Problems with Tplots

[pbaldrich]

Hi,
I am running CleaveLand 4.5 with some Rice public data with no trouble. However, as soon as I ask for the Tplots to be generated I get an error. Here is the commands and the output.

Thank you in advance for your help.

This command works perfect:
./CleaveLand4-master/CleaveLand4.pl -e BSS_m18.fastq.fa -u miR75_T.fa -n MSU7_cDNA.fa -t > BSSAll_MSU7_cDNA.txt

This command give me error:
./CleaveLand4-master/CleaveLand4.pl -e BSS_m18.fastq.fa -u miR75_T.fa -n MSU7_cDNA.fa -o TplotsAll -t > BSSAll_MSU7_cDNA.txt

CleaveLand4 version 4.5
Mon Jun 1 13:44:48 CDT 2020

Mode: 1
Checking Dependencies
bowtie: PASS: /usr/local/bowtie-1.2.3-linux-x86_64/bowtie
bowtie-build: PASS: /usr/local/bowtie-1.2.3-linux-x86_64/bowtie-build
RNAplex: PASS RNAplex 2.1.1
GSTAr: PASS GSTAr.pl version 1.0
samtools: PASS Version: 1.5 (using htslib 1.5)
R: PASS R version 3.2.1 (2015-06-18) -- "World-Famous Astronaut"

Created directory TplotsAll for T-plots.

Initiating alignment of degradome reads to transcriptome.
Bowtie index files for MSU7_cDNA.fa PRESENT

reads processed: 100638282

reads with at least one reported alignment: 71749113 (71.29%)

reads that failed to align: 28889169 (28.71%)

Reported 71749113 alignments
Alignments complete. Generating degradome density file.
Degradome density file completed ... BSS_m18.fastq.fa_dd.txt
Loaded degradome density data from file BSS_m18.fastq.fa_dd.txt
Transcriptome: MSU7_cDNA.fa
Initiating GSTAr run.
GSTAr command is GSTAr.pl -t miR75_T.fa MSU7_cDNA.fa > miR75_T.fa_GSTAr.txt

GSTAr version 1.0
Mon Jun 1 14:32:36 CDT 2020

Dependency checks:
RNAplex: PASS RNAplex 2.1.1

Hashing the transcriptome data... Done

Working on query miR-75-5p_1 ... Found 148 valid alignments
Working on query miR-75-5p_2 ... Found 324 valid alignments
Working on query miR-75-5p_3 ... Found 816 valid alignments
Working on query miR-75-5p_4 ... Found 425 valid alignments
Working on query miR-75_3p_1 ... Found 156 valid alignments
Working on query miR-75_3p_2 ... Found 240 valid alignments
Working on query miR-75_3p_3 ... Found 205 valid alignments
Working on query miR-75_3p_4 ... Found 159 valid alignments
Working on query miR-75_3p_5 ... Found 378 valid alignments

GSTAr run complete
Loaded GSTAr alignment file miR75_T.fa_GSTAr.txt
Transcriptome: MSU7_cDNA.fa
Queries: miR75_T.fa
Ranked by: MFEratio

Beginning analysis phase...

Finished with Query: miR-75-5p_1
Finished with Query: miR-75-5p_2
Finished with Query: miR-75-5p_3
Finished with Query: miR-75-5p_4
Finished with Query: miR-75_3p_1
Finished with Query: miR-75_3p_2
Finished with Query: miR-75_3p_3
Finished with Query: miR-75_3p_4
Finished with Query: miR-75_3p_5

Found a total of 90 non-redundant putative slicing sites with p-values <= 1 and categories <= 4. Outputting results.
sh: aspartic_proteinase_oryzasin-1_precursor,_putative,_expressed_1159_TPlot.pdf: command not found
Error: ignoring SIGPIPE signal

[MikeAxtell]

Based on the errors,
sh: aspartic_proteinase_oryzasin-1_precursor,_putative,_expressed_1159_TPlot.pdf: command not found Error: ignoring SIGPIPE signal
, this is likely due to the names of the cDNAs you are using. If the cDNA names have characters with special meaning in the shell (like SPACE and | , for instance), that will break the process. Suggest to rename cDNAs to remove spaces, pipes, commas, and anything else that might be interpreted as a special shell character. Simple gene names like 'AT1G12345' are the best.

[pbaldrich]

Thank you Mike! I fixed the names as you suggested and it worked.

Stay safe!
Pat