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Hi, I am trying to use RNAEditor and fixed most issues from the posted issues here. However, the following error I couldn't able fix. Need help.
ERROR: No Variants left RNAEditor failed
Below is the error log file *** INFO: CHECK DEPENDENCIES *** *** INFO: Dependencies satisfied *** *** INFO: *** Start RnaEditor with: *** *** *** INFO: FastQ-File: /home/owner/RNAEditor/sample.fastq *** *** INFO: outfilePrefix:/home/owner/RNAEditor/rnaEditor/sample/sample *** *** INFO: refGenome:/home/owner/RNAEditor/rnaEditor_annotations/human/GRCH38/Homo_sapiens.GRCh38.dna.primary_assembly.fa *** *** INFO: dbsnp:/home/owner/RNAEditor/rnaEditor_annotations/human/GRCH38/dbSNP.vcf *** *** INFO: sourceDir:/usr/local/bin/ *** *** INFO: threads:5 *** *** INFO: maxDiff:0.04 *** *** INFO: seedDiff:2 *** *** INFO: paired:False *** *** INFO: keepTemp:True *** *** INFO: overwrite:False *** *** INFO: *** *** INFO: [Sun 11 Aug 2019 01:07:22 PM ] * * * Align Reads with BWA * * * *** [bwa_aln] 17bp reads: max_diff = 2 [bwa_aln] 38bp reads: max_diff = 3 [bwa_aln] 64bp reads: max_diff = 4 [bwa_aln] 93bp reads: max_diff = 5 [bwa_aln] 124bp reads: max_diff = 6 [bwa_aln] 157bp reads: max_diff = 7 [bwa_aln] 190bp reads: max_diff = 8 [bwa_aln] 225bp reads: max_diff = 9 [bwa_aln_core] calculate SA coordinate... 0.06 sec [bwa_aln_core] write to the disk... 0.00 sec [bwa_aln_core] 125 sequences have been processed. [main] Version: 0.7.17-r1188 [main] CMD: /usr/local/bin/bwa aln -t 5 -n 0.04 -k 2 /home/owner/RNAEditor/rnaEditor_annotations/human/GRCH38/Homo_sapiens.GRCh38.dna.primary_assembly.fa /home/owner/RNAEditor/sample.fastq [main] Real time: 2.035 sec; CPU: 1.997 sec *** [DONE] Duration [0:00:02.044751] *** *** INFO: [Sun 11 Aug 2019 01:07:24 PM ] * * * convert sai to sam * * * *** [bwa_aln_core] convert to sequence coordinate... 3.54 sec [bwa_aln_core] refine gapped alignments... 0.88 sec [bwa_aln_core] print alignments... 0.00 sec [bwa_aln_core] 125 sequences have been processed. [main] Version: 0.7.17-r1188 [main] CMD: /usr/local/bin/bwa samse -r @rg\tID:bwa\tSM:A\tPL:ILLUMINA\tPU:HiSEQ2000 /home/owner/RNAEditor/rnaEditor_annotations/human/GRCH38/Homo_sapiens.GRCh38.dna.primary_assembly.fa /home/owner/RNAEditor/rnaEditor/sample/sample.sai /home/owner/RNAEditor/sample.fastq [main] Real time: 6.896 sec; CPU: 4.422 sec *** [DONE] Duration [0:00:06.905157] *** *** INFO: [Sun 11 Aug 2019 01:07:31 PM ] * * * Sort Bam File * * * *** *** [DONE] Duration [0:00:00.020746] *** *** INFO: [Sun 11 Aug 2019 01:07:31 PM ] * * * Index Bam File * * * *** *** [DONE] Duration [0:00:00.013919] *** *** INFO: [Sun 11 Aug 2019 01:07:31 PM ] * * * Remove PCR duplicates * * * *** [Sun Aug 11 13:07:32 EDT 2019] picard.sam.MarkDuplicates INPUT=[/home/owner/RNAEditor/rnaEditor/sample/sample.bam] OUTPUT=/home/owner/RNAEditor/rnaEditor/sample/sample.noDup.bam METRICS_FILE=/home/owner/RNAEditor/rnaEditor/sample/sample.pcr.metrics VALIDATION_STRINGENCY=LENIENT CREATE_INDEX=true PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates REMOVE_DUPLICATES=false ASSUME_SORTED=false MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 READ_NAME_REGEX=[a-zA-Z0-9]+:[0-9]:([0-9]+):([0-9]+):([0-9]+).* OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 VERBOSITY=INFO QUIET=false COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_MD5_FILE=false [Sun Aug 11 13:07:32 EDT 2019] Executing as owner@owner-Latitude-E7240 on Linux 5.0.0-23-generic amd64; OpenJDK 64-Bit Server VM 1.8.0_192-b01; Picard version: 1.119(d44cdb51745f5e8075c826430a39d8a61f1dd832_1408991805) JdkDeflater INFO 2019-08-11 13:07:32 MarkDuplicates Start of doWork freeMemory: 249134512; totalMemory: 251658240; maxMemory: 15271460864 INFO 2019-08-11 13:07:32 MarkDuplicates Reading input file and constructing read end information. INFO 2019-08-11 13:07:32 MarkDuplicates Will retain up to 60601035 data points before spilling to disk. WARNING 2019-08-11 13:07:32 AbstractDuplicateFindingAlgorithm Default READ_NAME_REGEX '[a-zA-Z0-9]+:[0-9]:([0-9]+):([0-9]+):([0-9]+).*' did not match read name 'SRR006041.4'. You may need to specify a READ_NAME_REGEX in order to correctly identify optical duplicates. Note that this message will not be emitted again even if other read names do not match the regex. INFO 2019-08-11 13:07:32 MarkDuplicates Read 2 records. 0 pairs never matched. INFO 2019-08-11 13:07:32 MarkDuplicates After buildSortedReadEndLists freeMemory: 249394760; totalMemory: 737148928; maxMemory: 15271460864 INFO 2019-08-11 13:07:32 MarkDuplicates Will retain up to 477233152 duplicate indices before spilling to disk. INFO 2019-08-11 13:07:34 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2019-08-11 13:07:34 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2019-08-11 13:07:34 MarkDuplicates Sorting list of duplicate records. INFO 2019-08-11 13:07:35 MarkDuplicates After generateDuplicateIndexes freeMemory: 735176432; totalMemory: 4555538432; maxMemory: 15271460864 INFO 2019-08-11 13:07:35 MarkDuplicates Marking 0 records as duplicates. INFO 2019-08-11 13:07:35 MarkDuplicates Found 0 optical duplicate clusters. INFO 2019-08-11 13:07:35 MarkDuplicates Before output close freeMemory: 4552131608; totalMemory: 4555538432; maxMemory: 15271460864 INFO 2019-08-11 13:07:35 MarkDuplicates After output close freeMemory: 4552348152; totalMemory: 4555538432; maxMemory: 15271460864 [Sun Aug 11 13:07:35 EDT 2019] picard.sam.MarkDuplicates done. Elapsed time: 0.06 minutes. Runtime.totalMemory()=4555538432 *** [DONE] Duration [0:00:04.235546] *** *** INFO: [Sun 11 Aug 2019 01:07:36 PM ] * * * Identify Target Regions for realignment * * * *** *** [DONE] Duration [0:06:42.567531] *** *** INFO: [Sun 11 Aug 2019 01:14:18 PM ] * * * Proceed Realignement * * * *** *** [DONE] Duration [0:00:18.616889] *** *** INFO: [Sun 11 Aug 2019 01:14:37 PM ] * * * Find Quality Score recalibration spots * * * *** *** [DONE] Duration [0:00:23.163883] *** *** INFO: [Sun 11 Aug 2019 01:15:00 PM ] * * * Proceed Quality Score recalibration * * * *** *** [DONE] Duration [0:00:18.871437] *** *** INFO: *** CALL VARIANTS WITH FOLLOWING ATTRIBUTES *** *** *** INFO: Bam-File: /home/owner/RNAEditor/rnaEditor/sample/sample.noDup.realigned.recalibrated.bam *** *** INFO: outfilePrefix:/home/owner/RNAEditor/rnaEditor/sample/sample *** *** INFO: refGenome:/home/owner/RNAEditor/rnaEditor_annotations/human/GRCH38/Homo_sapiens.GRCh38.dna.primary_assembly.fa *** *** INFO: dbsnp:/home/owner/RNAEditor/rnaEditor_annotations/human/GRCH38/dbSNP.vcf *** *** INFO: HapMap:/home/owner/RNAEditor/rnaEditor_annotations/human/GRCH38/HAPMAP.vcf *** *** INFO: 1000G Omni:/home/owner/RNAEditor/rnaEditor_annotations/human/GRCH38/1000GenomeProject.vcf *** *** INFO: Alu-Regions:/home/owner/RNAEditor/rnaEditor_annotations/human/GRCH38/repeats.bed *** *** INFO: sourceDir:/usr/local/bin/ *** *** INFO: threads:5 *** *** INFO: StandCall:1 *** *** INFO: standEmit:1 *** *** INFO: keepTemp:True *** *** INFO: overwrite:False *** *** INFO: [Sun 11 Aug 2019 01:15:19 PM ] * * * Call variants * * * *** *** [DONE] Duration [0:26:24.021020] *** *** INFO: [Sun 11 Aug 2019 01:41:43 PM ] Parsing Variant Data from /home/owner/RNAEditor/rnaEditor/sample/sample.vcf *** *** [DONE] Duration [0:00:00.003397] *** *** INFO: [Sun 11 Aug 2019 01:41:43 PM ] Delete overlapps from /home/owner/RNAEditor/rnaEditor_annotations/human/GRCH38/dbSNP.vcf *** *** [DONE] Duration [0:05:13.119562] *** *** INFO: [Sun 11 Aug 2019 01:46:56 PM ] Delete overlapps from /home/owner/RNAEditor/rnaEditor_annotations/human/GRCH38/1000GenomeProject.vcf *** *** [DONE] Duration [0:00:00.001128] *** *** INFO: [Sun 11 Aug 2019 01:46:56 PM ] Delete overlapps from /home/owner/RNAEditor/rnaEditor_annotations/human/GRCH38/ESP_filtered *** *** [DONE] Duration [0:00:00.430060] *** *** INFO: [Sun 11 Aug 2019 01:46:56 PM ] Print Variants to /home/owner/RNAEditor/rnaEditor/sample/sample.noSNPs.vcf *** *** INFO: [Sun 11 Aug 2019 01:46:56 PM ] remove Missmatches from the first 3 bp from read edges *** *** STATUS: 0 of 0variants were deleted *** *** [DONE] Duration [0:00:00.003831] *** *** INFO: [Sun 11 Aug 2019 01:46:56 PM ] Print Variants to /home/owner/RNAEditor/rnaEditor/sample/sample.noReadEdges.vcf *** *** INFO: [Sun 11 Aug 2019 01:46:56 PM ] Split Variants by Bed File /home/owner/RNAEditor/rnaEditor_annotations/human/GRCH38/repeats.bed *** *** STATUS: 100000 Bed Feautes parsed *** *** STATUS: 200000 Bed Feautes parsed *** *** STATUS: 300000 Bed Feautes parsed *** *** STATUS: 400000 Bed Feautes parsed *** *** STATUS: 500000 Bed Feautes parsed *** *** STATUS: 600000 Bed Feautes parsed *** *** STATUS: 700000 Bed Feautes parsed *** *** STATUS: 800000 Bed Feautes parsed *** *** STATUS: 900000 Bed Feautes parsed *** *** STATUS: 1000000 Bed Feautes parsed *** *** STATUS: 1100000 Bed Feautes parsed *** *** STATUS: 1200000 Bed Feautes parsed *** *** STATUS: 1300000 Bed Feautes parsed *** *** STATUS: 1400000 Bed Feautes parsed *** *** STATUS: 1500000 Bed Feautes parsed *** *** STATUS: 1600000 Bed Feautes parsed *** *** STATUS: 1700000 Bed Feautes parsed *** *** STATUS: 1800000 Bed Feautes parsed *** *** STATUS: 1900000 Bed Feautes parsed *** *** STATUS: 2000000 Bed Feautes parsed *** *** STATUS: 2100000 Bed