Multiple bugfix

.gitignore

@@ -128,22 +128,19 @@ dmypy.json
 # Pyre type checker
 .pyre/
 example/Homo_sapiens.GRCh38.dna.chromosome.13.fa
-example/SQANTI3_output/STAR_index/SA
-example/SQANTI3_output/STAR_index/SAindex
+# SQANTI example big output files
+example/SQANTI3_QC_output/STAR_index/SA
+example/SQANTI3_QC_output/STAR_index/SAindex
 
 # PyCharm
 .idea/
 
 .emacs.bak/
 
-/example/SQANTI3_output/
-
 # Hidden directories
 .pytest_cache
 .vscode
 #Examples Pablo
-/example/SQANTI3_QC_output2
-/example/run_sqanti3_pablo.sh
 sqanti_qc.out
 /pablo_tests
 /wiki

example/SQANTI3_QC_output/GMST/GMST_tmp

@@ -1,5 +1,5 @@
 GeneMark.hmm PROKARYOTIC (Version 3.20)
-Date: Tue Dec 10 17:23:36 2024
+Date: Wed Jan 29 15:06:55 2025
 Sequence file name: /home/pabloati/Programs/sqanti3/example/SQANTI3_QC_output/UHR_chr22_corrected.fasta
 Model file name: GeneMark_hmm.mod
 RBS: true

example/SQANTI3_QC_output/STAR_index/Log.out

@@ -1,35 +1,35 @@
 STAR version=2.7.11b
 STAR compilation time,server,dir=2024-11-25T09:14:51+0000 :/opt/conda/conda-bld/star_1732525954305/work/source
 ##### Command Line:
-/home/pabloati/miniforge3/envs/sqanti3/bin/STAR-avx2 --runThreadN 4 --runMode genomeGenerate --genomeDir /home/pabloati/Programs/sqanti3/example/SQANTI3_QC_output/STAR_index/ --genomeFastaFiles /home/pabloati/Programs/sqanti3/example/GRCh38.p13_chr22.fasta --outTmpDir /home/pabloati/Programs/sqanti3/example/SQANTI3_QC_output/STAR_index//_STARtmp/
+/home/pabloati/miniforge3/envs/sqanti3/bin/STAR-avx2 --runThreadN 4 --runMode genomeGenerate --genomeDir example/SQANTI3_QC_output/STAR_index/ --genomeFastaFiles example/GRCh38.p13_chr22.fasta --outTmpDir example/SQANTI3_QC_output/STAR_index//_STARtmp/
 ##### Initial USER parameters from Command Line:
-outTmpDir                         /home/pabloati/Programs/sqanti3/example/SQANTI3_QC_output/STAR_index//_STARtmp/
+outTmpDir                         example/SQANTI3_QC_output/STAR_index//_STARtmp/
 ###### All USER parameters from Command Line:
 runThreadN                    4     ~RE-DEFINED
 runMode                       genomeGenerate        ~RE-DEFINED
-genomeDir                     /home/pabloati/Programs/sqanti3/example/SQANTI3_QC_output/STAR_index/     ~RE-DEFINED
-genomeFastaFiles              /home/pabloati/Programs/sqanti3/example/GRCh38.p13_chr22.fasta        ~RE-DEFINED
-outTmpDir                     /home/pabloati/Programs/sqanti3/example/SQANTI3_QC_output/STAR_index//_STARtmp/     ~RE-DEFINED
+genomeDir                     example/SQANTI3_QC_output/STAR_index/     ~RE-DEFINED
+genomeFastaFiles              example/GRCh38.p13_chr22.fasta        ~RE-DEFINED
+outTmpDir                     example/SQANTI3_QC_output/STAR_index//_STARtmp/     ~RE-DEFINED
 ##### Finished reading parameters from all sources
 
