List index out of range error
Closed this issue · 6 comments
mahesh-panchal commented
Hi.
I'm running SPADE within a singularity container. This is the Dockerfile:
FROM continuumio/miniconda3:4.8.2
SHELL ["/bin/bash", "-c"]
LABEL description="Spade (Search for Patterned DNA Elements) container" \
version="1.0.0"
RUN apt-get update --fix-missing && \
apt-get install -y procps
RUN conda update -n base conda && \
conda install -c conda-forge -c bioconda \
python=3.6 mafft=7.455 blast=2.9.0 openssl=1.1.1e && \
conda clean --all -f -y
WORKDIR /opt
RUN git clone --depth 1 https://github.com/yachielab/SPADE && \
cd SPADE && chmod u+x *.py && \
pip install matplotlib==2.2.3 && \
pip install seaborn==0.8.1 && \
pip install weblogo==3.6.0 && \
pip install biopython
ENV PATH="/opt/SPADE:${PATH}"
CMD [ "SPADE.py" ]
When running spade (via workflow package Nextflow):
Command executed:
SPADE.py -i DA34821_pseudomolecule.fasta -f fasta -t nucl -d -n 4
I get the following error:
Command output:
Error in make_se_sets_all. dir pseudo_used_ENA_CP029567_CP029567.1 nucl_3328933_3329044
list index out of range
Error in make_se_sets_all. dir pseudo_used_ENA_CP029567_CP029567.1 nucl_3375436_3377156
list index out of range
Error in make_se_sets_all. dir pseudo_used_ENA_CP029567_CP029567.1 nucl_3481197_3481657
list index out of range
Error in make_se_sets_all. dir pseudo_used_ENA_CP029567_CP029567.1 nucl_3785859_3785893
list index out of range
Error in make_se_sets_all. dir pseudo_used_ENA_CP029567_CP029567.1 nucl_3956278_3956881
list index out of range
Error in make_se_sets_all. dir pseudo_used_ENA_CP029567_CP029567.1 nucl_4010576_4011560
list index out of range
Error in make_se_sets_all. dir pseudo_used_ENA_CP029567_CP029567.1 nucl_4018737_4019448
list index out of range
Error in make_se_sets_all. dir pseudo_used_ENA_CP029567_CP029567.1 nucl_4020959_4021133
list index out of range
Error in make_se_sets_all. dir pseudo_used_ENA_CP029567_CP029567.1 nucl_4023623_4024253
list index out of range
Error in make_se_sets_all. dir pseudo_used_ENA_CP029567_CP029567.1 nucl_4093472_4094076
list index out of range
Error in make_se_sets_all. dir pseudo_used_ENA_CP029567_CP029567.1 nucl_4100467_4105660
list index out of range
Error in make_se_sets_all. dir pseudo_used_ENA_CP029567_CP029567.1 nucl_4271700_4271796
list index out of range
Error in make_se_sets_all. dir pseudo_used_ENA_CP029567_CP029567.1 nucl_4313171_4313782
list index out of range
Error in make_se_sets_all. dir pseudo_used_ENA_CP029567_CP029567.1 nucl_4344856_4345464
list index out of range
Error in make_se_sets_all. dir pseudo_used_ENA_CP029567_CP029567.1 nucl_4370863_4371272
list index out of range
Error in make_se_sets_all. dir pseudo_used_ENA_CP029567_CP029567.1 nucl_4414478_4415085
list index out of range
Error in make_se_sets_all. dir pseudo_used_ENA_CP029567_CP029567.1 nucl_4550143_4556044
list index out of range
Error in make_se_sets_all. dir pseudo_used_ENA_CP029567_CP029567.1 nucl_4562903_4563392
list index out of range
Error in make_se_sets_all. dir pseudo_used_ENA_CP029567_CP029567.1 nucl_4563693_4563864
list index out of range
Error in make_se_sets_all. dir pseudo_used_ENA_CP029567_CP029567.1 nucl_4566812_4566973
list index out of range
Error in make_se_sets_all. dir pseudo_used_ENA_CP029567_CP029567.1 nucl_4615514_4615606
list index out of range
Error in make_se_sets_all. dir pseudo_used_ENA_CP029567_CP029567.1 nucl_4834118_4834398
list index out of range
Error in make_se_sets_all. dir pseudo_used_ENA_CP029567_CP029567.1 nucl_4857100_4857156
list index out of range
Error in make_se_sets_all. dir pseudo_used_ENA_CP029567_CP029567.1 nucl_4857637_4857655
list index out of range
Error in make_se_sets_all. dir pseudo_used_ENA_CP029567_CP029567.1 nucl_4894389_4894563
list index out of range
Command error:
Command line argument error: Argument "query". File is not accessible: `./nucl_4313171_4313782/query.fasta'
Command line argument error: Argument "query". File is not accessible: `./nucl_4344856_4345464/query.fasta'
Command line argument error: Argument "query". File is not accessible: `./nucl_4370863_4371272/query.fasta'
Command line arr: Argument "query". File is not accessible: `./nucl_1663958_1669493/query.fasta'
Command line argument error: Argument "query". File is not accessible: `./nucl_1892097_1894787/query.fasta'
Command line argument error: Argument "query". File is not accessible: `./nucl_2177089_2177696/query.fasta'
Command line argument error: Argument "query". File is not accessible: `./nucl_2219687_2220166/query.fasta'
