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WGLab / doc-ANNOVAR

Documentation for the ANNOVAR software
http://annovar.openbioinformatics.org
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Help!!! Error: invalid record found in exonic_variant_function file (exonic format error): <line73 #101

Open jigaoxiang opened 4 years ago

jigaoxiang commented 4 years ago

Dear professor Kai: When I try to use annovar with code perl ../table_annovar.pl sample.avinput ../testdb --buildver * --outfile *.test --protocol refGene --operation g there are some problem happen "Error: invalid record found in exonic_variant_function file (exonic format error): <line73 nonsynonymous SNV". The annovar was download by an email link from you in Dec 10 2019.

kaichop commented 4 years ago

you output file is not complete (may be a file system issue). Just run it again.

On Mon, Aug 3, 2020 at 9:46 AM jigaoxiang notifications@github.com wrote:

Dear professor Kai: When I try to use annovar with code perl ../table_annovar.pl sample.avinput ../testdb --buildver --outfile .test --protocol refGene --operation g there are some problem happen "Error: invalid record found in exonic_variant_function file (exonic format error): <line73 nonsynonymous SNV". The annovar was download by an email link from you in Dec 10 2019.

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jigaoxiang commented 4 years ago

the same Error info, Maybe some problem with my vcf file? image

kaichop commented 4 years ago

Your file has no chromosome number. It should be something like "1" or "chr1". By default, ANNOVAR uses hg18 coordinate, and most likely you are not using it and need to add -buildvar argument as well.

On Mon, Aug 3, 2020 at 10:35 AM jigaoxiang notifications@github.com wrote:

the same Error info, Maybe some problem with my vcf file? [image: image] https://user-images.githubusercontent.com/65279501/89194128-85585680-d5d9-11ea-8fa8-745342ae3623.png

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TingLi-2022 commented 3 years ago

Dear professor Kai: I had the same problem when running table annovar.pl, but it was OK when running the annotate Variation.pl command. I've used test data and it's OK when it runs (https://github.com/quanrd/CandiHap). I think it may be a problem with my data, but i can't solve it. F32I755YKWA%BCQ7DV6@CMG

kaichop commented 3 years ago

You used a file called "sample.avinput", but you supplied a "-vcfinput" argument which means the input file should be VCF file. I assume that it is not VCF, and this argument should not be present.

On Sun, Aug 1, 2021 at 9:33 PM lovetingli @.***> wrote:

Dear professor Kai: I had the same problem when running table annovar.pl, but it was OK when running the annotate Variation.pl command. I've used test data and it's OK when it runs (https://github.com/quanrd/CandiHap). I think it may be a problem with my data, but i can't solve it. [image: @.*** https://user-images.githubusercontent.com/88281408/127792996-00cb5be3-cc80-4b95-9a40-01ba7796dc95.png

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TingLi-2022 commented 3 years ago

Sorry, I forgot to modify the parameters. But, there will be the same error when I use the vcf file by -vcfinput and aviput file by the following command. ZT)K0IIJ%5{SFD{T{C% 3%C

kaichop commented 3 years ago

What is "ma" in the -buildver? It looks like there is no transcript name in the file. If you show a few lines of the ma_refGene.txt (such as the line for Zm00001d023225_P001) that can help check what is wrong.

On Mon, Aug 2, 2021 at 1:26 AM lovetingli @.***> wrote:

Sorry, I forgot to modify the parameters. But, there will be the same error when I use the vcf file by -vcfinput and aviput file by the following command. [image: ZT)K0IIJ%5{SFD{T{C% 3%C] https://user-images.githubusercontent.com/88281408/127808357-350c41f6-0d56-4ce8-9345-87d4beb4142b.png

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TingLi-2022 commented 3 years ago