 ##### Final user re-defined parameters-----------------:
 runMode                           genomeGenerate   
 runThreadN                        4
-genomeDir                         /home/pabloati/Programs/sqanti3/example/SQANTI3_QC_output/STAR_index/
-genomeFastaFiles                  /home/pabloati/Programs/sqanti3/example/GRCh38.p13_chr22.fasta   
-outTmpDir                         /home/pabloati/Programs/sqanti3/example/SQANTI3_QC_output/STAR_index//_STARtmp/
+genomeDir                         example/SQANTI3_QC_output/STAR_index/
+genomeFastaFiles                  example/GRCh38.p13_chr22.fasta   
+outTmpDir                         example/SQANTI3_QC_output/STAR_index//_STARtmp/
 
 -------------------------------
 ##### Final effective command line:
-/home/pabloati/miniforge3/envs/sqanti3/bin/STAR-avx2   --runMode genomeGenerate      --runThreadN 4   --genomeDir /home/pabloati/Programs/sqanti3/example/SQANTI3_QC_output/STAR_index/   --genomeFastaFiles /home/pabloati/Programs/sqanti3/example/GRCh38.p13_chr22.fasta      --outTmpDir /home/pabloati/Programs/sqanti3/example/SQANTI3_QC_output/STAR_index//_STARtmp/
+/home/pabloati/miniforge3/envs/sqanti3/bin/STAR-avx2   --runMode genomeGenerate      --runThreadN 4   --genomeDir example/SQANTI3_QC_output/STAR_index/   --genomeFastaFiles example/GRCh38.p13_chr22.fasta      --outTmpDir example/SQANTI3_QC_output/STAR_index//_STARtmp/
 ----------------------------------------
 
 Number of fastq files for each mate = 1
 ParametersSolo: --soloCellFilterType CellRanger2.2 filtering parameters:  3000 0.99 10
 Finished loading and checking parameters
---genomeDir directory exists and will be overwritten: /home/pabloati/Programs/sqanti3/example/SQANTI3_QC_output/STAR_index/
-Dec 10 17:02:16 ... starting to generate Genome files
-/home/pabloati/Programs/sqanti3/example/GRCh38.p13_chr22.fasta : chr # 0  "chr22" chrStart: 0
+--genomeDir directory exists and will be overwritten: example/SQANTI3_QC_output/STAR_index/
+Jan 29 15:06:56 ... starting to generate Genome files
+example/GRCh38.p13_chr22.fasta : chr # 0  "chr22" chrStart: 0
 Chromosome sequence lengths: 
 chr22	50818468
 Genome sequence total length = 50818468
@@ -38,6 +38,25 @@ Genome size with padding = 50855936
 Estimated genome size with padding and SJs: total=genome+SJ=251855936 = 50855936 + 201000000
 GstrandBit=32
 Number of SA indices: 78319554
-Dec 10 17:02:17 ... starting to sort Suffix Array. This may take a long time...
+Jan 29 15:06:57 ... starting to sort Suffix Array. This may take a long time...
 Number of chunks: 4;   chunks size limit: 208852144 bytes
-Dec 10 17:02:17 ... sorting Suffix Array chunks and saving them to disk...
+Jan 29 15:06:57 ... sorting Suffix Array chunks and saving them to disk...
+Writing 208178008 bytes into example/SQANTI3_QC_output/STAR_index//SA_0 ; empty space on disk = 140059475968 bytes ... done
+Writing 206604960 bytes into example/SQANTI3_QC_output/STAR_index//SA_1 ; empty space on disk = 139851251712 bytes ... done
+Writing 203895040 bytes into example/SQANTI3_QC_output/STAR_index//SA_2 ; empty space on disk = 139644608512 bytes ... done
+Writing 7878424 bytes into example/SQANTI3_QC_output/STAR_index//SA_3 ; empty space on disk = 139440717824 bytes ... done
+Jan 29 15:07:33 ... loading chunks from disk, packing SA...
+Jan 29 15:07:34 ... finished generating suffix array
+Jan 29 15:07:34 ... generating Suffix Array index
+Jan 29 15:07:48 ... completed Suffix Array index
+Jan 29 15:07:48 ... writing Genome to disk ...
+Writing 50855936 bytes into example/SQANTI3_QC_output/STAR_index//Genome ; empty space on disk = 140059385856 bytes ... done
+SA size in bytes: 323068164
+Jan 29 15:07:48 ... writing Suffix Array to disk ...
+Writing 323068164 bytes into example/SQANTI3_QC_output/STAR_index//SA ; empty space on disk = 140008529920 bytes ... done
+Jan 29 15:07:48 ... writing SAindex to disk
+Writing 8 bytes into example/SQANTI3_QC_output/STAR_index//SAindex ; empty space on disk = 139685457920 bytes ... done
+Writing 120 bytes into example/SQANTI3_QC_output/STAR_index//SAindex ; empty space on disk = 139685457920 bytes ... done
+Writing 1565873491 bytes into example/SQANTI3_QC_output/STAR_index//SAindex ; empty space on disk = 139685453824 bytes ... done
+Jan 29 15:07:49 ..... finished successfully
+DONE: Genome generation, EXITING

