RDorney
commented
1 year ago More information on the error messages I receive while the pipeline is running and files are progressing through stages
For several (but not all) files I will run into errors like:
=== Stage minimap2_transcriptome (positive_control_nanopore2020_D10x_M90) ===
Mismatch between length of bases and qualities for read 9276039 (id=2db111e8-9f27-5a08-a383-d2af7b6d92bd ENST00000391975.5|ENSG00000115677.1 8|OTTHUMG00000133391.10|OTTHUMT00000257245.6|HDLBP-203|HDLBP|6372|protein_coding|,+strand,0-6372 length=5861 error-free_length=6383 read_ide ntity=78.63%).
# qualities=138, # bases=5861
....
at stream.Read.validate(Read.java:114)
at stream.Read.<init>(Read.java:78)
at stream.Read.<init>(Read.java:61)
at stream.FASTQ.quadToRead(FASTQ.java:872)
at stream.FASTQ.toReadList(FASTQ.java:705)
at stream.FastqReadInputStream.fillBuffer(FastqReadInputStream.java:111)
at stream.FastqReadInputStream.nextList(FastqReadInputStream.java:96)
at stream.ConcurrentGenericReadInputStream$ReadThread.readLists(ConcurrentGenericReadInputStream.java:656)
at stream.ConcurrentGenericReadInputStream$ReadThread.run(ConcurrentGenericReadInputStream.java:635)
Input: 9276000 reads 16463207847 bases
Output: 9276000 reads (100.00%) 16463207847 bases (100.00%)
Time: 251.239 seconds.
Reads Processed: 9276k 36.92k reads/sec
Bases Processed: 16463m 65.53m bases/sec
Exception in thread "main" java.lang.RuntimeException: ReformatReads terminated in an error state; the output may be corrupt.
at jgi.ReformatReads.process(ReformatReads.java:1103)
at jgi.ReformatReads.main(ReformatReads.java:43)
ERROR: Command failed with exit status = 1 :
/opt/JAFFA-version-2.3/tools/bin/reformat ignorebadquality=t in=../positive_control_nanopore2020_D100x_M90.fastq.gz out=positive_control_nan opore2020_D100x_M90.fastq/positive_control_nanopore2020_D100x_M90.fastq.fasta threads=1 ;= Stage minimap2_transcriptome (positive_control_nanopore2020_D10x_M95) ~runs without error
== Stage filter_transcripts (positive_control_nanopore2020_D10x_M95) ==
java.lang.AssertionError:
Mismatch between length of bases and qualities for read 1934044 (id=d642ebd4-a024-95da-520b-1b29b14a4348 ENST00000361624.2|ENSG00000198804.2|-|-|MT-CO1-201|MT-CO1|1542|protein_coding|,-strand,0-1542 chimera ENST00000582467.2|ENSG000001716 34.19|OTTHUMG00000132254.6|OTTHUMT00000448091.2|BPTF-215|BPTF|11789|protein_coding|,+strand,0-11789 length=12759 error-free_length=13347 read_identity=87.51%).
# qualities=12894, # bases=12759
at stream.Read.validate(Read.java:114)
at stream.Read.<init>(Read.java:78)
at stream.Read.<init>(Read.java:61)
at stream.FASTQ.quadToRead(FASTQ.java:872)
at stream.FASTQ.toReadList(FASTQ.java:705)
at stream.FastqReadInputStream.fillBuffer(FastqReadInputStream.java:111)
at stream.FastqReadInputStream.nextList(FastqReadInputStream.java:96)
at stream.ConcurrentGenericReadInputStream$ReadThread.readLists(ConcurrentGenericReadInputStream.java:656)
at stream.ConcurrentGenericReadInputStream$ReadThread.run(ConcurrentGenericReadInputStream.java:635)
Input: 1934000 reads 3369013255 bases
Output: 1934000 reads (100.00%) 3369013255 bases (100.00%)
Time: 50.653 seconds.