Below is my ma_refGene.txt file ma_refGene txt

chenqing-1996 commented 2 years ago

Dear kaichop and lovetingli, I had the same problem when running table annovar.pl, my command is : perl /home/cq/biosoft/ANNOVAR/annovar/table_annovar.pl /home/cq/data/vcf/SC_addAA.vcf /home/cq/data/sequencing/SC -buildver SC -out scanno -protocol refGene --operation g -nastring . --vcfinput --otherinfo error is : Error: invalid record found in exonic_variant_function file (exonic format error): <line36 synonymous SNV :Maker06611:exon2:c.T120C:p.T40T Contig0000002 90010 90010 T C 0.08824 893.43 22 Contig0000002 90010 Contig0000002_90010_T_C T C 893.43 PASS AC=3;AF=0.088;AN=34;BaseQRankSum=1.69;ClippingRankSum=0;DP=325;ExcessHet=3.4242;FS=4.124;InbreedingCoeff=-0.0968;MLEAC=3;MLEAF=0.088;MQ=60;MQRankSum=0;QD=17.87;ReadPosRankSum=1.36;SOR=0.283;AA=C GT:AD:DP:GQ:PL 0/0:27,0:27:81:0,81,1094 0/0:20,0:20:60:0,60,777 0/0:16,0:16:45:0,45,675 0/0:10,0:10:30:0,30,379 0/0:13,0:13:39:0,39,497 0/0:15,0:15:42:0,42,630 0/0:23,0:23:60:0,60,900 0/1:5,6:11:99:211,0,141 0/1:10,13:23:99:421,0,269 0/0:22,0:22:45:0,45,708 0/0:20,0:20:60:0,60,711 0/0:23,0:23:60:0,60,900 0/1:7,9:16:99:314,0,198 0/0:26,0:26:72:0,72,1080 0/0:14,0:14:42:0,42,525 0/0:24,0:24:72:0,72,876 0/0:22,0:22:66:0,66,837> at /home/cq/biosoft/ANNOVAR/annovar/coding_change.pl line 77, line 1. Error running system command: <coding_change.pl scanno.refGene.exonic_variant_function.orig /home/cq/data/sequencing/SC//SC_refGene.txt /home/cq/data/sequencing/SC//SC_refGeneMrna.fa -alltranscript -out scanno.refGene.fa -newevf scanno.refGene.exonic_variant_function> Error running system command: </home/cq/biosoft/ANNOVAR/annovar/table_annovar.pl scanno.avinput /home/cq/data/sequencing/SC/ -buildver SC -outfile scanno -protocol refGene -operation g -nastring . -otherinfo -otherinfo> I haven't found any solution. What exactly is the problem?

Yixiangzhang1996 commented 2 years ago

Dear kaichop and lovetingli, I had the same problem when running table annovar.pl, my command is : perl /home/cq/biosoft/ANNOVAR/annovar/table_annovar.pl /home/cq/data/vcf/SC_addAA.vcf /home/cq/data/sequencing/SC -buildver SC -out scanno -protocol refGene --operation g -nastring . --vcfinput --otherinfo error is : Error: invalid record found in exonic_variant_function file (exonic format error): <line36 synonymous SNV :Maker06611:exon2:c.T120C:p.T40T Contig0000002 90010 90010 T C 0.08824 893.43 22 Contig0000002 90010 Contig0000002_90010_T_C T C 893.43 PASS AC=3;AF=0.088;AN=34;BaseQRankSum=1.69;ClippingRankSum=0;DP=325;ExcessHet=3.4242;FS=4.124;InbreedingCoeff=-0.0968;MLEAC=3;MLEAF=0.088;MQ=60;MQRankSum=0;QD=17.87;ReadPosRankSum=1.36;SOR=0.283;AA=C GT:AD:DP:GQ:PL 0/0:27,0:27:81:0,81,1094 0/0:20,0:20:60:0,60,777 0/0:16,0:16:45:0,45,675 0/0:10,0:10:30:0,30,379 0/0:13,0:13:39:0,39,497 0/0:15,0:15:42:0,42,630 0/0:23,0:23:60:0,60,900 0/1:5,6:11:99:211,0,141 0/1:10,13:23:99:421,0,269 0/0:22,0:22:45:0,45,708 0/0:20,0:20:60:0,60,711 0/0:23,0:23:60:0,60,900 0/1:7,9:16:99:314,0,198 0/0:26,0:26:72:0,72,1080 0/0:14,0:14:42:0,42,525 0/0:24,0:24:72:0,72,876 0/0:22,0:22:66:0,66,837> at /home/cq/biosoft/ANNOVAR/annovar/coding_change.pl line 77, line 1. Error running system command: <coding_change.pl scanno.refGene.exonic_variant_function.orig /home/cq/data/sequencing/SC//SC_refGene.txt /home/cq/data/sequencing/SC//SC_refGeneMrna.fa -alltranscript -out scanno.refGene.fa -newevf scanno.refGene.exonic_variant_function> Error running system command: </home/cq/biosoft/ANNOVAR/annovar/table_annovar.pl scanno.avinput /home/cq/data/sequencing/SC/ -buildver SC -outfile scanno -protocol refGene -operation g -nastring . -otherinfo -otherinfo> I haven't found any solution. What exactly is the problem?