Feautes parsed *** *** STATUS: 2200000 Bed Feautes parsed *** *** STATUS: 2300000 Bed Feautes parsed *** *** STATUS: 2400000 Bed Feautes parsed *** *** STATUS: 2500000 Bed Feautes parsed *** *** STATUS: 2600000 Bed Feautes parsed *** *** STATUS: 2700000 Bed Feautes parsed *** *** STATUS: 2800000 Bed Feautes parsed *** *** STATUS: 2900000 Bed Feautes parsed *** *** STATUS: 3000000 Bed Feautes parsed *** *** STATUS: 3100000 Bed Feautes parsed *** *** STATUS: 3200000 Bed Feautes parsed *** *** STATUS: 3300000 Bed Feautes parsed *** *** STATUS: 3400000 Bed Feautes parsed *** *** STATUS: 3500000 Bed Feautes parsed *** *** STATUS: 3600000 Bed Feautes parsed *** *** STATUS: 3700000 Bed Feautes parsed *** *** STATUS: 3800000 Bed Feautes parsed *** *** STATUS: 3900000 Bed Feautes parsed *** *** STATUS: 4000000 Bed Feautes parsed *** *** STATUS: 4100000 Bed Feautes parsed *** *** STATUS: 4200000 Bed Feautes parsed *** *** STATUS: 4300000 Bed Feautes parsed *** *** STATUS: 4400000 Bed Feautes parsed *** *** STATUS: 4500000 Bed Feautes parsed *** *** STATUS: 4600000 Bed Feautes parsed *** *** STATUS: 4700000 Bed Feautes parsed *** *** STATUS: 4800000 Bed Feautes parsed *** *** STATUS: 4900000 Bed Feautes parsed *** *** STATUS: 5000000 Bed Feautes parsed *** *** STATUS: 5100000 Bed Feautes parsed *** *** STATUS: 5200000 Bed Feautes parsed *** *** STATUS: 5300000 Bed Feautes parsed *** *** STATUS: 5400000 Bed Feautes parsed *** *** STATUS: 5500000 Bed Feautes parsed *** *** INFO: finished parsing Bed file *** *** [DONE] Duration [0:00:10.589523] *** *** INFO: finished creating overlaps *** *** [DONE] Duration [0:00:10.590025] *** *** [DONE] Duration [0:00:10.590296] *** *** INFO: [Sun 11 Aug 2019 01:47:07 PM ] Print Variants to /home/owner/RNAEditor/rnaEditor/sample/sample.alu.vcf *** *** INFO: [Sun 11 Aug 2019 01:47:07 PM ] Print Variants to /home/owner/RNAEditor/rnaEditor/sample/sample.nonAlu.vcf *** *** INFO: [Sun 11 Aug 2019 01:47:07 PM ] Assembling Genome from /home/owner/RNAEditor/rnaEditor_annotations/human/GRCH38/Homo_sapiens.GRCh38.83.gtf *** *** [DONE] Duration [0:02:40.692249] *** *** INFO: [Sun 11 Aug 2019 01:49:48 PM ] remove Missmatches from the intronic splice junctions *** *** [DONE] Duration [0:00:00.119274] *** *** INFO: [Sun 11 Aug 2019 01:49:48 PM ] Print Variants to /home/owner/RNAEditor/rnaEditor/sample/sample.noSpliceJunction.vcf *** *** INFO: [Sun 11 Aug 2019 01:49:48 PM ] remove Missmatches from homopolymers *** *** INFO: 0 out of 0 passed the Homopolymer-Filter *** *** [DONE] Duration [0:00:00.001687] *** *** INFO: [Sun 11 Aug 2019 01:49:48 PM ] Print Variants to /home/owner/RNAEditor/rnaEditor/sample/sample.noHomo.vcf *** *** INFO: [Sun 11 Aug 2019 01:49:48 PM ] Search non uniquely mapped reads *** *** INFO: [Sun 11 Aug 2019 01:49:48 PM ] Create fasta file for blat *** *** ERROR: No Variants left *** *** ERROR: RnaEditor Failed ***
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Hi,
I am trying to use RNAEditor and fixed most issues from the posted issues here. However, the following error I couldn't able fix. Need help.