example/SQANTI3_QC_output/STAR_index/genomeParameters.txt

@@ -0,0 +1,19 @@
+### /home/pabloati/miniforge3/envs/sqanti3/bin/STAR-avx2   --runMode genomeGenerate      --runThreadN 4   --genomeDir example/SQANTI3_QC_output/STAR_index/   --genomeFastaFiles example/GRCh38.p13_chr22.fasta      --outTmpDir example/SQANTI3_QC_output/STAR_index//_STARtmp/
+### GstrandBit 32
+versionGenome	2.7.4a
+genomeType	Full
+genomeFastaFiles	example/GRCh38.p13_chr22.fasta 
+genomeSAindexNbases	14
+genomeChrBinNbits	18
+genomeSAsparseD	1
+genomeTransformType	None
+genomeTransformVCF	-
+sjdbOverhang	0
+sjdbFileChrStartEnd	- 
+sjdbGTFfile	-
+sjdbGTFchrPrefix	-
+sjdbGTFfeatureExon	exon
+sjdbGTFtagExonParentTranscript	transcript_id
+sjdbGTFtagExonParentGene	gene_id
+sjdbInsertSave	Basic
+genomeFileSizes	50855936 323068164

example/SQANTI3_QC_output/STAR_mapping/UHR_Rep1_chr22Log.out

@@ -1,14 +1,14 @@
 STAR version=2.7.11b
 STAR compilation time,server,dir=2024-11-25T09:14:51+0000 :/opt/conda/conda-bld/star_1732525954305/work/source
 ##### Command Line:
-/home/pabloati/miniforge3/envs/sqanti3/bin/STAR-avx2 --runThreadN 4 --genomeDir /home/pabloati/Programs/sqanti3/example/SQANTI3_QC_output/STAR_index/ --readFilesIn example/UHR_Rep1_chr22.R1.fastq.gz example/UHR_Rep1_chr22.R2.fastq.gz --outFileNamePrefix /home/pabloati/Programs/sqanti3/example/SQANTI3_QC_output/STAR_mapping/UHR_Rep1_chr22 --alignSJoverhangMin 8 --alignSJDBoverhangMin 1 --outFilterType BySJout --outSAMunmapped Within --outFilterMultimapNmax 20 --outFilterMismatchNoverLmax 0.04 --outFilterMismatchNmax 999 --alignIntronMin 20 --alignIntronMax 1000000 --alignMatesGapMax 1000000 --sjdbScore 1 --genomeLoad NoSharedMemory --outSAMtype BAM SortedByCoordinate --readFilesCommand zcat --twopassMode Basic
+/home/pabloati/miniforge3/envs/sqanti3/bin/STAR-avx2 --runThreadN 4 --genomeDir example/SQANTI3_QC_output/STAR_index/ --readFilesIn example/UHR_Rep1_chr22.R1.fastq.gz example/UHR_Rep1_chr22.R2.fastq.gz --outFileNamePrefix example/SQANTI3_QC_output/STAR_mapping/UHR_Rep1_chr22 --alignSJoverhangMin 8 --alignSJDBoverhangMin 1 --outFilterType BySJout --outSAMunmapped Within --outFilterMultimapNmax 20 --outFilterMismatchNoverLmax 0.04 --outFilterMismatchNmax 999 --alignIntronMin 20 --alignIntronMax 1000000 --alignMatesGapMax 1000000 --sjdbScore 1 --genomeLoad NoSharedMemory --outSAMtype BAM SortedByCoordinate --readFilesCommand zcat --twopassMode Basic