Command line argument error: Argument "query". File is not accessible: `./nucl_2496611_2502210/query.fasta'
Command line argument error: Argument "query". File is not accessible: `./nucl_2535334_2535963/query.fasta'
Command line argument error: Argument "query". File is not accessible: `./nucl_2540192_2541435/query.fasta'
Command line argument error: Argument "query". File is not accessible: `./nucl_2541821_2545685/query.fasta'
Command line argument error: Argument "query". File is not accessible: `./nucl_2695205_2700564/query.fasta'
Command line argument error: Argument "query". File is not accessible: `./nucl_2791127_2796412/query.fasta'
Command line argument error: Argument "query". File is not accessible: `./nucl_2877855_2883756/query.fasta'
Command line argument error: Argument "query". File is not accessible: `./nucl_3213117_3213377/query.fasta'
Command line argument error: Argument "query". File is not accessible: `./nucl_3260582_3261345/query.fasta'
Command line argument error: Argument "query". File is not accessible: `./nucl_3297030_3297896/query.fasta'
Command line argument error: Argument "query". File is not accessible: `./nucl_3323972_3324117/query.fasta'
Command line argument error: Argument "query". File is not accessible: `./nucl_3324408_3326112/query.fasta'
Command line argument error: Argument "query". File is not accessible: `./nucl_3326614_3327904/query.fasta'
Command line argument error: Argument "query". File is not accessible: `./nucl_3328933_3329044/query.fasta'
Command line argument error: Argument "query". File is not accessible: `./nucl_3375436_3377156/query.fasta'
Command line argument error: Argument "query". File is not accessible: `./nucl_3481197_3481657/query.fasta'
Command line argument error: Argument "query". File is not accessible: `./nucl_3785859_3785893/query.fasta'
Command line argument error: Argument "query". File is not accessible: `./nucl_3956278_3956881/query.fasta'
Command line argument error: Argument "query". File is not accessible: `./nucl_4010576_4011560/query.fasta'
Command line argument error: Argument "query". File is not accessible: `./nucl_4018737_4019448/query.fasta'
Command line argument error: Argument "query". File is not accessible: `./nucl_4020959_4021133/query.fasta'
Command line argument error: Argument "query". File is not accessible: `./nucl_4023623_4024253/query.fasta'
Command line argument error: Argument "query". File is not accessible: `./nucl_4093472_4094076/query.fasta'
Command line argument error: Argument "query". File is not accessible: `./nucl_4100467_4105660/query.fasta'
Command line argument error: Argument "query". File is not accessible: `./nucl_4271700_4271796/query.fasta'
Command line argument error: Argument "query". File is not accessible: `./nucl_4313171_4313782/query.fasta'
Command line argument error: Argument "query". File is not accessible: `./nucl_4344856_4345464/query.fasta'
Command line argument error: Argument "query". File is not accessible: `./nucl_4370863_4371272/query.fasta'
Command line argument error: Argument "query". File is not accessible: `./nucl_4414478_4415085/query.fasta'
Command line argument error: Argument "query". File is not accessible: `./nucl_4550143_4556044/query.fasta'
Command line argument error: Argument "query". File is not accessible: `./nucl_4562903_4563392/query.fasta'
Command line argument error: Argument "query". File is not accessible: `./nucl_4563693_4563864/query.fasta'
Command line argument error: Argument "query". File is not accessible: `./nucl_4566812_4566973/query.fasta'
Command line argument error: Argument "query". File is not accessible: `./nucl_4615514_4615606/query.fasta'
Command line argument error: Argument "query". File is not accessible: `./nucl_4834118_4834398/query.fasta'
Command line argument error: Argument "query". File is not accessible: `./nucl_4857100_4857156/query.fasta'
Command line argument error: Argument "query". File is not accessible: `./nucl_4857637_4857655/query.fasta'
Command line argument error: Argument "query". File is not accessible: `./nucl_4894389_4894563/query.fasta'
/opt/conda/lib/python3.6/site-packages/matplotlib/font_manager.py:1331: UserWarning: findfont: Font family ['Arial'] not found. Falling back to DejaVu Sans
(prop.get_family(), self.defaultFamily[fontext]))
/opt/SPADE/visualisation.py:330: UserWarning: Ghostscript was not found. If you want to generate LOGO in pdf format, please install Ghostscript.
