mutiple "is not defined in the header" issues

[jacopoM28]

Hello,

I am having some issues using TELR and I think the problem arise after calling the SVs with SNIFFLE. Here the complete log file:

ngmlr 0.2.7 (build: Feb 21 2022 18:53:53, start: 2022-11-27.14:47:42)
Contact: philipp.rescheneder@univie.ac.at
Writing output (SAM) to stdout
Encoding reference sequence.
Size of reference genome 648 Mbp (max. 68719 Mbp)
0 reference sequences were skipped (length < 10).
Writing encoded reference to /proj/sllstore2017073/private/Jacopo/Ostreida_SVs/Analyses/Hemizigosity/Cgig/TELR/intermediate_files/Cgig_Ref.PacBio_genome.fa-enc.2.ngm
Writing to disk took 0.35s
Building reference index #0 (kmer length: 13, reference skip: 2)
3624 prefixes were ignored due to the frequency cutoff (1000)
Overall time for creating RefTable: 60.55s
Writing reference index to /proj/sllstore2017073/private/Jacopo/Ostreida_SVs/Analyses/Hemizigosity/Cgig/TELR/intermediate_files/Cgig_Ref.PacBio_genome.fa-ht-13-2.2.ngm
Writing to disk took 1.01s
Opening query file /proj/sllstore2017073/private/Jacopo/Ostreida_SVs/Analyses/Hemizigosity/Cgig/TELR/intermediate_files/Cgig_Ref.PacBio.fastq
No progress information (use --progress)
Mapping reads...
Done (5506263 reads mapped (76.91%), 1653020 reads not mapped, 9646255 lines written)(elapsed: 916m, 100 r/s)
[bam_sort_core] merging from 208 files and 16 in-memory blocks...
[W::vcf_parse] Contig 'NC_047559.1STRANDBIAS' is not defined in the header. (Quick workaround: index the file with tabix.)
[W::vcf_parse] FILTER 'SVMETHOD=Snifflesv1.0.12' is not defined in the header
[W::vcf_parse] FILTER 'CHR2=NC_047559.1' is not defined in the header
[W::vcf_parse] FILTER 'END=551219' is not defined in the header
[W::vcf_parse] FILTER 'STD_quant_start=0.316228' is not defined in the header
[W::vcf_parse] FILTER 'STD_quant_stop=5.205766' is not defined in the header
[W::vcf_parse] FILTER 'Kurtosis_quant_start=1.819916' is not defined in the header
[W::vcf_parse] FILTER 'Kurtosis_quant_stop=1.632353' is not defined in the header
[W::vcf_parse] FILTER 'SVTYPE=DEL' is not defined in the header
[W::vcf_parse] FILTER 'RNAMES=ERR3760406.339883,ERR3760406.383956,ERR3760407.390592,ERR3760535.30124,ERR3760540.62198,ERR3760540.62199,ERR3760971.475923,ERR3760971.523277,ERR3761162.734890,ERR3761191.363478,ERR3761191.385042,ERR3761191.497920,ERR3761192.353508,ERR3761192.353510,ERR3761192.502379,ERR3761418.266094' is not defined in the header
[E::bcf_hdr_parse_line] Could not parse the header line: "##FILTER=<ID=RNAMES=ERR3760406.339883,ERR3760406.383956,ERR3760407.390592,ERR3760535.30124,ERR3760540.62198,ERR3760540.62199,ERR3760971.475923,ERR3760971.523277,ERR3761162.734890,ERR3761191.363478,ERR3761191.385042,ERR3761191.497920,ERR3761192.353508,ERR3761192.353510,ERR3761192.502379,ERR3761418.266094,Description="Dummy">"
[E::vcf_parse] Could not add dummy header for FILTER 'RNAMES=ERR3760406.339883,ERR3760406.383956,ERR3760407.390592,ERR3760535.30124,ERR3760540.62198,ERR3760540.62199,ERR3760971.475923,ERR3760971.523277,ERR3761162.734890,ERR3761191.363478,ERR3761191.385042,ERR3761191.497920,ERR3761192.353508,ERR3761192.353510,ERR3761192.502379,ERR3761418.266094'
[W::vcf_parse] FILTER 'END=826354' is not defined in the header
[W::vcf_parse] FILTER 'STD_quant_start=12.041595' is not defined in the header
[W::vcf_parse] FILTER 'STD_quant_stop=36.029155' is not defined in the header
[W::vcf_parse] FILTER 'Kurtosis_quant_start=3.277955' is not defined in the header
[W::vcf_parse] FILTER 'Kurtosis_quant_stop=-0.673460' is not defined in the header
