCAGGGACAACGCCAAGAACACGCTGTATCTGCAAATGAACAGTCGGAGAGCCGACGCCACGGCTCTCCAGTTCTAAGTA","FW3_AA":"?GRFTISRDNAKNTLYLQMNSRRADATALQFXV","CDR3":"TCAAGG","CDR3_AA":"SR","JUNCTION":"","JUNCTION_AA":"","D_ALLELE":<HyPhy Base Object>,"D":<HyPhy Base Object>,"D_AA":<HyPhy Base Object>,"D_SCORE":<HyPhy Base Object>,"D/INV_ALLELE":<HyPhy Base Object>,"D/INV":<HyPhy Base Object>,"D/INV_AA":<HyPhy Base Object>,"D/INV_SCORE":<HyPhy Base Object>,"J":"AATTGGCTTCATTTTTGGGGCCAGGGA","J_AA":"NWLHFWGQG","Mapped Read":"------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------NNGGGCCGATTCACCATCTCCAGGGACAACGCCAAGAACACGCTGTATCTGCAAATGAACAGTCGGAGAGCCGACGCCACGGCTCTCCAGTTCTAAGTATCA---AGG------------AATTGGCTTCATTTTTGGGGCCAGGGA","ALIGNMENT_SPANS":{{0}{0}{0}{0}{0}{309}{318}{357}}},"BREAKPOINTS":{{83}},"BREAKPOINT_SUPPORT":{{0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.1456930636871952,0.2703689890077469,0.4998401229266012,1.989057611030079,0.1060029818613149,0.2003780448756747,0.05065952770098886,0.01039759491221152,0.01695390692930668,0.002792155360233929,0.005016239937116403,0.0006589674772842443,0.001122935525891838,0.0002356821939785753,5.581693287826438e-05,5.761665779748163e-06,3.30598232412334e-06,2.697791988406645e-06,1.558849211755474e-05,1.146899474055181e-05,1.831144527194329e-05,6.874526493384023e-06,3.897117281356305e-06,1.799020120012361e-06,2.957274409543752e-06,5.23041815475654e-06,7.741882881598341e-07,1.116849384987805e-07,1.613979262227906e-07,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0}},"BRANCH_SUPPORT":{"IGHV3_OR16_13_01_CRF_1":0.2355769565450195,"IGHJ5_02_CRF_01":0.505197630560812,"NODE418":0.2685987492996635,"NODE215":0.0006646798602217707,"NODE223":0.2747536601683747,"IGHJ4_01_CRF_01":0.002036010173577946,"IGHV3_7_03_CRF_1":2.11990314494291e-06,"IGHJ4_02_CRF_01":0.007872780349331679,"IGHV3_74_01_CRF_1":0.2663617158075827,"NODE213":0.001169021672724645,"IGHV3_7_01_CRF_1":1.88172605079868e-07,"IGHJ1_01_CRF_01":0.002978418270986093,"NODE218":9.621083301398733e-06,"IGHV3_11_03_CRF_1":1.377037426536239e-07,"IGHJ5_01_CRF_01":0.1723445890638802,"NODE222":0.005023733867614126,"IGHJ6_02_CRF_01":1.098134971540044e-05,"IGHJ2_01_CRF_01":0.0005193745003022194,"IGHV3_33_01_CRF_1":7.217116947125665e-06,"IGHJ6_01_CRF_01":9.974348263729893e-06,"IGHJ4_03_CRF_01":0.001719786938219417,"NODE426":9.318921841915733e-05,"NODE210":0.001144857939214975,"IGHJ3_01_CRF_01":0.0002560899245278436,"NODE209":0.01955209979253981,"NODE413":5.223131880025091e-05,"IGHV3_30_11_CRF_1":4.519107406008061e-07,"IGHV3_74_02_CRF_1":0.1874488922176568,"NODE383":4.344635723758386e-07,"IGHJ3_02_CRF_01":0.0003603656309201829,"NODE217":3.955360387340337e-06,"NODE226":0.0043673811723453,"IGHJ6_03_CRF_01":3.324376589818147e-06,"NODE474":1.763468152859612e-06,"NODE529":1.001940803517348e-07,"NODE445":8.399571690048901e-08,"IGHV3_30_15_CRF_1":3.729288354108478e-08,"IGHV3_30_03_CRF_1":3.665557320488754e-08,"IGHV3_30_10_CRF_1":3.665557320488754e-08,"IGHV3_21_03_CRF_1":1.649234682777622e-07,"NODE362":1.621809308835362e-07,"NODE417":2.985150774309586e-06,"NODE443":3.665557320488754e-08,"IGHV3_20_01_CRF_1":2.032417135315628e-07,"IGHV3_30_01_CRF_1":1.843819333586962e-07,"IGHV3_30_05_CRF_1":4.541270587174071e-08,"NODE360":1.621809309794129e-07,"NODE411":4.733616245074128e-05,"NODE359":0.0002926829837711942,"IGHV3_48_01_CRF_1":1.406929185064368e-08,"IGHJ6_04_CRF_01":1.663596148482191e-06,"IGHV3_74_03_CRF_1":0.04149946926596937,"NODE475":6.232104550923576e-09,"IGHV3_66_01_CRF_1":1.438865568447491e-08,"NODE433":5.709593674570826e-07,"IGHV3_30_17_CRF_1":2.613509056183398e-07,"NODE358":4.751834529420488e-06,"IGHV3_66_03_CRF_1":2.426522623244322e-08,"IGHV3_7_02_CRF_1":2.781840291921345e-08,"NODE450":1.269030583128618e-07,"NODE518":1.02050722187214e-06,"NODE405":3.97676965278125e-06,"NODE437":6.525763531629453e-07,"IGHV3_OR16_12_01_CRF_1":6.534431786251058e-07,"NODE373":9.65616275673788e-08,"IGHV3_30_16_CRF_1":2.784032698171134e-08},"FRAME":0}
-------
2 : ExecuteCommands in string "returnAVL = "+returnValue using basepath /fh/fast/matsen_e/dralph/work/igscueal/A/data/istartstop-0-10000/igs-567/.
-------
3 : mpiNode=ReceiveAJob(0)
-------
4 : SendAJob(seqID)
-------
-----
err----
srun: job 26096298 queued and waiting for resources
srun: job 26096298 has been allocated resources
--------------------------------------------------------------------------
MPI_ABORT was invoked on rank 0 in communicator MPI_COMM_WORLD
with errorcode 1.
NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI processes.
You may or may not see output from other processes, depending on
exactly when Open MPI kills them.
--------------------------------------------------------------------------
[gizmof32:26131] *** Process received signal ***
[gizmof32:26131] Signal: Segmentation fault (11)
[gizmof32:26131] Signal code: Address not mapped (1)
[gizmof32:26131] Failing at address: 0x31
HYPHYMPI terminated.
Error:
HyPhy killed by signal 15
--------------------------------------------------------------------------
mpirun noticed that process rank 0 with PID 26131 on node gizmof32 exited on signal 11 (Segmentation fault).