Reads Processed: 1934k 38.18k reads/sec
Bases Processed: 3369m 66.51m bases/sec
Exception in thread "main" java.lang.RuntimeException: ReformatReads terminated in an error state; the output may be corrupt.
at jgi.ReformatReads.process(ReformatReads.java:1103)
at jgi.ReformatReads.main(ReformatReads.java:43)
ERROR: Command failed with exit status = 1 :
/opt/JAFFA-version-2.3/tools/bin/reformat ignorebadquality=t in=../positive_control_nanopore2020_D20x_M85.fastq.gz out=positive_control_nanopore2020_D20x_M85.fastq/positive_control_nanopore2020_D20x_M85.fastq.fasta threads=1 ;================ Stage filter_transcripts (positive_control_nanopore2020_D10x_M95) =================
java -ea -Xmx200m -cp /opt/JAFFA-version-2.3/tools/bbmap/current/ jgi.ReformatReads ignorebadquality=t in=../positive_control_nanopore2020_D20x_M85.fastq.gz out=positive_control_nanopore2020_D20x_M85.fastq/positive_control_nanopore2020_D2 0x_M85.fastq.fasta threads=1
Executing jgi.ReformatReads [ignorebadquality=t, in=../positive_control_nanopore2020_D20x_M85.fastq.gz, out=positive_control_nanopore2020_D20x_M85.fastq/positive_control_nanopore2020_D20x_M85.fastq.fasta, threads=1]
Set threads to 1
Input is being processed as unpaired
[M::worker_pipeline::3857.303*1.00] mapped 286876 sequences
java.lang.AssertionError:
Mismatch between length of bases and qualities for read 1934044 (id=d642ebd4-a024-95da-520b-1b29b14a4348 ENST00000361624.2|ENSG00000198804.2|-|-|MT-CO1-201|MT-CO1|1542|protein_coding|,-strand,0-1542 chimera ENST00000582467.2|ENSG000001716 34.19|OTTHUMG00000132254.6|OTTHUMT00000448091.2|BPTF-215|BPTF|11789|protein_coding|,+strand,0-11789 length=12759 error-free_length=13347 read_identity=87.51%).
# qualities=12894, # bases=12759
......
at stream.Read.validate(Read.java:114)
at stream.Read.<init>(Read.java:78)
at stream.Read.<init>(Read.java:61)
at stream.FASTQ.quadToRead(FASTQ.java:872)
at stream.FASTQ.toReadList(FASTQ.java:705)
at stream.FastqReadInputStream.fillBuffer(FastqReadInputStream.java:111)
at stream.FastqReadInputStream.nextList(FastqReadInputStream.java:96)
at stream.ConcurrentGenericReadInputStream$ReadThread.readLists(ConcurrentGenericReadInputStream.java:656)
at stream.ConcurrentGenericReadInputStream$ReadThread.run(ConcurrentGenericReadInputStream.java:635)
Input: 1934000 reads 3369013255 bases
Output: 1934000 reads (100.00%) 3369013255 bases (100.00%)
Time: 50.653 seconds.
Reads Processed: 1934k 38.18k reads/sec
Bases Processed: 3369m 66.51m bases/sec
Exception in thread "main" java.lang.RuntimeException: ReformatReads terminated in an error state; the output may be corrupt.
at jgi.ReformatReads.process(ReformatReads.java:1103)
at jgi.ReformatReads.main(ReformatReads.java:43)
ERROR: Command failed with exit status = 1 :
/opt/JAFFA-version-2.3/tools/bin/reformat ignorebadquality=t in=../positive_control_nanopore2020_D20x_M85.fastq.gz out=positive_control_nanopore2020_D20x_M85.fastq/positive_control_nanopore2020_D20x_M85.fastq.fasta threads=1 ;Despite these errors, the files will continue into later stages:
============= Stage extract_fusion_sequences (positive_control_nanopore2020_D10x_M95) ==============
java -ea -Xmx200m -cp /opt/JAFFA-version-2.3/tools/bbmap/current/ jgi.ReformatReads ignorebadquality=t in=../positive_control_nanopore2020_D20x_M90.fastq.gz out=positive_control_nanopore2020_D20x_M90.fastq/positive_control_nanopore2020_D20x_M90.fastq.fasta threads=1
Executing jgi.ReformatReads [ignorebadquality=t, in=../positive_control_nanopore2020_D20x_M90.fastq.gz, out=positive_control_nanopore2020_D20x_M90.fastq/positive_control_nanopore2020_D20x_M90.fastq.fasta, threads=1]
Set threads to 1
Input is being processed as unpaired
[M::worker_pipeline::4170.854*1.00] mapped 207573 sequences
[M::main] Version: 2.17-r941
[M::main] CMD: /opt/JAFFA-version-2.3/tools/bin/minimap2 -t 1 -x map-ont -c /opt/JAFFA-version-2.3/hg38_genCode22.fa positive_control_nanopore2020_D10x_M90.fastq/positive_control_nanopore2020_D10x_M90.fastq.fasta
[M::main] Real time: 4170.911 sec; CPU: 4170.349 sec; Peak RSS: 2.835 GB
================ Stage filter_transcripts (positive_control_nanopore2020_D10x_M90) =================
Done reading in transcript IDs
Reading the input alignment file, jaffal_edited_positive_control_nanopore2020_D100x_M85.fastq/jaffal_edited_positive_control_nanopore2020_D100x_M85.fastq.paf
0
1000000
2000000
3000000
3038753 reads processed. Finished.
