Comments (1)
rpetrovski
commented on July 23, 2024
The example data seems to have been built with iSAAC-01. Both iSAAC-01 and iSAAC-02 are not being supported anymore. Please let me know if the issue still exists with iSAAC-03
Roman.
$ samtools view bam/problem.bam -H |grep VN
@hd VN:1.0 SO:coordinate
@pg ID:iSAAC PN:iSAAC CL:/opt/illumina/Isis/2.5.26.13/Workflows/ResequencingWorker/isaac-align -t /home/ec2-user/compute/scratch/isaacTemp -o /home/ec2-user/compute/344404/isaac_align/Alignment -r /opt/genomes/Homo_sapiens/UCSC/hg38-hli/Sequence/IsaacIndex/sorted-reference.xml --base-calls HLVMVCCXX -s HLVMVCCXX/SampleSheetNew.csv --ignore-missing-filters 1 --base-quality-cutoff 15 --use-bases-mask Y150N1,Y150N1 --default-adapters AGATCGGAAGAGCACACGTCTGAACTCCAGTCA_,_TGACTGGAGTTCAGACGTGTGCTCTTCCGATCT --variable-read-length yes --barcode-mismatches 1 --ignore-missing-bcls 1 --stop-at Finish --allow-empty-flowcell 1 --seed-length 32 --cleanup-intermediary 1 --verbosity 3 --start-from Start --lane-number-max 8 --memory-limit 56 --base-calls-format fastq-gz --stats-image-format none --per-tile-tls 1 VN:iSAAC-01.14.02.06
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Related Issues (14)
- Compile error HOT 10
- mm10 reference HOT 1
- make error HOT 1
- isaac-sort-reference: --jobs 1 results in 2400% CPU load? HOT 9
- error building isaac2 HOT 2
- contigs.xml does not support seed length 32 HOT 7
- isaac-sort-reference: --jobs N is ignored HOT 4
- Compile on Mac HOT 2
- isaac-sort-preferenc: space in file path HOT 3
- Error occurs when isaac-unpack-reference HOT 1
- Can Isaac2 align fasta files? HOT 1
- Aligned reads only have 25 bases. HOT 4
- Base quality scores [0-63] supported only. HOT 1
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