--------------------------------------------------------------------------
[gizmof32:26125] 1 more process has sent help message help-mpi-api.txt / mpi-abort
[gizmof32:26125] Set MCA parameter "orte_base_help_aggregate" to 0 to see all help / error messages
srun: error: gizmof32: task 0: Exited with exit code 139
-----
proc 739
out----
Read 10 sequences
[SEND] Sequence 04-A-M_1552639 to MPI node 1
[RECEIVE] Sequence 04-A-M_1552639 from node 1 (9 alignments remaining): V3-20*01,J3*02
[SEND] Sequence 04-A-M_0296250 to MPI node 1
[RECEIVE] Sequence 04-A-M_0296250 from node 1 (8 alignments remaining): V4-4*07,J5*02
[SEND] Sequence 04-A-M_1646678 to MPI node 1
[RECEIVE] Sequence 04-A-M_1646678 from node 1 (7 alignments remaining): V3-48*02,J5*02
[SEND] Sequence 04-A-M_0621520 to MPI node 1
Error:
Master node received an error:Bad binary operator placement in the following context: '<<ERROR HERE>HyPhy Base Object>'
Function call stack
1 : returnAVL={"SEQUENCE_NAME":"04-A-M_0621520","REFERENCE":"Human IgG (heavy chain) with all unique F+ORF alleles, based on IMGT from Dec 2014","BEST_REARRANGEMENT":"V1-38-4*01,J5*01","SUPPORT":0.4308637519637646,"SCORE":8382.398066699145,"DELTA_IC":-8382.398066699145,"TERMINATOR":0,"SEQUENCE":"GTCACCGTGACCAGGGACATGTCCAAAACCACAGCCTACACAGACCTGACCGGCCTGACATCTGAGGACATGGCTGTTTATTACTATGCATTGGATCGGCAGTACGACTCCTGGGGTCAGGGA","SISTER_SEQUENCES":{"0":"IGHV1_38_4_01_CRF_1","1":"NODE223"},"BRANCH_LENGTHS":{"TO_SISTER":{{0.02421824621219878}{0.06695779922190059}},"TO_PARENT":{{0.3139389687983632}{0.3549767255936095}},"TO_QUERY":{{0.1397280685416624}{1.058491458942536}}},"REARRANGEMENTS":{"V1-38-4*01,J5*01":0.4308637519637646,"V1-38-4*01,J5*02":0.4269675648157789,"V1-38-4*01,J?":0.05203935769589174,"V1-38-4*01,J4*01":0.03212512562639346,"V1-38-4*01,J4*02":0.02437258790848295,"V1-38-4*01,J1*01":0.01345667990319248},"MODELS_TRIED":16221,"EXTRA":{"FW1":"","FW1_AA":"","CDR1":"","CDR1_AA":"","FW2":"","FW2_AA":"","CDR2":"","CDR2_AA":"","FW3":"GTCACCGTGACCAGGGACATGTCCAAAACCACAGCCTACACAGACCTGACCGGCCTGACATCTGAGGACATGGCTGTTTATTACTAT","FW3_AA":"VTVTRDMSKTTAYTDLTGLTSEDMAVYYY","CDR3":"GCATTG","CDR3_AA":"AL","JUNCTION":"","JUNCTION_AA":"","D_ALLELE":<HyPhy Base Object>,"D":<HyPhy Base Object>,"D_AA":<HyPhy Base Object>,"D_SCORE":<HyPhy Base Object>,"D/INV_ALLELE":<HyPhy Base Object>,"D/INV":<HyPhy Base Object>,"D/INV_AA":<HyPhy Base Object>,"D/INV_SCORE":<HyPhy Base Object>,"J":"GATCGGCAGTACTAGGAAGACTCCTGGGGTCAGGGA","J_AA":"DRQYXEDSWGQG","Mapped Read":"---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------GTCACCGTGACCAGGGACATGTCCAAAACCACAGCCTACACAGACCTGACCGGCCTGACATCTGAGGACATGGCTGTTTATTACTATGCA---TTG---------GATCGGCAGTACTAGGAAGACTCCTGGGGTCAGGGA","ALIGNMENT_SPANS":{{0}{0}{0}{0}{0}{306}{315}{360}}},"BREAKPOINTS":{{91}},"BREAKPOINT_SUPPORT":{{0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.000102643871589471,0.0001637797429837243,0.0002575945840991782,0.001568693877394063,0.00158429532408744,0.004320384121405998,0.0005844502879769086,0.0005787815646683817,0.000844335782330171,0.00240628407440603,0.004135725472794098,0.006404766884057242,0.01105270629626681,0.01999216573525903,0.06844337501210934,0.1231110584776146,0.2290800902923942,0.4162012139592099,1.267665428357383,0.1061751074428939,0.01672124721255037,0.003880915540585277,0.001444485897468202,0.001316367873300754,0.001930838364837214,0.009845557946803958,0.01604055953920919,0.03376995216898496,0.07278529410980344,0.4387125288275071,0.09332232776955285,0.04313896808210355,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0}},"BRANCH_SUPPORT":{"IGHV1_38_4_01_CRF_1":1,"IGHJ4_03_CRF_01":0.008960243005382156,"NODE215":0.001982776334721728,"IGHJ6_02_CRF_01":3.154305567308635e-05,"IGHJ5_01_CRF_01":0.1949676784801738,"IGHJ4_01_CRF_01":0.006601546436270827,"NODE213":0.001757688736531886,"NODE217":2.065825952975476e-05,"NODE226":0.02552357919012263,"NODE222":0.03489406877949004,"IGHJ5_02_CRF_01":0.4269675648157789,"IGHJ3_01_CRF_01":7.3416843958388e-05,"IGHJ3_02_CRF_01":7.086121200081458e-05,"NODE218":3.246261395686035e-05,"IGHJ4_02_CRF_01":0.02437258790848295,"NODE209":0.01538760017986984,"IGHJ6_01_CRF_01":3.286188420632628e-05,"IGHJ2_01_CRF_01":0.007405295128649624,"NODE210":0.001522463687933825,"IGHJ6_04_CRF_01":9.902711975388886e-06,"NODE223":0.2358960734835908,"IGHJ1_01_CRF_01":0.01345667990319248,"IGHJ6_03_CRF_01":3.244734850748162e-05},"FRAME":0}
-------
2 : ExecuteCommands in string "returnAVL = "+returnValue using basepath /fh/fast/matsen_e/dralph/work/igscueal/A/data/istartstop-0-10000/igs-739/.
-------
3 : mpiNode=ReceiveAJob(0)
-------
4 : SendAJob(seqID)
-------
-----
err----
srun: job 26096312 queued and waiting for resources
srun: job 26096312 has been allocated resources
--------------------------------------------------------------------------
MPI_ABORT was invoked on rank 0 in communicator MPI_COMM_WORLD
with errorcode 1.
NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI processes.
You may or may not see output from other processes, depending on
exactly when Open MPI kills them.
--------------------------------------------------------------------------
[gizmof35:15940] *** Process received signal ***
[gizmof35:15940] Signal: Segmentation fault (11)
[gizmof35:15940] Signal code: Address not mapped (1)
[gizmof35:15940] Failing at address: 0x31
HYPHYMPI terminated.
Error:
HyPhy killed by signal 15
--------------------------------------------------------------------------
mpirun noticed that process rank 0 with PID 15940 on node gizmof35 exited on signal 11 (Segmentation fault).
--------------------------------------------------------------------------
[gizmof35:15934] 1 more process has sent help message help-mpi-api.txt / mpi-abort
[gizmof35:15934] Set MCA parameter "orte_base_help_aggregate" to 0 to see all help / error messages
srun: error: gizmof35: task 0: Exited with exit code 139
-----
proc 783
out----
Read 10 sequences
[SEND] Sequence 04-A-M_3225224 to MPI node 1
[RECEIVE] Sequence 04-A-M_3225224 from node 1 (9 alignments remaining): V5-51*01,J4*02
[SEND] Sequence 04-A-M_0010237 to MPI node 1
[RECEIVE] Sequence 04-A-M_0010237 from node 1 (8 alignments remaining): Error/ alignment failed
[SEND] Sequence 04-A-M_0820911 to MPI node 1
[RECEIVE] Sequence 04-A-M_0820911 from node 1 (7 alignments remaining): V4-61*06,J6*03
[SEND] Sequence 04-A-M_1331287 to MPI node 1
[RECEIVE] Sequence 04-A-M_1331287 from node 1 (6 alignments remaining): Error/ alignment failed
[SEND] Sequence 04-A-M_0641793 to MPI node 1
[RECEIVE] Sequence 04-A-M_0641793 from node 1 (5 alignments remaining): V3-48*03,J6*03