[W::vcf_parse] FILTER 'SVTYPE=INS' is not defined in the header
[W::vcf_parse] FILTER 'RNAMES=ERR3760535.423133,ERR3760540.7045,ERR3760540.71827,ERR3761162.202711,ERR3761190.301933,ERR3761190.353649,ERR3761192.16072,ERR3761192.406381,ERR3761192.85484,ERR3761418.266450,ERR3761418.405198,ERR3761418.81695' is not defined in the header
[E::bcf_hdr_parse_line] Could not parse the header line: "##FILTER=<ID=RNAMES=ERR3760535.423133,ERR3760540.7045,ERR3760540.71827,ERR3761162.202711,ERR3761190.301933,ERR3761190.353649,ERR3761192.16072,ERR3761192.406381,ERR3761192.85484,ERR3761418.266450,ERR3761418.405198,ERR3761418.81695,Description="Dummy">"
[E::vcf_parse] Could not add dummy header for FILTER 'RNAMES=ERR3760535.423133,ERR3760540.7045,ERR3760540.71827,ERR3761162.202711,ERR3761190.301933,ERR3761190.353649,ERR3761192.16072,ERR3761192.406381,ERR3761192.85484,ERR3761418.266450,ERR3761418.405198,ERR3761418.81695'
[W::vcf_parse] FILTER 'END=12109963' is not defined in the header
[W::vcf_parse] FILTER 'STD_quant_start=0.000000' is not defined in the header
[W::vcf_parse] FILTER 'STD_quant_stop=0.000000' is not defined in the header
[W::vcf_parse] FILTER 'Kurtosis_quant_start=2.000000' is not defined in the header
[W::vcf_parse] FILTER 'Kurtosis_quant_stop=0.333333' is not defined in the header
[W::vcf_parse] FILTER 'SVTYPE=INV' is not defined in the header
[W::vcf_parse] FILTER 'RNAMES=ERR3761418.607683,ERR3761418.607684,ERR3761418.607685,ERR3761418.607686,ERR3761418.607687,ERR3761418.607688,ERR3761418.607689,ERR3761418.607690,ERR3761418.607691,ERR3761418.607692,ERR3761418.607693,ERR3761418.607694,ERR3761418.607695,ERR3761418.607696,ERR3761418.607697,ERR3761418.607698,ERR3761418.607699' is not defined in the header
[E::bcf_hdr_parse_line] Could not parse the header line: "##FILTER=<ID=RNAMES=ERR3761418.607683,ERR3761418.607684,ERR3761418.607685,ERR3761418.607686,ERR3761418.607687,ERR3761418.607688,ERR3761418.607689,ERR3761418.607690,ERR3761418.607691,ERR3761418.607692,ERR3761418.607693,ERR3761418.607694,ERR3761418.607695,ERR3761418.607696,ERR3761418.607697,ERR3761418.607698,ERR3761418.607699,Description="Dummy">"
[E::vcf_parse] Could not add dummy header for FILTER 'RNAMES=ERR3761418.607683,ERR3761418.607684,ERR3761418.607685,ERR3761418.607686,ERR3761418.607687,ERR3761418.607688,ERR3761418.607689,ERR3761418.607690,ERR3761418.607691,ERR3761418.607692,ERR3761418.607693,ERR3761418.607694,ERR3761418.607695,ERR3761418.607696,ERR3761418.607697,ERR3761418.607698,ERR3761418.607699'
[W::vcf_parse] FILTER 'END=44450593' is not defined in the header
[W::vcf_parse] FILTER 'STD_quant_start=0.447214' is not defined in the header
[W::vcf_parse] FILTER 'STD_quant_stop=1.870829' is not defined in the header
[W::vcf_parse] FILTER 'Kurtosis_quant_start=4.877882' is not defined in the header
[W::vcf_parse] FILTER 'Kurtosis_quant_stop=4.745380' is not defined in the header
[W::vcf_parse] FILTER 'RNAMES=ERR3760406.12623,ERR3760406.19446,ERR3760406.312202,ERR3760406.341147,ERR3760407.418135,ERR3760441.530513,ERR3760971.107122,ERR3760971.258653,ERR3761190.117976,ERR3761190.117977,ERR3761190.117978,ERR3761190.494622,ERR3761191.299530,ERR3761192.187745,ERR3761192.45148,ERR3761418.45724,ERR3761418.604736' is not defined in the header
[E::bcf_hdr_parse_line] Could not parse the header line: "##FILTER=<ID=RNAMES=ERR3760406.12623,ERR3760406.19446,ERR3760406.312202,ERR3760406.341147,ERR3760407.418135,ERR3760441.530513,ERR3760971.107122,ERR3760971.258653,ERR3761190.117976,ERR3761190.117977,ERR3761190.117978,ERR3761190.494622,ERR3761191.299530,ERR3761192.187745,ERR3761192.45148,ERR3761418.45724,ERR3761418.604736,Description="Dummy">"