For the present, LOGO was output in EPS format
warnings.warn("Ghostscript was not found. If you want to generate LOGO in pdf format, please install Ghostscript.\n For the present, LOGO was output in EPS format")
Could you help me solve the index out of range error?
ponnhide commented
I'm sorry for the inconvenience and the late response.
Since I want to reproduce the above error, could you share the sequence information you used?
mahesh-panchal commented
Hi, I haven't received permission from my collaborators to share the sequence, so I've created a toy sequence that generates the same error.
seq.fasta:
>random sequence
ccgccaagagaatgtatgaataggttgagtataagacagccctatgttcaccgtctgcag
actccggacatggggtcacggagtaaagtcgtgctgagcacataaagtttagccatcagc
ctgaagtactgcagtatgtagagcgtctataggacgcagctctcacatatgtggatcccg
aagctcaactatactgaggagaggtcagtgtccgtagattcgaccgcaccaccgacaact
cccaactgctcggaggtaatcggcgcggggtcgcgagatcttggttgtcgggtgaatttg
attccactctttcgctgtaggcaaattccatttagttgcctccggggatagcctcactaa
tttattttgaaagtgtctgggtacacattagttggctacgccaccacgagcgttaaaccc
aacctcttagcctgggtaccctgactcgctcctccatatttttgattcagctccggcggg
tcaataacccgtggctggcgagactaacggattcccgtgccccagcctcaggcttaaagc
ctctttagaattaggcggtccgatactgagtcagtctaaaaaaatagtttagagtggtcc
atatgacgacctcgcggcattcatggtatttcgctaccgatcccctcctcaggggcacct
atacggcctacgagactaggctactcgggctctcctaagtgccggagaacttaaggcctg
gcccatacaatcctttccccaataagttggaccactatatatgccgtgagacgtcttcta
tccggagaaccaaatgttgggggccaaacaggctaagagttcgagttccgagccttggca
attagctcgatcgggtgaaaaaaagagaagagtccattaagagttacatgttgttttcag
gcgatctggtccacactggtactgtccgtatgcactagctagagttcagtacagttttac
atgcttcttccgtctagagcctatcgcggtctcatcgaagctacagagtaaatagggccg
gactaggatgtgtcccgtccttgtggtttattgagcactccaggcgcttgggtacctgta
ctcagagtaacgaactcgtccagtagcgttctagagttcctaatatatgagtcgaggtcc
tgcgcctaaggaagaaatggtcattatgcgataagtgacccgcttagaaggggtaggagg
taactcaccttggtcaattttaccatctgtacctaaaagtctcctgattagtgtcccgat
atcccacggttaagtcagcannnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnn
nnnnnnnnnnnnnnnnnnnngtactcgagaatgcactcccgacgtgatgatggttcatcg
gaaaacgtacggctaccacggaatactttccactccttaccctacgccggcacgacccga
gaattagacactagcccgaacggcatggagtgcccagaacgtggggacgtaggatgttag
tagaacgtcaataggcgcgggagtctaggtaccgcactgatcatactctatagggtgtcg
caaagcggatattcagaaatgactagtcagcatgcacgtctgatggcgaactcttgggcg
cttggttcttggcgataatccgacatgggatgttcgatacggtcgcggtctgtcccgccg
agatagtgcgggttcgcctcactctgctaaagtctccggtacttgccagactccacatac
tgggtgtgccgaccgaggtggtgcaggaggggtcatacaggacccttgtaccctcctgtt
ccgctcgctgcaaaatggtgtggtaagttcgaggctgttgaggcaatggtcccataaatc
agtgactgaccaccaactactagcggggtgcgggacgataccgactcggccatctgctcc
aggcgttatgtccctagtttcacggtgattagtaaccatttggccaaacagcgaaatact
acaataggaaataccggctattcaaacggctatcgtggatcggccaccgagggtttacgc
ataaagatttcggcattagttctcacctgtgtgccccacgaacgaacaggcttccggtgc
tacgacgctgccagctttctttcgttacataattcttggtgaaaataacattgacctgcg
gctcatcacgtattatcctacgtgaaattcgcctggaagttgtgaaccattaatatagtc
agtgcatttttatcgcagggccagtaacacgcgcgtcgtccattacgctttcatgggtat
ttagacttcaagtattagggttagaaactgagcaagctggctcgtgtggcatccgccacg
cctaacgctctctatagacatcattagaaaggcatctgctatcacagtatgagtgctttc
