Hello,
I am using QuasR to do spliced alignment of paired end reads to the human genome. This is done through SpliceMap. I have received an error message, which I have been unable to find in any forums. Is it possible for anyone to assist me?
My read length is 76, if this is relevant. It occurred to me that the problem could be short reads, since Splicemap does not work for short reads, but I do not think that this is the issue.
Thank you so much for your assistance! This is my first time going through the RNA-seq analysis pipeline, and this forum has been invaluable.
Cheers, Gabriella
The log message is as follows:
[1] "Decompressing file on Theory9 : /home/Lab/Desktop/Gabriella/RNA_Seq/Epidermis/Basal_Ker_S2_R1_001.fastq.gz" [1] "Decompressing file on Theory9 : /home/Lab/Desktop/Gabriella/RNA_Seq/Epidermis/Basal_Ker_S2_R2_001.fastq.gz" [1] "Writing BSgenome to disk on Theory9 : /home/Lab/Desktop/Gabriella/RNA_Seq/Epidermis/TempDir/RtmpKW69pw/file28337981ede.fa" [1] "Executing Splicemap on Theory9 using 6 cores. Parameters:" [1] "-max_intron 400000 -min_intron 20000 -max_multi_hit 10 -selectSingleHit TRUE -seed_mismatch 1 -read_mismatch 2 -try_hard yes -genome_dir /home/Lab/Desktop/Gabriella/RNA_Seq/Epidermis/TempDir/RtmpKW69pw/file28337981ede.fa -reads_list1 /home/Lab/Desktop/Gabriella/RNA_Seq/Epidermis/TempDir/RtmpKW69pw/Basal_Ker_S2_R1_001.fastq.gz2833a4169e3.fastq -reads_list2 /home/Lab/Desktop/Gabriella/RNA_Seq/Epidermis/TempDir/RtmpKW69pw/Basal_Ker_S2_R2_001.fastq.gz283311e34d93.fastq -read_format FASTQ -quality_format phred-33 -temp_path /home/Lab/Desktop/Gabriella/RNA_Seq/Epidermis/TempDir/RtmpKW69pw -num_chromosome_together 6 -num_threads 6 -bowtie_base_dir /home/Lab/R/x86_64-redhat-linux-gnu-library/3.2/BSgenome.Hsapiens.UCSC.hg19.Rbowtie/alignmentIndex/bowtieIndex -outfile /home/Lab/Desktop/Gabriella/RNA_Seq/Epidermis/TempDir/RtmpKW69pw/Basal_Ker_S2_R1_001.fastq.gz2833a4169e3.fastq2833355d17a6.sam" [1] "Error on Theory9 processing sample /home/Lab/Desktop/Gabriella/RNA_Seq/Epidermis/TempDir/RtmpKW69pw/Basal_Ker_S2_R1_001.fastq.gz2833a4169e3.fastq : failed while aligning 25mers"
Here is my session info:
R version 3.2.3 (2015-12-10) Platform: x86_64-redhat-linux-gnu (64-bit) Running under: CentOS release 6.7 (Final)
locale:
[1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C
[3] LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8
[5] LC_MONETARY=en_US.UTF-8 LC_MESSAGES=en_US.UTF-8
[7] LC_PAPER=en_US.UTF-8 LC_NAME=C
[9] LC_ADDRESS=C LC_TELEPHONE=C
[11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C
attached base packages: [1] stats4 parallel stats graphics grDevices utils datasets [8] methods base
other attached packages:
[1] BSgenome.Hsapiens.UCSC.hg19_1.4.0 BSgenome_1.38.0
[3] rtracklayer_1.30.2 Biostrings_2.38.4
[5] XVector_0.10.0 QuasR_1.10.1
[7] Rbowtie_1.10.0 GenomicRanges_1.22.4
[9] GenomeInfoDb_1.6.3 IRanges_2.4.8
[11] S4Vectors_0.8.11 BiocGenerics_0.16.1
[13] BiocInstaller_1.20.1
loaded via a namespace (and not attached):
[1] AnnotationDbi_1.32.3 GenomicAlignments_1.6.3
[3] zlibbioc_1.16.0 BiocParallel_1.4.3
[5] lattice_0.20-33 hwriter_1.3.2
[7] tools_3.2.3 grid_3.2.3
[9] SummarizedExperiment_1.0.2 Biobase_2.30.0
[11] DBI_0.3.1 latticeExtra_0.6-28
[13] lambda.r_1.1.7 futile.logger_1.4.1
[15] GenomicFiles_1.6.2 RColorBrewer_1.1-2
[17] futile.options_1.0.0 bitops_1.0-6
[19] biomaRt_2.26.1 RCurl_1.95-4.8
[21] RSQLite_1.0.0 GenomicFeatures_1.22.13
[23] Rsamtools_1.22.0 ShortRead_1.28.0
[25] XML_3.98-1.4