[SEND] Sequence 04-A-M_0340093 to MPI node 1
[RECEIVE] Sequence 04-A-M_0340093 from node 1 (4 alignments remaining): Error/ alignment failed
[SEND] Sequence 04-A-M_0362177 to MPI node 1
Error:
Master node received an error:Bad binary operator placement in the following context: '<<ERROR HERE>HyPhy Base Object>'
Function call stack
1 : returnAVL={"SEQUENCE_NAME":"04-A-M_0362177","REFERENCE":"Human IgG (heavy chain) with all unique F+ORF alleles, based on IMGT from Dec 2014","BEST_REARRANGEMENT":"V3-7*01","SUPPORT":0.09524867792594588,"SCORE":7938.291781241467,"DELTA_IC":-7938.291781241467,"TERMINATOR":0,"SEQUENCE":"TCACCACCTCCAGAGACAACGCCAAGAACTCACTGTATCTGCAGATGAACAGCCTGAGAGCCGAAGACACGGCTGTGTATTACTGTGCGAGAGATTCGGCGGGAGA","SISTER_SEQUENCES":{"0":"NODE426"},"BRANCH_LENGTHS":{"TO_SISTER":{{5.000000025e-09}},"TO_PARENT":{{0.1330022910594508}},"TO_QUERY":{{0.09623785515861556}}},"REARRANGEMENTS":{"V3-7*01":0.09524867792594588,"V3-21*01":0.09115831069832338,"V3-48*04":0.09115830737698748,"V3-11*06":0.0666642937226508,"V3":0.04973686368060667,"V3-11*04":0.04726634065758437,"V3-11*05":0.04720650698848655,"V3-48*02":0.04557930412018402,"V3-21*04":0.04557922692734276,"V3-21*02":0.04557915617948531,"V3-11":0.04557915127435799,"V3-48":0.04557915119136709,"V3-21*03":0.04557914925791128,"V3-48*01":0.04557914768750963,"V3-48*03":0.04557914709007468,"V3-7*03":0.04551152734912011,"V3-7*02":0.04551149859769659,"V3-21*01,J?":0.01255207892805976},"MODELS_TRIED":25486,"EXTRA":{"FW1":"","FW1_AA":"","CDR1":"","CDR1_AA":"","FW2":"","FW2_AA":"","CDR2":"","CDR2_AA":"","FW3":"NTCACCACCTCCAGAGACAACGCCAAGAACTCACTGTATCTGCAGATGAACAGCCTGAGAGCCGAAGACACGGCTGTGTATTACTGT","FW3_AA":"?TTSRDNAKNSLYLQMNSLRAEDTAVYYC","CDR3":"GCGAGA","CDR3_AA":"AR","JUNCTION":"","JUNCTION_AA":"","D_ALLELE":<HyPhy Base Object>,"D":<HyPhy Base Object>,"D_AA":<HyPhy Base Object>,"D_SCORE":<HyPhy Base Object>,"D/INV_ALLELE":<HyPhy Base Object>,"D/INV":<HyPhy Base Object>,"D/INV_AA":<HyPhy Base Object>,"D/INV_SCORE":<HyPhy Base Object>,"J":"GATTCGGCGGGACAGTAACTACCCCCGGGGGCCAGGGA","J_AA":"DSAGQXLPPGAR?","Mapped Read":"---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------NTCACCACCTCCAGAGACAACGCCAAGAACTCACTGTATCTGCAGATGAACAGCCTGAGAGCCGAAGACACGGCTGTGTATTACTGTGCG---AGA---------GATTCGGCGGGACAGTAACTACCCCCGGGGGCCAGGGA","ALIGNMENT_SPANS":{{0}{0}{0}{0}{0}{306}{315}{362}}},"BREAKPOINTS":{},"BREAKPOINT_SUPPORT":{{0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0}},"BRANCH_SUPPORT":{"IGHV3_11_03_CRF_1":0.001883663113886366,"NODE209":0.05242175556074671,"NODE373":0.05265642347906777,"NODE359":0.05717391785665003,"IGHJ4_03_CRF_01":1.443545230823916e-06,"NODE210":2.425495642073759e-07,"NODE213":1.32259864675077e-06,"NODE217":2.146206208572208e-06,"NODE226":1.130512383065938e-07,"IGHJ6_03_CRF_01":2.284393338724968e-07,"IGHV3_11_01_CRF_1":0.001850373019909466,"NODE222":5.207892302091906e-07,"NODE426":0.04977033271343621,"IGHV3_21_01_CRF_1":0.05105484224343071,"IGHV3_74_01_CRF_1":6.081971969180779e-08,"IGHV3_48_02_CRF_1":0.04724559323151421,"IGHJ2_01_CRF_01":1.074972020894901e-06,"IGHV3_48_03_CRF_1":0.04557916414753405,"IGHV3_11_04_CRF_1":0.00170365482860882,"IGHV3_48_01_CRF_1":0.04557983955583472,"IGHJ6_04_CRF_01":7.22491230459313e-06,"IGHV3_11_05_CRF_1":0.001627370529779283,"NODE362":0.04611310283750515,"IGHJ3_02_CRF_01":3.846954188549019e-07,"IGHJ5_01_CRF_01":7.830105786410569e-08,"NODE215":3.602172499794586e-06,"IGHJ4_02_CRF_01":5.94981970755335e-07,"IGHJ5_02_CRF_01":2.820773960137988e-07,"IGHJ4_01_CRF_01":1.003720863621954e-06,"NODE223":7.905687050284397e-07,"IGHJ1_01_CRF_01":4.979590545016634e-08,"IGHV3_48_04_CRF_1":0.04773294633778306,"NODE363":0.05265831963514057,"IGHV3_21_03_CRF_1":0.04557915626504374,"IGHV3_21_04_CRF_1":0.04740737088739835,"IGHV3_21_02_CRF_1":0.04557916312465859,"NODE360":0.04943182654497387,"IGHV3_OR16_9_01_CRF_1":2.032409669381561e-05,"IGHV3_11_06_CRF_1":0.06998814791741476,"NODE374":0.05274001757674431,"IGHJ6_01_CRF_01":4.598703718644364e-07,"IGHJ3_01_CRF_01":1.255667570452723e-07,"NODE377":0.04611016898899611,"IGHV3_7_02_CRF_1":0.04934984138955492,"NODE356":4.341233847537849e-09,"NODE416":4.165072740486585e-09,"NODE474":4.16507216425803e-09,"NODE518":4.165097914708248e-09,"NODE475":4.165072314161164e-09,"NODE507":4.165143190593753e-09,"NODE476":4.655904871965033e-06,"NODE492":1.428623075663451e-06,"NODE495":2.381485407235793e-08,"IGHV3_20_02_CRF_1":1.169452495352359e-08,"IGHV3_20_01_CRF_1":1.169452495352359e-08,"NODE477":1.305823260168116e-06,"NODE417":3.390335854848945e-08,"NODE425":4.165077223673607e-09,"NODE430":4.165079801422719e-09,"IGHV3_30_07_CRF_1":8.247190479237974e-09,"IGHV3_33_05_CRF_1":8.247190980754878e-09,"IGHV3_30_12_CRF_1":8.247190980762379e-09,"NODE437":8.254486777588145e-09,"IGHV3_33_02_CRF_1":8.140472552196335e-09,"IGHV3_33_01_CRF_1":8.14044505478729e-09,"IGHV3_33_04_CRF_1":8.14044505478729e-09,"IGHV3_33_03_CRF_1":5.807166296107867e-09,"IGHV3_7_01_CRF_1":0.04551149859769659,"IGHV3_7_03_CRF_1":0.04551152734912011,"NODE418":3.604000764441901e-07,"IGHV3_OR16_13_01_CRF_1":2.186813473966455e-08,"IGHV3_74_02_CRF_1":2.186791163587924e-08,"IGHV3_74_03_CRF_1":2.186791163587924e-08,"NODE405":1.249959616617895e-07,"NODE411":0.0001281620944227646,"NODE413":5.024017157015633e-06,"NODE406":3.929026961581791e-08,"NODE358":4.16507261239917e-09,"NODE382":4.165078786014021e-09},"FRAME":0}
-------
2 : ExecuteCommands in string "returnAVL = "+returnValue using basepath /fh/fast/matsen_e/dralph/work/igscueal/A/data/istartstop-0-10000/igs-783/.
-------
3 : mpiNode=ReceiveAJob(0)
-------
4 : SendAJob(seqID)
-------
-----
err----
srun: job 26096316 queued and waiting for resources
srun: job 26096316 has been allocated resources
--------------------------------------------------------------------------
MPI_ABORT was invoked on rank 0 in communicator MPI_COMM_WORLD
with errorcode 1.
NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI processes.
You may or may not see output from other processes, depending on
exactly when Open MPI kills them.
--------------------------------------------------------------------------
[gizmof36:14467] *** Process received signal ***
[gizmof36:14467] Signal: Segmentation fault (11)
[gizmof36:14467] Signal code: Address not mapped (1)
[gizmof36:14467] Failing at address: 0x31
HYPHYMPI terminated.
Error:
HyPhy killed by signal 15
--------------------------------------------------------------------------
mpirun noticed that process rank 0 with PID 14467 on node gizmof36 exited on signal 11 (Segmentation fault).