java -ea -Xmx200m -cp /opt/JAFFA-version-2.3/tools/bbmap/current/ jgi.ReformatReads in=jaffal_edited_positive_control_nanopore2020_D10x_M85.fastq/jaffal_edited_positive_control_nanopore2020_D10x_M85.fastq.fasta out=stdout.fasta fastawrap=0
....
============= Stage extract_fusion_sequences (positive_control_nanopore2020_D10x_M90) ==============
Executing jgi.ReformatReads [in=jaffal_edited_positive_control_nanopore2020_D100x_M85.fastq/jaffal_edited_positive_control_nanopore2020_D100x_M85.fastq.fasta, out=stdout.fasta, fastawrap=0]
Input is being processed as unpaired
Input: 2418119 reads 4376157978 bases
Output: 2418119 reads (100.00%) 4376157978 bases (100.00%)
Time: 74.634 seconds.
Reads Processed: 2418k 32.40k reads/sec
Bases Processed: 4376m 58.64m bases/sec
================== Stage minimap2_genome (positive_control_nanopore2020_D10x_M95) ==================
[M::mm_idx_gen::11.980*0.83] collected minimizers
[M::mm_idx_gen::16.631*0.88] sorted minimizers
[M::main::16.631*0.88] loaded/built the index for 195175 target sequence(s)
[M::mm_mapopt_update::17.107*0.88] mid_occ = 110
[M::mm_idx_stat] kmer size: 15; skip: 10; is_hpc: 0; #seq: 195175
[M::mm_idx_stat::17.405*0.88] distinct minimizers: 16950829 (43.60% are singletons); average occurrences: 3.243; average spacing: 5.406
[M::worker_pipeline::3316.073*1.00] mapped 276210 sequences
Input: 3432565 reads 6048616768 bases
Output: 3432565 reads (100.00%) 6048616768 bases (100.00%)
Time: 104.254 seconds.
Reads Processed: 3432k 32.92k reads/sec
Bases Processed: 6048m 58.02m bases/sec
================== Stage minimap2_genome (positive_control_nanopore2020_D10x_M90) ==================
[M::mm_idx_gen::129.049*0.96] collected minimizers
[M::worker_pipeline::961.815*1.00] mapped 282471 sequences
[M::worker_pipeline::4260.013*1.00] mapped 276724 sequences
[M::mm_idx_gen::217.976*0.98] sorted minimizers
[M::main::217.976*0.98] loaded/built the index for 455 target sequence(s)
[M::mm_mapopt_update::221.762*0.98] mid_occ = 792
[M::mm_idx_stat] kmer size: 15; skip: 5; is_hpc: 0; #seq: 455
[M::mm_idx_stat::224.110*0.98] distinct minimizers: 167291034 (34.68% are singletons); average occurrences: 6.239; average spacing: 3.075
[M::worker_pipeline::1435.168*1.00] mapped 281994 sequences
[M::worker_pipeline::4730.434*1.00] mapped 276264 sequences
[M::worker_pipeline::1019.761*0.99] mapped 12621 sequences
[M::main] Version: 2.17-r941
[M::main] CMD: /opt/JAFFA-version-2.3/tools/bin/minimap2 -t 1 -x splice -c /opt/JAFFA-version-2.3/hg38.fa positive_control_nanopore2020_D10x_M95.fastq/positive_control_nanopore2020_D10x_M95.fastq.fusions.fa
[M::main] Real time: 1019.905 sec; CPU: 1014.720 sec; Peak RSS: 18.983 GB
============== Stage make_fasta_reads_table (positive_control_nanopore2020_D10x_M95) ===============
[M::worker_pipeline::1907.097*1.00] mapped 282043 sequences
[M::worker_pipeline::5201.252*1.00] mapped 276573 sequences
[M::mm_idx_gen::144.855*0.86] collected minimizers
[M::mm_idx_gen::233.550*0.91] sorted minimizers
[M::main::233.550*0.91] loaded/built the index for 455 target sequence(s)
[M::mm_mapopt_update::237.213*0.92] mid_occ = 792
[M::mm_idx_stat] kmer size: 15; skip: 5; is_hpc: 0; #seq: 455