[E::vcf_parse] Could not add dummy header for FILTER 'RNAMES=ERR3760406.12623,ERR3760406.19446,ERR3760406.312202,ERR3760406.341147,ERR3760407.418135,ERR3760441.530513,ERR3760971.107122,ERR3760971.258653,ERR3761190.117976,ERR3761190.117977,ERR3761190.117978,ERR3761190.494622,ERR3761191.299530,ERR3761192.187745,ERR3761192.45148,ERR3761418.45724,ERR3761418.604736'
[W::vcf_parse] FILTER 'END=9665029' is not defined in the header
[W::vcf_parse] FILTER 'STD_quant_stop=3.041381' is not defined in the header
[W::vcf_parse] FILTER 'Kurtosis_quant_start=2.165993' is not defined in the header
[W::vcf_parse] FILTER 'Kurtosis_quant_stop=11.444586' is not defined in the header
[W::vcf_parse] FILTER 'RNAMES=ERR3760406.387959,ERR3760407.191552,ERR3760407.329352,ERR3760441.410502,ERR3760535.333619,ERR3760540.371375,ERR3760540.415044,ERR3760540.70847,ERR3760540.89907,ERR3760540.89908,ERR3760540.89909,ERR3760540.89910,ERR3760540.89911,ERR3760540.89912,ERR3760971.352776,ERR3760971.507254,ERR3760971.564010,ERR3760971.605529,ERR3760971.92497,ERR3761162.400746,ERR3761162.510584,ERR3761190.326603,ERR3761191.13867,ERR3761191.237926,ERR3761191.392956,ERR3761191.560311,ERR3761191.580931,ERR3761191.580932,ERR3761191.580934,ERR3761192.161893,ERR3761192.58385,ERR3761418.237605,ERR3761418.378934' is not defined in the header
[E::bcf_hdr_parse_line] Could not parse the header line: "##FILTER=<ID=RNAMES=ERR3760406.387959,ERR3760407.191552,ERR3760407.329352,ERR3760441.410502,ERR3760535.333619,ERR3760540.371375,ERR3760540.415044,ERR3760540.70847,ERR3760540.89907,ERR3760540.89908,ERR3760540.89909,ERR3760540.89910,ERR3760540.89911,ERR3760540.89912,ERR3760971.352776,ERR3760971.507254,ERR3760971.564010,ERR3760971.605529,ERR3760971.92497,ERR3761162.400746,ERR3761162.510584,ERR3761190.326603,ERR3761191.13867,ERR3761191.237926,ERR3761191.392956,ERR3761191.560311,ERR3761191.580931,ERR3761191.580932,ERR3761191.580934,ERR3761192.161893,ERR3761192.58385,ERR3761418.237605,ERR3761418.378934,Description="Dummy">"
[E::vcf_parse] Could not add dummy header for FILTER 'RNAMES=ERR3760406.387959,ERR3760407.191552,ERR3760407.329352,ERR3760441.410502,ERR3760535.333619,ERR3760540.371375,ERR3760540.415044,ERR3760540.70847,ERR3760540.89907,ERR3760540.89908,ERR3760540.89909,ERR3760540.89910,ERR3760540.89911,ERR3760540.89912,ERR3760971.352776,ERR3760971.507254,ERR3760971.564010,ERR3760971.605529,ERR3760971.92497,ERR3761162.400746,ERR3761162.510584,ERR3761190.326603,ERR3761191.13867,ERR3761191.237926,ERR3761191.392956,ERR3761191.560311,ERR3761191.580931,ERR3761191.580932,ERR3761191.580934,ERR3761192.161893,ERR3761192.58385,ERR3761418.237605,ERR3761418.378934'
[W::vcf_parse] FILTER 'END=30200860' is not defined in the header
[W::vcf_parse] FILTER 'STD_quant_start=0.480384' is not defined in the header
[W::vcf_parse] FILTER 'STD_quant_stop=1.074172' is not defined in the header
[W::vcf_parse] FILTER 'Kurtosis_quant_start=9.988983' is not defined in the header
[W::vcf_parse] FILTER 'Kurtosis_quant_stop=-0.287836' is not defined in the header
[W::vcf_parse] FILTER 'RNAMES=ERR3760291.200003,ERR3760291.308034,ERR3760291.382195,ERR3760441.526162,ERR3760534.149009,ERR3760535.216304,ERR3760971.588350,ERR3760971.588351,ERR3760971.588352,ERR3760971.588353,ERR3760971.642513,ERR3760971.642515,ERR3760971.90717,ERR3761162.691358,ERR3761190.507341,ERR3761190.507342,ERR3761190.649401,ERR3761190.69904,ERR3761191.143361,ERR3761191.546829,ERR3761192.186068,ERR3761192.246170,ERR3761192.445510,ERR3761418.139626,ERR3761418.378570,ERR3761418.534223' is not defined in the header
