johnstonmj
johnstonmj
A small subset of samples were failing with: ``` circlemap/extract_circle_SV_reads.py", line 123, in extract_sv_circleReads if read.is_read2 and read.qname == read1.qname: AttributeError: 'str' object has no attribute 'qname' ``` The loop...
Hi Iñigo, I was performing the Circle-Map Realign tutorial, and encountered a few warnings. My command: ``` Circle-Map Realign -t 4 -i sort_circular_read_candidates.bam -qbam qname_unknown_circle.bam -sbam sorted_unknown_circle.bam -fasta $ref_genome -o...
Hi Inigo, I have multiple samples where Circle-Map will fail with: `"An error happenend during execution. Exiting"` stderr: ``` [E::idx_find_and_load] Could not retrieve index file for 'output/circle-map/namesort_bams/tissue1.namesort.bam' 0%| | 0/800...
I encountered the error: `ImportError: Bio.Alphabet has been removed from Biopython. In many cases, the alphabet can simply be ignored and removed from scripts. In a few cases, you may...
Hi Inigo, While running my samples, I encountered some warnings that I believe come from divide-by-zero during certain coverage calculations. ``` /home/michael/circles/.snakemake/conda/68e54810/lib/python3.8/site-packages/circlemap/Coverage.py:149: RuntimeWarning: invalid value encountered in ulong_scalars start_coverage_ratio =...
I recently re-installed sleuth in a conda environment, re-ran a previously functioning sleuth script, and encountered this error in sleuth_prep: ``` Error in `[.data.table`(counts_test, , .(total = sum(est_counts)), by =...
I was excited to try scRNA analysis through this Snakemake workflow, however, I encountered multiple errors trying to run the test dataset. I believe that I've corrected them here. In...
I would like to go from transcripts back to the annotated gene names in a GTF. I am trying this command: `geneoverlaps = getGenes("/media/michael/Storage Drive/Desktop/20161117rnaseq/reference/Mus_musculus.GRCm38.86.gtf", structure(bg_AM1)$trans, UCSC=FALSE, attribute="gene_id") ` I...
I have encountered an issue with large INDELs being silently discarded from my results. This is the offending VCF entry: `contig_xyz 133527 Sniffles2.DEL.50S0 GGATGAACTCTTGGATTCTTGGGCTCATGTCGGACAGGATGCCGCCCCAGCTTCTCAGGTTGATGCCCTGGGATCTAGAATCCAGCAGTGTGGGCAGCACCCGGAACAGCTTGAAGAAGTCCACGTTGGCGTACAGGGTATCCTCGATCCACTGCAGGGTTCCCTGGCTCAGACTGCACAGGGCATATCTGACGGTCTTGGCGCCTCTCCGCTGGCTGAAGATGATGAACCGTTCCAGCAGGGCCTCAGAACAGGCGATATCCTTCAGGGCGAGATCTGGCACGCCATGAGCAAACTGCTCGGGCCGCACTTGGCTGTTGATCAGCAGGTACACCACGCTGTCGCTCAGGCCGATGTTCTTGATGAGGAACAGTGTCAGGGTTTCCTCGTCCTTCAGGATGTCCCGGATTCTGATGCCCCTGCCGGCGATTCTCTCGGGGTGTGTTCTCAGGGTGTCCATGAACTGGCTCAGGATGTGCAGCTCGGTCCAGATTCTGCCCAGGTGCTGAGACTCAGGGGCGTTCATCAGCAGCTCTTGGAAGTCCCGGTACACTCTGGCCAGGATGCTGTTGTTGTAGTTGGACACGATGCCAGGGCTTTCGCCAGGTGTGGGGCTCTGAAAGCAGGGGTTGTTCACGTTGCAGAAGATGCCCTGCAGCCAAGGCAGCATTCCGGCAGAAGGCATGGCCTTGTTGGGGAAGTGACACTCGTGGTGGCTGTACAGAGGATTGGCGTTCCGCAGCCAGATCAGCACCAGAAACAGGCTCAGGGGCCACACGAGTTCCACCACGAATCTGATTTTCTGCCGCTTCCGCAGGGTCCAGTTCTTCCACAGCAGCAGCTGAATCTGCCGCACGAATCCCATGGTGGCCAGCTCGGTCGTCCCGGGGCCTCTACTGTCCAGAGTCCTCCGCGGATCCCGATCTGACGGTTCACTAAACGAGCTCTGTTTATATAGACCTCCCACCGTACACGCCTACCGCCCATTTGCGTCAACGGGGCGGGCGATCGCAGTTGTTACGACATTTTGGAAAGTCCCGTTGATTTTGGTGCCAAAACAAACTCCCATTGACGTCAATGGGGTGGAGACTTGGAAATCCCCGTGAGTCAAACCGCTATCCACGCCCATTGGTGTACTGCCAAAACCGCATCACCATGGTAATAGCGATGACTAATACGTAGATGTACTGCCAAGTAGGAAAGTCCCGTAAGGTCATGTACTGGGCATAATGCCAGGCGGGCCATTTACCGTCATTGACGTCAATAGGGGGCGGACTTGGCATATGATACACTTGATGTACTGCCAAGTGGGCAGTTTACCGTAAATACTCCACCCATTGACGTCAATGGAAAGTCCCTATTGGCGTTACTATGGGAACATACGTCATTATTGACGTCAATGGGCGGGGGTCGTTGGGCGGTCAGCCAGGCGGGCCATTTACCGTAAGTTATGTAACGCGGAACTCCATATATGGGCTATGAACTAATGACCCCGTAATTGATTACTATTAATAACTAGTCAATAATCAATGCCAACATGGCGGTCATATTGGACATGAGCCAATATAAATGTACATATTATGATATAGATACAACGTATGCAATGGCCAATAGCCAATATTGATTTATGCTATATAACCAATGAATAATATGGCTAATGGCCAATATTGAAGATCCCCGGGTACCGAGCTCGAATTCATCGATGATGATCCACTAGTAACGGCCGCCAGTGTGCTGGAATTCGCCCTTCCCGCATGGCATCTCATTACCGCCCGATCCGGCGGTTTCCGCTTCCGTTCCGCATGCTAACGAGGAACGGGCAGGGGGCGGGGCCCGGGCCCCGACTTCCCGGTTCGGCGGTAATGTGATACGAGCCCCGCGCGCCCGTTGGCCGTCCCCGGGCCCCCGGTCCCGCCCGCCGGACGCCGGGACCAACGGGACGGCGGGCGGCCCTTGGGCCGCCCGCCTTGCCGCCCCCCCATTGGCCGGCGGGCGGGACCGCCCCAAGGGGGCGGGGCCGCCGGGTAAAAGAAGTGAGAACGCGAAGCGTTCGCACTTCGTCCCAATATATATATATTATTAGGGCGAAGTGCGAGCACTGGCGCCGTGCCCGACTCCGCGCCGGCCCCGGGGGCGGACCCGGGCGGCGGGGGGCGGGTCTCTCCGGCGCACATAAAGGCCCGGCGCGACCGACGCCCGCAGACGGCGCCGGCCACGAACGACGGGAGCGGCTGCGGAGCACGCGGACCGGGAGCGGGAGTCGCAGAGGGCCGTCGGAGCGGACGGCGTCGGCATCGCGACGCCCCGGCTCGGGATCGGGATCGCATCGGAAAGGGACACGCGGACGCGGGGGGGAAAGACCCGCCCACCCCACCCACGAAACACAGGGGACGCACCCCGGGGGCCTCCGACGACAGAAACCCACCGGTCCGCCTTTTTTGCACGGGTAAGCACCTTGGGTGGGCGGAGGAGGGGGGACGCGGGGGCGGAGGAGGGGGGACGCGGGGGCCGGAGGAGGGGGGACGCGGGGGCGGAGGAGGGGG G 59 PASS PRECISE;SVTYPE=DEL;SVLEN=-2542;END=136069;SUPPORT=259;COVERAGE=335,326,308,260,257;STRAND=+-;AF=0.869;STDEV_LEN=0;STDEV_POS=0 GT:GQ:DR:DV 1/1:60:39:259`...
[Snakemake 8.0](https://snakemake.readthedocs.io/en/stable/project_info/history.html) has been released. This removes the snakemake option '--reason', and causes ipa to fail. **Operating system** Ubuntu 22.04.3 LTS **Package name** ipa (wrapper) version=1.8.0 **Conda environment** ``` #...