ERROR: No Variants left
RNAEditor failed
Below is the error log file
*** INFO: CHECK DEPENDENCIES ***
*** INFO: Dependencies satisfied ***
*** INFO: *** Start RnaEditor with: *** ***
*** INFO: FastQ-File: /home/owner/RNAEditor/sample.fastq ***
*** INFO: outfilePrefix:/home/owner/RNAEditor/rnaEditor/sample/sample ***
*** INFO: refGenome:/home/owner/RNAEditor/rnaEditor_annotations/human/GRCH38/Homo_sapiens.GRCh38.dna.primary_assembly.fa ***
*** INFO: dbsnp:/home/owner/RNAEditor/rnaEditor_annotations/human/GRCH38/dbSNP.vcf ***
*** INFO: sourceDir:/usr/local/bin/ ***
*** INFO: threads:5 ***
*** INFO: maxDiff:0.04 ***
*** INFO: seedDiff:2 ***
*** INFO: paired:False ***
*** INFO: keepTemp:True ***
*** INFO: overwrite:False ***
*** INFO: ***
*** INFO: [Sun 11 Aug 2019 01:07:22 PM ] * * * Align Reads with BWA * * * ***
[bwa_aln] 17bp reads: max_diff = 2
[bwa_aln] 38bp reads: max_diff = 3
[bwa_aln] 64bp reads: max_diff = 4
[bwa_aln] 93bp reads: max_diff = 5
[bwa_aln] 124bp reads: max_diff = 6
[bwa_aln] 157bp reads: max_diff = 7
[bwa_aln] 190bp reads: max_diff = 8
[bwa_aln] 225bp reads: max_diff = 9
[bwa_aln_core] calculate SA coordinate... 0.06 sec
[bwa_aln_core] write to the disk... 0.00 sec
[bwa_aln_core] 125 sequences have been processed.
[main] Version: 0.7.17-r1188
[main] CMD: /usr/local/bin/bwa aln -t 5 -n 0.04 -k 2 /home/owner/RNAEditor/rnaEditor_annotations/human/GRCH38/Homo_sapiens.GRCh38.dna.primary_assembly.fa /home/owner/RNAEditor/sample.fastq
[main] Real time: 2.035 sec; CPU: 1.997 sec
*** [DONE] Duration [0:00:02.044751] ***
*** INFO: [Sun 11 Aug 2019 01:07:24 PM ] * * * convert sai to sam * * * ***
[bwa_aln_core] convert to sequence coordinate... 3.54 sec
[bwa_aln_core] refine gapped alignments... 0.88 sec
[bwa_aln_core] print alignments... 0.00 sec
[bwa_aln_core] 125 sequences have been processed.
[main] Version: 0.7.17-r1188
[main] CMD: /usr/local/bin/bwa samse -r @rg\tID:bwa\tSM:A\tPL:ILLUMINA\tPU:HiSEQ2000 /home/owner/RNAEditor/rnaEditor_annotations/human/GRCH38/Homo_sapiens.GRCh38.dna.primary_assembly.fa /home/owner/RNAEditor/rnaEditor/sample/sample.sai /home/owner/RNAEditor/sample.fastq
[main] Real time: 6.896 sec; CPU: 4.422 sec
*** [DONE] Duration [0:00:06.905157] ***
*** INFO: [Sun 11 Aug 2019 01:07:31 PM ] * * * Sort Bam File * * * ***
*** [DONE] Duration [0:00:00.020746] ***
*** INFO: [Sun 11 Aug 2019 01:07:31 PM ] * * * Index Bam File * * * ***
*** [DONE] Duration [0:00:00.013919] ***
*** INFO: [Sun 11 Aug 2019 01:07:31 PM ] * * * Remove PCR duplicates * * * ***
[Sun Aug 11 13:07:32 EDT 2019] picard.sam.MarkDuplicates INPUT=[/home/owner/RNAEditor/rnaEditor/sample/sample.bam] OUTPUT=/home/owner/RNAEditor/rnaEditor/sample/sample.noDup.bam METRICS_FILE=/home/owner/RNAEditor/rnaEditor/sample/sample.pcr.metrics VALIDATION_STRINGENCY=LENIENT CREATE_INDEX=true PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates REMOVE_DUPLICATES=false ASSUME_SORTED=false MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 READ_NAME_REGEX=[a-zA-Z0-9]+:[0-9]:([0-9]+):([0-9]+):([0-9]+).* OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 VERBOSITY=INFO QUIET=false COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_MD5_FILE=false
[Sun Aug 11 13:07:32 EDT 2019] Executing as owner@owner-Latitude-E7240 on Linux 5.0.0-23-generic amd64; OpenJDK 64-Bit Server VM 1.8.0_192-b01; Picard version: 1.119(d44cdb51745f5e8075c826430a39d8a61f1dd832_1408991805) JdkDeflater
INFO 2019-08-11 13:07:32 MarkDuplicates Start of doWork freeMemory: 249134512; totalMemory: 251658240; maxMemory: 15271460864
INFO 2019-08-11 13:07:32 MarkDuplicates Reading input file and constructing read end information.