[E::bcf_hdr_parse_line] Could not parse the header line: "##FILTER=<ID=RNAMES=ERR3760291.200003,ERR3760291.308034,ERR3760291.382195,ERR3760441.526162,ERR3760534.149009,ERR3760535.216304,ERR3760971.588350,ERR3760971.588351,ERR3760971.588352,ERR3760971.588353,ERR3760971.642513,ERR3760971.642515,ERR3760971.90717,ERR3761162.691358,ERR3761190.507341,ERR3761190.507342,ERR3761190.649401,ERR3761190.69904,ERR3761191.143361,ERR3761191.546829,ERR3761192.186068,ERR3761192.246170,ERR3761192.445510,ERR3761418.139626,ERR3761418.378570,ERR3761418.534223,Description="Dummy">"
[E::vcf_parse] Could not add dummy header for FILTER 'RNAMES=ERR3760291.200003,ERR3760291.308034,ERR3760291.382195,ERR3760441.526162,ERR3760534.149009,ERR3760535.216304,ERR3760971.588350,ERR3760971.588351,ERR3760971.588352,ERR3760971.588353,ERR3760971.642513,ERR3760971.642515,ERR3760971.90717,ERR3761162.691358,ERR3761190.507341,ERR3761190.507342,ERR3761190.649401,ERR3761190.69904,ERR3761191.143361,ERR3761191.546829,ERR3761192.186068,ERR3761192.246170,ERR3761192.445510,ERR3761418.139626,ERR3761418.378570,ERR3761418.534223'
[W::vcf_parse] FILTER 'END=10889086' is not defined in the header
[W::vcf_parse] FILTER 'STD_quant_start=5.907622' is not defined in the header
[W::vcf_parse] FILTER 'STD_quant_stop=5.594640' is not defined in the header
[W::vcf_parse] FILTER 'Kurtosis_quant_start=2.138888' is not defined in the header
[W::vcf_parse] FILTER 'Kurtosis_quant_stop=-1.790606' is not defined in the header
[W::vcf_parse] FILTER 'SVTYPE=INVDUP' is not defined in the header
[W::vcf_parse] FILTER 'RNAMES=ERR3760971.441164,ERR3760971.441165,ERR3760971.441166,ERR3760971.441167,ERR3760971.441168,ERR3760971.441169,ERR3760971.441170,ERR3760971.441171,ERR3760971.441172,ERR3760971.441173,ERR3760971.441174' is not defined in the header
[E::bcf_hdr_parse_line] Could not parse the header line: "##FILTER=<ID=RNAMES=ERR3760971.441164,ERR3760971.441165,ERR3760971.441166,ERR3760971.441167,ERR3760971.441168,ERR3760971.441169,ERR3760971.441170,ERR3760971.441171,ERR3760971.441172,ERR3760971.441173,ERR3760971.441174,Description="Dummy">"
[E::vcf_parse] Could not add dummy header for FILTER 'RNAMES=ERR3760971.441164,ERR3760971.441165,ERR3760971.441166,ERR3760971.441167,ERR3760971.441168,ERR3760971.441169,ERR3760971.441170,ERR3760971.441171,ERR3760971.441172,ERR3760971.441173,ERR3760971.441174'
[W::vcf_parse] FILTER 'END=11582792' is not defined in the header
[W::vcf_parse] FILTER 'STD_quant_start=10.397115' is not defined in the header
[W::vcf_parse] FILTER 'STD_quant_stop=11.462984' is not defined in the header
[W::vcf_parse] FILTER 'Kurtosis_quant_start=4.354947' is not defined in the header
[W::vcf_parse] FILTER 'Kurtosis_quant_stop=6.685802' is not defined in the header
[W::vcf_parse] FILTER 'RNAMES=ERR3760291.129347,ERR3760406.134299,ERR3760406.26917,ERR3760441.142506,ERR3760441.295921,ERR3760540.95078,ERR3760971.148634,ERR3761162.283343,ERR3761162.727098,ERR3761190.550259,ERR3761190.86006,ERR3761192.171017,ERR3761192.501025,ERR3761192.562491' is not defined in the header
[E::bcf_hdr_parse_line] Could not parse the header line: "##FILTER=<ID=RNAMES=ERR3760291.129347,ERR3760406.134299,ERR3760406.26917,ERR3760441.142506,ERR3760441.295921,ERR3760540.95078,ERR3760971.148634,ERR3761162.283343,ERR3761162.727098,ERR3761190.550259,ERR3761190.86006,ERR3761192.171017,ERR3761192.501025,ERR3761192.562491,Description="Dummy">"
