Error occurred when processing GFF file, need more than 1 value to unpack

Question

[rebeccakurtz62]

I am trying to create a count matrix using htseq. My commands are below:

htseq-count -m union -s yes -t exon --idattr=Parent data1.sam GENE.gff > data1.counts

Here is a sample of my GENE.gff

##gff-version 3
# File name: 
# Organism: Candida albicans SC5314
# Genome version: A22-s07-m01-r20
# Date created: Sun Feb 19 07:02:19 2017
# Created by: The Candida Genome Database (http://www.candidagenome.org/)
# Contact Email: candida-curator AT lists DOT stanford DOT edu
# Funding: NIDCR at US NIH, grant number 1-R01-DE015873-01
#
Ca22chr1A_C_albicans_SC5314 CGD chromosome  1   3188341 .   .   .   ID=Ca22chr1A_C_albicans_SC5314;Name=Ca22chr1A_C_albicans_SC5314
Ca22chr1B_C_albicans_SC5314 CGD chromosome  1   3188396 .   .   .   ID=Ca22chr1B_C_albicans_SC5314;Name=Ca22chr1B_C_albicans_SC5314
Ca22chr2A_C_albicans_SC5314 CGD chromosome  1   2231883 .   .   .   ID=Ca22chr2A_C_albicans_SC5314;Name=Ca22chr2A_C_albicans_SC5314
Ca22chr2B_C_albicans_SC5314 CGD chromosome  1   2231750 .   .   .   ID=Ca22chr2B_C_albicans_SC5314;Name=Ca22chr2B_C_albicans_SC5314
Ca22chr3A_C_albicans_SC5314 CGD chromosome  1   1799298 .   .   .   ID=Ca22chr3A_C_albicans_SC5314;Name=Ca22chr3A_C_albicans_SC5314
Ca22chr3B_C_albicans_SC5314 CGD chromosome  1   1799271 .   .   .   ID=Ca22chr3B_C_albicans_SC5314;Name=Ca22chr3B_C_albicans_SC5314
Ca22chr4A_C_albicans_SC5314 CGD chromosome  1   1603259 .   .   .   ID=Ca22chr4A_C_albicans_SC5314;Name=Ca22chr4A_C_albicans_SC5314
Ca22chr4B_C_albicans_SC5314 CGD chromosome  1   1603311 .   .   .   ID=Ca22chr4B_C_albicans_SC5314;Name=Ca22chr4B_C_albicans_SC5314
Ca22chr5A_C_albicans_SC5314 CGD chromosome  1   1190869 .   .   .   ID=Ca22chr5A_C_albicans_SC5314;Name=Ca22chr5A_C_albicans_SC5314
Ca22chr5B_C_albicans_SC5314 CGD chromosome  1   1190991 .   .   .   ID=Ca22chr5B_C_albicans_SC5314;Name=Ca22chr5B_C_albicans_SC5314
Ca22chr6A_C_albicans_SC5314 CGD chromosome  1   1033292 .   .   .   ID=Ca22chr6A_C_albicans_SC5314;Name=Ca22chr6A_C_albicans_SC5314
Ca22chr6B_C_albicans_SC5314 CGD chromosome  1   1033212 .   .   .   ID=Ca22chr6B_C_albicans_SC5314;Name=Ca22chr6B_C_albicans_SC5314
Ca22chr7A_C_albicans_SC5314 CGD chromosome  1   949580  .   .   .   ID=Ca22chr7A_C_albicans_SC5314;Name=Ca22chr7A_C_albicans_SC5314
Ca22chr7B_C_albicans_SC5314 CGD chromosome  1   949611  .   .   .   ID=Ca22chr7B_C_albicans_SC5314;Name=Ca22chr7B_C_albicans_SC5314
Ca22chrM_C_albicans_SC5314  CGD chromosome  1   40420   .   .   .   ID=Ca22chrM_C_albicans_SC5314;Name=Ca22chrM_C_albicans_SC5314
Ca22chrRA_C_albicans_SC5314 CGD chromosome  1   2286237 .   .   .   ID=Ca22chrRA_C_albicans_SC5314;Name=Ca22chrRA_C_albicans_SC5314
Ca22chrRB_C_albicans_SC5314 CGD chromosome  1   2285697 .   .   .   ID=Ca22chrRB_C_albicans_SC5314;Name=Ca22chrRB_C_albicans_SC5314
Ca22chr1A_C_albicans_SC5314 CGD gene    4059    4397    .   +   .   ID=C1_00010W_A;Name=C1_00010W_A;Note=%28orf19.6115%29%20Dubious%20open%20reading%20frame;orf_classification=Dubious;Alias=C1_00010W,C1_00010W_B,CaO19.11880,CaO19.13534,CaO19.4402,CaO19.6115,IPF21113.1,IPF27828.1,orf19.13534,orf19.6115
Ca22chr1A_C_albicans_SC5314 CGD mRNA    4059    4397    .   +   .   ID=C1_00010W_A-T;Parent=C1_00010W_A;Name=C1_00010W_A;Note=%28orf19.6115%29%20Dubious%20open%20reading%20frame;orf_classification=Dubious;Alias=C1_00010W,C1_00010W_B,CaO19.11880,CaO19.13534,CaO19.4402,CaO19.6115,IPF21113.1,IPF27828.1,orf19.13534,orf19.6115
Ca22chr1A_C_albicans_SC5314 CGD exon    4059    4397    .   +   .   ID=C1_00010W_A-T-E1;Parent=C1_00010W_A-T