ctttcctttatacccgtgtgttgactccgttttcaggctgggcccacctcgataacgccc
tatcaacacacagcatttcaatataacccggtagcgaatgcgccttgcggctctcccggg
ccgccgctcacaacaggaagtaacatacgtccggaatccgctgctgggtaattcagttca
taaaggtcactgaagcggaaagggctctcgacgcgagtatcgtctacagctggttccagc
ctaccactccgccgtgtacggactgataccgcttagtagggattgagatgagcggaccat
ggtaatgggttacatattgagctgaattttactcagggcggtattattactatgtttagt
tatccgataagtgttataccgcgtccgaaggtcagtaagattcactacgcaccggtagtg
cagggtcccttttgctctcaggtgacactgcaattctaggcgaggcccattccccgttgg
attaaaacagaactcggcgtatggtttagtttgagcccatatcagcaagatgactgcccc
actgtgtgacccatcaccctaccattgagcctaggtgatcgttgtcaattgctgttcaga
taggagcgcagagcccgaaaacagagtaatatgtcatgtaaccagtcgcgtggtgacatc
tggggtcttcatggtctggatgcccataccaacgcgtagtcgctggtccctacatgcctt
agacacgttatcggccactcnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnn
nnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnn
nnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnn
nnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnn
nnnnnnnnnnnnnnnnnnnnggtatttgcgtggatatccatagtcgatccttgcggcaag
tcctacactgacatccccgaactccgtccattatgctcaaactatatcaccttggggcgc
caaggcatccataatgacctaagattttgtagccccccgccgcaacttgacgctcgaacg
acctatgcccggctctcagcttaacacgggtcggttatcataaaacgataaagagaaccg
tgttttgggcacgtgaggagcgccacgctccgacgcctatctaaccaatctatacgtaca
ggaagggcccaatgagtgtgcatagcgatgctgcgtttccagtacagtccatctccgcct
ctaatagggcacgccaccgcaccttgagctacggtgcccgcgaaaccgtagatgcggttt
gaacttggcagcgttattgccgaaccagcacgtgcgttgggtttatcatacgatggctgt
ttagggacatagtgggatcactagtattagcccttcacgtcttttcaggtgtagtaaaaa
actttgagcaacgttcttcgttaaacatacatgctgaaactcacgtggccgacatcccct
ctcacaagcgagtctttgtacattgatacgtgaagttgccctcctaactttaaagaagca
tgccacgatttcggtaagctttgcaaaaacaacgggcaaccttcagctgcctctcataag
atagcgcatgcttggcccccgcgctttcatagtcagaaacaacccctttcacccacatat
gtagactaaggtctgtccgagtgacagacagttttacggcacagattgtacgacgcctcc
gtctatcttacgtggttccccgatattcatggggtgcggtgctgacacaagctcttttat
aaggcatgatgaatgggtcctagacgctctgtggttccaactggtttttgcgtagtcgtt
tttagataagatatacccgccccttcctcccgaggcaactaggactgtaagcatgtacac
cggtactaccccttaggaatgtcacttcttgtcttggatatcgtctagcgcttgactcca
ctgcgcagttttgtgtagggttaccgatctaacaaaactgacggccctttgacgcccgca
aggggctccactcttacgagcctcagggaaagagattcagcacctgcgcactatggaggt
acaatttccgattcagtatcccatttacagataagcttggaaaccccagtcgctcattag
tggcaacgtgaagaccgaattcattcaatgccgatatccgccgtccgtgaattggtttca
acgtcgcccagtgtccgtcaggctcgaatggataacgcacgcctacgctatatgttgaca
aataaactactacacctctgaccatttactccaaattaacccatttgctatcgatcattt
ggagaaggcctttcacagataaagcacaccatttattctaccccgaaggcagcgttctac
gactgccccgctcccgatattggcatagcttcgaggtcagaataagtgagattacaccac
gcgcggggccaaacaccagggagtctcgcattttcttgtattgctgtgtttagagagaca
attgagtttccgagtgcggagttgtgagttttatcttgacttaatactcctctcgagcta
acgcagtgagcgtctcacaaccagcttaattcgcatcatcggacattccttgtgaacaat
cgatcgcccacaacgagtcccgctaggggcttgtgtagatatctggaaccagttacaaat
cagatatacagcactgtgttggcttactactgaagaacagatggcaccgtaagtcgcggc
agcgttttcgaaactagctgtgagaccaagcgatctaagtggcagcatagcttggacggg
ctatgcacgaagccacgctc
This is the command line instruction:
SPADE.py -i seq.fasta -f fasta -t nucl -d -n 4Error:
Error in decide_query_all. dir random nucl_1280_1340
No counts.