[E::vcf_parse] Could not add dummy header for FILTER 'RNAMES=ERR3760291.129347,ERR3760406.134299,ERR3760406.26917,ERR3760441.142506,ERR3760441.295921,ERR3760540.95078,ERR3760971.148634,ERR3761162.283343,ERR3761162.727098,ERR3761190.550259,ERR3761190.86006,ERR3761192.171017,ERR3761192.501025,ERR3761192.562491'
[W::vcf_parse] FILTER 'END=11756236' is not defined in the header
[W::vcf_parse] FILTER 'STD_quant_start=4.219005' is not defined in the header
[W::vcf_parse] FILTER 'STD_quant_stop=4.679744' is not defined in the header
[W::vcf_parse] FILTER 'Kurtosis_quant_start=-1.568951' is not defined in the header
[W::vcf_parse] FILTER 'Kurtosis_quant_stop=-1.427588' is not defined in the header
[W::vcf_parse] FILTER 'RNAMES=ERR3760291.207635,ERR3760291.207636,ERR3760406.475306,ERR3760407.111404,ERR3760441.17646,ERR3760441.280909,ERR3760534.85196,ERR3760535.225000,ERR3760535.225002,ERR3760535.225003,ERR3760535.225004,ERR3760540.86004,ERR3760971.73448,ERR3761162.582738,ERR3761192.115719,ERR3761192.370338,ERR3761192.378198,ERR3761418.152193,ERR3761418.396639,ERR3761418.398875,ERR3761418.77738' is not defined in the header
[E::bcf_hdr_parse_line] Could not parse the header line: "##FILTER=<ID=RNAMES=ERR3760291.207635,ERR3760291.207636,ERR3760406.475306,ERR3760407.111404,ERR3760441.17646,ERR3760441.280909,ERR3760534.85196,ERR3760535.225000,ERR3760535.225002,ERR3760535.225003,ERR3760535.225004,ERR3760540.86004,ERR3760971.73448,ERR3761162.582738,ERR3761192.115719,ERR3761192.370338,ERR3761192.378198,ERR3761418.152193,ERR3761418.396639,ERR3761418.398875,ERR3761418.77738,Description="Dummy">"
[E::vcf_parse] Could not add dummy header for FILTER 'RNAMES=ERR3760291.207635,ERR3760291.207636,ERR3760406.475306,ERR3760407.111404,ERR3760441.17646,ERR3760441.280909,ERR3760534.85196,ERR3760535.225000,ERR3760535.225002,ERR3760535.225003,ERR3760535.225004,ERR3760540.86004,ERR3760971.73448,ERR3761162.582738,ERR3761192.115719,ERR3761192.370338,ERR3761192.378198,ERR3761418.152193,ERR3761418.396639,ERR3761418.398875,ERR3761418.77738'
[W::vcf_parse] FILTER 'END=11841324' is not defined in the header
[W::vcf_parse] FILTER 'STD_quant_start=5.735852' is not defined in the header
[W::vcf_parse] FILTER 'STD_quant_stop=17.421251' is not defined in the header
[W::vcf_parse] FILTER 'Kurtosis_quant_start=1.864860' is not defined in the header
[W::vcf_parse] FILTER 'Kurtosis_quant_stop=0.270179' is not defined in the header
[W::vcf_parse] FILTER 'RNAMES=ERR3760406.122170,ERR3760407.374218,ERR3760535.441952,ERR3760971.278722,ERR3761162.170941,ERR3761162.236551,ERR3761162.74803,ERR3761162.74804,ERR3761190.586868,ERR3761191.416395,ERR3761191.641891,ERR3761191.692732,ERR3761192.400591,ERR3761192.540717' is not defined in the header
[E::bcf_hdr_parse_line] Could not parse the header line: "##FILTER=<ID=RNAMES=ERR3760406.122170,ERR3760407.374218,ERR3760535.441952,ERR3760971.278722,ERR3761162.170941,ERR3761162.236551,ERR3761162.74803,ERR3761162.74804,ERR3761190.586868,ERR3761191.416395,ERR3761191.641891,ERR3761191.692732,ERR3761192.400591,ERR3761192.540717,Description="Dummy">"
[E::vcf_parse] Could not add dummy header for FILTER 'RNAMES=ERR3760406.122170,ERR3760407.374218,ERR3760535.441952,ERR3760971.278722,ERR3761162.170941,ERR3761162.236551,ERR3761162.74803,ERR3761162.74804,ERR3761190.586868,ERR3761191.416395,ERR3761191.641891,ERR3761191.692732,ERR3761192.400591,ERR3761192.540717'
[W::vcf_parse] FILTER 'END=11864978' is not defined in the header
[W::vcf_parse] FILTER 'STD_quant_start=8.526429' is not defined in the header
[W::vcf_parse] FILTER 'STD_quant_stop=37.680234' is not defined in the header