 ##### Initial USER parameters from Command Line:
-outFileNamePrefix                 /home/pabloati/Programs/sqanti3/example/SQANTI3_QC_output/STAR_mapping/UHR_Rep1_chr22
+outFileNamePrefix                 example/SQANTI3_QC_output/STAR_mapping/UHR_Rep1_chr22
 ###### All USER parameters from Command Line:
 runThreadN                    4     ~RE-DEFINED
-genomeDir                     /home/pabloati/Programs/sqanti3/example/SQANTI3_QC_output/STAR_index/     ~RE-DEFINED
+genomeDir                     example/SQANTI3_QC_output/STAR_index/     ~RE-DEFINED
 readFilesIn                   example/UHR_Rep1_chr22.R1.fastq.gz   example/UHR_Rep1_chr22.R2.fastq.gz        ~RE-DEFINED
-outFileNamePrefix             /home/pabloati/Programs/sqanti3/example/SQANTI3_QC_output/STAR_mapping/UHR_Rep1_chr22     ~RE-DEFINED
+outFileNamePrefix             example/SQANTI3_QC_output/STAR_mapping/UHR_Rep1_chr22     ~RE-DEFINED
 alignSJoverhangMin            8     ~RE-DEFINED
 alignSJDBoverhangMin          1     ~RE-DEFINED
 outFilterType                 BySJout     ~RE-DEFINED
@@ -28,11 +28,11 @@ twopassMode                   Basic     ~RE-DEFINED
 
 ##### Final user re-defined parameters-----------------:
 runThreadN                        4
-genomeDir                         /home/pabloati/Programs/sqanti3/example/SQANTI3_QC_output/STAR_index/
+genomeDir                         example/SQANTI3_QC_output/STAR_index/
 genomeLoad                        NoSharedMemory
 readFilesIn                       example/UHR_Rep1_chr22.R1.fastq.gz   example/UHR_Rep1_chr22.R2.fastq.gz   
 readFilesCommand                  zcat   
-outFileNamePrefix                 /home/pabloati/Programs/sqanti3/example/SQANTI3_QC_output/STAR_mapping/UHR_Rep1_chr22
+outFileNamePrefix                 example/SQANTI3_QC_output/STAR_mapping/UHR_Rep1_chr22
 outSAMtype                        BAM   SortedByCoordinate   
 outSAMunmapped                    Within   
 outFilterType                     BySJout
@@ -49,33 +49,129 @@ twopassMode                       Basic
 