Here is a sample of my .sam file:

D00743:137:CAAWDANXX:1:1101:1129:76971  256 Ca22chr5A_C_albicans_SC5314 148153  3   51M *   0   0   CNGCTGGTTCAGTAGGTAAAACCACCATTGAACTATAATCAGGGTCAGGCA B#<<BFFFFFFFFFFFFFFFFFFFFFFFFFFBFFFFFFFFFFFFFFFFFFF AS:i:-1 XN:i:0  XM:i:1  XO:i:0  XG:i:0  NM:i:1  MD:Z:1T49   YT:Z:UU NH:i:2  CC:Z:Ca22chr5B_C_albicans_SC5314    CP:i:148147 HI:i:0
D00743:137:CAAWDANXX:1:1101:1129:76971  0   Ca22chr5B_C_albicans_SC5314 148147  3   51M *   0   0   CNGCTGGTTCAGTAGGTAAAACCACCATTGAACTATAATCAGGGTCAGGCA B#<<BFFFFFFFFFFFFFFFFFFFFFFFFFFBFFFFFFFFFFFFFFFFFFF AS:i:-1 XN:i:0  XM:i:1  XO:i:0  XG:i:0  NM:i:1  MD:Z:1T49   YT:Z:UU NH:i:2  HI:i:1
D00743:137:CAAWDANXX:1:1101:1129:87845  272 Ca22chr7A_C_albicans_SC5314 613287  3   51M *   0   0   GTTGGTTGGTCTAAGGATTTTAATAGCAACATCAACAACACATGGTTTCNC F<B/FFFFFFFFFFFFFFFFFFFFF<FFBBFFBFFBFFBFBFFFFFB<<#B AS:i:-1 XN:i:0  XM:i:1  XO:i:0  XG:i:0  NM:i:1  MD:Z:49A1   YT:Z:UU NH:i:2  CC:Z:Ca22chr7B_C_albicans_SC5314    CP:i:613307 HI:i:0
D00743:137:CAAWDANXX:1:1101:1129:87845  16  Ca22chr7B_C_albicans_SC5314 613307  3   51M *   0   0   GTTGGTTGGTCTAAGGATTTTAATAGCAACATCAACAACACATGGTTTCNC F<B/FFFFFFFFFFFFFFFFFFFFF<FFBBFFBFFBFFBFBFFFFFB<<#B AS:i:-1 XN:i:0  XM:i:1  XO:i:0  XG:i:0  NM:i:1  MD:Z:49A1   YT:Z:UU NH:i:2  HI:i:1
D00743:137:CAAWDANXX:1:1101:1129:90895  0   Ca22chr3B_C_albicans_SC5314 1786020 3   51M *   0   0   GNCGGCCAAAGCTTCGATTTGGTGCAAGATCATTGGTCTGTTACCGAACTC B#<<BFFFFFFFFFFF/FFFFFBFFFFFFFFFFFFFFFFFFFFFFFFFFFF AS:i:-6 XN:i:0  XM:i:2  XO:i:0  XG:i:0  NM:i:2  MD:Z:0A0G49 YT:Z:UU NH:i:2  HI:i:1
D00743:137:CAAWDANXX:1:1101:1129:90895  256 Ca22chr3A_C_albicans_SC5314 1786049 3   51M *   0   0   GNCGGCCAAAGCTTCGATTTGGTGCAAGATCATTGGTCTGTTACCGAACTC B#<<BFFFFFFFFFFF/FFFFFBFFFFFFFFFFFFFFFFFFFFFFFFFFFF AS:i:-6 XN:i:0  XM:i:2  XO:i:0  XG:i:0  NM:i:2  MD:Z:0A0G49 YT:Z:UU NH:i:2  CC:Z:Ca22chr3B_C_albicans_SC5314    CP:i:1786020    HI:i:0
D00743:137:CAAWDANXX:1:1101:1129:91175  16  Ca22chrRA_C_albicans_SC5314 1494150 3   51M *   0   0   AAAAGCTGTATGTATTGACCATGTTTATATTTACTACTAATTAAATGTCNA FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFB<<#B AS:i:-1 XN:i:0  XM:i:1  XO:i:0  XG:i:0  NM:i:1  MD:Z:49C1   YT:Z:UU NH:i:2  CC:Z:Ca22chrRB_C_albicans_SC5314    CP:i:1494053    HI:i:0
D00743:137:CAAWDANXX:1:1101:1129:91175  272 Ca22chrRB_C_albicans_SC5314 1494053 3   51M *   0   0   AAAAGCTGTATGTATTGACCATGTTTATATTTACTACTAATTAAATGTCNA FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFB<<#B AS:i:-1 XN:i:0  XM:i:1  XO:i:0  XG:i:0  NM:i:1  MD:Z:49C1   YT:Z:UU NH:i:2  HI:i:1
D00743:137:CAAWDANXX:1:1101:1130:83249  272 Ca22chr2A_C_albicans_SC5314 1454537 3   51M *   0   0   TAATTTAGTGTTTGGGTCATCGGATTTTCTCAATTTCGATATAGGATTGNC FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFB<<#B AS:i:-1 XN:i:0  XM:i:1  XO:i:0  XG:i:0  NM:i:1  MD:Z:49G1   YT:Z:UU NH:i:2  CC:Z:Ca22chr2B_C_albicans_SC5314    CP:i:1454552    HI:i:0
D00743:137:CAAWDANXX:1:1101:1130:83249  16  Ca22chr2B_C_albicans_SC5314 1454552 3   51M *   0   0   TAATTTAGTGTTTGGGTCATCGGATTTTCTCAATTTCGATATAGGATTGNC FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFB<<#B AS:i:-1 XN:i:0  XM:i:1  XO:i:0  XG:i:0  NM:i:1  MD:Z:49G1   YT:Z:UU NH:i:2  HI:i:1
D00743:137:CAAWDANXX:1:1101:1130:86865  16  Ca22chr3B_C_albicans_SC5314 177846  3   51M *   0   0   ATCCATTGGCAAGATCTAACTTGTCGGAATTCACCGGTGACTCACACTTNC FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFB<<#B AS:i:-1 XN:i:0  XM:i:1  XO:i:0  XG:i:0  NM:i:1  MD:Z:49C1   YT:Z:UU NH:i:2  HI:i:1
D00743:137:CAAWDANXX:1:1101:1130:86865  272 Ca22chr3A_C_albicans_SC5314 177843  3   51M *   0   0   ATCCATTGGCAAGATCTAACTTGTCGGAATTCACCGGTGACTCACACTTNC FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFB<<#B AS:i:-1 XN:i:0  XM:i:1  XO:i:0  XG:i:0  NM:i:1  MD:Z:49C1   YT:Z:UU NH:i:2  CC:Z:Ca22chr3B_C_albicans_SC5314    CP:i:177846 HI:i:0