[W::vcf_parse] FILTER 'Kurtosis_quant_start=4.037530' is not defined in the header
[W::vcf_parse] FILTER 'Kurtosis_quant_stop=-0.669853' is not defined in the header
[W::vcf_parse] FILTER 'RNAMES=ERR3760291.318843,ERR3760406.323693,ERR3760407.195868,ERR3760407.217213,ERR3760441.150261,ERR3760441.357345,ERR3760540.174394,ERR3760971.12283,ERR3761162.338041,ERR3761162.466722,ERR3761190.454105,ERR3761191.248494,ERR3761418.66786' is not defined in the header
[E::bcf_hdr_parse_line] Could not parse the header line: "##FILTER=<ID=RNAMES=ERR3760291.318843,ERR3760406.323693,ERR3760407.195868,ERR3760407.217213,ERR3760441.150261,ERR3760441.357345,ERR3760540.174394,ERR3760971.12283,ERR3761162.338041,ERR3761162.466722,ERR3761190.454105,ERR3761191.248494,ERR3761418.66786,Description="Dummy">"
[E::vcf_parse] Could not add dummy header for FILTER 'RNAMES=ERR3760291.318843,ERR3760406.323693,ERR3760407.195868,ERR3760407.217213,ERR3760441.150261,ERR3760441.357345,ERR3760540.174394,ERR3760971.12283,ERR3761162.338041,ERR3761162.466722,ERR3761190.454105,ERR3761191.248494,ERR3761418.66786'
[W::vcf_parse] FILTER 'END=11962116' is not defined in the header
[W::vcf_parse] FILTER 'Kurtosis_quant_start=6.940882' is not defined in the header
[W::vcf_parse] FILTER 'Kurtosis_quant_stop=5.684161' is not defined in the header
[W::vcf_parse] FILTER 'RNAMES=ERR3760406.508284,ERR3760441.3402,ERR3760535.203630,ERR3760540.379618,ERR3760971.173116,ERR3760971.464366,ERR3761190.494189,ERR3761192.10961,ERR3761192.372853,ERR3761192.372855,ERR3761192.372856,ERR3761192.372857,ERR3761192.372858,ERR3761192.452014,ERR3761192.520627,ERR3761418.276998' is not defined in the header
[E::bcf_hdr_parse_line] Could not parse the header line: "##FILTER=<ID=RNAMES=ERR3760406.508284,ERR3760441.3402,ERR3760535.203630,ERR3760540.379618,ERR3760971.173116,ERR3760971.464366,ERR3761190.494189,ERR3761192.10961,ERR3761192.372853,ERR3761192.372855,ERR3761192.372856,ERR3761192.372857,ERR3761192.372858,ERR3761192.452014,ERR3761192.520627,ERR3761418.276998,Description="Dummy">"
[E::vcf_parse] Could not add dummy header for FILTER 'RNAMES=ERR3760406.508284,ERR3760441.3402,ERR3760535.203630,ERR3760540.379618,ERR3760971.173116,ERR3760971.464366,ERR3761190.494189,ERR3761192.10961,ERR3761192.372853,ERR3761192.372855,ERR3761192.372856,ERR3761192.372857,ERR3761192.372858,ERR3761192.452014,ERR3761192.520627,ERR3761418.276998'
[W::vcf_parse] FILTER 'END=11962680' is not defined in the header
[W::vcf_parse] FILTER 'STD_quant_stop=179.002235' is not defined in the header
[W::vcf_parse] FILTER 'Kurtosis_quant_start=3.800000' is not defined in the header
[W::vcf_parse] FILTER 'Kurtosis_quant_stop=3.240435' is not defined in the header
[W::vcf_parse] FILTER 'RNAMES=ERR3760535.203630,ERR3760540.379618,ERR3760540.56696,ERR3760540.56697,ERR3760971.173116,ERR3761162.219486,ERR3761162.665170,ERR3761190.345431,ERR3761192.10961,ERR3761192.372857,ERR3761192.372858' is not defined in the header
[E::bcf_hdr_parse_line] Could not parse the header line: "##FILTER=<ID=RNAMES=ERR3760535.203630,ERR3760540.379618,ERR3760540.56696,ERR3760540.56697,ERR3760971.173116,ERR3761162.219486,ERR3761162.665170,ERR3761190.345431,ERR3761192.10961,ERR3761192.372857,ERR3761192.372858,Description="Dummy">"
[E::vcf_parse] Could not add dummy header for FILTER 'RNAMES=ERR3760535.203630,ERR3760540.379618,ERR3760540.56696,ERR3760540.56697,ERR3760971.173116,ERR3761162.219486,ERR3761162.665170,ERR3761190.345431,ERR3761192.10961,ERR3761192.372857,ERR3761192.372858'
Warning...unknown stuff <
>
Warning...unknown stuff <
>
Warning...unknown stuff <
>