--------------------------------------------------------------------------
[gizmof36:14461] 1 more process has sent help message help-mpi-api.txt / mpi-abort
[gizmof36:14461] Set MCA parameter "orte_base_help_aggregate" to 0 to see all help / error messages
srun: error: gizmof36: task 0: Exited with exit code 139
-----
proc 830
out----
Read 10 sequences
[SEND] Sequence 04-A-M_1068194 to MPI node 1
[RECEIVE] Sequence 04-A-M_1068194 from node 1 (9 alignments remaining): Error/ alignment failed
[SEND] Sequence 04-A-M_2644068 to MPI node 1
[RECEIVE] Sequence 04-A-M_2644068 from node 1 (8 alignments remaining): V3-49*03,J6*02
[SEND] Sequence 04-A-M_1626214 to MPI node 1
[RECEIVE] Sequence 04-A-M_1626214 from node 1 (7 alignments remaining): V5-51*01,J4*02
[SEND] Sequence 04-A-M_4565883 to MPI node 1
Error:
Master node received an error:Bad binary operator placement in the following context: '<<ERROR HERE>HyPhy Base Object>'
Function call stack
1 : returnAVL={"SEQUENCE_NAME":"04-A-M_4565883","REFERENCE":"Human IgG (heavy chain) with all unique F+ORF alleles, based on IMGT from Dec 2014","BEST_REARRANGEMENT":"V1-8*02,J3*01","SUPPORT":0.1675642805239802,"SCORE":8006.016851524969,"DELTA_IC":-8006.016851524969,"TERMINATOR":0,"SEQUENCE":"ACCATGACCAGGAACACCTCCGTAAGCACAGCCTACATGGAGCTGAGCAGCCTGAGACTTGCGGACACGGCCGTGTATTCCTGTGCGAGAGCCCGGGGAACGGTGACTACTGGACGTCTG","SISTER_SEQUENCES":{"0":"NODE275","1":"NODE210"},"BRANCH_LENGTHS":{"TO_SISTER":{{5.000000025e-09}{5.000000025e-09}},"TO_PARENT":{{0.07485338105370724}{0.33195194982656}},"TO_QUERY":{{0.1352749331276989}{2.562125831919472}}},"REARRANGEMENTS":{"V1-8*02,J3*01":0.1675642805239802,"V1-8*02,J3*02":0.109901035217694,"V1-8*02,J5*02":0.06470990285832555,"V1-8*01,J3*01":0.05968932045974096,"V1-8*02,J4*02":0.05747331145518882,"V1-8*01,J5*02":0.05580803453988294,"V1-8*02,J?":0.05054132609041564,"V1-8*02,J5*01":0.03733789651726765,"V1-8*02,J4*01":0.03362656369221666,"V1-8*01,J3*02":0.0321223569392235,"V1-8*02,J2*01":0.0286430906600452,"V1-8*02,J1*01":0.02715374985914839,"V1-8*01,J4*02":0.0265511464060391,"V1-8*02,J6*03":0.02505848361058418,"V1-8*02,J4*03":0.02317094775408541,"V1-8*01,J5*01":0.02218766501609468,"V1-8*02,J6*02":0.02215862003646322,"V1-8*01,J4*03":0.01898020013553821,"V1-8*02,J6*01":0.01854211376532585,"V1-8*01,J4*01":0.01827797374738222,"V1-8*01,J?":0.01656374314606726,"V1-8*01,J6*02":0.01411034847734025,"V1-8*01,J6*03":0.0140279043968909,"V1-8*01,J1*01":0.01399493904332097,"V1-8*01,J2*01":0.01313370898919676,"V1-8*02,J6*04":0.01160772044645099},"MODELS_TRIED":16903,"EXTRA":{"FW1":"","FW1_AA":"","CDR1":"","CDR1_AA":"","FW2":"","FW2_AA":"","CDR2":"","CDR2_AA":"","FW3":"ACCATGACCAGGAACACCTCCGTAAGCACAGCCTACATGGAGCTGAGCAGCCTGAGACTTGCGGACACGGCCGTGTATTCCTGT","FW3_AA":"TMTRNTSVSTAYMELSSLRLADTAVYSC","CDR3":"GCGAGA","CDR3_AA":"AR","JUNCTION":"","JUNCTION_AA":"","D_ALLELE":<HyPhy Base Object>,"D":<HyPhy Base Object>,"D_AA":<HyPhy Base Object>,"D_SCORE":<HyPhy Base Object>,"D/INV_ALLELE":<HyPhy Base Object>,"D/INV":<HyPhy Base Object>,"D/INV_AA":<HyPhy Base Object>,"D/INV_SCORE":<HyPhy Base Object>,"J":"GCCCGGGGAACGGTGACTACTGGACGTCTG","J_AA":"ARGTVTTGRL","Mapped Read":"------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ACCATGACCAGGAACACCTCCGTAAGCACAGCCTACATGGAGCTGAGCAGCCTGAGACTTGCGGACACGGCCGTGTATTCCTGTGCG---AGA------------------------------GCCCGGGGAACGGTGACTACTGGACGTCTG","ALIGNMENT_SPANS":{{0}{0}{0}{0}{0}{306}{315}{375}}},"BREAKPOINTS":{{101}},"BREAKPOINT_SUPPORT":{{0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,2.897300916944107e-05,4.556180016092084e-05,7.041407155913674e-05,0.0001144616296506973,0.0003480762854720991,0.0005834465989088492,0.0009963806687823536,0.0009017688448823036,0.001388438011298971,0.002456525808931469,0.00442991484846933,0.0004817758678238635,0.001592370046670961,0.001475167205144382,0.002725288593089371,0.005126486036278713,0.009922206981694248,0.01864157179234921,0.08059635810945689,0.07139280918492044,0.1520415959764563,0.2804172506770611,0.4037132220612455,0.2649224912791938,0.370979375074005,0.5372401696356475,0.7872047353201881,0.5965501815607246,0.4736203441982177,1.426844604154726,1.223481807450559,2.822574129690265,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0}},"BRANCH_SUPPORT":{"IGHV1_8_02_CRF_1":0.5867080644320249,"NODE222":0.03808733007657278,"IGHJ5_02_CRF_01":0.1205187880200728,"NODE218":0.02383587943092867,"IGHJ4_01_CRF_01":0.04258464263073224,"NODE297":1.391718519111695e-07,"NODE305":8.253829990766924e-07,"IGHJ1_01_CRF_01":0.04114869186695105,"NODE213":0.01368085719250226,"NODE226":0.009320741807578983,"IGHJ6_01_CRF_01":0.02766877134572506,"IGHJ4_02_CRF_01":0.08402543420619966,"NODE209":0.01533697564703212,"IGHV1_8_01_CRF_1":0.3224899351331709,"IGHV1_46_01_CRF_1":9.7821320509553e-09,"NODE286":7.264520582960659e-07,"NODE298":2.274102949006495e-07,"NODE274":9.212886956118884e-06,"IGHV1_38_4_01_CRF_1":2.538733039789863e-07,"IGHJ2_01_CRF_01":0.0417768416555036,"NODE215":0.03233320131225051,"IGHJ3_01_CRF_01":0.04847303019046937,"IGHJ5_01_CRF_01":0.03994981560702184,"NODE210":0.1787896804486472,"NODE217":0.009348181506037476,"NODE223":0.01957597968100644,"IGHJ4_03_CRF_01":0.04215115084781694,"NODE273":1.249360373002448e-07,"NODE296":1.242218908000579e-07,"NODE310":1.249087575313444e-07,"NODE278":8.54586634048558e-06,"NODE279":6.666179200871117e-07,"NODE275":0.09078097805516665,"IGHJ6_04_CRF_01":0.010175511881231,"IGHJ6_02_CRF_01":0.0124331055627459,"IGHJ6_03_CRF_01":0.006753204053262773,"NODE264":1.249933228199587e-09,"NODE272":1.249909854287576e-09,"NODE316":3.176533451514625e-09,"IGHV1_46_02_CRF_1":8.439560160113187e-09,"IGHV1_46_03_CRF_1":8.439564607719365e-09,"NODE281":1.105489110268879e-09,"IGHV1_OR15_1_04_CRF_1":1.105487753556839e-09,"NODE265":1.249909855383438e-09,"NODE269":8.780527984614766e-09,"IGHV1_3_01_CRF_1":1.254844095594349e-09,"IGHV1_3_02_CRF_1":1.255157200015511e-09,"NODE266":3.562177369430081e-09,"IGHJ3_02_CRF_01":0.1420321850297108},"FRAME":0}
-------
2 : ExecuteCommands in string "returnAVL = "+returnValue using basepath /fh/fast/matsen_e/dralph/work/igscueal/A/data/istartstop-0-10000/igs-830/.
-------
3 : mpiNode=ReceiveAJob(0)
-------
4 : SendAJob(seqID)
-------
-----
err----
srun: job 26096321 queued and waiting for resources
srun: job 26096321 has been allocated resources
--------------------------------------------------------------------------
MPI_ABORT was invoked on rank 0 in communicator MPI_COMM_WORLD
with errorcode 1.
NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI processes.
You may or may not see output from other processes, depending on
exactly when Open MPI kills them.
--------------------------------------------------------------------------
[gizmof38:11884] *** Process received signal ***
[gizmof38:11884] Signal: Segmentation fault (11)
[gizmof38:11884] Signal code: Address not mapped (1)
[gizmof38:11884] Failing at address: 0x31
HYPHYMPI terminated.
Error:
HyPhy killed by signal 15
--------------------------------------------------------------------------
mpirun noticed that process rank 0 with PID 11884 on node gizmof38 exited on signal 11 (Segmentation fault).
--------------------------------------------------------------------------
[gizmof38:11878] 1 more process has sent help message help-mpi-api.txt / mpi-abort
[gizmof38:11878] Set MCA parameter "orte_base_help_aggregate" to 0 to see all help / error messages
srun: error: gizmof38: task 0: Exited with exit code 139
-----
proc 868
out----
Read 10 sequences
[SEND] Sequence 04-A-M_1948220 to MPI node 1
[RECEIVE] Sequence 04-A-M_1948220 from node 1 (9 alignments remaining): V1-69*11,J4*02
[SEND] Sequence 04-A-M_4775500 to MPI node 1
[RECEIVE] Sequence 04-A-M_4775500 from node 1 (8 alignments remaining): V3-15*01,J4*02
[SEND] Sequence 04-A-M_2305425 to MPI node 1
[RECEIVE] Sequence 04-A-M_2305425 from node 1 (7 alignments remaining): V3-48*03,J4*02
[SEND] Sequence 04-A-M_1400046 to MPI node 1
Error:
Master node received an error:Bad binary operator placement in the following context: '<<ERROR HERE>HyPhy Base Object>'
Function call stack
1 : returnAVL={"SEQUENCE_NAME":"04-A-M_1400046","REFERENCE":"Human IgG (heavy chain) with all unique F+ORF alleles, based on IMGT from Dec 2014","BEST_REARRANGEMENT":"V1-69*05,J3*01","SUPPORT":0.1758418012064633,"SCORE":7907.580825235807,"DELTA_IC":-7907.580825235807,"TERMINATOR":0,"SEQUENCE":"CTCCATTACTACCGCCGAATCCACGAGCACAGCCTACATGGAACTCAGCAGCCTGAGATCTGAGGACACGGCCGTCTATTATTGTGCGACAGAGGGGGTAACTGGAGCGACTTCCCCC","SISTER_SEQUENCES":{"0":"NODE322","1":"NODE210"},"BRANCH_LENGTHS":{"TO_SISTER":{{0.02694049973111257}{5.000000025e-09}},"TO_PARENT":{{0.05652609867914878}{0.2096178561836136}},"TO_QUERY":{{0.23586117168111}{3.043381161855358}}},"REARRANGEMENTS":{"V1-69*05,J3*01":0.1758418012064633,"V1-69*05,J6*03":0.1336256377164861,"V1-69*05,J6*04":0.1308370702227491,"V1-69*05,J6*01":0.1210484290771364,"V1-69*05,J6*02":0.1121928276155664,"V1-69*05,J?":0.08429540474790131,"V1-69*05,J3*02":0.06904563314271567,"V1-69*05,J2*01":0.03146559288814196,"V1-69*05,J5*01":0.02466425599359217,"V1-69*05,J4*01":0.02058787850133421,"V1-69*05,J4*02":0.01702846571858076,"V1-69*05,J4*03":0.01690159805327694,"V1-69*05,J1*01":0.01459928080460862,"V1-69*12,J3*01":0.01375335389987834,"V1-69*05,J5*02":0.01093467388074798},"MODELS_TRIED":12065,"EXTRA":{"FW1":"","FW1_AA":"","CDR1":"","CDR1_AA":"","FW2":"","FW2_AA":"","CDR2":"","CDR2_AA":"","FW3":"NNCTCCATTACTACCGCCGAATCCACGAGCACAGCCTACATGGAACTCAGCAGCCTGAGATCTGAGGACACGGCCGTCTATTATTGT","FW3_AA":"?SITTAESTSTAYMELSSLRSEDTAVYYC","CDR3":"GCG","CDR3_AA":"A","JUNCTION":"","JUNCTION_AA":"","D_ALLELE":<HyPhy Base Object>,"D":<HyPhy Base Object>,"D_AA":<HyPhy Base Object>,"D_SCORE":<HyPhy Base Object>,"D/INV_ALLELE":<HyPhy Base Object>,"D/INV":<HyPhy Base Object>,"D/INV_AA":<HyPhy Base Object>,"D/INV_SCORE":<HyPhy Base Object>,"J":"ACAGAGGGGGTAACTGGAGCGACTTCCCCC","J_AA":"TEGVTGATSP","Mapped Read":"---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------NNCTCCATTACTACCGCCGAATCCACGAGCACAGCCTACATGGAACTCAGCAGCCTGAGATCTGAGGACACGGCCGTCTATTATTGTGCG------------------------------------ACAGAGGGGGTAACTGGAGCGACTTCCCCC","ALIGNMENT_SPANS":{{0}{0}{0}{0}{0}{306}{309}{375}}},"BREAKPOINTS":{{89}},"BREAKPOINT_SUPPORT":{{0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.0001310710454037902,0.0001932042364155736,0.0003063744857198927,0.0005141436689568915,0.001547513432603232,0.001486479044453484,0.002619878381723223,0.004835340293618706,0.009314888772649035,0.001528058560204877,0.002898418429262686,0.004931448275673128,0.009825367785066885,0.0201336895408048,0.0366153054001051,0.008689015492664379,0.01842362807318606,0.04621376718842608,0.09029793732388793,0.2092523928019326,0.8454242456139121,2.361512681271983,1.528403321864571,0.5524799525113536,0.5370934036821691,0.2021702732890599,0.2473530471972929,0.1895229625434973,0.5259617649093626,0.5094177481796935,0.8398868136104161,0.6297830095206495,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0}},"BRANCH_SUPPORT":{"NODE322":0.8335985563987657,"IGHJ6_03_CRF_01":0.07143119227571236,"IGHV1_18_03_CRF_1":8.61032854074848e-08,"IGHJ6_01_CRF_01":0.125659515974051,"NODE223":0.0126513046159699,"NODE274":7.096917416365591e-08,"IGHV1_69_05_CRF_1":0.1294699931705351,"IGHJ3_02_CRF_01":0.06957267301808906,"IGHJ5_02_CRF_01":0.0110075778465735,"NODE305":1.813988210385695e-07,"IGHJ6_04_CRF_01":0.06017948844571726,"NODE338":0.005069707746932834,"IGHJ3_01_CRF_01":0.05371153508347072,"IGHV1_69_09_CRF_1":4.214389615870958e-05,"IGHJ4_03_CRF_01":0.01695228291172191,"NODE209":0.02892700460467768,"IGHV1_18_04_CRF_1":9.002894146303091e-08,"NODE226":0.00915111857025192,"IGHJ6_02_CRF_01":0.04211695159493954,"NODE323":0.02302057919346618,"NODE213":0.03657567618648833,"IGHJ1_01_CRF_01":0.01467738367667886,"NODE217":0.07149690493042513,"NODE298":9.12328346501519e-08,"NODE222":0.02068628026260964,"NODE215":0.0628117531990124,"NODE336":0.001818115714339123,"IGHJ4_01_CRF_01":0.012444084372294,"IGHJ5_01_CRF_01":0.01228356593378083,"IGHJ2_01_CRF_01":0.03290078658573792,"IGHJ4_02_CRF_01":0.02041413015303647,"NODE218":0.0732652756715185,"IGHV1_18_02_CRF_1":2.661192261128038e-08,"NODE210":0.141083514087244,"IGHV1_18_01_CRF_1":3.986135260054165e-09,"IGHV1_69_02_CRF_1":7.630818264848599e-05,"IGHV1_69_11_CRF_1":0.001063383273092001,"IGHV1_69_14_CRF_1":8.717120733411641e-05,"NODE316":2.246920604246586e-06,"NODE266":2.294209084951067e-06,"IGHV1_58_01_CRF_1":1.165379673416276e-08,"NODE334":0.0002712339516051824,"NODE342":2.949102257951889e-05,"NODE264":0.0001401590046693688,"NODE348":1.847118161222567e-05,"IGHV1_3_01_CRF_1":2.927171080487451e-07,"NODE297":8.103906842486713e-08,"NODE340":2.175681135646649e-05,"IGHV1_69_04_CRF_1":6.700584519460484e-05,"IGHV1_69_10_CRF_1":4.962484354145754e-05,"IGHV1_69_08_CRF_1":7.046068308623292e-05,"NODE331":0.0008896434556657609,"IGHV1_69_06_CRF_1":8.806862973898626e-05,"IGHV1_69_03_CRF_1":0.0006369940453127153,"IGHV1_69_13_CRF_1":0.001097588545016872,"IGHV1_69D_01_CRF_1":0.001364572492187601,"IGHV1_69_12_CRF_1":0.0009898658877978213,"NODE272":2.086748744436206e-06,"NODE273":2.087561152901495e-06,"IGHV1_38_4_01_CRF_1":6.366488362518788e-08,"NODE296":5.972623215372523e-08,"NODE310":5.972814504913622e-08,"NODE265":2.086748494613254e-06,"NODE269":4.242838044699463e-06,"IGHV1_3_02_CRF_1":3.116258254765393e-07,"IGHV1_46_02_CRF_1":6.947403435521872e-09,"IGHV1_46_01_CRF_1":6.947403435521872e-09,"IGHV1_46_03_CRF_1":1.24199464335613e-08,"IGHV1_58_02_CRF_1":1.197695538296431e-08,"NODE263":2.591013355461415e-06},"FRAME":0}
-------
2 : ExecuteCommands in string "returnAVL = "+returnValue using basepath /fh/fast/matsen_e/dralph/work/igscueal/A/data/istartstop-0-10000/igs-868/.