INFO 2019-08-11 13:07:32 MarkDuplicates Will retain up to 60601035 data points before spilling to disk.
WARNING 2019-08-11 13:07:32 AbstractDuplicateFindingAlgorithm Default READ_NAME_REGEX '[a-zA-Z0-9]+:[0-9]:([0-9]+):([0-9]+):([0-9]+).*' did not match read name 'SRR006041.4'. You may need to specify a READ_NAME_REGEX in order to correctly identify optical duplicates. Note that this message will not be emitted again even if other read names do not match the regex.
INFO 2019-08-11 13:07:32 MarkDuplicates Read 2 records. 0 pairs never matched.
INFO 2019-08-11 13:07:32 MarkDuplicates After buildSortedReadEndLists freeMemory: 249394760; totalMemory: 737148928; maxMemory: 15271460864
INFO 2019-08-11 13:07:32 MarkDuplicates Will retain up to 477233152 duplicate indices before spilling to disk.
INFO 2019-08-11 13:07:34 MarkDuplicates Traversing read pair information and detecting duplicates.
INFO 2019-08-11 13:07:34 MarkDuplicates Traversing fragment information and detecting duplicates.
INFO 2019-08-11 13:07:34 MarkDuplicates Sorting list of duplicate records.
INFO 2019-08-11 13:07:35 MarkDuplicates After generateDuplicateIndexes freeMemory: 735176432; totalMemory: 4555538432; maxMemory: 15271460864
INFO 2019-08-11 13:07:35 MarkDuplicates Marking 0 records as duplicates.
INFO 2019-08-11 13:07:35 MarkDuplicates Found 0 optical duplicate clusters.
INFO 2019-08-11 13:07:35 MarkDuplicates Before output close freeMemory: 4552131608; totalMemory: 4555538432; maxMemory: 15271460864
INFO 2019-08-11 13:07:35 MarkDuplicates After output close freeMemory: 4552348152; totalMemory: 4555538432; maxMemory: 15271460864
[Sun Aug 11 13:07:35 EDT 2019] picard.sam.MarkDuplicates done. Elapsed time: 0.06 minutes.
Runtime.totalMemory()=4555538432
*** [DONE] Duration [0:00:04.235546] ***
*** INFO: [Sun 11 Aug 2019 01:07:36 PM ] * * * Identify Target Regions for realignment * * * ***
*** [DONE] Duration [0:06:42.567531] ***
*** INFO: [Sun 11 Aug 2019 01:14:18 PM ] * * * Proceed Realignement * * * ***
*** [DONE] Duration [0:00:18.616889] ***
*** INFO: [Sun 11 Aug 2019 01:14:37 PM ] * * * Find Quality Score recalibration spots * * * ***
*** [DONE] Duration [0:00:23.163883] ***
*** INFO: [Sun 11 Aug 2019 01:15:00 PM ] * * * Proceed Quality Score recalibration * * * ***
*** [DONE] Duration [0:00:18.871437] ***
*** INFO: *** CALL VARIANTS WITH FOLLOWING ATTRIBUTES *** ***
*** INFO: Bam-File: /home/owner/RNAEditor/rnaEditor/sample/sample.noDup.realigned.recalibrated.bam ***
*** INFO: outfilePrefix:/home/owner/RNAEditor/rnaEditor/sample/sample ***
*** INFO: refGenome:/home/owner/RNAEditor/rnaEditor_annotations/human/GRCH38/Homo_sapiens.GRCh38.dna.primary_assembly.fa ***
*** INFO: dbsnp:/home/owner/RNAEditor/rnaEditor_annotations/human/GRCH38/dbSNP.vcf ***
*** INFO: HapMap:/home/owner/RNAEditor/rnaEditor_annotations/human/GRCH38/HAPMAP.vcf ***
*** INFO: 1000G Omni:/home/owner/RNAEditor/rnaEditor_annotations/human/GRCH38/1000GenomeProject.vcf ***
*** INFO: Alu-Regions:/home/owner/RNAEditor/rnaEditor_annotations/human/GRCH38/repeats.bed ***
*** INFO: sourceDir:/usr/local/bin/ ***
*** INFO: threads:5 ***
*** INFO: StandCall:1 ***
*** INFO: standEmit:1 ***
*** INFO: keepTemp:True ***
*** INFO: overwrite:False ***
*** INFO: [Sun 11 Aug 2019 01:15:19 PM ] * * * Call variants * * * ***
*** [DONE] Duration [0:26:24.021020] ***
*** INFO: [Sun 11 Aug 2019 01:41:43 PM ] Parsing Variant Data from /home/owner/RNAEditor/rnaEditor/sample/sample.vcf ***
*** [DONE] Duration [0:00:00.003397] ***
*** INFO: [Sun 11 Aug 2019 01:41:43 PM ] Delete overlapps from /home/owner/RNAEditor/rnaEditor_annotations/human/GRCH38/dbSNP.vcf ***
*** [DONE] Duration [0:05:13.119562] ***
*** INFO: [Sun 11 Aug 2019 01:46:56 PM ] Delete overlapps from /home/owner/RNAEditor/rnaEditor_annotations/human/GRCH38/1000GenomeProject.vcf ***
*** [DONE] Duration [0:00:00.001128] ***
*** INFO: [Sun 11 Aug 2019 01:46:56 PM ] Delete overlapps from /home/owner/RNAEditor/rnaEditor_annotations/human/GRCH38/ESP_filtered ***
*** [DONE] Duration [0:00:00.430060] ***
*** INFO: [Sun 11 Aug 2019 01:46:56 PM ] Print Variants to /home/owner/RNAEditor/rnaEditor/sample/sample.noSNPs.vcf ***
*** INFO: [Sun 11 Aug 2019 01:46:56 PM ] remove Missmatches from the first 3 bp from read edges ***
*** STATUS: 0 of 0variants were deleted ***
*** [DONE] Duration [0:00:00.003831] ***
*** INFO: [Sun 11 Aug 2019 01:46:56 PM ] Print Variants to /home/owner/RNAEditor/rnaEditor/sample/sample.noReadEdges.vcf ***
*** INFO: [Sun 11 Aug 2019 01:46:56 PM ] Split Variants by Bed File /home/owner/RNAEditor/rnaEditor_annotations/human/GRCH38/repeats.bed ***
*** STATUS: 100000 Bed Feautes parsed ***
*** STATUS: 200000 Bed Feautes parsed ***
*** STATUS: 300000 Bed Feautes parsed ***
*** STATUS: 400000 Bed Feautes parsed ***
*** STATUS: 500000 Bed Feautes parsed ***
*** STATUS: 600000 Bed Feautes parsed ***
*** STATUS: 700000 Bed Feautes parsed ***
*** STATUS: 800000 Bed Feautes parsed ***
*** STATUS: 900000 Bed Feautes parsed ***
*** STATUS: 1000000 Bed Feautes parsed ***
*** STATUS: 1100000 Bed Feautes parsed ***
*** STATUS: 1200000 Bed Feautes parsed ***
*** STATUS: 1300000 Bed Feautes parsed ***
*** STATUS: 1400000 Bed Feautes parsed ***
*** STATUS: 1500000 Bed Feautes parsed ***
*** STATUS: 1600000 Bed Feautes parsed ***
*** STATUS: 1700000 Bed Feautes parsed ***
*** STATUS: 1800000 Bed Feautes parsed ***
*** STATUS: 1900000 Bed Feautes parsed ***
*** STATUS: 2000000 Bed Feautes parsed ***
*** STATUS: 2100000 Bed Feautes parsed ***
*** STATUS: 2200000 Bed Feautes parsed ***
*** STATUS: 2300000 Bed Feautes parsed ***
*** STATUS: 2400000 Bed Feautes