how to solve？same problem

kaichop commented 2 years ago

This problem happens for new genome assemblies when there is no gene annotation but there is transcript annotation. The ":Maker06611:exon2:c.T120C:p.T40T" string is not treated as valid in coding_change.pl and therefore there is an error message. If a user can manually change the file in the line for Maker06611, add a gene name there (for example, just call it "Maker06611gene", then it should work. Alternatively, I have made slight modifications to coding_change.pl that ignores this "missing gene name" issue, and attached it here. You can replace the old coding_change.pl to address this problem. coding_change.pl.txt

jiangxiaokanggg commented 1 year ago

Dear professor Kai: I had the same problem when running table annovar.pl, my command is : perl /data/software/Annovar/table_annovar.pl --vcfinput bsa_sigregion.vcf ../glymadb --buildver glyma --protocol refGene --operation g --remove --outfile bsa_sig_annovar --otherinfo

error is: `NOTICE: the --polish argument is set ON automatically (use --nopolish to change this behavior) NOTICE: Running with system command <convert2annovar.pl -includeinfo -allsample -withfreq -format vcf4 bsa_sigregion.vcf > bsa_sig_annovar.avinput> NOTICE: Finished reading 3696 lines from VCF file NOTICE: A total of 3372 locus in VCF file passed QC threshold, representing 2779 SNPs (1560 transitions and 1219 transversions) and 635 indels/substitutions NOTICE: Finished writing allele frequencies based on 11116 SNP genotypes (6240 transitions and 4876 transversions) and 2540 indels/substitutions for 4 samples WARNING: 11 invalid alternative alleles found in input file

NOTICE: Running with system command </data/software/Annovar/table_annovar.pl bsa_sig_annovar.avinput ../glymadb --buildver glyma --protocol refGene --operation g --remove -outfile bsa_sig_annovar --otherinfo -otherinfo -nastring .> NOTICE: the --polish argument is set ON automatically (use --nopolish to change this behavior)

NOTICE: Processing operation=g protocol=refGene

NOTICE: Running with system command <annotate_variation.pl -geneanno -buildver glyma -dbtype refGene -outfile bsa_sig_annovar.refGene -exonsort -nofirstcodondel bsa_sig_annovar.avinput ../glymadb> NOTICE: Output files are written to bsa_sig_annovar.refGene.variant_function, bsa_sig_annovar.refGene.exonic_variant_function NOTICE: Reading gene annotation from ../glymadb/glyma_refGene.txt ... Done with 86256 transcripts (including 0 without coding sequence annotation) for 52872 unique genes NOTICE: Processing next batch with 3425 unique variants in 3425 input lines NOTICE: Reading FASTA sequences from ../glymadb/glyma_refGeneMrna.fa ... Done with 89 sequences