-------
3 : mpiNode=ReceiveAJob(0)
-------
4 : SendAJob(seqID)
-------
-----
err----
srun: job 26096328 queued and waiting for resources
srun: job 26096328 has been allocated resources
--------------------------------------------------------------------------
MPI_ABORT was invoked on rank 0 in communicator MPI_COMM_WORLD
with errorcode 1.
NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI processes.
You may or may not see output from other processes, depending on
exactly when Open MPI kills them.
--------------------------------------------------------------------------
[gizmof39:14335] *** Process received signal ***
[gizmof39:14335] Signal: Segmentation fault (11)
[gizmof39:14335] Signal code: Address not mapped (1)
[gizmof39:14335] Failing at address: 0x31
HYPHYMPI terminated.
Error:
HyPhy killed by signal 15
--------------------------------------------------------------------------
mpirun noticed that process rank 0 with PID 14335 on node gizmof39 exited on signal 11 (Segmentation fault).
--------------------------------------------------------------------------
[gizmof39:14331] 1 more process has sent help message help-mpi-api.txt / mpi-abort
[gizmof39:14331] Set MCA parameter "orte_base_help_aggregate" to 0 to see all help / error messages
srun: error: gizmof39: task 0: Exited with exit code 139
-----
proc 893
out----
Read 10 sequences
[SEND] Sequence 04-A-M_3703765 to MPI node 1
[RECEIVE] Sequence 04-A-M_3703765 from node 1 (9 alignments remaining): V3-48*03,J5*01
[SEND] Sequence 04-A-M_3877474 to MPI node 1
Error:
Master node received an error:Bad binary operator placement in the following context: '<<ERROR HERE>HyPhy Base Object>'
Function call stack
1 : returnAVL={"SEQUENCE_NAME":"04-A-M_3877474","REFERENCE":"Human IgG (heavy chain) with all unique F+ORF alleles, based on IMGT from Dec 2014","BEST_REARRANGEMENT":"V3-30*02","SUPPORT":0.1260836271203857,"SCORE":9693.712033866159,"DELTA_IC":-9693.712033866159,"TERMINATOR":0,"SEQUENCE":"ATGCAGACTCCGTGAAGGCCCGATTCACCATCTCCAGAGACAACTCCAAGAACACCCTGTATCTCCACATGAACAGCCTGAGAGCTGAGGACACGGCTCTGTATTGCTGTGCGACAACTGGGGCCGGGGA","SISTER_SEQUENCES":{"0":"NODE430"},"BRANCH_LENGTHS":{"TO_SISTER":{{5.000000025e-09}},"TO_PARENT":{{0.05033329049390001}},"TO_QUERY":{{0.1858917164453578}}},"REARRANGEMENTS":{"V3-30*02":0.1260836271203857,"V3-30*18":0.1251384771749349,"V3-30*03":0.1166580656857181,"V3-NL1*01":0.1137003297770463,"V3":0.07710518456420976,"V3-33*06":0.06623470564284771,"V3-30":0.06256922690908076,"V3-33*03":0.05518271748886507,"V3-33*05":0.03206693761300343,"V3-66*02":0.0288804205491709,"V3-66*03":0.01783918315106901,"V3-30*14":0.01770020882202635,"V3-66*01":0.01440334357988199,"V3-33*01":0.01114230909587544,"V3-30*01":0.01114209614399057,"V3-30*06":0.01111523601168212},"MODELS_TRIED":25365,"EXTRA":{"FW1":"","FW1_AA":"","CDR1":"","CDR1_AA":"","FW2":"","FW2_AA":"","CDR2":"","CDR2_AA":"","FW3":"NATGCAGACTCCGTGAAGGCCCGATTCACCATCTCCAGAGACAACTCCAAGAACACCCTGTATCTCCACATGAACAGCCTGAGAGCTGAGGACACGGCTCTGTATTGCTGT","FW3_AA":"?ADSVKARFTISRDNSKNTLYLHMNSLRAEDTALYCC","CDR3":"GCGACA","CDR3_AA":"AT","JUNCTION":"","JUNCTION_AA":"","D_ALLELE":<HyPhy Base Object>,"D":<HyPhy Base Object>,"D_AA":<HyPhy Base Object>,"D_SCORE":<HyPhy Base Object>,"D/INV_ALLELE":<HyPhy Base Object>,"D/INV":<HyPhy Base Object>,"D/INV_AA":<HyPhy Base Object>,"D/INV_SCORE":<HyPhy Base Object>,"J":"ACTGGGGCCGGGGA","J_AA":"TGAG?","Mapped Read":"---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------NATGCAGACTCCGTGAAGGCCCGATTCACCATCTCCAGAGACAACTCCAAGAACACCCTGTATCTCCACATGAACAGCCTGAGAGCTGAGGACACGGCTCTGTATTGCTGTGCG---ACA---------ACTGGGGCCGGGGA","ALIGNMENT_SPANS":{{0}{0}{0}{0}{0}{306}{315}{338}}},"BREAKPOINTS":{},"BREAKPOINT_SUPPORT":{{0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0}},"BRANCH_SUPPORT":{"NODE425":0.004342727496289033,"NODE222":2.920474088606741e-06,"NODE209":0.001237038754967854,"NODE430":0.06404425979972835,"IGHJ6_04_CRF_01":4.46131157145119e-06,"IGHV3_35_01_CRF_1":6.634336355381047e-06,"NODE223":2.285695875041109e-06,"IGHV3_30_08_CRF_1":0.005565676057067111,"IGHJ4_03_CRF_01":5.632942462503304e-06,"IGHV3_53_03_CRF_1":5.652661625049139e-05,"IGHV3_30_18_CRF_1":0.06297926043458058,"NODE215":2.5314618786227e-06,"NODE443":0.06264509815259728,"IGHJ2_01_CRF_01":2.393043240714896e-06,"NODE218":3.720894935545659e-07,"NODE226":2.765954714160783e-06,"IGHV3_NL1_01_CRF_1":0.1137284617160054,"NODE432":0.0626808177842537,"NODE213":2.263576695290638e-06,"NODE217":3.963893877393722e-06,"IGHJ5_01_CRF_01":9.69855000420834e-07,"IGHJ3_02_CRF_01":1.53333516492202e-05,"IGHV3_30_06_CRF_1":0.005557666703895695,"IGHJ4_02_CRF_01":1.749262778086634e-06,"IGHJ1_01_CRF_01":6.549537259229358e-06,"IGHV3_33_05_CRF_1":0.03208758365985277,"IGHV3_30_12_CRF_1":0.005563711499444642,"NODE417":0.0001917789494875712,"IGHV3_66_03_CRF_1":0.0178610956989318,"NODE442":0.06268251992118176,"NODE477":2.489381920581276e-05,"IGHJ3_01_CRF_01":5.606849588804475e-05,"IGHV3_30_3_03_CRF_1":0.005557660777050328,"IGHV3_33_03_CRF_1":0.05518344152561689,"NODE475":0.0001749395008496655,"NODE476":0.005736153882511684,"NODE384":0.001768851952959304,"IGHV3_30_3_01_CRF_1":0.005557667438498375,"IGHV3_30_13_CRF_1":0.005557659894202696,"NODE446":0.005557660777050328,"IGHV3_30_3_02_CRF_1":0.003665441696591134,"NODE394":0.01447723630631767,"IGHV3_66_02_CRF_1":0.01440905087550038,"IGHV3_30_01_CRF_1":0.005557658315979299,"IGHV3_30_11_CRF_1":0.005557660777050328,"NODE433":0.06257612115615195,"IGHV3_OR16_12_01_CRF_1":8.330757358011954e-05,"NODE382":0.0001145707761322435,"NODE397":0.002023649491398694,"NODE391":0.001771894952321696,"NODE383":0.001784745869398201,"NODE406":0.0001870357012162168,"IGHJ5_02_CRF_01":1.126792748544727e-06,"IGHV3_66_01_CRF_1":0.01441378353652223,"IGHJ4_01_CRF_01":2.257