[M::mm_idx_stat::239.559*0.92] distinct minimizers: 167291034 (34.68% are singletons); average occurrences: 6.239; average spacing: 3.075
[M::worker_pipeline::2381.133*1.00] mapped 281944 sequences
[M::worker_pipeline::5674.755*1.00] mapped 276818 sequences
[M::worker_pipeline::2854.149*1.00] mapped 281181 sequences
[M::worker_pipeline::6145.728*1.00] mapped 276402 sequences
[M::worker_pipeline::3327.070*1.00] mapped 281324 sequences
[M::worker_pipeline::6616.826*1.00] mapped 276139 sequences
[M::worker_pipeline::3799.048*1.00] mapped 282279 sequences
[M::worker_pipeline::7087.283*1.00] mapped 275430 sequences
[M::worker_pipeline::2286.720*0.99] mapped 25347 sequences
[M::main] Version: 2.17-r941
[M::main] CMD: /opt/JAFFA-version-2.3/tools/bin/minimap2 -t 1 -x splice -c /opt/JAFFA-version-2.3/hg38.fa jaffal_edited_positive_control_nanopore2020_D100x_M85.fastq/jaffal_edited_positive_control_nanopore2020_D100x_M85.fastq.fusions.fa
[M::main] Real time: 2286.867 sec; CPU: 2266.908 sec; Peak RSS: 18.982 GB
============== Stage make_fasta_reads_table (positive_control_nanopore2020_D10x_M90) ===============
================== Stage get_final_list (positive_control_nanopore2020_D10x_M95) ===================
================== Stage get_final_list (positive_control_nanopore2020_D10x_M90) ===================
R version 4.3.0 (2023-04-21) -- "Already Tomorrow"
Copyright (C) 2023 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (64-bit)
R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.
Natural language support but running in an English locale
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> options(echo=FALSE)
[1] "Getting the location of fusion transcripts in the genome.."
Calculating gap size in the genome...
Checking if the fusions are in frame...
[M::worker_pipeline::6645.681*1.00] mapped 281746 sequences
[M::worker_pipeline::9932.681*1.00] mapped 276604 sequences
Merging with read coverage data...
Reassigning Low Confidence breakpoints
Done producing summary file
=============== Stage report_3_gene_fusions (positive_control_nanopore2020_D10x_M95) ===============
read id: f0b35753-71f3-f9c3-9a50-77dbb994040b does not conform to 3 gene fusion structure.However I then get the same error message again in
== Stage report_3_gene_fusions (positive_control_nanopore2020_D10x_M90) ==
java -ea -Xmx200m -cp /opt/JAFFA-version-2.3/tools/bbmap/current/ jgi.ReformatReads ignorebadquality=t in=../positive_control_nanopore2020_D50x_M85.fastq.gz out=positive_control_nanopore2020_D50x_M85.fastq/positive_control_nanopore2020_D50x_M85.fastq.fasta threads=1
Executing jgi.ReformatReads [ignorebadquality=t, in=../positive_control_nanopore2020_D50x_M85.fastq.gz, out=positive_control_nanopore2020_D50x_M85.fastq/positive_control_nanopore2020_D50x_M85.fastq.fasta, threads=1]
Set threads to 1
Input is being processed as unpaired
java.lang.AssertionError:
Mismatch between length of bases and qualities for read 2524899 (id=8f66a3fe-c408-fef8-1779-6ce91cc4a34f ENST00000344063.7|ENSG00000108107.15|OTTHUMG00000171991.4|OTTHUMT00000416277.2|RPL28-201|RPL28|4209|protein_coding|,+strand,0-4209 length=4170 error-free_length=4235 read_identity=94.79%).