NOTICE: Running with system command <coding_change.pl bsa_sig_annovar.refGene.exonic_variant_function.orig ../glymadb/glyma_refGene.txt ../glymadb/glyma_refGeneMrna.fa -alltranscript -out bsa_sig_annovar.refGene.fa -newevf bsa_sig_annovar.refGene.exonic_variant_function> Error: invalid record found in exonic_variant_function file (exonic format error): <line1 synonymous SNV glyma.Wm82.gnm4.ann1.Glyma.04G234600:glyma.Wm82.gnm4.ann1.Glyma.04G234600.1#glyma.Wm82.gnm4.Gm04#49128351:exon2:c.C351T:p.S117S,glyma.Wm82.gnm4.ann1.Glyma.04G234600:glyma.Wm82.gnm4.ann1.Glyma.04G234600.2#glyma.Wm82.gnm4.Gm04#49128351:exon2:c.C258T:p.S86S glyma.Wm82.gnm4.Gm04 49129130 49129130 C T 0.375 3103.11 96 glyma.Wm82.gnm4.Gm04 49129130 . C 3103.11 PASS AC=3;AF=0.375;AN=8;BaseQRankSum=-1.7;DP=365;ExcessHet=2.4304;FS=5.768;MLEAC=3;MLEAF=0.375;MQ=60;MQRankSum=0;QD=11.67;ReadPosRankSum=-1.464;SOR=0.81 GT:AD:DP:GQ:PGT:PID:PL:PS 0/0:73,0:73:99:.:.:0,120,1800:. 0/1:23,55:78:99:.:.:1616,0,801:. 0/1:60,32:92:99:.:.:812,0,2015:. 0|1:73,23:96:99:1|0:49129123_C_T:687,0,2966:49129123> at /data/software/Annovar/coding_change.pl line 77, line 1. Error running system command: <coding_change.pl bsa_sig_annovar.refGene.exonic_variant_function.orig ../glymadb/glyma_refGene.txt ../glymadb/glyma_refGeneMrna.fa -alltranscript -out bsa_sig_annovar.refGene.fa -newevf bsa_sig_annovar.refGene.exonic_variant_function> Error running system command: </data/software/Annovar/table_annovar.pl bsa_sig_annovar.avinput ../glymadb --buildver glyma --protocol refGene --operation g --remove -outfile bsa_sig_annovar --otherinfo -otherinfo -nastring .>`

this is the head of my vcf: `#CHROM POS ID REF ALT QUAL FILTER INFO FORMAT 2018 842 H1 S1 glyma.Wm82.gnm4.Gm04 49129130 . C T 3103.11 PASS AC=3;AF=0.375;AN=8;BaseQRankSum=-1.7;DP=365;ExcessHet=2.4304;FS=5.768;MLEAC=3;MLEAF=0.375;MQ =60;MQRankSum=0;QD=11.67;ReadPosRankSum=-1.464;SOR=0.81 GT:AD:DP:GQ:PGT:PID:PL:PS 0/0:73,0:73:99:.:.:0,120,1800:. 0/1:23,55:78:99:.:.:1616,0,801:. 0/1:60,32:92 :99:.:.:812,0,2015:. 0|1:73,23:96:99:1|0:49129123_C_T:687,0,2966:49129123 glyma.Wm82.gnm4.Gm04 49129364 . T C 753.11 PASS AC=3;AF=0.375;AN=8;BaseQRankSum=-1.563;DP=306;ExcessHet=2.4304;FS=20.781;MLEAC=3;MLEAF=0.375 ;MQ=59.34;MQRankSum=-3.091;QD=3.22;ReadPosRankSum=0.432;SOR=1.544 GT:AD:DP:GQ:PL 0/0:32,0:32:90:0,90,1350 0/1:47,18:65:99:344,0,1555 0/1:75,7:82:44:44,0, 2454 0/1:66,21:87:99:377,0,2023 glyma.Wm82.gnm4.Gm04 49129439 . G C 1839.11 PASS AC=3;AF=0.375;AN=8;BaseQRankSum=0.762;DP=274;ExcessHet=2.4304;FS=10.22;MLEAC=3;MLEAF=0.375;M Q=59.91;MQRankSum=0;QD=8;ReadPosRankSum=-0.91;SOR=1.369 GT:AD:DP:GQ:PL 0/0:24,0:24:66:0,66,990 0/1:44,18:62:99:587,0,1418 0/1:59,10:69:99:243,0,2027 0/1:68,31:99 :99:1021,0,2117 glyma.Wm82.gnm4.Gm04 49129456 . C T 1993.11 PASS AC=3;AF=0.375;AN=8;BaseQRankSum=0.811;DP=284;ExcessHet=2.4304;FS=8.268;MLEAC=3;MLEAF=0.375;M Q=59.97;MQRankSum=0;QD=8.17;ReadPosRankSum=0.465;SOR=1.182 GT:AD:DP:GQ:PL 0/0:19,0:19:57:0,57,689 0/1:46,17:63:99:548,0,1462 0/1:65,11:76:99:243,0,2189 0/1: 67,38:105:99:1214,0,2111 glyma.Wm82.gnm4.Gm04 49129478 . G C 2059.11 PASS AC=3;AF=0.375;AN=8;BaseQRankSum=0.366;DP=280;ExcessHet=2.4304;FS=10.971;MLEAC=3;MLEAF=0.375; MQ=59.97;MQRankSum=0;QD=8.8;ReadPosRankSum=0.372;SOR=1.376 GT:AD:DP:GQ:PL 0/0:21,0:21:60:0,60,775 0/1:36,16:52:99:540,0,1138 0/1:66,11:77:99:240,0,2263 0/1: 66,39:105:99:1291,0,1964 glyma.Wm82.gnm4.Gm04 49129503 . T G 2353.11 PASS AC=3;AF=0.375;AN=8;BaseQRankSum=0.89;DP=286;ExcessHet=2.4304;FS=15.565;MLEAC=3;MLEAF=0.375;M Q=59.97;MQRankSum=0;QD=9.6;ReadPosRankSum=1.47;SOR=1.346 GT:AD:DP:GQ:PL 0/0:21,0:21:60:0,60,775 0/1:36,19:55:99:630,0,1062 0/1:69,12:81:99:247,0,2243 0/1: 63,46:109:99:1488,0,1842

