__STDOUT LOG__ Job runs on fgcz-h-161 at /scratch/FastqScreen_2024-12-04--22-19-01_temp1453771 Starting EzAppFastqScreen FastqScreen_Result FastqScreen_2024-12-04--22-19-01_temp1453771 2024-12-04 22:19:10 touch S1_undiff_preprocessing.log fastp --in1 /scratch/FastqScreen_2024-12-04--22-19-01_temp1453771/S1_undiff-subsample_R1.fastq.gz --out1 trimmed_R1.fastq.gz --thread 8 --trim_front1 0 --trim_tail1 0 --average_qual 0 --adapter_fasta adapters.fa --max_len1 0 --max_len2 0 --trim_poly_x --poly_x_min_len 10 --length_required 18 --compression 4 2> S1_undiff_preprocessing.log cat fastp.json >> S1_undiff_preprocessing.log touch S2_undiff_preprocessing.log fastp --in1 /scratch/FastqScreen_2024-12-04--22-19-01_temp1453771/S2_undiff-subsample_R1.fastq.gz --out1 trimmed_R1.fastq.gz --thread 8 --trim_front1 0 --trim_tail1 0 --average_qual 0 --adapter_fasta adapters.fa --max_len1 0 --max_len2 0 --trim_poly_x --poly_x_min_len 10 --length_required 18 --compression 4 2> S2_undiff_preprocessing.log cat fastp.json >> S2_undiff_preprocessing.log touch S3_undiff_preprocessing.log fastp --in1 /scratch/FastqScreen_2024-12-04--22-19-01_temp1453771/S3_undiff-subsample_R1.fastq.gz --out1 trimmed_R1.fastq.gz --thread 8 --trim_front1 0 --trim_tail1 0 --average_qual 0 --adapter_fasta adapters.fa --max_len1 0 --max_len2 0 --trim_poly_x --poly_x_min_len 10 --length_required 18 --compression 4 2> S3_undiff_preprocessing.log cat fastp.json >> S3_undiff_preprocessing.log touch S4_diff_preprocessing.log fastp --in1 /scratch/FastqScreen_2024-12-04--22-19-01_temp1453771/S4_diff-subsample_R1.fastq.gz --out1 trimmed_R1.fastq.gz --thread 8 --trim_front1 0 --trim_tail1 0 --average_qual 0 --adapter_fasta adapters.fa --max_len1 0 --max_len2 0 --trim_poly_x --poly_x_min_len 10 --length_required 18 --compression 4 2> S4_diff_preprocessing.log cat fastp.json >> S4_diff_preprocessing.log touch S5_diff_preprocessing.log fastp --in1 /scratch/FastqScreen_2024-12-04--22-19-01_temp1453771/S5_diff-subsample_R1.fastq.gz --out1 trimmed_R1.fastq.gz --thread 8 --trim_front1 0 --trim_tail1 0 --average_qual 0 --adapter_fasta adapters.fa --max_len1 0 --max_len2 0 --trim_poly_x --poly_x_min_len 10 --length_required 18 --compression 4 2> S5_diff_preprocessing.log cat fastp.json >> S5_diff_preprocessing.log touch S6_diff_preprocessing.log fastp --in1 /scratch/FastqScreen_2024-12-04--22-19-01_temp1453771/S6_diff-subsample_R1.fastq.gz --out1 trimmed_R1.fastq.gz --thread 8 --trim_front1 0 --trim_tail1 0 --average_qual 0 --adapter_fasta adapters.fa --max_len1 0 --max_len2 0 --trim_poly_x --poly_x_min_len 10 --length_required 18 --compression 4 2> S6_diff_preprocessing.log cat fastp.json >> S6_diff_preprocessing.log fastq_screen --threads 8 --conf /usr/local/ngseq/packages/QC/FastQScreen/conf/adapters_20170421.txt /scratch/FastqScreen_2024-12-04--22-19-01_temp1453771/S1_undiff-subsample_R1.fastq.gz /scratch/FastqScreen_2024-12-04--22-19-01_temp1453771/S2_undiff-subsample_R1.fastq.gz /scratch/FastqScreen_2024-12-04--22-19-01_temp1453771/S3_undiff-subsample_R1.fastq.gz /scratch/FastqScreen_2024-12-04--22-19-01_temp1453771/S4_diff-subsample_R1.fastq.gz /scratch/FastqScreen_2024-12-04--22-19-01_temp1453771/S5_diff-subsample_R1.fastq.gz /scratch/FastqScreen_2024-12-04--22-19-01_temp1453771/S6_diff-subsample_R1.fastq.gz --outdir rawReads --nohits --aligner bowtie2 > fastqscreen.out 2> fastqscreen.err fastq_screen --threads 8 --conf /usr/local/ngseq/packages/QC/FastQScreen/conf/variousSpecies_rRNA_20160826_silva123.conf /scratch/FastqScreen_2024-12-04--22-19-01_temp1453771/S1_undiff-trimmed_R1.fastq.gz /scratch/FastqScreen_2024-12-04--22-19-01_temp1453771/S2_undiff-trimmed_R1.fastq.gz /scratch/FastqScreen_2024-12-04--22-19-01_temp1453771/S3_undiff-trimmed_R1.fastq.gz /scratch/FastqScreen_2024-12-04--22-19-01_temp1453771/S4_diff-trimmed_R1.fastq.gz /scratch/FastqScreen_2024-12-04--22-19-01_temp1453771/S5_diff-trimmed_R1.fastq.gz /scratch/FastqScreen_2024-12-04--22-19-01_temp1453771/S6_diff-trimmed_R1.fastq.gz --outdir procReads --nohits --aligner bowtie2 > fastqscreen.out 2> fastqscreen.err bowtie2 -x /srv/GT/reference/Viruses/ncbi/humanPathogenic_20170419/Sequence/BOWTIE2Index/genome -U procReads/S1_undiff-trimmed_R1.tagged_filter.fastq.gz -k 10 --trim5 4 --trim3 4 --very-sensitive -p 8 --no-unal --no-hd 2> virusResult/S1_undiff_bowtie2.err | cut -f1,3,12 |sed s/AS:i://g >> virusResult/S1_undiff-counts.txt bowtie2 -x /srv/GT/reference/Viruses/ncbi/humanPathogenic_20170419/Sequence/BOWTIE2Index/genome -U procReads/S2_undiff-trimmed_R1.tagged_filter.fastq.gz -k 10 --trim5 4 --trim3 4 --very-sensitive -p 8 --no-unal --no-hd 2> virusResult/S2_undiff_bowtie2.err | cut -f1,3,12 |sed s/AS:i://g >> virusResult/S2_undiff-counts.txt bowtie2 -x /srv/GT/reference/Viruses/ncbi/humanPathogenic_20170419/Sequence/BOWTIE2Index/genome -U procReads/S3_undiff-trimmed_R1.tagged_filter.fastq.gz -k 10 --trim5 4 --trim3 4 --very-sensitive -p 8 --no-unal --no-hd 2> virusResult/S3_undiff_bowtie2.err | cut -f1,3,12 |sed s/AS:i://g >> virusResult/S3_undiff-counts.txt bowtie2 -x /srv/GT/reference/Viruses/ncbi/humanPathogenic_20170419/Sequence/BOWTIE2Index/genome -U procReads/S4_diff-trimmed_R1.tagged_filter.fastq.gz -k 10 --trim5 4 --trim3 4 --very-sensitive -p 8 --no-unal --no-hd 2> virusResult/S4_diff_bowtie2.err | cut -f1,3,12 |sed s/AS:i://g >> virusResult/S4_diff-counts.txt bowtie2 -x /srv/GT/reference/Viruses/ncbi/humanPathogenic_20170419/Sequence/BOWTIE2Index/genome -U procReads/S5_diff-trimmed_R1.tagged_filter.fastq.gz -k 10 --trim5 4 --trim3 4 --very-sensitive -p 8 --no-unal --no-hd 2> virusResult/S5_diff_bowtie2.err | cut -f1,3,12 |sed s/AS:i://g >> virusResult/S5_diff-counts.txt bowtie2 -x /srv/GT/reference/Viruses/ncbi/humanPathogenic_20170419/Sequence/BOWTIE2Index/genome -U procReads/S6_diff-trimmed_R1.tagged_filter.fastq.gz -k 10 --trim5 4 --trim3 4 --very-sensitive -p 8 --no-unal --no-hd 2> virusResult/S6_diff_bowtie2.err | cut -f1,3,12 |sed s/AS:i://g >> virusResult/S6_diff-counts.txt java -Xms1g -Xmx10g -Djava.io.tmpdir=. -jar /usr/local/ngseq/packages/Tools/Picard/3.2.0/picard.jar FastqToSam F1=/scratch/FastqScreen_2024-12-04--22-19-01_temp1453771/S1_undiff-trimmed_R1.fastq.gz O=S1_undiff-trimmed_R1.bam SAMPLE_NAME=S1_undiff LIBRARY_NAME=S1_undiff READ_GROUP_NAME=S1_undiff RUN_DATE=2024-12-04T22:25:14+00:00 PLATFORM=illumina SEQUENCING_CENTER=FGCZ java -Xms1g -Xmx10g -Djava.io.tmpdir=. -jar /usr/local/ngseq/packages/Tools/Picard/3.2.0/picard.jar FastqToSam F1=/scratch/FastqScreen_2024-12-04--22-19-01_temp1453771/S2_undiff-trimmed_R1.fastq.gz O=S2_undiff-trimmed_R1.bam SAMPLE_NAME=S2_undiff LIBRARY_NAME=S2_undiff READ_GROUP_NAME=S2_undiff RUN_DATE=2024-12-04T22:25:14+00:00 PLATFORM=illumina SEQUENCING_CENTER=FGCZ java -Xms1g -Xmx10g -Djava.io.tmpdir=. -jar /usr/local/ngseq/packages/Tools/Picard/3.2.0/picard.jar FastqToSam F1=/scratch/FastqScreen_2024-12-04--22-19-01_temp1453771/S3_undiff-trimmed_R1.fastq.gz O=S3_undiff-trimmed_R1.bam SAMPLE_NAME=S3_undiff LIBRARY_NAME=S3_undiff READ_GROUP_NAME=S3_undiff RUN_DATE=2024-12-04T22:25:14+00:00 PLATFORM=illumina SEQUENCING_CENTER=FGCZ java -Xms1g -Xmx10g -Djava.io.tmpdir=. -jar /usr/local/ngseq/packages/Tools/Picard/3.2.0/picard.jar FastqToSam F1=/scratch/FastqScreen_2024-12-04--22-19-01_temp1453771/S4_diff-trimmed_R1.fastq.gz O=S4_diff-trimmed_R1.bam SAMPLE_NAME=S4_diff LIBRARY_NAME=S4_diff READ_GROUP_NAME=S4_diff RUN_DATE=2024-12-04T22:25:14+00:00 PLATFORM=illumina SEQUENCING_CENTER=FGCZ java -Xms1g -Xmx10g -Djava.io.tmpdir=. -jar /usr/local/ngseq/packages/Tools/Picard/3.2.0/picard.jar FastqToSam F1=/scratch/FastqScreen_2024-12-04--22-19-01_temp1453771/S5_diff-trimmed_R1.fastq.gz O=S5_diff-trimmed_R1.bam SAMPLE_NAME=S5_diff LIBRARY_NAME=S5_diff READ_GROUP_NAME=S5_diff RUN_DATE=2024-12-04T22:25:14+00:00 PLATFORM=illumina SEQUENCING_CENTER=FGCZ java -Xms1g -Xmx10g -Djava.io.tmpdir=. -jar /usr/local/ngseq/packages/Tools/Picard/3.2.0/picard.jar FastqToSam F1=/scratch/FastqScreen_2024-12-04--22-19-01_temp1453771/S6_diff-trimmed_R1.fastq.gz O=S6_diff-trimmed_R1.bam SAMPLE_NAME=S6_diff LIBRARY_NAME=S6_diff READ_GROUP_NAME=S6_diff RUN_DATE=2024-12-04T22:25:14+00:00 PLATFORM=illumina SEQUENCING_CENTER=FGCZ java -Xms1g -Xmx10g -Djava.io.tmpdir=. -jar /usr/local/ngseq/packages/Tools/Picard/3.2.0/picard.jar MergeSamFiles I=S1_undiff-trimmed_R1.bam I=S2_undiff-trimmed_R1.bam I=S3_undiff-trimmed_R1.bam I=S4_diff-trimmed_R1.bam I=S5_diff-trimmed_R1.bam I=S6_diff-trimmed_R1.bam O=refseqResult/allSamples_unmapped.bam USE_THREADING=true SORT_ORDER=queryname samtools view refseqResult/allSamples_unmapped.bam |cut -f 1,12| sed s/RG:Z:// > refseqResult/readID2RG.txt