556762725675e-06,"IGHJ6_02_CRF_01":3.486445671743047e-07,"IGHJ6_03_CRF_01":2.250670329363065e-06,"NODE210":1.397446392973075e-05,"IGHJ6_01_CRF_01":2.41523696091405e-06,"IGHV3_53_04_CRF_1":0.00201451474516879,"NODE445":0.005584585708139527,"IGHV3_30_09_CRF_1":0.005557659632465241,"NODE355":9.316122711809691e-06,"NODE529":7.951240699609057e-06,"NODE531":1.980840922569316e-08,"IGHV3_25_04_CRF_1":1.502345003422824e-08,"NODE356":5.196446868872397e-05,"NODE416":0.0001939220136587237,"NODE474":0.0001749261139593156,"NODE518":0.000747003392985857,"NODE526":0.0002075632704231022,"IGHV3_64_02_CRF_1":3.127763504568954e-07,"IGHV3_64_01_CRF_1":3.1277637133375e-07,"NODE519":6.952591711155332e-05,"NODE521":2.317430998767057e-06,"IGHV3_64D_06_CRF_1":2.460497717582961e-07,"NODE522":9.231801914281842e-09,"IGHV3_64_04_CRF_1":2.834769974934213e-05,"NODE507":0.0001751202858448405,"IGHV3_23_04_CRF_1":7.858115467986893e-08,"NODE508":7.858118988371888e-08,"IGHV3_23_02_CRF_1":7.858130763777916e-08,"IGHV3_23_01_CRF_1":7.858117486397272e-08,"NODE509":1.08888735033599e-06,"NODE511":1.084770909569322e-06,"IGHV3_23_03_CRF_1":1.084770761923658e-06,"IGHV3_23_05_CRF_1":1.084770920085421e-06,"NODE492":9.409699690578357e-05,"NODE494":1.536317866485956e-06,"NODE498":1.547321749443437e-06,"IGHV3_9_01_CRF_1":1.323393993163571e-07,"IGHV3_9_03_CRF_1":1.323394353987179e-07,"IGHV3_9_02_CRF_1":1.323394620386861e-07,"NODE495":5.046133289410468e-06,"IGHV3_20_02_CRF_1":2.2609572940756e-07,"IGHV3_20_01_CRF_1":2.2609572940756e-07,"NODE483":7.307799341332711e-07,"NODE478":7.383590841753349e-07,"NODE480":8.736681973593393e-08,"IGHV3_OR16_10_02_CRF_1":8.736682145806315e-08,"IGHV3_OR16_10_01_CRF_1":8.736682145806315e-08,"IGHV3_OR16_10_03_CRF_1":8.736681973593393e-08,"IGHV3_30_14_CRF_1":0.01770020882202635,"IGHV3_30_16_CRF_1":0.005557619034838671,"IGHV3_30_17_CRF_1":0.005557619034838671,"IGHV3_30_07_CRF_1":0.005557617981298213,"IGHV3_30_15_CRF_1":0.005557622488124207,"IGHV3_30_10_CRF_1":0.005557616591959131,"NODE450":0.005557619169195662,"IGHV3_30_03_CRF_1":0.1166580656857181,"IGHV3_30_19_CRF_1":0.0055576193035476,"IGHV3_30_05_CRF_1":0.005557619454847702,"NODE437":0.005584612757893979,"IGHV3_33_02_CRF_1":0.00555769759927469,"IGHV3_33_01_CRF_1":0.005557696337981465,"IGHV3_33_04_CRF_1":0.005557698799077805,"IGHV3_33_06_CRF_1":0.003665482847984288,"IGHV3_30_02_CRF_1":0.06256924976291492,"NODE426":0.00537410195848496,"IGHV3_7_02_CRF_1":8.40592886890368e-09,"IGHV3_7_01_CRF_1":8.40592886890368e-09,"IGHV3_7_03_CRF_1":8.405929362352113e-09,"NODE418":0.0002745950725491216,"IGHV3_OR16_13_01_CRF_1":1.495864988358199e-07,"IGHV3_74_02_CRF_1":3.418050986771827e-08,"IGHV3_74_01_CRF_1":3.418050986771827e-08,"IGHV3_74_03_CRF_1":3.418050986771827e-08,"NODE405":7.471560404087536e-05,"NODE411":3.637564188945651e-05,"NODE407":3.715813417177525e-06,"NODE358":5.077495003384471e-05,"IGHV3_53_01_CRF_1":5.649734687869786e-05,"IGHV3_53_02_CRF_1":5.649737202024508e-05,"NODE386":2.486223784188187e-07,"IGHV3_38_3_01_CRF_1":1.944811115317316e-07,"NODE359":8.961945697585266e-05,"NODE373":5.110365519775789e-08,"NODE377":5.110368823668753e-08,"IGHV3_11_06_CRF_1":6.098269507793912e-08,"NODE374":5.11036447818798e-08,"NODE360":5.110365508063206e-08,"NODE362":5.110365626165085e-08,"IGHV3_48_02_CRF_1":5.1103647440961e-08,"IGHV3_48_01_CRF_1":5.110364644808736e-08,"IGHV3_48_04_CRF_1":5.110363458133866e-08,"NODE363":5.110364360625278e-08,"IGHV3_21_01_CRF_1":1.435055793363471e-08,"IGHV3_21_03_CRF_1":1.435058181652851e-08,"IGHV3_21_04_CRF_1":1.435055936825774e-08,"IGHV3_21_02_CRF_1":1.435056098167696e-08,"IGHV3_48_03_CRF_1":5.110363266191671e-08},"FRAME":0}
-------
2 : ExecuteCommands in string "returnAVL = "+returnValue using basepath /fh/fast/matsen_e/dralph/work/igscueal/A/data/istartstop-0-10000/igs-893/.
-------
3 : mpiNode=ReceiveAJob(0)
-------
4 : SendAJob(seqID)
-------
-----
err----
srun: job 26096329 queued and waiting for resources
srun: job 26096329 has been allocated resources
--------------------------------------------------------------------------
MPI_ABORT was invoked on rank 0 in communicator MPI_COMM_WORLD
with errorcode 1.
NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI processes.
You may or may not see output from other processes, depending on
exactly when Open MPI kills them.
--------------------------------------------------------------------------
[gizmof40:19304] *** Process received signal ***
[gizmof40:19304] Signal: Segmentation fault (11)
[gizmof40:19304] Signal code: Address not mapped (1)
[gizmof40:19304] Failing at address: 0x31
HYPHYMPI terminated.
Error:
HyPhy killed by signal 15
--------------------------------------------------------------------------
mpirun noticed that process rank 0 with PID 19304 on node gizmof40 exited on signal 11 (Segmentation fault).
--------------------------------------------------------------------------
[gizmof40:19299] 1 more process has sent help message help-mpi-api.txt / mpi-abort
[gizmof40:19299] Set MCA parameter "orte_base_help_aggregate" to 0 to see all help / error messages
srun: error: gizmof40: task 0: Exited with exit code 139
-----
Allow non-coding query sequences
This is an enhancement, but an important one; can we accommodate sequences that aren't coding (e.g. by masking stop codons, accommodating frame shifts etc.)
Junction finding when there is no 'C' in FW3
At the moment, an absent 'C' in FW3 is handled as an unproductive junction; resolve by mapping to the MSA position for the the 'C'.
404 on link from wiki
Hello gentlemen--
I am getting a 404 when trying to access
https://github.com/spond/IgSCUEAL/blob/master/viz/test/test-heavy.html
which is pointed to from the "template" link at the bottom of
https://github.com/spond/IgSCUEAL/wiki/IgSCUEAL-usage
Thanks!