 -------------------------------
 ##### Final effective command line:
-/home/pabloati/miniforge3/envs/sqanti3/bin/STAR-avx2   --runThreadN 4   --genomeDir /home/pabloati/Programs/sqanti3/example/SQANTI3_QC_output/STAR_index/   --genomeLoad NoSharedMemory   --readFilesIn example/UHR_Rep1_chr22.R1.fastq.gz   example/UHR_Rep1_chr22.R2.fastq.gz      --readFilesCommand zcat      --outFileNamePrefix /home/pabloati/Programs/sqanti3/example/SQANTI3_QC_output/STAR_mapping/UHR_Rep1_chr22   --outSAMtype BAM   SortedByCoordinate      --outSAMunmapped Within      --outFilterType BySJout   --outFilterMultimapNmax 20   --outFilterMismatchNmax 999   --outFilterMismatchNoverLmax 0.04   --alignIntronMin 20   --alignIntronMax 1000000   --alignMatesGapMax 1000000   --alignSJoverhangMin 8   --alignSJDBoverhangMin 1   --sjdbScore 1   --twopassMode Basic
+/home/pabloati/miniforge3/envs/sqanti3/bin/STAR-avx2   --runThreadN 4   --genomeDir example/SQANTI3_QC_output/STAR_index/   --genomeLoad NoSharedMemory   --readFilesIn example/UHR_Rep1_chr22.R1.fastq.gz   example/UHR_Rep1_chr22.R2.fastq.gz      --readFilesCommand zcat      --outFileNamePrefix example/SQANTI3_QC_output/STAR_mapping/UHR_Rep1_chr22   --outSAMtype BAM   SortedByCoordinate      --outSAMunmapped Within      --outFilterType BySJout   --outFilterMultimapNmax 20   --outFilterMismatchNmax 999   --outFilterMismatchNoverLmax 0.04   --alignIntronMin 20   --alignIntronMax 1000000   --alignMatesGapMax 1000000   --alignSJoverhangMin 8   --alignSJDBoverhangMin 1   --sjdbScore 1   --twopassMode Basic
 ----------------------------------------
 
 Number of fastq files for each mate = 1
 
    Input read files for mate 1 :
--rwxrwxr-x 1 pabloati pabloati 13464036 dic  9 12:15 example/UHR_Rep1_chr22.R1.fastq.gz
+-rwxrwxr-x 1 pabloati pabloati 13464036 ene 29 13:07 example/UHR_Rep1_chr22.R1.fastq.gz
 
    readsCommandsFile:
-exec > "/home/pabloati/Programs/sqanti3/example/SQANTI3_QC_output/STAR_mapping/UHR_Rep1_chr22_STARtmp/tmp.fifo.read1"
+exec > "example/SQANTI3_QC_output/STAR_mapping/UHR_Rep1_chr22_STARtmp/tmp.fifo.read1"
 echo FILE 0
 zcat      "example/UHR_Rep1_chr22.R1.fastq.gz"
 
 
    Input read files for mate 2 :
--rwxrwxr-x 1 pabloati pabloati 14475272 dic  9 12:15 example/UHR_Rep1_chr22.R2.fastq.gz
+-rwxrwxr-x 1 pabloati pabloati 14475272 ene 29 13:07 example/UHR_Rep1_chr22.R2.fastq.gz
 
    readsCommandsFile:
-exec > "/home/pabloati/Programs/sqanti3/example/SQANTI3_QC_output/STAR_mapping/UHR_Rep1_chr22_STARtmp/tmp.fifo.read2"
+exec > "example/SQANTI3_QC_output/STAR_mapping/UHR_Rep1_chr22_STARtmp/tmp.fifo.read2"
 echo FILE 0
 zcat      "example/UHR_Rep1_chr22.R2.fastq.gz"
 