samtools bam2fq refseqResult/allSamples_unmapped.bam > refseqResult/allSamples.fastq bowtie2 -x /srv/GT/reference/RefSeq/mRNA/20170510/Sequence/BOWTIE2Index/transcriptome -U refseqResult/allSamples.fastq -k 10 --trim5 4 --trim3 4 --very-sensitive -p 8 -t --no-unal 2> refseqResult/bowtie2.err | grep ^@ -v|cut -f1,3,12 |sed s/AS:i://g > refseqResult/refSeq_Counts.txt sort -k1 refseqResult/refSeq_Counts.txt > refseqResult/refSeq_Counts_allSamples.txt bowtie2 -x /srv/GT/reference/Silva/silva/release_123_1/SILVA_123.1_LSU_SSU -U /scratch/FastqScreen_2024-12-04--22-19-01_temp1453771/S1_undiff-trimmed_R1.fastq.gz -k 10 --trim5 4 --trim3 4 --very-sensitive -p 8 --no-unal --no-hd --mm 2> S1_undiff_bowtie2.err | cut -f1,2,3,12 |sed s/AS:i://g >> S1_undiff-counts.txt bowtie2 -x /srv/GT/reference/Silva/silva/release_123_1/SILVA_123.1_LSU_SSU -U /scratch/FastqScreen_2024-12-04--22-19-01_temp1453771/S2_undiff-trimmed_R1.fastq.gz -k 10 --trim5 4 --trim3 4 --very-sensitive -p 8 --no-unal --no-hd --mm 2> S2_undiff_bowtie2.err | cut -f1,2,3,12 |sed s/AS:i://g >> S2_undiff-counts.txt bowtie2 -x /srv/GT/reference/Silva/silva/release_123_1/SILVA_123.1_LSU_SSU -U /scratch/FastqScreen_2024-12-04--22-19-01_temp1453771/S3_undiff-trimmed_R1.fastq.gz -k 10 --trim5 4 --trim3 4 --very-sensitive -p 8 --no-unal --no-hd --mm 2> S3_undiff_bowtie2.err | cut -f1,2,3,12 |sed s/AS:i://g >> S3_undiff-counts.txt bowtie2 -x /srv/GT/reference/Silva/silva/release_123_1/SILVA_123.1_LSU_SSU -U /scratch/FastqScreen_2024-12-04--22-19-01_temp1453771/S4_diff-trimmed_R1.fastq.gz -k 10 --trim5 4 --trim3 4 --very-sensitive -p 8 --no-unal --no-hd --mm 2> S4_diff_bowtie2.err | cut -f1,2,3,12 |sed s/AS:i://g >> S4_diff-counts.txt bowtie2 -x /srv/GT/reference/Silva/silva/release_123_1/SILVA_123.1_LSU_SSU -U /scratch/FastqScreen_2024-12-04--22-19-01_temp1453771/S5_diff-trimmed_R1.fastq.gz -k 10 --trim5 4 --trim3 4 --very-sensitive -p 8 --no-unal --no-hd --mm 2> S5_diff_bowtie2.err | cut -f1,2,3,12 |sed s/AS:i://g >> S5_diff-counts.txt bowtie2 -x /srv/GT/reference/Silva/silva/release_123_1/SILVA_123.1_LSU_SSU -U /scratch/FastqScreen_2024-12-04--22-19-01_temp1453771/S6_diff-trimmed_R1.fastq.gz -k 10 --trim5 4 --trim3 4 --very-sensitive -p 8 --no-unal --no-hd --mm 2> S6_diff_bowtie2.err | cut -f1,2,3,12 |sed s/AS:i://g >> S6_diff-counts.txt kraken2 --db /srv/GT/databases/kraken2/minikraken_20200917/minikraken_8GB_20200312 /scratch/FastqScreen_2024-12-04--22-19-01_temp1453771/S1_undiff-trimmed_R1.fastq.gz --gzip-compressed --threads 8 --report report_S1_undiff.kraken >sequences.kraken kraken2 --db /srv/GT/databases/kraken2/minikraken_20200917/minikraken_8GB_20200312 /scratch/FastqScreen_2024-12-04--22-19-01_temp1453771/S2_undiff-trimmed_R1.fastq.gz --gzip-compressed --threads 8 --report report_S2_undiff.kraken >sequences.kraken kraken2 --db /srv/GT/databases/kraken2/minikraken_20200917/minikraken_8GB_20200312 /scratch/FastqScreen_2024-12-04--22-19-01_temp1453771/S3_undiff-trimmed_R1.fastq.gz --gzip-compressed --threads 8 --report report_S3_undiff.kraken >sequences.kraken kraken2 --db /srv/GT/databases/kraken2/minikraken_20200917/minikraken_8GB_20200312 /scratch/FastqScreen_2024-12-04--22-19-01_temp1453771/S4_diff-trimmed_R1.fastq.gz --gzip-compressed --threads 8 --report report_S4_diff.kraken >sequences.kraken kraken2 --db /srv/GT/databases/kraken2/minikraken_20200917/minikraken_8GB_20200312 /scratch/FastqScreen_2024-12-04--22-19-01_temp1453771/S5_diff-trimmed_R1.fastq.gz --gzip-compressed --threads 8 --report report_S5_diff.kraken >sequences.kraken kraken2 --db /srv/GT/databases/kraken2/minikraken_20200917/minikraken_8GB_20200312 /scratch/FastqScreen_2024-12-04--22-19-01_temp1453771/S6_diff-trimmed_R1.fastq.gz --gzip-compressed --threads 8 --report report_S6_diff.kraken >sequences.kraken ezRun tag: 733d7a85c98ed8bb0732c178986b67ce4584e581 ezRun github link: https://github.com/uzh/ezRun/tree/733d7a85c98ed8bb0732c178986b67ce4584e581 R version 4.4.0 (2024-04-24) Platform: x86_64-pc-linux-gnu Running under: Debian GNU/Linux 12 (bookworm) Matrix products: default BLAS: /usr/lib/x86_64-linux-gnu/blas/libblas.so.3.11.0 LAPACK: /usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3.11.0 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 time zone: Europe/Zurich tzcode source: system (glibc) attached base packages: [1] parallel grid stats4 stats graphics grDevices utils [8] datasets methods base other attached packages: [1] htmltools_0.5.8.1 DT_0.33 [3] plotly_4.10.4 kableExtra_1.4.0 [5] knitr_1.47 withr_3.0.0 [7] ShortRead_1.62.0 GenomicAlignments_1.40.0 [9] SummarizedExperiment_1.34.0 Biobase_2.64.0 [11] MatrixGenerics_1.16.0 matrixStats_1.3.0 [13] Rsamtools_2.20.0 BiocParallel_1.38.0 [15] seqLogo_1.70.0 ezRun_3.19.1 [17] lubridate_1.9.3 forcats_1.0.0 [19] stringr_1.5.1 dplyr_1.1.4 [21] purrr_1.0.2 readr_2.1.5 [23] tidyr_1.3.1 tibble_3.2.1 [25] ggplot2_3.5.1 tidyverse_2.0.0 [27] GenomicRanges_1.56.1 Biostrings_2.72.1 [29] GenomeInfoDb_1.40.1 XVector_0.44.0 [31] IRanges_2.38.0 S4Vectors_0.42.0 [33] BiocGenerics_0.50.0 data.table_1.15.4 loaded via a namespace (and not attached): [1] tidyselect_1.2.1 viridisLite_0.4.2 bitops_1.0-7 [4] lazyeval_0.2.2 fastmap_1.2.0 digest_0.6.35 [7] timechange_0.3.0 lifecycle_1.0.4 pwalign_1.0.0 [10] magrittr_2.0.3 compiler_4.4.0 rlang_1.1.4 [13] sass_0.4.9 tools_4.4.0 utf8_1.2.4 [16] yaml_2.3.8 htmlwidgets_1.6.4 S4Arrays_1.4.1 [19] interp_1.1-6 DelayedArray_0.30.1 xml2_1.3.6 [22] RColorBrewer_1.1-3 abind_1.4-5 hwriter_1.3.2.1 [25] fansi_1.0.6 latticeExtra_0.6-30 colorspace_2.1-1 [28] scales_1.3.0 cli_3.6.2 rmarkdown_2.27 [31] crayon_1.5.2 generics_0.1.3 rstudioapi_0.16.0 [34] httr_1.4.7 tzdb_0.4.0 cachem_1.1.0 [37] zlibbioc_1.50.0 vctrs_0.6.5 Matrix_1.7-0 [40] jsonlite_1.8.8 hms_1.1.3 crosstalk_1.2.1 [43] systemfonts_1.1.0 jpeg_0.1-10 jquerylib_0.1.4 [46] glue_1.7.0 codetools_0.2-20 stringi_1.8.4 [49] gtable_0.3.5 deldir_2.0-4 UCSC.utils_1.0.0 [52] munsell_0.5.1 pillar_1.9.0 GenomeInfoDbData_1.2.12 [55] R6_2.5.1 evaluate_0.24.0 lattice_0.22-6 [58] highr_0.11 png_0.1-8 bslib_0.7.0 [61] Rcpp_1.0.12 svglite_2.1.3 SparseArray_1.4.8 [64] xfun_0.45 pkgconfig_2.0.3 Finished EzAppFastqScreen FastqScreen_Result FastqScreen_2024-12-04--22-19-01_temp1453771 2024-12-04 22:40:13 [1] "Success" __SCRIPT END__ __STDERR LOG__ Loading required package: data.table Loading required package: Biostrings Loading required package: BiocGenerics Attaching package: ‘BiocGenerics’ The following objects are masked from ‘package:stats’: IQR, mad, sd, var, xtabs The following objects are masked from ‘package:base’: anyDuplicated, aperm, append, as.data.frame, basename, cbind, colnames, dirname, do.call, duplicated, eval, evalq, Filter, Find, get, grep, grepl, intersect, is.unsorted, lapply, Map, mapply, match, mget, order, paste, pmax, pmax.int, pmin, pmin.int, Position, rank, rbind, Reduce, rownames, sapply, setdiff, table, tapply, union, unique, unsplit, which.max, which.min Loading required package: S4Vectors Loading required package: stats4 Attaching package: ‘S4Vectors’ The following objects are masked from ‘package:data.table’: first, second The following object is masked from ‘package:utils’: findMatches The following objects are masked from ‘package:base’: expand.grid, I, unname Loading required package: IRanges Attaching package: ‘IRanges’ The following object is masked from ‘package:data.table’: shift Loading required package: XVector Loading required package: GenomeInfoDb Attaching package: ‘Biostrings’ The following object is masked from ‘package:base’: strsplit Loading required package: GenomicRanges Loading required package: tidyverse ── Attaching core tidyverse packages ──────────────────────── tidyverse 2.0.0 ── ✔ dplyr 1.1.4 ✔ readr 2.1.5 ✔ forcats 1.0.0 ✔ stringr 1.5.1 ✔ ggplot2 3.5.1 ✔ tibble 3.2.1 ✔ lubridate 1.9.3 ✔ tidyr 1.3.1 ✔ purrr 1.0.2 ── Conflicts ────────────────────────────────────────── tidyverse_conflicts() ── ✖ lubridate::%within%() masks IRanges::%within%() ✖ dplyr::between() masks data.table::between() ✖ dplyr::collapse() masks Biostrings::collapse(), IRanges::collapse() ✖ dplyr::combine() masks BiocGenerics::combine() ✖ purrr::compact() masks XVector::compact() ✖ dplyr::desc() masks IRanges::desc() ✖ tidyr::expand() masks S4Vectors::expand() ✖ dplyr::filter() masks stats::filter() ✖ dplyr::first() masks S4Vectors::first(), data.table::first() ✖ lubridate::hour() masks data.table::hour() ✖ lubridate::isoweek() masks data.table::isoweek() ✖ dplyr::lag() masks stats::lag() ✖ dplyr::last() masks data.table::last() ✖ lubridate::mday() masks data.table::mday() ✖ lubridate::minute() masks data.table::minute() ✖ lubridate::month() masks