Long ids in fasta query cause issues in GSTAr phase

[juancresc]

Just in case this happens to someone, when the query miRNA file has long names (ids) there's an issue in the analysis phase, and the results file is then incomplete.

This is solved by shorten the name of the queries

Checking Dependencies
	bowtie: PASS: /home/juan/Desktop/juan/bio/sw/bowtie-1.2.2-linux-x86_64/bowtie
	bowtie-build: PASS: /home/juan/Desktop/juan/bio/sw/bowtie-1.2.2-linux-x86_64/bowtie-build
	RNAplex: PASS RNAplex 2.4.11
	GSTAr: PASS GSTAr.pl version 1.0
	samtools: PASS Version: 1.2 (using htslib 1.2.1)
	R: PASS R version 3.4.4 (2018-03-15) -- "Someone to Lean On"

T-plot directory /home/juan/Desktop/juan/bio/mirna_mite/data/res/sun_plots/SRR1197125 already exists, new T-plots will be placed there.

Initiating alignment of degradome reads to transcriptome.
Bowtie index files for /home/juan/Desktop/juan/bio/mirna_mite/data/fixed.cdna.all.fa PRESENT
# reads processed: 18494868
# reads with at least one reported alignment: 11870760 (64.18%)
# reads that failed to align: 6624108 (35.82%)
Reported 11870760 alignments
[bam_sort_core] merging from 5 files...
Alignments complete. Generating degradome density file.
Degradome density file completed ... /home/juan/Desktop/juan/bio/mirna_mite/data/sun/degradome/SRR1197125.trimmed.21.fasta_dd.txt
Loaded degradome density data from file /home/juan/Desktop/juan/bio/mirna_mite/data/sun/degradome/SRR1197125.trimmed.21.fasta_dd.txt
	Transcriptome: /home/juan/Desktop/juan/bio/mirna_mite/data/fixed.cdna.all.fa
Initiating GSTAr run.
GSTAr command is GSTAr.pl -t /home/juan/Desktop/juan/bio/mirna_mite/data/res/mirna.y.trep.fasta /home/juan/Desktop/juan/bio/mirna_mite/data/fixed.cdna.all.fa > /home/juan/Desktop/juan/bio/mirna_mite/data/res/mirna.y.trep.fasta_GSTAr.txt


GSTAr version 1.0
jue jul 25 13:32:03 -03 2019

Dependency checks:
	RNAplex: PASS RNAplex 2.4.11


Hashing the transcriptome data... Done

Working on query sun_all_Cluster_8835 1B:161992200-161992280 ... Found 327 valid alignments
Working on query mrcv_all_Cluster_2513 1B:565664575-565664794 ... Found 1497 valid alignments
Working on query mrcv_mites_MITE_T_120271|chr2D|74975911|74975992|TA|85|F5488 1D:147896240-147896319 ... Found 5050 valid alignments
Working on query sun_mites_MITE_T_99232|chr3B|765723509|765723619|TA|116|F4321 2A:133702671-133702770 ... Found 510 valid alignments
Working on query mrcv_mites_MITE_T_102616|chr1B|301273397|301273500|TA|109|F4546 2A:168984136-168984233 ... Found 275 valid alignments
Working on query sun_all_Cluster_28681 2B:5671327-5671460 ... Found 433 valid alignments
Working on query sun_mites_MITE_T_100846|chr5D|282007012|282007117|AGT|113|F4436 2B:207058615-207058716 ... Found 3785 valid alignments
Working on query sun_all_Cluster_33132 2B:482720682-482720772 ... Found 945 valid alignments
Working on query mrcv_all_Cluster_8534 2B:720801630-720801713 ... Found 2082 valid alignments
Working on query mrcv_mites_MITE_T_105526|chr3A|638201844|638201940|AA|97|F4730 3A:19302861-19302943 ... Found 3552 valid alignments
Working on query mrcv_all_Cluster_12767 3A:746087222-746087306 ... Found 8030 valid alignments
Working on query mrcv_mites_MITE_T_120628|chr4D|230912845|230912926|TA|86|F5513 3B:253488744-253488823 ... Found 839 valid alignments
Working on query mrcv_all_Cluster_13743 3B:587564305-587564383 ... Found 2387 valid alignments
Working on query mrcv_mites_MITE_T_110611|chr6B|503544571|503544661|TA|94|F5029 3D:472405006-472405092 ... Found 531 valid alignments
Working on query mrcv_mites_MITE_T_121053|chr7D|349263971|349264052|TA|85|F5551 3D:508204974-508205052 ... Found 4383 valid alignments
Working on query mrcv_mites_MITE_T_21345|chr5D|55587099|55587407|TT|100|F866 4A:67171695-67171971 ... Found 1826 valid alignments
Working on query mrcv_mites_MITE_T_37538|chr7B|129805762|129806026|AT|279|F1550 4B:429353827-429354091 ... Found 1078 valid alignments
Working on query sun_all_Cluster_82408 4D:142764794-142764971 ... Found 1115 valid alignments
Working on query mrcv_mites_MITE_T_95924|chr2B|774087848|774087962|TA|122|F4206 5A:552632192-552632284 ... Found 2460 valid alignments
Working on query GGGACG ...
	WARNING: query sequence GGGACG has non AUTGC characters. It is not being analyzed!
Working on query UUGUAGAGCUUUCAUUAUGGA ...
	WARNING: query sequence UUGUAGAGCUUUCAUUAUGGA has non AUTGC characters. It is not being analyzed!
Working on query UUUGGACAUCUGACAAGCUCU ...
	WARNING: query sequence UUUGGACAUCUGACAAGCUCU has non AUTGC characters. It is not being analyzed!
Working on query UUAGAGGUUUCAAUACGGACU ...
	WARNING: query sequence UUAGAGGUUUCAAUACGGACU has non AUTGC characters. It is not being analyzed!
Working on query UUAGAGAUUUCAAUGUGGAUU ...
	WARNING: query sequence UUAGAGAUUUCAAUGUGGAUU has non AUTGC characters. It is not being analyzed!
Working on query AGAUGACCAAAUGAGCUGAAACUU ...
	WARNING: query sequence AGAUGACCAAAUGAGCUGAAACUU has non AUTGC characters. It is not being analyzed!
Working on query AUGACGAGUAAAUCAGAACGG ...
	WARNING: query sequence AUGACGAGUAAAUCAGAACGG has non AUTGC characters. It is not being analyzed!
Working on query CUUCUGAUUUACUCGUCGUGG ...
	WARNING: query sequence CUUCUGAUUUACUCGUCGUGG has non AUTGC characters. It is not being analyzed!
Working on query UGUCGUAGAUUUGUCUAGAUA ...
	WARNING: query sequence UGUCGUAGAUUUGUCUAGAUA has non AUTGC characters. It is not being analyzed!
Use of uninitialized value in uc at /home/juan/Desktop/juan/bio/mirna_mite/sw/CleaveLand4/GSTAr_v1-0/GSTAr.pl line 97, <QUERIES> line 57.
Working on query UGGCAAAUCUAGUUGGUGAGC ...
	WARNING: query sequence UGGCAAAUCUAGUUGGUGAGC has non AUTGC characters. It is not being analyzed!