This is my glyma_refGeneMrna.fa: `>glyma.Wm82.gnm4.ann1.Glyma.01G000100.1 Comment: this sequence (leftmost exon at glyma.Wm82.gnm4.Gm01:27343) is generated by ANNOVAR on Thu May 25 21:25:31 2023, based on regions speficied in ./glyma_refGene.txt and the sequence file ./glyma.Wm82.gnm4.4PTR.genome_main.fna. CTATTGAGCAAAAATGTTGTAATCTATCTATCTAATCTACACACACACATATTAAATTTTGTATTTTCTTTGAAATTAAATATTTTTCCCAATTGTTTTGATATTCACGCCATGTTCTACCAATGCTACCTTTTCTTTCCTAAGGAAAAAATCAATATACTTGCAGCGTCAAACATTTGCATGTGAAGACAAAGGCAGAACTTAAAGAAGCTATGTGTGTAGCACAACATGAGCAAATGGACTGTATGGTTGAGATTGAGAGTTCCATTAATGCCAATGCCAATTTCCACAGTCAAGGCTCAATAAAGGACAAGTTCTATTTATACAAAATCCGTGAAATACAGTGTTCTAAATATAGAATTGCACTTGAAGCTCCGCCAACATCAACATTTGTTACTGATAGTTGTAAGGAATTTTATAGAGAAGGATTTATTTTATCTTTAGTGCTTGAAGAGGGAAGCGTTGGTTATGGTGAGGTTGGTATCAGTTTCATGTTATATCATGTCTTGTATCTTGCTTTACATTAATGTCTTGCTTTATAATAACGTTGGGCTGTTAAAAAACTGAAGATTAGATAAAAGCTAAATTTCTTAGTAAATGTATTTATAGAGTTAGAGTTCATAGCTCTAATACAAGATATGGATAGCGGTGTGGAGTGGCTGCCACAAAAAAATGAGATAGTAGATAGTGAGATGACCGCTACTCTAATATTTTCGTAAATGTTAAATAATTATTATTATATATATACTCTTTGGAGTCAAATATGAGCAAAAAAAATTTGTGAGTTATGGAACATAATATAAATTTTTTCTAGCTATTTTTACCTTATTTAATGACAC