data.table::month() ✖ ggplot2::Position() masks BiocGenerics::Position(), base::Position() ✖ lubridate::quarter() masks data.table::quarter() ✖ purrr::reduce() masks GenomicRanges::reduce(), IRanges::reduce() ✖ dplyr::rename() masks S4Vectors::rename() ✖ lubridate::second() masks S4Vectors::second(), data.table::second() ✖ lubridate::second<-() masks S4Vectors::second<-() ✖ dplyr::slice() masks XVector::slice(), IRanges::slice() ✖ purrr::transpose() masks data.table::transpose() ✖ lubridate::wday() masks data.table::wday() ✖ lubridate::week() masks data.table::week() ✖ lubridate::yday() masks data.table::yday() ✖ lubridate::year() masks data.table::year() ℹ Use the conflicted package () to force all conflicts to become errors unknown param: partition unknown param: trim_front1 unknown param: trim_tail1 unknown param: cut_front_window_size unknown param: cut_front_mean_quality unknown param: cut_tail_window_size unknown param: cut_tail_mean_quality unknown param: cut_right_window_size unknown param: cut_right_mean_quality unknown param: average_qual unknown param: poly_x_min_len unknown param: length_required unknown param: cmdOptionsFastp unknown param: sushi_app unknown param: isLastJob Loading required package: seqLogo Loading required package: grid Attaching package: ‘grid’ The following object is masked from ‘package:Biostrings’: pattern Loading required package: ShortRead Loading required package: BiocParallel Loading required package: Rsamtools Loading required package: GenomicAlignments Loading required package: SummarizedExperiment Loading required package: MatrixGenerics Loading required package: matrixStats Attaching package: ‘matrixStats’ The following object is masked from ‘package:dplyr’: count Attaching package: ‘MatrixGenerics’ The following objects are masked from ‘package:matrixStats’: colAlls, colAnyNAs, colAnys, colAvgsPerRowSet, colCollapse, colCounts, colCummaxs, colCummins, colCumprods, colCumsums, colDiffs, colIQRDiffs, colIQRs, colLogSumExps, colMadDiffs, colMads, colMaxs, colMeans2, colMedians, colMins, colOrderStats, colProds, colQuantiles, colRanges, colRanks, colSdDiffs, colSds, colSums2, colTabulates, colVarDiffs, colVars, colWeightedMads, colWeightedMeans, colWeightedMedians, colWeightedSds, colWeightedVars, rowAlls, rowAnyNAs, rowAnys, rowAvgsPerColSet, rowCollapse, rowCounts, rowCummaxs, rowCummins, rowCumprods, rowCumsums, rowDiffs, rowIQRDiffs, rowIQRs, rowLogSumExps, rowMadDiffs, rowMads, rowMaxs, rowMeans2, rowMedians, rowMins, rowOrderStats, rowProds, rowQuantiles, rowRanges, rowRanks, rowSdDiffs, rowSds, rowSums2, rowTabulates, rowVarDiffs, rowVars, rowWeightedMads, rowWeightedMeans, rowWeightedMedians, rowWeightedSds, rowWeightedVars Loading required package: Biobase Welcome to Bioconductor Vignettes contain introductory material; view with 'browseVignettes()'. To cite Bioconductor, see 'citation("Biobase")', and for packages 'citation("pkgname")'. Attaching package: ‘Biobase’ The following object is masked from ‘package:MatrixGenerics’: rowMedians The following objects are masked from ‘package:matrixStats’: anyMissing, rowMedians Attaching package: ‘GenomicAlignments’ The following object is masked from ‘package:dplyr’: last The following object is masked from ‘package:data.table’: last Attaching package: ‘ShortRead’ The following object is masked from ‘package:ezRun’: readData The following object is masked from ‘package:dplyr’: id The following object is masked from ‘package:purrr’: compose The following object is masked from ‘package:tibble’: view The following object is masked from ‘package:data.table’: tables Loading required package: withr Loading required package: parallel INFO 2024-12-04 22:25:17 FastqToSam ********** NOTE: Picard's command line syntax is changing. ********** ********** For more information, please see: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** ********** The command line looks like this in the new syntax: ********** ********** FastqToSam -F1 /scratch/FastqScreen_2024-12-04--22-19-01_temp1453771/S2_undiff-trimmed_R1.fastq.gz -O S2_undiff-trimmed_R1.bam -SAMPLE_NAME S2_undiff -LIBRARY_NAME S2_undiff -READ_GROUP_NAME S2_undiff -RUN_DATE 2024-12-04T22:25:14+00:00 -PLATFORM illumina -SEQUENCING_CENTER FGCZ ********** INFO 2024-12-04 22:25:17 FastqToSam ********** NOTE: Picard's command line