I am getting the following error message though

[bam_sort_core] merging from 14 files... Error occured when processing GFF file (line 53257 of file C_albicans.gff need more than 1 value to unpack [Exception type: ValueError, raised in ___init___.py:207]

I am really new to this and am totally lost as to what is wrong. Any advice would be appreciated!

[WouterDeCoster]

So how does line 53257 of file C_albicans.gff look like?

[Santosh Anand]

can you uppload the Gene.gff file here http://www.tinyupload.com , and post the download link?

Answer 1

[rebeccakurtz62]

Line 53257:

Ca22chrRB_C_albicans_SC5314 CGD exon    2284837 2285658 .   -   .   ID=CR_10860C_B-T-E1;Parent=CR_10860C_B-T
Ca22chrRB_C_albicans_SC5314 CGD CDS 2284837 2285658 .   -   0   ID=CR_10860C_B-P;Parent=CR_10860C_B-T;orf_classification=Verified;parent_feature_type=ORF
##FASTA
>Ca22chr1A_C_albicans_SC5314 (3188341 nucleotides)
GAGTCACGCCAATCACAAATTCCTTTGAAAAACTTGATTCGACCACATTCACAAGTTTGA

[WouterDeCoster]

Please use ADD REPLY to answer to earlier reactions, as such this thread remains logically structured and easy to follow. I have now moved your reply, but as you can see it's not optimal.

So which line is it? The exon or CDS line? Both look normal to me...