Any suggestion on what is going on?

Thanks in advanced!
Jacopo

[shunhuahan]

Hi @jacopoM28,

Thanks for reporting this issue. On first glance, it appears that the SV VCF generated by Sniffles hassle format issues. Could you send the gzipped Sniffles VCF file and the full standard output to hanshunhua0829@gmail.com so I can take a look?

Also, could you share the conda package list you installed under TELR env using the following commands? This should be helpful in assessing whether the issue is caused by Sniffles/NGMLR/bcftools versions.

conda activate TELR
conda list

Thanks,
Shunhua

[jacopoM28]

Hi Shunhua,

thank you very much, I just sent you all the files!

Best
Jacopo

[shunhuahan]

@jacopoM28 Thanks for sending over the files and sorry for the late response (end of the year push).

I noticed two issues in the standard error log file. The first issue seems to be caused by Sniffles producing non-standard VCF format, which doesn't seem to affect the results (expect for having those format related warning messages), but I will keep it in my backlog.

The second issue is an actual error. Basically TELR will repeatmask the reference genome for reference TE insertions and use this annotation in the non-reference TE identification process. Currently, the reference TE BED file (Cgig_Ref.PacBio_genome.fa.te.bed) is not properly sorted. I have now added a patch in TELR to fix the TE.bed out of sort error (see #27). Please activate TELR conda env, pull the new patch in the GitHub repo, install the new TELR package locally using pip, and test on your failed sample jobs. Let me know if you can get normal TELR output files, or are stilling having issues. Thanks!

conda activate TELR

cd TELR # this is the TELR git folder
git pull # necessary to use this patched update
pip install . # necessary to use this patched update

Best,
Shunhua