syntax is changing. ********** ********** For more information, please see: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** ********** The command line looks like this in the new syntax: ********** ********** FastqToSam -F1 /scratch/FastqScreen_2024-12-04--22-19-01_temp1453771/S3_undiff-trimmed_R1.fastq.gz -O S3_undiff-trimmed_R1.bam -SAMPLE_NAME S3_undiff -LIBRARY_NAME S3_undiff -READ_GROUP_NAME S3_undiff -RUN_DATE 2024-12-04T22:25:14+00:00 -PLATFORM illumina -SEQUENCING_CENTER FGCZ ********** INFO 2024-12-04 22:25:17 FastqToSam ********** NOTE: Picard's command line syntax is changing. ********** ********** For more information, please see: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** ********** The command line looks like this in the new syntax: ********** ********** FastqToSam -F1 /scratch/FastqScreen_2024-12-04--22-19-01_temp1453771/S5_diff-trimmed_R1.fastq.gz -O S5_diff-trimmed_R1.bam -SAMPLE_NAME S5_diff -LIBRARY_NAME S5_diff -READ_GROUP_NAME S5_diff -RUN_DATE 2024-12-04T22:25:14+00:00 -PLATFORM illumina -SEQUENCING_CENTER FGCZ ********** INFO 2024-12-04 22:25:17 FastqToSam ********** NOTE: Picard's command line syntax is changing. ********** ********** For more information, please see: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** ********** The command line looks like this in the new syntax: ********** ********** FastqToSam -F1 /scratch/FastqScreen_2024-12-04--22-19-01_temp1453771/S1_undiff-trimmed_R1.fastq.gz -O S1_undiff-trimmed_R1.bam -SAMPLE_NAME S1_undiff -LIBRARY_NAME S1_undiff -READ_GROUP_NAME S1_undiff -RUN_DATE 2024-12-04T22:25:14+00:00 -PLATFORM illumina -SEQUENCING_CENTER FGCZ ********** INFO 2024-12-04 22:25:17 FastqToSam ********** NOTE: Picard's command line syntax is changing. ********** ********** For more information, please see: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** ********** The command line looks like this in the new syntax: ********** ********** FastqToSam -F1 /scratch/FastqScreen_2024-12-04--22-19-01_temp1453771/S4_diff-trimmed_R1.fastq.gz -O S4_diff-trimmed_R1.bam -SAMPLE_NAME S4_diff -LIBRARY_NAME S4_diff -READ_GROUP_NAME S4_diff -RUN_DATE 2024-12-04T22:25:14+00:00 -PLATFORM illumina -SEQUENCING_CENTER FGCZ ********** INFO 2024-12-04 22:25:17 FastqToSam ********** NOTE: Picard's command line syntax is changing. ********** ********** For more information, please see: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** ********** The command line looks like this in the new syntax: ********** ********** FastqToSam -F1 /scratch/FastqScreen_2024-12-04--22-19-01_temp1453771/S6_diff-trimmed_R1.fastq.gz -O S6_diff-trimmed_R1.bam -SAMPLE_NAME S6_diff -LIBRARY_NAME S6_diff -READ_GROUP_NAME S6_diff -RUN_DATE 2024-12-04T22:25:14+00:00 -PLATFORM illumina -SEQUENCING_CENTER FGCZ ********** 22:25:17.147 INFO NativeLibraryLoader - Loading libgkl_compression.so from jar:file:/misc/ngseq12/packages/Tools/Picard/3.2.0/picard.jar!/com/intel/gkl/native/libgkl_compression.so 22:25:17.150 INFO NativeLibraryLoader - Loading libgkl_compression.so from jar:file:/misc/ngseq12/packages/Tools/Picard/3.2.0/picard.jar!/com/intel/gkl/native/libgkl_compression.so 22:25:17.145 INFO NativeLibraryLoader - Loading libgkl_compression.so from jar:file:/misc/ngseq12/packages/Tools/Picard/3.2.0/picard.jar!/com/intel/gkl/native/libgkl_compression.so 22:25:17.170 INFO NativeLibraryLoader - Loading libgkl_compression.so from jar:file:/misc/ngseq12/packages/Tools/Picard/3.2.0/picard.jar!/com/intel/gkl/native/libgkl_compression.so 22:25:17.175 INFO NativeLibraryLoader - Loading libgkl_compression.so from jar:file:/misc/ngseq12/packages/Tools/Picard/3.2.0/picard.jar!/com/intel/gkl/native/libgkl_compression.so 22:25:17.187 INFO NativeLibraryLoader - Loading libgkl_compression.so from jar:file:/misc/ngseq12/packages/Tools/Picard/3.2.0/picard.jar!