parsed ***
*** STATUS: 2500000 Bed Feautes parsed ***
*** STATUS: 2600000 Bed Feautes parsed ***
*** STATUS: 2700000 Bed Feautes parsed ***
*** STATUS: 2800000 Bed Feautes parsed ***
*** STATUS: 2900000 Bed Feautes parsed ***
*** STATUS: 3000000 Bed Feautes parsed ***
*** STATUS: 3100000 Bed Feautes parsed ***
*** STATUS: 3200000 Bed Feautes parsed ***
*** STATUS: 3300000 Bed Feautes parsed ***
*** STATUS: 3400000 Bed Feautes parsed ***
*** STATUS: 3500000 Bed Feautes parsed ***
*** STATUS: 3600000 Bed Feautes parsed ***
*** STATUS: 3700000 Bed Feautes parsed ***
*** STATUS: 3800000 Bed Feautes parsed ***
*** STATUS: 3900000 Bed Feautes parsed ***
*** STATUS: 4000000 Bed Feautes parsed ***
*** STATUS: 4100000 Bed Feautes parsed ***
*** STATUS: 4200000 Bed Feautes parsed ***
*** STATUS: 4300000 Bed Feautes parsed ***
*** STATUS: 4400000 Bed Feautes parsed ***
*** STATUS: 4500000 Bed Feautes parsed ***
*** STATUS: 4600000 Bed Feautes parsed ***
*** STATUS: 4700000 Bed Feautes parsed ***
*** STATUS: 4800000 Bed Feautes parsed ***
*** STATUS: 4900000 Bed Feautes parsed ***
*** STATUS: 5000000 Bed Feautes parsed ***
*** STATUS: 5100000 Bed Feautes parsed ***
*** STATUS: 5200000 Bed Feautes parsed ***
*** STATUS: 5300000 Bed Feautes parsed ***
*** STATUS: 5400000 Bed Feautes parsed ***
*** STATUS: 5500000 Bed Feautes parsed ***
*** INFO: finished parsing Bed file ***
*** [DONE] Duration [0:00:10.589523] ***
*** INFO: finished creating overlaps ***
*** [DONE] Duration [0:00:10.590025] ***
*** [DONE] Duration [0:00:10.590296] ***
*** INFO: [Sun 11 Aug 2019 01:47:07 PM ] Print Variants to /home/owner/RNAEditor/rnaEditor/sample/sample.alu.vcf ***
*** INFO: [Sun 11 Aug 2019 01:47:07 PM ] Print Variants to /home/owner/RNAEditor/rnaEditor/sample/sample.nonAlu.vcf ***
*** INFO: [Sun 11 Aug 2019 01:47:07 PM ] Assembling Genome from /home/owner/RNAEditor/rnaEditor_annotations/human/GRCH38/Homo_sapiens.GRCh38.83.gtf ***
*** [DONE] Duration [0:02:40.692249] ***
*** INFO: [Sun 11 Aug 2019 01:49:48 PM ] remove Missmatches from the intronic splice junctions ***
*** [DONE] Duration [0:00:00.119274] ***
*** INFO: [Sun 11 Aug 2019 01:49:48 PM ] Print Variants to /home/owner/RNAEditor/rnaEditor/sample/sample.noSpliceJunction.vcf ***
*** INFO: [Sun 11 Aug 2019 01:49:48 PM ] remove Missmatches from homopolymers ***
*** INFO: 0 out of 0 passed the Homopolymer-Filter ***
*** [DONE] Duration [0:00:00.001687] ***
*** INFO: [Sun 11 Aug 2019 01:49:48 PM ] Print Variants to /home/owner/RNAEditor/rnaEditor/sample/sample.noHomo.vcf ***
*** INFO: [Sun 11 Aug 2019 01:49:48 PM ] Search non uniquely mapped reads ***
*** INFO: [Sun 11 Aug 2019 01:49:48 PM ] Create fasta file for blat ***
*** ERROR: No Variants left ***
*** ERROR: RnaEditor Failed ***
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