# qualities=135, # bases=4170
@c9990bd9-8607-294c-8734-feb361710e64 ref|NM_018666-NM_001330000,+strand,0-5484 length=5419 error-free_length=5485 read_identity=89.20%
CGTTCAGTTACGTATTGCTCTCTTTCCGGTCATCAGGTCGCCGCTGCGAAGGGGCCGCCACCATGTCTGCGCATCTGCAATGGATGGTCGTGCGGAACTGCTCCAGTTTCCTGATCAACGAGGAATAAGCAGACCTACAGCACTGAGCCCAATAACTTGAAGGCCCGCAATTCAACTTCCGCTACAGCGGATGATTCACGCAGGACTGTGGGCGTGGAGCCGGCGGCCGACGGCAAAGTGTCGTGGTGGTCATTAAGCAGATCCGGCCAGCGGAAGCCTGCCACCTCCTATGTGCGGACACCATCAACAAGAATGCTCGCGCCCACGCTCAGCAGCATCAGACACATGATCCGCAAGAACAAGTACCGCCCCGACCTGCTGATGGCAGCCATCCGCAGGGCCAGCGCCATCCTGTGCAGCCAGAAGCCTGTGATGGTGAAGAAAGCGGACCGCCCCACCAAGAGCTCCTGAGCCCCCTGCCCCCAGAGCAATAAAGTCAGCTGCTTTCTCACCCTGCCTCGACGGGCCTCCCTTTTTTGAAACGCTCTGGGGAGCTCTGGCCTATGTTGTCATTCAGGCCATGTCATCAAACTCTGCATGTCACCTTGTCCATCTGGAGGTGATGTCAATGGCTGGCCACATGCAGGAGGGGTGGGGTAGCTGCCTTGTCCTTTGGTGGCAAGGGTCACTGTCTTCACAGAAAAATTTGCTGACTTGTGATTGAACCTACTGTCCCATTGTGAGGTGGCCTGAAGAATCCCAGCTGGGGAGTGGCTTCCATTCAGAAGAAGAAAGGCCTTTTCTAGCCCAGAAGGGTGCAGGCTGAGGCTGGGCCCTGGGCCCTGGTGCTGTAGCACGGTTTGGGGACTTGGGGTGTTCCCAAGACCTGGGGGACGACGAACATCCGGGAGGAAGATGAGAGACTTTTGCATCCAGGAGTGGGTGCGGCCACATTTGGAGGGGATGGAGCTTTGATGCAACCTGTCTCTGAGATGGGCAACTTTGGTGGGTGGTGGCTTATAACTGTAAGGGGATGGCTGACCAGGGTACAGCCAGCAGGCATTGAGCAGCCTTAGCATTGTCCCCCTACTCCCGTCCTCCAGGTGTCCGCATCCCTCCCCTATCTCTTTGAGCTGGCTCTTGTCACCTTAGGACTCATCTAGTGGCCGCTCTTTGGGCCACCCTGTCACCCAAGCTTTCCTGATTGCCCAGCCCTCTTGTTTCCTTTGGCCTGTTTGCTCCCTAGTGTTTATTACAGCTTGTGAGGCCAGGAGTTTGAGACCATCCTAGGCAACACCAATGAGACACCGTCTCTAAAATAAAATTAGCTGGGTGTGGTGGTCACCGCCTGTGGTCCCAGCTCCTCAGAGGTTGAGTGGGGCTGAGGGACGGAGCACTTGAACCAAGAATATGGGGCTGCAGTAGCCCAGAGCCCCACCACCACACTCCAGCCTGGAAGACACCATGACACAGTGAGGCCTGGATGGAAAAGAGTCCTGTGTTGATCCTCACATGTTTCCTGAACACTAACTCTGTCAGCCACTGCCAGGACCAAAGGATCAGCATCATGGCACCCCTGGTTCCACTGCCATCCTGGGGGTACCGATTCAAAGAAGGACTCTGCTCCCTGTCTGAGACCACCCCCCGGCTCTGACTGAGATAAGGGGACTGTCAGGGCCTCGACTTGCCATTGGTTGGGGTCGTACGGGGCTGGGAGCCTGCGTTTTGAGGCGGGCCTGCCCTTCCGACCTCAGTCCTGTCTGCTCCAGTCTTGCCCAACTCGAAGGGAGCAGATCTGACCACTTGCCAGCCCCTGTCTGCTGTGAATTACATTTCCTTTGTCTTCCTTAGTTGGGTCTATTAGCTCAGATTGAGGTGTTACCTTAAAATGAGTTGGGTGACTTGGTACCTGCTCAGGACTCCCCCGCACTGTCCGTCCCACTCAGGCCCACCTCCAGCTGGCCTCACTCCGCTGAGTGACTTCGTACCTGCTCAGGAGCCCCCACTGTCCCAGTCCCACTCAGGCCCATCTCGCTGGCCTCACTGCGCTGGGACTCCGCCTTCATAAAGGAGAGCTCACTGCTCACGTTAGTAAGATGGCCCCTTCTCGTGAGGCCTCTCCCTGGCACCTGCTTCAGTTGTCCTCCACAGCACTGATTTGCAGCCCACAAGCTGGCAGGTTTATCTGTCTCATGTTTGTCTTGTGCTGGTCGGCAAGGGGTTTAGTCTAGCACACCAGCATATAATGAGATGCTTGATGAATGGTACATATTGAATGTATAAAGCCCACCGGTCCTGAGTTTGCTCACTGGAGACTTTCTGGAGATGGAGTCTCGCTCTGTGCCCGGCTGGCGAAGTGCAATGGCGCGATCTTGGCTCACTGCAGCCTCCCACCTCCTGGGTTCAACGATTCTCCTGCCTCAGCCTCCCGAGTAGCTGGGATTACAGGTGGTATGCCACACCCAGCTCAGTATTGTATTTTTAGCAGAGATCGGGTTTCACCATTGCAGGCTGGTTTGGAACTCCTGACTTCAAATTACCCACCTGCCTCAACCTCCCAAAGTGCTGGCATTACAAGCGCTCGAGGCTTCTGATGTGGCTGCTGCTGCTCAGAAGGCCTTGTCCTTAACCACCTCCTTGCCTGCCCTGGAGGCTTGTGCCTCTAGGACCCCACCCCTGTGGAGTCCTGCTGGCTTTCTCCATCCCTATCTGAATCCTCCTGCTGTGTGGCCTCCCCTGGTCTCATCCGTAACACAGCCCAACAGTGGCCTCTGTTCCTGCGGGTGGCCAGCCCATCTGTGTGTGGCTGGGCTGGGGAGGCCACGCGTCTGGTATCTGAATGCTATCGGTGGGTTGGGGTGGAGGAACCAGGAGAGGGCTGGAGGGAGAGGAGATGGTCTCAGCCCCACAGAGTTTGGATGTCATCAGTGTGCTGAGCAAACGTGAACACCATTTCCCTCCTCTAGACCTCATCTTGGAGAGAGAGATGTTGGATGGGGCCATCTATTCCAGCTTTATTCACAAATCATGTCTGTTGGCCTGGAAATTGGAAAACCAGTTAAACCAAAAACGTGATATTAAGAAAACAGGCGGAGCTCACCATTGTAAAAATGCTGAAAGCCAAAGACAAAGTGGAGAACAAAGAAAAGCGTCTTGTCACATTACAGAAGGTCCTGATAAAGTAGTAGCTGCCCTCATCTAGAAACCAGGCCCAGGCAGTGGGGACACATCCAGTGCTGAAAGAACCTCCCCCAGGTCATCTATCCCAAGAGTGATGCCCGGCAGCATTCCAAGCTCAAGGGCTAATGGTTCACGGAAGCCAGGAATCAAACTGCCTGGGTTCCAGTCCCAGCTCTGCCAGTTATGCCCAGCTGTGGGACTTGGGCAACTCGTTTAGTAGCACCGTGCCTCAGTTCCCAATATGTAAAAGGCCATTTGAGTGCCTTTCACAGCCCTGCATAAGGCAGGTGTCTCAGTGTTCACTGCTATCTCTCCAGCTCTTAGTCCAGTAGCTACATGGTGAGTGAGCGTAGGGCGCACCCTGGAAGGCTGCCCAGCCCAAAGTTGTGCCAGAGCGCTGGGGATCAGACTCCCCACAGCAGCAGAGACTCAGGGACTGAGGCATCCTCTGTCACAGGACATGCTGCGTCTACTGGGTCAGGGCTCTGCTGCTCGGTGGCTGTGAACCTTAGGCAAGTTCCTCAACCTCTCTGTGTCTTCGTACCCTCATCTGTAACATGCGTGTCGATAGACCCTACTACTCCGGGTTGGTGAAGATTAAATGTGCAAAACCTGCTTGACGCTGTGCCCACAAATCCTGATTGTAGGAATAAATTAATGACTTTTTATAAATATTTTGATCGATGGACTCATGATCTGGATGTCTCACATGCCAATGACTAATTTGTACACAAACTAATGCTCGTGTTTCCCGAGCACCTGGAGAGACATAGCCAGATCCATGTGCGATAATGCCTGGTGGCTCCAGGTTGCCCCGCCGTCCTGTGGGCTGTGAGCTTTCCCAGCCTCCTGCCCGTGTTTGTGAATATCATTCTGTCCTCCAGCTGCATTTCCAGCCGAGCTCTTTGGCGCTGCCCAGGAATGGTATCAATTCCCCTGTTTCTCTGTAGCCAGTTACTAGAATAAAATCATCTACTTTAAAAGCAATAC
at stream.Read.validate(Read.java:114)
at stream.Read.<init>(Read.java:78)
at stream.Read.<init>(Read.java:61)
at stream.FASTQ.quadToRead(FASTQ.java:872)
at stream.FASTQ.toReadList(FASTQ.java:705)
at stream.FastqReadInputStream.fillBuffer(FastqReadInputStream.java:111)