/com/intel/gkl/native/libgkl_compression.so [Wed Dec 04 22:25:17 CET 2024] FastqToSam FASTQ=/scratch/FastqScreen_2024-12-04--22-19-01_temp1453771/S1_undiff-trimmed_R1.fastq.gz OUTPUT=S1_undiff-trimmed_R1.bam READ_GROUP_NAME=S1_undiff SAMPLE_NAME=S1_undiff LIBRARY_NAME=S1_undiff PLATFORM=illumina SEQUENCING_CENTER=FGCZ RUN_DATE=2024-12-04T23:25:14+0100 USE_SEQUENTIAL_FASTQS=false SORT_ORDER=queryname MIN_Q=0 MAX_Q=93 STRIP_UNPAIRED_MATE_NUMBER=false ALLOW_AND_IGNORE_EMPTY_LINES=false ALLOW_EMPTY_FASTQ=false VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Wed Dec 04 22:25:17 CET 2024] FastqToSam FASTQ=/scratch/FastqScreen_2024-12-04--22-19-01_temp1453771/S6_diff-trimmed_R1.fastq.gz OUTPUT=S6_diff-trimmed_R1.bam READ_GROUP_NAME=S6_diff SAMPLE_NAME=S6_diff LIBRARY_NAME=S6_diff PLATFORM=illumina SEQUENCING_CENTER=FGCZ RUN_DATE=2024-12-04T23:25:14+0100 USE_SEQUENTIAL_FASTQS=false SORT_ORDER=queryname MIN_Q=0 MAX_Q=93 STRIP_UNPAIRED_MATE_NUMBER=false ALLOW_AND_IGNORE_EMPTY_LINES=false ALLOW_EMPTY_FASTQ=false VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Wed Dec 04 22:25:17 CET 2024] FastqToSam FASTQ=/scratch/FastqScreen_2024-12-04--22-19-01_temp1453771/S2_undiff-trimmed_R1.fastq.gz OUTPUT=S2_undiff-trimmed_R1.bam READ_GROUP_NAME=S2_undiff SAMPLE_NAME=S2_undiff LIBRARY_NAME=S2_undiff PLATFORM=illumina SEQUENCING_CENTER=FGCZ RUN_DATE=2024-12-04T23:25:14+0100 USE_SEQUENTIAL_FASTQS=false SORT_ORDER=queryname MIN_Q=0 MAX_Q=93 STRIP_UNPAIRED_MATE_NUMBER=false ALLOW_AND_IGNORE_EMPTY_LINES=false ALLOW_EMPTY_FASTQ=false VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Wed Dec 04 22:25:17 CET 2024] FastqToSam FASTQ=/scratch/FastqScreen_2024-12-04--22-19-01_temp1453771/S3_undiff-trimmed_R1.fastq.gz OUTPUT=S3_undiff-trimmed_R1.bam READ_GROUP_NAME=S3_undiff SAMPLE_NAME=S3_undiff LIBRARY_NAME=S3_undiff PLATFORM=illumina SEQUENCING_CENTER=FGCZ RUN_DATE=2024-12-04T23:25:14+0100 USE_SEQUENTIAL_FASTQS=false SORT_ORDER=queryname MIN_Q=0 MAX_Q=93 STRIP_UNPAIRED_MATE_NUMBER=false ALLOW_AND_IGNORE_EMPTY_LINES=false ALLOW_EMPTY_FASTQ=false VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Wed Dec 04 22:25:17 CET 2024] FastqToSam FASTQ=/scratch/FastqScreen_2024-12-04--22-19-01_temp1453771/S5_diff-trimmed_R1.fastq.gz OUTPUT=S5_diff-trimmed_R1.bam READ_GROUP_NAME=S5_diff SAMPLE_NAME=S5_diff LIBRARY_NAME=S5_diff PLATFORM=illumina SEQUENCING_CENTER=FGCZ RUN_DATE=2024-12-04T23:25:14+0100 USE_SEQUENTIAL_FASTQS=false SORT_ORDER=queryname MIN_Q=0 MAX_Q=93 STRIP_UNPAIRED_MATE_NUMBER=false ALLOW_AND_IGNORE_EMPTY_LINES=false ALLOW_EMPTY_FASTQ=false VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Wed Dec 04 22:25:17 CET 2024] FastqToSam FASTQ=/scratch/FastqScreen_2024-12-04--22-19-01_temp1453771/S4_diff-trimmed_R1.fastq.gz OUTPUT=S4_diff-trimmed_R1.bam READ_GROUP_NAME=S4_diff SAMPLE_NAME=S4_diff LIBRARY_NAME=S4_diff PLATFORM=illumina SEQUENCING_CENTER=FGCZ RUN_DATE=2024-12-04T23:25:14+0100 USE_SEQUENTIAL_FASTQS=false SORT_ORDER=queryname MIN_Q=0 MAX_Q=93 STRIP_UNPAIRED_MATE_NUMBER=false ALLOW_AND_IGNORE_EMPTY_LINES=false ALLOW_EMPTY_FASTQ=false VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Wed Dec 04 22:25:17 CET 2024] Executing as trxcopy@fgcz-h-161 on Linux 6.1.0-26-cloud-amd64 amd64; OpenJDK 64-Bit Server VM 21.0.4+7-LTS; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: 3.2.0-1-g3948afb6b [Wed Dec 04 22:25:17 CET 2024] Executing as trxcopy@fgcz-h-161 on Linux 6.1.0-26-cloud-amd64 amd64; OpenJDK 64-Bit Server VM 21.0.4+7-LTS; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: 3.2.0-1-g3948afb6b [Wed Dec 04 22:25:17 CET 2024] Executing as trxcopy@fgcz-h-161 on Linux 6.1.0-26-cloud-amd64 amd64; OpenJDK 64-Bit Server VM 21.0.4+7-LTS; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: 3.2.0-1-g3948afb6b [Wed Dec 04 22:25:17 CET 2024] Executing as trxcopy@fgcz-h-161 on Linux 6.1.0-26-cloud-amd64 amd64; OpenJDK 64-Bit Server VM 21.0.4+7-LTS; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: 3.2.0-1-g3948afb6b [Wed Dec 04 22:25:17 CET 2024] Executing as trxcopy@fgcz-h-161 on Linux 6.1.0-26-cloud-amd64 amd64; OpenJDK 64-Bit Server VM 21.0.4+7-LTS; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: 3.2.0-1-g3948afb6b [Wed Dec 04 22:25:17 CET 2024] Executing as trxcopy@fgcz-h-161 on Linux 6.1.0-26-cloud-amd64 amd64; OpenJDK 64-Bit Server VM 21.0.4+7-LTS; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: 3.2.0-1-g3948afb6b INFO 2024-12-04 22:25:17 FastqToSam Auto-detected quality format as: Standard. INFO 2024-12-04 22:25:17 FastqToSam Auto-detected quality format as: Standard. INFO 2024-12-04 22:25:17 FastqToSam Auto-detected quality format as: Standard. INFO 2024-12-04 22:25:17 FastqToSam Auto-detected quality format as: Standard. INFO 2024-12-04 22:25:17 FastqToSam Auto-detected quality format as: Standard. INFO 2024-12-04 