 ParametersSolo: --soloCellFilterType CellRanger2.2 filtering parameters:  3000 0.99 10
 WARNING: --limitBAMsortRAM=0, will use genome size as RAM limit for BAM sorting
 Finished loading and checking parameters
+Reading genome generation parameters:
+### /home/pabloati/miniforge3/envs/sqanti3/bin/STAR-avx2   --runMode genomeGenerate      --runThreadN 4   --genomeDir example/SQANTI3_QC_output/STAR_index/   --genomeFastaFiles example/GRCh38.p13_chr22.fasta      --outTmpDir example/SQANTI3_QC_output/STAR_index//_STARtmp/
+### GstrandBit=32
+versionGenome                 2.7.4a     ~RE-DEFINED
+genomeType                    Full     ~RE-DEFINED
+genomeFastaFiles              example/GRCh38.p13_chr22.fasta        ~RE-DEFINED
+genomeSAindexNbases           14     ~RE-DEFINED
+genomeChrBinNbits             18     ~RE-DEFINED
+genomeSAsparseD               1     ~RE-DEFINED
+genomeTransformType           None     ~RE-DEFINED
+genomeTransformVCF            -     ~RE-DEFINED
+sjdbOverhang                  0     ~RE-DEFINED
+sjdbFileChrStartEnd           -        ~RE-DEFINED
+sjdbGTFfile                   -     ~RE-DEFINED
+sjdbGTFchrPrefix              -     ~RE-DEFINED
+sjdbGTFfeatureExon            exon     ~RE-DEFINED
+sjdbGTFtagExonParentTranscripttranscript_id     ~RE-DEFINED
+sjdbGTFtagExonParentGene      gene_id     ~RE-DEFINED
+sjdbInsertSave                Basic     ~RE-DEFINED
+genomeFileSizes               50855936   323068164        ~RE-DEFINED
+Genome version is compatible with current STAR
+Number of real (reference) chromosomes= 1
+1	chr22	50818468	0
+Started loading the genome: Wed Jan 29 15:07:49 2025
 
-EXITING because of FATAL ERROR: could not open genome file /home/pabloati/Programs/sqanti3/example/SQANTI3_QC_output/STAR_index//genomeParameters.txt
-SOLUTION: check that the path to genome files, specified in --genomeDir is correct and the files are present, and have user read permsissions
+Genome: size given as a parameter = 50855936
+SA: size given as a parameter = 323068164
+SAindex: size given as a parameter = 1
+Read from SAindex: pGe.gSAindexNbases=14  nSAi=357913940
+nGenome=50855936;  nSAbyte=323068164
+GstrandBit=32   SA number of indices=78319554
+Shared memory is not used for genomes. Allocated a private copy of the genome.
+Genome file size: 50855936 bytes; state: good=1 eof=0 fail=0 bad=0
+Loading Genome ... done! state: good=1 eof=0 fail=0 bad=0; loaded 50855936 bytes
+SA file size: 323068164 bytes; state: good=1 eof=0 fail=0 bad=0
+Loading SA ... done! state: good=1 eof=0 fail=0 bad=0; loaded 323068164 bytes
+Loading SAindex ... done: 1565873619 bytes
+Finished loading the genome: Wed Jan 29 15:07:50 2025
 
