panchyni
commented
1 year ago Hello,
Thanks for reaching out to us. Unfortunately, this appears to be an issue with RepeatMasker itself as the program is not running properly and might be related to an issue with the recent conda build (see https://github.com/rmhubley/RepeatMasker/issues/221). If you can, I would wait until you can get the official version and try that.
Nick
On Mon, Jun 26, 2023 at 1:40 PM Wenwen @.***> wrote:
Dear @panchyni https://github.com/panchyni @shinhanshiu https://github.com/shinhanshiu
Hello there! This is a very good tool that suits my needs very well and I look forward to referencing it later. I'm having a RepeatMasker problem while running the test pipeline for PseudogenePipeline, please review? I have the conda version of RepeatMasker. Due to internet speed problems I may not be able to get the official version until two days later. Anyway, I'm not quite sure what the problem is at the moment.
(base) @.***:~/tool/PseudogenePipeline-master/_test25$ python ~/tool/PseudogenePipeline-master/_scripts/PseudogenePipeline.py test_parameter_file here
Step 0: read, check, and set parameters
Check parameter file... Check names among genome/protein seq, and blast output Determining intron length using provided 95th percentile intron length 95th percentile intron legnth is 456 Set default values default: ev_t=5 default: id_t=40 default: ml_t=30 default: ml_p=0.05
Step 1. Filtering BLAST output...
Filter test_prot25_tblastn6... E:5 I:40 L:30 P:0.05
Step 2. Get pseudoexon
Pseudoexon file: test_prot25_tblastn6_parsed_G456.PE
Step 3. Get phase 1 pseudogene
Get initial phase 1 pseudogene phase1 file: test_prot25_tblastn6_parsed_G456.PE_I456.PS1 Get pair file and subject coordinates pair file: test_prot25_tblastn6_parsed_G456.PE_I456.PS1.pairs coordinates file:test_prot25_tblastn6_parsed_G456.PE_I456.PS1.subj_coord Get phase 1 pseudogene sequences phase 1 seq: test_prot25_tblastn6_parsed_G456.PE_I456.PS1.subj_coord.fa
Step 4. Get Smith-Waterman alignments with fasta
Find stop and framshifts
here Program : tfasty36 Pair list: test_prot25_tblastn6_parsed_G456.PE_I456.PS1.pairs Fasta1 : test_prot25.fa Fasta2 : test_prot25_tblastn6_parsed_G456.PE_I456.PS1.subj_coord.fa Fasta dir: /home/w/tool/fasta36-36.3.8/bin Working d: tmp_1687798035.136786/ Flags : -m 3 -q E thres : 1.0 Read gene pairs... 52 pairs Read fasta files... Do sw... 0 x 100
Done! smith-Waterman outputs: test_prot25_tblastn6_parsed_G456.PE_I456.PS1_pairs.sw* Read BLOSUM50 matrix... Read the sw.out file... Compare sequences: total: 52 alignments 0.0 Done! disable_count file: test_prot25_tblastn6_parsed_G456.PE_I456.PS1.pairs.sw.out.disable_count
Step 5. Convert coordinates
Convert S-W coordinates to genome-based ones processed Disable_count file: test_prot25_tblastn6_parsed.4col Process Maker format GFF if necessary
Step 6. Determine overlap with annotated genes
Find Overlaps between predicted pseudogenes and genes output: test_prot25_tblastn6_parsed.4col.onlyoverlap overlap file: test_prot25_tblastn6_parsed.4col.onlyoverlap Do not filter pseudogene predictions overlapping with genes output file: test_prot25_tblastn6_parsed.fullyFiltered.disable_count
Step 7. Repeat masking
Repeat masking prep here Sequence to dict... Read coordinates... 0 k shortened name file: test_prot25_tblastn6_parsed.4col.true.fa.mod 2 col reference file: test_prot25_tblastn6_parsed.4col.true.fa.ref
Run RepeatMasker /home/w/miniconda3/pkgs/repeatmasker-4.1.5-pl5321hdfd78af_0/share/RepeatMasker/RepeatMasker: 45: =head1: not found /home/w/miniconda3/pkgs/repeatmasker-4.1.5-pl5321hdfd78af_0/share/RepeatMasker/RepeatMasker: 47: RepeatMasker: not found /home/w/miniconda3/pkgs/repeatmasker-4.1.5-pl5321hdfd78af_0/share/RepeatMasker/RepeatMasker: 49: =head1: not found /home/w/miniconda3/pkgs/repeatmasker-4.1.5-pl5321hdfd78af_0/share/RepeatMasker/RepeatMasker: 51: Syntax error: "(" unexpected
Parse RepeatMasker output Traceback (most recent call last): File "/home/w/tool/PseudogenePipeline-master/_test25/../_scripts/parse_RepeatMasker_gff.py", line 5, in
file1=open(sys.argv[1],'r') FileNotFoundError: [Errno 2] No such file or directory: 'test_prot25_tblastn6_parsed.4col.true.fa.mod.mod.out' Traceback (most recent call last): File "/home/w/tool/PseudogenePipeline-master/_test25/../_scripts/1_3_removeCodeNamesFromRM4col.py", line 9, in four = open(sys.argv[1]) #4input coded file FileNotFoundError: [Errno 2] No such file or directory: 'test_prot25_tblastn6_parsed.4col.true.fa.mod.mod.out.300Cutoff30.0divg.4col' Get simple repeats grep: test_prot25_tblastn6_parsed.4col.true.fa.mod.mod.out.300Cutoff30.0divg.4col.longNames: 没有那个文件或目录
Filter out repeats disable_count output file: test_prot25_tblastn6_parsed.fullyFiltered.disable_count.RMfilt 4col format output file: test_prot25_tblastn6_parsed.4col.true.RMfilt fasta format output file: test_prot25_tblastn6_parsed.4col.true.fa.RMfilt repeat Masked files end with '.RMfilt'
Step 8. Run high-confidence filter
Get genome and protein sequence sizes here Total length: 18585056 here Total length: 10253
Run High-Confidence Filter high-Confidence files: '.hiConf'
Replace gene-names here name corrected files end with '.cdnm'
Write Pseudogene GFF GFF files: test_prot25_tblastn6_parsed.4col.true.fa.ref test_prot25_tblastn6_parsed.4col.true.RMfilt.hiConf.cdnm.gff
Step 9. Clean up
Removing temporary genome and protein sequences files Moving intermediate files to _intermediate Move hiConf, codename and gff files to _results Move log files to _logs
Done!!!
log 1.txt https://github.com/ShiuLab/PseudogenePipeline/files/11872123/log.1.txt
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Wenwen012345
Dear @panchyni @shinhanshiu
Hello there! This is a very good tool that suits my needs very well and I look forward to referencing it later. I'm having a RepeatMasker problem while running the test pipeline for PseudogenePipeline, please review? I have the conda version of RepeatMasker. Due to internet speed problems I may not be able to get the official version until two days later. Anyway, I'm not quite sure what the problem is at the moment.
test_parameter_file.txt