22:25:17 FastqToSam Auto-detected quality format as: Standard. INFO 2024-12-04 22:25:17 FastqToSam Processed 84972 fastq reads INFO 2024-12-04 22:25:18 FastqToSam Processed 87800 fastq reads INFO 2024-12-04 22:25:18 FastqToSam Processed 94664 fastq reads INFO 2024-12-04 22:25:18 FastqToSam Processed 97136 fastq reads INFO 2024-12-04 22:25:18 FastqToSam Processed 94502 fastq reads INFO 2024-12-04 22:25:18 FastqToSam Processed 96993 fastq reads [Wed Dec 04 22:25:18 CET 2024] picard.sam.FastqToSam done. Elapsed time: 0.03 minutes. Runtime.totalMemory()=1082130432 [Wed Dec 04 22:25:18 CET 2024] picard.sam.FastqToSam done. Elapsed time: 0.03 minutes. Runtime.totalMemory()=1082130432 [Wed Dec 04 22:25:19 CET 2024] picard.sam.FastqToSam done. Elapsed time: 0.03 minutes. Runtime.totalMemory()=1082130432 [Wed Dec 04 22:25:19 CET 2024] picard.sam.FastqToSam done. Elapsed time: 0.03 minutes. Runtime.totalMemory()=1082130432 [Wed Dec 04 22:25:19 CET 2024] picard.sam.FastqToSam done. Elapsed time: 0.03 minutes. Runtime.totalMemory()=1082130432 [Wed Dec 04 22:25:19 CET 2024] picard.sam.FastqToSam done. Elapsed time: 0.04 minutes. Runtime.totalMemory()=1082130432 INFO 2024-12-04 22:25:21 MergeSamFiles ********** NOTE: Picard's command line syntax is changing. ********** ********** For more information, please see: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** ********** The command line looks like this in the new syntax: ********** ********** MergeSamFiles -I S1_undiff-trimmed_R1.bam -I S2_undiff-trimmed_R1.bam -I S3_undiff-trimmed_R1.bam -I S4_diff-trimmed_R1.bam -I S5_diff-trimmed_R1.bam -I S6_diff-trimmed_R1.bam -O refseqResult/allSamples_unmapped.bam -USE_THREADING true -SORT_ORDER queryname ********** 22:25:21.193 INFO NativeLibraryLoader - Loading libgkl_compression.so from jar:file:/misc/ngseq12/packages/Tools/Picard/3.2.0/picard.jar!/com/intel/gkl/native/libgkl_compression.so [Wed Dec 04 22:25:21 CET 2024] MergeSamFiles INPUT=[S1_undiff-trimmed_R1.bam, S2_undiff-trimmed_R1.bam, S3_undiff-trimmed_R1.bam, S4_diff-trimmed_R1.bam, S5_diff-trimmed_R1.bam, S6_diff-trimmed_R1.bam] OUTPUT=refseqResult/allSamples_unmapped.bam SORT_ORDER=queryname USE_THREADING=true ASSUME_SORTED=false MERGE_SEQUENCE_DICTIONARIES=false VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Wed Dec 04 22:25:21 CET 2024] Executing as trxcopy@fgcz-h-161 on Linux 6.1.0-26-cloud-amd64 amd64; OpenJDK 64-Bit Server VM 21.0.4+7-LTS; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: 3.2.0-1-g3948afb6b INFO 2024-12-04 22:25:21 MergeSamFiles Input files are in same order as output so sorting to temp directory is not needed. INFO 2024-12-04 22:25:24 MergeSamFiles Finished reading inputs. [Wed Dec 04 22:25:24 CET 2024] picard.sam.MergeSamFiles done. Elapsed time: 0.06 minutes. Runtime.totalMemory()=1082130432 [M::bam2fq_mainloop] discarded 0 singletons [M::bam2fq_mainloop] processed 556067 reads join: refseqResult/readID2RG.txt:19: is not sorted: NS500415:272:HKV57AFXY:1:11101:1023:2685 S2_undiff join: refseqResult/refSeq_Counts_allSamples.txt:345945: is not sorted: NS500415:272:HKV57AFXY:1:11208:26666:1022 9483_1060966216 -51 join: input is not in sorted order Loading database information... done. 97136 sequences (12.65 Mbp) processed in 0.277s (21019.3 Kseq/m, 2737.95 Mbp/m). 84854 sequences classified (87.36%) 12282 sequences unclassified (12.64%) Loading database information... done. 87800 sequences (7.33 Mbp) processed in 0.182s (28901.1 Kseq/m, 2412.76 Mbp/m). 48533 sequences classified (55.28%) 39267 sequences unclassified (44.72%) Loading database information... done. 94664 sequences (11.71 Mbp) processed in 0.257s (22130.9 Kseq/m, 2738.70 Mbp/m). 78465 sequences classified (82.89%) 16199 sequences unclassified (17.11%) Loading database information... done. 96993 sequences (12.33 Mbp) processed in 0.265s (21952.4 Kseq/m, 2789.75 Mbp/m). 84064 sequences classified (86.67%) 12929 sequences unclassified (13.33%) Loading database information... done. 84972 sequences (6.38 Mbp) processed in 0.161s (31749.2 Kseq/m, 2384.81 Mbp/m). 39910 sequences classified (46.97%) 45062 sequences unclassified (53.03%) Loading database information... done. 94502 sequences (10.05 Mbp) processed in 0.243s (23356.1 Kseq/m, 2484.01 Mbp/m). 68923 sequences classified (72.93%) 25579 sequences unclassified (27.07%)