Restriction on the header line for running 'ThreadNucOntoAA.bf'
It seems like 'ThreadNucOntoAA.bf' does not work with sequences having accession numbers with underscore. I checked 'ThreadNucOntoAA.bf' after replacing the '_' with letters and it worked fine.
Fix CDR/J regions in JSON
JSON output from ScreenFromAlignment does not correctly annotate CDR3 and J region boundaries.
Gaps that are not multiples of 3
Reference alignment scripts must check that all sequences in the file have indels whose length is divisible by 3; otherwise misalignment will result during screening.
Add allele information to postprocessing?
The reference alignments only contain the *01 alleles for the V genes. Should there be an additional postprocessing step to compare the query sequence to the different allelic forms, if the family and gene is identified?
AuxBF/SplitIMGTV.bf throws an error
Using the latest HyPhy from veg/hyphy:
$ HYPHYMP AuxBF/SplitIMGTV.bf
AuxBF/IMGT V-region protein alignment:homo_sapiens/ighv_imgt_aa.txt
Regular expression to filter annotation with (e.g. F for functional, F|ORF for function or ORF):F
Error:
Operation 'MAccess' is not implemented/defined for a Number
Function call stack
1 : Branch under condition 'match[0]==0&&match[1]==Abs(annotation[5])-1'
to
v_region=imgt_aa[k+1]^{{"\\.",""}}
else
k+=2
-------
Segmentation fault
Improve J performance on v2 cf v1
The performance of IgSCUEAL v2 is poorer for J regions than V1: see here.
Generate valid .TSV
Add tabs to the lines for which alignment has failed.
Add branch length to output
It would be convenient to get an idea of how divergent each fragment is from germline. Could the divergence for each segment be included in the output? Would also be good to add this information to he visualisation.
AuxBF/MergeVRegionAlignments.bf doesn't read the directory
I've checked and double-checked that I'm entering the directory right - both with and without the trailing forward slash, but the BF can't seem to find my alignments (named CDR3.fas.aligned etc.) (my directories are removed from the below output).
$ HYPHYMP AuxBF/MergeVRegionAlignments.bf
The directory containing V-region amino-acid alignments:/homo_sapiens/regions/
Error:
Could not find source dataset file:filesIn[fileID] Path stack: {/usr/local/lib/hyphy,AuxBF/}
Function call stack
1 : Read Data Set current from file filesIn[fileID]
-------
Segmentation fault
IGH-Full reference does not annotate by D region
Dear @spond ,
My bad, I'm sure, but the IGH-full reference alignment doesn't annotate the D regions properly.
Fail test case
Sequence 2 breaks IgSCUEAL.
>V36_a_DS_58
GAGGTGCAGCTGGTGGAGTCTGGGGGAGGCTTGGCAAAGCCTGGGGGGTCCCTTAGACTCTCCTGTGTAG
CCTCTGGATTCATTTTCAGTAACGCCTGGATGAGTTGGGTCCGCCAGGCTCCAGGGAAGGGGCTGGAGTG
GGTTGGTCACATTAAAAGCAAAACTGATGGTGGGACAACAGACTACGCCGCACCCGTGAAGGGCAGATTC
ACCATCTCAAGAGATGAGTCAAAAAACACACTATATCTGCAAATGAACAGCCTGAAAACCGGGGACACAG
CCGTATATTACTGTACCACAGGGAAGTGGCAACGAGATTTTGACTGGTCCGGGGACTACTTCTACTACAT
GGACGTCTGGGGCAAAGGGACCACGGTCACCGTCTCCTCA
>V36_a_DS_59
GAGGTGCAGCTGGTGGAGTCTGGGGGAGGCTTGGTAAAGCCTGGGGGGTCCCTTAGACTCTCCTGTGCAG
CCTCTGGATTCACTTTCAGTAACGCCTGGATGAGCTGGGTCCGCCAGGCTCCAGGGAAGGGGCTGGAGTG
GGTTGGCCGTATTAAAAGCAAAACTGATGGTGGGACAACAGACTACGCTGCACCCGTGAAAGGCAGATTC
ACCATCTCAAGAGATGATTCAAAAAACACGCTGTATCTGCAAATGAACAGCCTGAAAACCGAGGACACAG
CCGTGTATTACTGTACCACAGGACGGAACTACTGGGGCCAGGGAACCCTGGTCACCGTCTCCTCAG
>V36_a_DS_60
GAGGTGCAGCTGGTGGAGTCTGGGGGAGGCTTGGTAAAGCCTGGGGGGTCCCTTAGACTCTCCTGTGTAG
CCTCTGGATTCACTTTCAGTAATGCCTGGATGAGTTGGGTCCGCCAGGCTCCAGGGAAGGGGCTGGAGTG
GGTTGGCCATATTAAAAGCAAAACTGATGGTGGGACAACAGACTACGCTGCACCCGTGAAAGGCAGATTC
ACCATCTCGAAGGATGATTCAAAAAACACGCTATATCTGCAAATGAACAGCCTGAAAACCGGGGACACAG
CCGTCTATTACTGTACCACAGGGAAGTGGCAACGATCTTTTGACTGGTCCGGGGACTACTTCTACTACAT
GGACGTCTGGGGCAAAGGGACCACGGTCACCGTCTCCTCA
AuxBF/TranslateIMGTJ.bf doesn't translate
HyPhy is clearly reading in the sequences, but is not translating in the correct frame. This was also an issue in the macaque alignments.
$ HYPHYMP AuxBF/TranslateIMGTJ.bf
AuxBF/IMGT J-region nucleotide sequences:homo_sapiens/ighj_edit.fas
[WARNING] Sequence J00256|IGHJ1*01|Homo sapiens|F|J-REGION|723..774|52 nt|1| | | | |52+0=52| | | appears to have premature stop codons or is empty and will be skipped
[WARNING] Sequence J00256|IGHJ2*01|Homo sapiens|F|J-REGION|932..984|53 nt|2| | | | |53+0=53| | | appears to have premature stop codons or is empty and will be skipped
[WARNING] Sequence J00256|IGHJ3*01|Homo sapiens|F|J-REGION|1537..1586|50 nt|2| | | | |50+0=50| | | appears to have premature stop codons or is empty and will be skipped
[WARNING] Sequence X86355|IGHJ3*02|Homo sapiens|F|J-REGION|1107..1156|50 nt|2| | | | |50+0=50| | | appears to have premature stop codons or is empty and will be skipped
[WARNING] Sequence J00256|IGHJ4*01|Homo sapiens|F|J-REGION|1912..1959|48 nt|3| | | | |48+0=48| | | appears to have premature stop codons or is empty and will be skipped
[WARNING] Sequence X86355|IGHJ4*02|Homo sapiens|F|J-REGION|1480..1527|48 nt|3| | | | |48+0=48| | | appears to have premature stop codons or is empty and will be skipped
[WARNING] Sequence M25625|IGHJ4*03|Homo sapiens|F|J-REGION|446..493|48 nt|3| | | | |48+0=48| | | appears to have premature stop codons or is empty and will be skipped
[WARNING] Sequence J00256|IGHJ5*01|Homo sapiens|F|J-REGION|2354..2404|51 nt|3| | | | |51+0=51| | | appears to have premature stop codons or is empty and will be skipped
[WARNING] Sequence X86355|IGHJ5*02|Homo sapiens|F|J-REGION|1878..1928|51 nt|3| | | | |51+0=51| | | appears to have premature stop codons or is empty and will be skipped
[WARNING] Sequence J00256|IGHJ6*01|Homo sapiens|F|J-REGION|2947..3009|63 nt|3| | | | |63+0=63| | | appears to have premature stop codons or is empty and will be skipped
[WARNING] Sequence X86355|IGHJ6*02|Homo sapiens|F|J-REGION|2482..2543|62 nt|3| | | | |62+0=62| | | appears to have premature stop codons or is empty and will be skipped
[WARNING] Sequence X86356|IGHJ6*03|Homo sapiens|F|J-REGION|2482..2543|62 nt|3| | | | |62+0=62| | | appears to have premature stop codons or is empty and will be skipped
[WARNING] Sequence AJ879487|IGHJ6*04|Homo sapiens|F|J-REGION|39..101|63 nt|3| | | | |63+0=63| | | appears to have premature stop codons or is empty and will be skipped
Error:
No fully annotated sequences found in call to assert(
Function call stack
1 : Assert 'Abs(sequences)>0'
-------
Segmentation fault
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