-Dec 10 17:25:24 ...... FATAL ERROR, exiting
+To accommodate alignIntronMax=1000000 redefined winBinNbits=18
+To accommodate alignIntronMax=1000000 and alignMatesGapMax=1000000, redefined winFlankNbins=4 and winAnchorDistNbins=8
+Opening the file: example/SQANTI3_QC_output/STAR_mapping/UHR_Rep1_chr22_STARtmp//FilterBySJoutFiles.mate1.thread0 ... ok
+Opening the file: example/SQANTI3_QC_output/STAR_mapping/UHR_Rep1_chr22_STARtmp//FilterBySJoutFiles.mate2.thread0 ... ok
+Opening the file: example/SQANTI3_QC_output/STAR_mapping/UHR_Rep1_chr22_STARtmp//FilterBySJoutFiles.mate1.thread1 ... ok
+Opening the file: example/SQANTI3_QC_output/STAR_mapping/UHR_Rep1_chr22_STARtmp//FilterBySJoutFiles.mate2.thread1 ... ok
+Opening the file: example/SQANTI3_QC_output/STAR_mapping/UHR_Rep1_chr22_STARtmp//FilterBySJoutFiles.mate1.thread2 ... ok
+Opening the file: example/SQANTI3_QC_output/STAR_mapping/UHR_Rep1_chr22_STARtmp//FilterBySJoutFiles.mate2.thread2 ... ok
+Opening the file: example/SQANTI3_QC_output/STAR_mapping/UHR_Rep1_chr22_STARtmp//FilterBySJoutFiles.mate1.thread3 ... ok
+Opening the file: example/SQANTI3_QC_output/STAR_mapping/UHR_Rep1_chr22_STARtmp//FilterBySJoutFiles.mate2.thread3 ... ok
+Created thread # 1
+Thread #1 end of input stream, nextChar=-1
+Thread #1 end of input stream, nextChar=-1
+Created thread # 2
+Completed: thread #2
+Completed: thread #1
+Created thread # 3
+Completed: thread #0
+Joined thread # 1
+Joined thread # 2
+Completed: thread #3
+Joined thread # 3
+Jan 29 15:07:51   Loaded database junctions from the 1st pass file: example/SQANTI3_QC_output/STAR_mapping/UHR_Rep1_chr22_STARpass1//SJ.out.tab: 0 total junctions
+
+Jan 29 15:07:51   Finished preparing junctions
+Jan 29 15:07:51 ..... finished inserting junctions into genome
+
+   Input read files for mate 1 :
+-rwxrwxr-x 1 pabloati pabloati 13464036 ene 29 13:07 example/UHR_Rep1_chr22.R1.fastq.gz
+
+   readsCommandsFile:
+exec > "example/SQANTI3_QC_output/STAR_mapping/UHR_Rep1_chr22_STARtmp/tmp.fifo.read1"
+echo FILE 0
+zcat      "example/UHR_Rep1_chr22.R1.fastq.gz"
+
+
+   Input read files for mate 2 :
+-rwxrwxr-x 1 pabloati pabloati 14475272 ene 29 13:07 example/UHR_Rep1_chr22.R2.fastq.gz
+
+   readsCommandsFile:
+exec > "example/SQANTI3_QC_output/STAR_mapping/UHR_Rep1_chr22_STARtmp/tmp.fifo.read2"
+echo FILE 0
+zcat      "example/UHR_Rep1_chr22.R2.fastq.gz"
+
+Opening the file: example/SQANTI3_QC_output/STAR_mapping/UHR_Rep1_chr22_STARtmp//FilterBySJoutFiles.mate1.thread0 ... ok
+Opening the file: example/SQANTI3_QC_output/STAR_mapping/UHR_Rep1_chr22_STARtmp//FilterBySJoutFiles.mate2.thread0 ... ok
+Opening the file: example/SQANTI3_QC_output/STAR_mapping/UHR_Rep1_chr22_STARtmp//FilterBySJoutFiles.mate1.thread1 ... ok
+Opening the file: example/SQANTI3_QC_output/STAR_mapping/UHR_Rep1_chr22_STARtmp//FilterBySJoutFiles.mate2.thread1 ... ok
+Opening the file: example/SQANTI3_QC_output/STAR_mapping/UHR_Rep1_chr22_STARtmp//FilterBySJoutFiles.mate1.thread2 ... ok
+Opening the file: example/SQANTI3_QC_output/STAR_mapping/UHR_Rep1_chr22_STARtmp//FilterBySJoutFiles.mate2.thread2 ... ok
+Opening the file: example/SQANTI3_QC_output/STAR_mapping/UHR_Rep1_chr22_STARtmp//FilterBySJoutFiles.mate1.thread3 ... ok
+Opening the file: example/SQANTI3_QC_output/STAR_mapping/UHR_Rep1_chr22_STARtmp//FilterBySJoutFiles.mate2.thread3 ... ok
+Created thread # 1
+Created thread # 2
+Created thread # 3
+
+ReadAlignChunk_processChunks.cpp:204:processChunks EXITING because of FATAL ERROR in input reads: wrong read ID line format: the read ID lines should start with @ or > 
+Offending line for read # 1
+JGHIIHDGGAHIJE8@GGIHIIIHHHHEFBDEEDEED9;=?BBDDCDCCCD4AC 
+SOLUTION: verify and correct the input read files
+
+Jan 29 15:07:51 ...... FATAL ERROR, exiting