GSTAr run complete
Loaded GSTAr alignment file /home/juan/Desktop/juan/bio/mirna_mite/data/res/mirna.y.trep.fasta_GSTAr.txt
	Transcriptome: /home/juan/Desktop/juan/bio/mirna_mite/data/fixed.cdna.all.fa
	Queries: /home/juan/Desktop/juan/bio/mirna_mite/data/res/mirna.y.trep.fasta
	Ranked by: MFEratio

Beginning analysis phase...

Finished with Query: sun_all_Cluster_8835 1B:161992200-161992280
Finished with Query: mrcv_all_Cluster_2513 1B:565664575-565664794
Finished with Query: mrcv_mites_MITE_T_120271|chr2D|74975911|74975992|TA|85|F5488 1D:147896240-147896319
Finished with Query: sun_mites_MITE_T_99232|chr3B|765723509|765723619|TA|116|F4321 2A:133702671-133702770
Finished with Query: mrcv_mites_MITE_T_102616|chr1B|301273397|301273500|TA|109|F4546 2A:168984136-168984233
Finished with Query: sun_all_Cluster_28681 2B:5671327-5671460
Finished with Query: sun_mites_MITE_T_100846|chr5D|282007012|282007117|AGT|113|F4436 2B:207058615-207058716
Finished with Query: sun_all_Cluster_33132 2B:482720682-482720772
Finished with Query: mrcv_all_Cluster_8534 2B:720801630-720801713
Finished with Query: mrcv_mites_MITE_T_105526|chr3A|638201844|638201940|AA|97|F4730 3A:19302861-19302943
Finished with Query: mrcv_all_Cluster_12767 3A:746087222-746087306
Finished with Query: mrcv_mites_MITE_T_120628|chr4D|230912845|230912926|TA|86|F5513 3B:253488744-253488823
Finished with Query: mrcv_all_Cluster_13743 3B:587564305-587564383
Finished with Query: mrcv_mites_MITE_T_110611|chr6B|503544571|503544661|TA|94|F5029 3D:472405006-472405092
Finished with Query: mrcv_mites_MITE_T_121053|chr7D|349263971|349264052|TA|85|F5551 3D:508204974-508205052
Finished with Query: mrcv_mites_MITE_T_21345|chr5D|55587099|55587407|TT|100|F866 4A:67171695-67171971
Finished with Query: mrcv_mites_MITE_T_37538|chr7B|129805762|129806026|AT|279|F1550 4B:429353827-429354091
Finished with Query: sun_all_Cluster_82408 4D:142764794-142764971
Finished with Query: mrcv_mites_MITE_T_95924|chr2B|774087848|774087962|TA|122|F4206 5A:552632192-552632284

Found a total of 503 non-redundant putative slicing sites with p-values <= 1 and categories <= 4. Outputting results.
sh: 1: chr5D: not found
sh: 1: sh: 1: 282007012: not found282007117: not found

sh: 1: AGT: not found
sh: 1: 113: not found
sh: 1: F4436: not found
sh: 1: chr5D: not found
sh: 1: 282007117: not found
sh: 1: 282007012: not found
sh: 1: 113: not found
sh: 1: AGT: not found
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