at stream.FastqReadInputStream.nextList(FastqReadInputStream.java:96)
at stream.ConcurrentGenericReadInputStream$ReadThread.readLists(ConcurrentGenericReadInputStream.java:656)
at stream.ConcurrentGenericReadInputStream$ReadThread.run(ConcurrentGenericReadInputStream.java:635)
Input: 2524800 reads 4397913090 bases
Output: 2524800 reads (100.00%) 4397913090 bases (100.00%)
Time: 66.580 seconds.
Reads Processed: 2524k 37.92k reads/sec
Bases Processed: 4397m 66.05m bases/sec
Exception in thread "main" java.lang.RuntimeException: ReformatReads terminated in an error state; the output may be corrupt.
at jgi.ReformatReads.process(ReformatReads.java:1103)
at jgi.ReformatReads.main(ReformatReads.java:43)
read id: 97bbcd5f-5c99-c079-08c5-f9de492e7062 does not conform to 3 gene fusion structure.
read id: 0ed90292-a03b-79f8-49c7-a0f6cad8a986 does not conform to 3 gene fusion structure.
read id: a8a332ef-bc95-08a1-ff04-adc08e25bde0 does not conform to 3 gene fusion structure.
read id: 785523d8-f840-1378-82ab-088fd95db875 does not conform to 3 gene fusion structure.
read id: 7ed251aa-ab58-b50a-fab5-1d65e4bc61f6 does not conform to 3 gene fusion structure.
read id: 13001a1f-1ef1-115e-16e8-6b80f23c960c does not conform to 3 gene fusion structure.
read id: 26a7d451-1849-ee01-4ef4-7e5b4f9731b4 does not conform to 3 gene fusion structure.
java -ea -Xmx200m -cp /opt/JAFFA-version-2.3/tools/bbmap/current/ jgi.ReformatReads ignorebadquality=t in=../positive_control_nanopore2020_D20x_M95.fastq.gz out=positive_control_nanopore2020_D20x_M95.fastq/positive_control_nanopore2020_D20x_M95.fastq.fasta threads=1
nadiadavidson
stefanc-sbg
Hello, I am currently testing JAFFAL and other long-read fusion finding tools on a simulated dataset ~generated using badread to simulate reads and FUSIM to simulate fusions (including tri-fusions). The command I use:
The pipeline runs successfully and (relatively) smoothly on my spiked-in simulated pacbio dataset. except for this error message when entering Stage report_3_gene_fusions :
(and I get this type of message for several reads in several data files). However, my main issue is when I run JAFFAL on my spiked-in simulated nanopore dataset where the pipeline fails, and I do not get a jaffa_results.csv or .fasta output file.