glyma.Wm82.gnm4.ann1.Glyma.01G000137.1 Comment: this sequence (leftmost exon at glyma.Wm82.gnm4.Gm01:52484) is generated by ANNOVAR on Thu May 25 21:25:31 2023, based on regions speficied in ./glyma_refGene.txt and the sequence file ./glyma.Wm82.gnm4.4PTR.genome_main.fna. ATGTTCTTTCCTCTGAGTCTGCCCTTTTTCTTAGTAATACTATGCCCATTCAGGATGCAAATATATATGGATGTAGTTGGTCTATATGCTATCAAAGTGTTTCATGACTCCTGTTAA glyma.Wm82.gnm4.ann1.Glyma.01G000174.1 Comment: this sequence (leftmost exon at glyma.Wm82.gnm4.Gm01:54355) is generated by ANNOVAR on Thu May 25 21:25:31 2023, based on regions speficied in ./glyma_refGene.txt and the sequence file ./glyma.Wm82.gnm4.4PTR.genome_main.fna. ATGTATTTTTACATTAAAAAAGGACTTCTATCATTTTACAATATATCCATTGTACTGAATTTTCACTGTTATTTGATGAGACTGCAAACTTTTGCTTCCCTATTTCATTCTTTTAGTCAATATTTTGCATCTCTTGATATAGTTGTCCAGGTGAAGTCCACACCAAAGGAAAAGCAGAAGAAGCAAGAGAGAGATGATGTTTCTTTTGGTATTAGTGGTGCAAGCTACTTCACTGGAACTTTCACTACTGTCGATCGCTCTACAGATGGAAGGTATGTTGTAGTCTCAAGTCGGGGAAACTTCTACTTAACCTGGGAGTCTGGTCAGGTGAGGGTTTTAGTTTGTGATGGCTTTTGCTTTTGCTTCTATTTGCCTGGTCTCCTAGATACTTTTATTTTTCACTCAACGTTTGACCATGGATAA

this is my glyma_refGene.txt glyma.Wm82.gnm4.ann1.Glyma.01G000100.1 glyma.Wm82.gnm4.Gm01 - 27343 28430 27655 28218 3 27343,27925,28138, 27824,27991,28430, 0 glyma.Wm82.gnm4.ann1.Glyma.01G000100 incmpl incmpl 2,2,0, glyma.Wm82.gnm4.ann1.Glyma.01G000137.1 glyma.Wm82.gnm4.Gm01 - 52484 52601 52484 52601 1 52484, 52601, 0 glyma.Wm82.gnm4.ann1.Glyma.01G000137 incmpl incmpl 0, glyma.Wm82.gnm4.ann1.Glyma.01G000174.1 glyma.Wm82.gnm4.Gm01 - 54355 55224 54355 55224 2 54355,55025, 54579,55224, 0 glyma.Wm82.gnm4.ann1.Glyma.01G000174 incmpl incmpl 1,0, glyma.Wm82.gnm4.ann1.Glyma.01G000211.1 glyma.Wm82.gnm4.Gm01 - 56131 64061 56131 64061 3 56131,63084,64054, 56139,63417,64061, 0 glyma.Wm82.gnm4.ann1.Glyma.01G000211 incmpl incmpl 1,1,0, glyma.Wm82.gnm4.ann1.Glyma.01G000248.1 glyma.Wm82.gnm4.Gm01 - 59056 60641 59056 60641 4 59056,59786,60351,60618, 59111,59827,60520,60641, 0 glyma.Wm82.gnm4.ann1.Glyma.01G000248 incmpl incmpl 2,0,2,0, glyma.Wm82.gnm4.ann1.Glyma.01G000285.1 glyma.Wm82.gnm4.Gm01 - 65652 67666 65652 67666 3 65652,66688,67659, 65684,67021,67666, 0 glyma.Wm82.gnm4.ann1.Glyma.01G000285 incmpl incmpl 1,1,0, glyma.Wm82.gnm4.ann1.Glyma.01G000322.1 glyma.Wm82.gnm4.Gm01 - 72972 77727 77109 77700 5 72972,76318,76555,76990,77183, 73056,76386,76617,77114,77727, 0 glyma.Wm82.gnm4.ann1.Glyma.01G000322 incmpl incmpl -1,-1,-1,1,0,

jiangyongsen121 commented 11 months ago

I had the same problem when running table annovar.pl, my command is : NOTICE: Running with system command <coding_change.pl test.refGene.exonic_variant_function.orig .//si_refGene.txt .//si_refGeneMrna.fa -alltranscript -out test.refGene.fa -newevf test.refGene.exonic_variant_function> Error: invalid record found in annovar outputfile: <ncRNA_exonic 16 8315086 8315086 G A 0.1625 . . 16 8315086 Chr16__8315086 G A . . PR GT 0/1 0/0 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0> Error running system command: </home/share_data1/zhongls/software/package/annovar//table_annovar.pl test.avinput ./ -outfile test --buildver si --protocol refGene --operation g -remove -otherinfo -nastring .> I haven't found any solution. What exactly is the problem?