Error in decide_query_all. dir random nucl_3140_3380
No counts.
Command line argument error: Argument "query". File is not accessible: `./nucl_1280_1340/query.fasta'
Command line argument error: Argument "query". File is not accessible: `./nucl_3140_3380/query.fasta'
Error in make_se_sets_all. dir random nucl_1280_1340
list index out of range
Error in make_se_sets_all. dir random nucl_3140_3380
list index out of range
ponnhide commented
I ran SPADE for the given sequence and faced the above error. There was a problem with the N-nucleotide manipulation, so I fixed it and updated the repository. Could you re-clone the git repository and run again?
mahesh-panchal commented
Hi, I'm still facing similar errors with my real dataset, after pulling the updated code.
The errors are reduced, but still present.
Command executed:
SPADE.py -i DA34821_pseudomolecule.fasta -f fasta -t nucl -d -n 4
Command exit status:
0
Command output:
Error in decide_query_all. dir pseudo_used_ENA_CP029567_CP029567.1 nucl_192268_193122
No counts.
Error in decide_query_all. dir pseudo_used_ENA_CP029567_CP029567.1 nucl_513395_513988
No counts.
Error in decide_query_all. dir pseudo_used_ENA_CP029567_CP029567.1 nucl_1137245_1138409
No counts.
Error in decide_query_all. dir pseudo_used_ENA_CP029567_CP029567.1 nucl_2219687_2220166
No counts.
Error in decide_query_all. dir pseudo_used_ENA_CP029567_CP029567.1 nucl_3481197_3481657
No counts.
Error in decide_query_all. dir pseudo_used_ENA_CP029567_CP029567.1 nucl_3956278_3956881
No counts.
Error in decide_query_all. dir pseudo_used_ENA_CP029567_CP029567.1 nucl_4370863_4371272
No counts.
Error in make_se_sets_all. dir pseudo_used_ENA_CP029567_CP029567.1 nucl_192268_193122
list index out of range
Error in make_se_sets_all. dir pseudo_used_ENA_CP029567_CP029567.1 nucl_513395_513988
list index out of range
Error in make_se_sets_all. dir pseudo_used_ENA_CP029567_CP029567.1 nucl_1137245_1138409
list index out of range
Error in make_se_sets_all. dir pseudo_used_ENA_CP029567_CP029567.1 nucl_2219687_2220166
list index out of range
Error in make_se_sets_all. dir pseudo_used_ENA_CP029567_CP029567.1 nucl_3481197_3481657
list index out of range
Error in make_se_sets_all. dir pseudo_used_ENA_CP029567_CP029567.1 nucl_3956278_3956881
list index out of range
Error in make_se_sets_all. dir pseudo_used_ENA_CP029567_CP029567.1 nucl_4370863_4371272
list index out of range
Command error:
Command line argument error: Argument "query". File is not accessible: `./nucl_192268_193122/query.fasta'
Command line argument error: Argument "query". File is not accessible: `./nucl_513395_513988/query.fasta'
Command line argument error: Argument "query". File is not accessible: `./nucl_1137245_1138409/query.fasta'
Command line argument error: Argument "query". File is not accessible: `./nucl_2219687_2220166/query.fasta'
Command line argument error: Argument "query". File is not accessible: `./nucl_3481197_3481657/query.fasta'
Command line argument error: Argument "query". File is not accessible: `./nucl_3956278_3956881/query.fasta'
Command line argument error: Argument "query". File is not accessible: `./nucl_4370863_4371272/query.fasta'
/opt/conda/lib/python3.6/site-packages/matplotlib/font_manager.py:1331: UserWarning: findfont: Font family ['Arial'] not found. Falling back to DejaVu Sans
(prop.get_family(), self.defaultFamily[fontext]))
Do lines 93, 108, and 189, also need to be changed from 'DNA' to 'nucl'?
ponnhide commented
Yes..., I was so ashamed. I updated the repository, so could you retry? I'm sorry for the inconvenience.
mahesh-panchal commented
Thank you for working on it so quickly. It seems to work now.