__STDOUT LOG__ Job runs on fgcz-h-166 at /scratch/o31309_FastqScreen_2024-12-11--13-20-51_temp1922338 Starting EzAppFastqScreen FastqScreen_Result o31309_FastqScreen_2024-12-11--13-20-51_temp1922338 2024-12-11 13:20:57 touch 313091_1-_preprocessing.log fastp --in1 /scratch/o31309_FastqScreen_2024-12-11--13-20-51_temp1922338/313091_1--subsample_R1.fastq.gz --out1 trimmed_R1.fastq.gz --thread 4 --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> 313091_1-_preprocessing.log cat fastp.json >> 313091_1-_preprocessing.log touch 313092_1-_preprocessing.log fastp --in1 /scratch/o31309_FastqScreen_2024-12-11--13-20-51_temp1922338/313092_1--subsample_R1.fastq.gz --out1 trimmed_R1.fastq.gz --thread 4 --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> 313092_1-_preprocessing.log cat fastp.json >> 313092_1-_preprocessing.log touch 313093_1-_preprocessing.log fastp --in1 /scratch/o31309_FastqScreen_2024-12-11--13-20-51_temp1922338/313093_1--subsample_R1.fastq.gz --out1 trimmed_R1.fastq.gz --thread 4 --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> 313093_1-_preprocessing.log cat fastp.json >> 313093_1-_preprocessing.log touch 313094_1-_preprocessing.log fastp --in1 /scratch/o31309_FastqScreen_2024-12-11--13-20-51_temp1922338/313094_1--subsample_R1.fastq.gz --out1 trimmed_R1.fastq.gz --thread 4 --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> 313094_1-_preprocessing.log cat fastp.json >> 313094_1-_preprocessing.log touch 313095_1-_preprocessing.log fastp --in1 /scratch/o31309_FastqScreen_2024-12-11--13-20-51_temp1922338/313095_1--subsample_R1.fastq.gz --out1 trimmed_R1.fastq.gz --thread 4 --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> 313095_1-_preprocessing.log cat fastp.json >> 313095_1-_preprocessing.log touch 313096_1-_preprocessing.log fastp --in1 /scratch/o31309_FastqScreen_2024-12-11--13-20-51_temp1922338/313096_1--subsample_R1.fastq.gz --out1 trimmed_R1.fastq.gz --thread 4 --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> 313096_1-_preprocessing.log cat fastp.json >> 313096_1-_preprocessing.log touch 313097_1-_preprocessing.log fastp --in1 /scratch/o31309_FastqScreen_2024-12-11--13-20-51_temp1922338/313097_1--subsample_R1.fastq.gz --out1 trimmed_R1.fastq.gz --thread 4 --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> 313097_1-_preprocessing.log cat fastp.json >> 313097_1-_preprocessing.log touch 313098_1-_preprocessing.log fastp --in1 /scratch/o31309_FastqScreen_2024-12-11--13-20-51_temp1922338/313098_1--subsample_R1.fastq.gz --out1 trimmed_R1.fastq.gz --thread 4 --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> 313098_1-_preprocessing.log cat fastp.json >> 313098_1-_preprocessing.log fastq_screen --threads 4 --conf /usr/local/ngseq/packages/QC/FastQScreen/conf/adapters_20170421.txt /scratch/o31309_FastqScreen_2024-12-11--13-20-51_temp1922338/313091_1--subsample_R1.fastq.gz /scratch/o31309_FastqScreen_2024-12-11--13-20-51_temp1922338/313092_1--subsample_R1.fastq.gz /scratch/o31309_FastqScreen_2024-12-11--13-20-51_temp1922338/313093_1--subsample_R1.fastq.gz /scratch/o31309_FastqScreen_2024-12-11--13-20-51_temp1922338/313094_1--subsample_R1.fastq.gz /scratch/o31309_FastqScreen_2024-12-11--13-20-51_temp1922338/313095_1--subsample_R1.fastq.gz /scratch/o31309_FastqScreen_2024-12-11--13-20-51_temp1922338/313096_1--subsample_R1.fastq.gz /scratch/o31309_FastqScreen_2024-12-11--13-20-51_temp1922338/313097_1--subsample_R1.fastq.gz /scratch/o31309_FastqScreen_2024-12-11--13-20-51_temp1922338/313098_1--subsample_R1.fastq.gz --outdir rawReads --nohits --aligner bowtie2 > fastqscreen.out 2> fastqscreen.err fastq_screen --threads 4 --conf /usr/local/ngseq/packages/QC/FastQScreen/conf/variousSpecies_rRNA_20160826_silva123.conf /scratch/o31309_FastqScreen_2024-12-11--13-20-51_temp1922338/313091_1--trimmed_R1.fastq.gz /scratch/o31309_FastqScreen_2024-12-11--13-20-51_temp1922338/313092_1--trimmed_R1.fastq.gz /scratch/o31309_FastqScreen_2024-12-11--13-20-51_temp1922338/313093_1--trimmed_R1.fastq.gz /scratch/o31309_FastqScreen_2024-12-11--13-20-51_temp1922338/313094_1--trimmed_R1.fastq.gz /scratch/o31309_FastqScreen_2024-12-11--13-20-51_temp1922338/313095_1--trimmed_R1.fastq.gz /scratch/o31309_FastqScreen_2024-12-11--13-20-51_temp1922338/313096_1--trimmed_R1.fastq.gz /scratch/o31309_FastqScreen_2024-12-11--13-20-51_temp1922338/313097_1--trimmed_R1.fastq.gz /scratch/o31309_FastqScreen_2024-12-11--13-20-51_temp1922338/313098_1--trimmed_R1.fastq.gz --outdir procReads --nohits --aligner bowtie2 > fastqscreen.out 2> fastqscreen.err java -Xms1g -Xmx10g -Djava.io.tmpdir=. -jar /usr/local/ngseq/packages/Tools/Picard/3.2.0/picard.jar FastqToSam F1=/scratch/o31309_FastqScreen_2024-12-11--13-20-51_temp1922338/313091_1--trimmed_R1.fastq.gz O=313091_1--trimmed_R1.bam SAMPLE_NAME=313091_1- LIBRARY_NAME=313091_1- READ_GROUP_NAME=313091_1- RUN_DATE=2024-12-11T13:27:18+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/o31309_FastqScreen_2024-12-11--13-20-51_temp1922338/313092_1--trimmed_R1.fastq.gz O=313092_1--trimmed_R1.bam SAMPLE_NAME=313092_1- LIBRARY_NAME=313092_1- READ_GROUP_NAME=313092_1- RUN_DATE=2024-12-11T13:27:18+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/o31309_FastqScreen_2024-12-11--13-20-51_temp1922338/313093_1--trimmed_R1.fastq.gz O=313093_1--trimmed_R1.bam SAMPLE_NAME=313093_1- LIBRARY_NAME=313093_1- READ_GROUP_NAME=313093_1- RUN_DATE=2024-12-11T13:27:18+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/o31309_FastqScreen_2024-12-11--13-20-51_temp1922338/313094_1--trimmed_R1.fastq.gz O=313094_1--trimmed_R1.bam SAMPLE_NAME=313094_1- LIBRARY_NAME=313094_1- READ_GROUP_NAME=313094_1- RUN_DATE=2024-12-11T13:27:18+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/o31309_FastqScreen_2024-12-11--13-20-51_temp1922338/313095_1--trimmed_R1.fastq.gz O=313095_1--trimmed_R1.bam SAMPLE_NAME=313095_1- LIBRARY_NAME=313095_1- READ_GROUP_NAME=313095_1- RUN_DATE=2024-12-11T13:27:18+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/o31309_FastqScreen_2024-12-11--13-20-51_temp1922338/313096_1--trimmed_R1.fastq.gz O=313096_1--trimmed_R1.bam SAMPLE_NAME=313096_1- LIBRARY_NAME=313096_1- READ_GROUP_NAME=313096_1- RUN_DATE=2024-12-11T13:27:18+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/o31309_FastqScreen_2024-12-11--13-20-51_temp1922338/313097_1--trimmed_R1.fastq.gz O=313097_1--trimmed_R1.bam SAMPLE_NAME=313097_1- LIBRARY_NAME=313097_1- READ_GROUP_NAME=313097_1- RUN_DATE=2024-12-11T13:27:18+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/o31309_FastqScreen_2024-12-11--13-20-51_temp1922338/313098_1--trimmed_R1.fastq.gz O=313098_1--trimmed_R1.bam SAMPLE_NAME=313098_1- LIBRARY_NAME=313098_1- READ_GROUP_NAME=313098_1- RUN_DATE=2024-12-11T13:27:18+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=313091_1--trimmed_R1.bam I=313092_1--trimmed_R1.bam I=313093_1--trimmed_R1.bam I=313094_1--trimmed_R1.bam I=313095_1--trimmed_R1.bam I=313096_1--trimmed_R1.bam I=313097_1--trimmed_R1.bam I=313098_1--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 4 -t --no-unal 2> refseqResult/bowtie2.err | grep ^@ -v|cut -f1,3,12 |sed s/AS:i://g > refseqResult/refSeq_Counts.txt bowtie2 -x /srv/GT/reference/Silva/silva/release_123_1/SILVA_123.1_LSU_SSU -U /scratch/o31309_FastqScreen_2024-12-11--13-20-51_temp1922338/313091_1--trimmed_R1.fastq.gz -k 10 --trim5 4 --trim3 4 --very-sensitive -p 4 --no-unal --no-hd --mm 2> 313091_1-_bowtie2.err | cut -f1,2,3,12 |sed s/AS:i://g >> 313091_1--counts.txt bowtie2 -x /srv/GT/reference/Silva/silva/release_123_1/SILVA_123.1_LSU_SSU -U /scratch/o31309_FastqScreen_2024-12-11--13-20-51_temp1922338/313092_1--trimmed_R1.fastq.gz -k 10 --trim5 4 --trim3 4 --very-sensitive -p 4 --no-unal --no-hd --mm 2> 313092_1-_bowtie2.err | cut -f1,2,3,12 |sed s/AS:i://g >> 313092_1--counts.txt bowtie2 -x /srv/GT/reference/Silva/silva/release_123_1/SILVA_123.1_LSU_SSU -U /scratch/o31309_FastqScreen_2024-12-11--13-20-51_temp1922338/313093_1--trimmed_R1.fastq.gz -k 10 --trim5 4 --trim3 4 --very-sensitive -p 4 --no-unal --no-hd --mm 2> 313093_1-_bowtie2.err | cut -f1,2,3,12 |sed s/AS:i://g >> 313093_1--counts.txt bowtie2 -x /srv/GT/reference/Silva/silva/release_123_1/SILVA_123.1_LSU_SSU -U /scratch/o31309_FastqScreen_2024-12-11--13-20-51_temp1922338/313094_1--trimmed_R1.fastq.gz -k 10 --trim5 4 --trim3 4 --very-sensitive -p 4 --no-unal --no-hd --mm 2> 313094_1-_bowtie2.err | cut -f1,2,3,12 |sed s/AS:i://g >> 313094_1--counts.txt bowtie2 -x /srv/GT/reference/Silva/silva/release_123_1/SILVA_123.1_LSU_SSU -U /scratch/o31309_FastqScreen_2024-12-11--13-20-51_temp1922338/313095_1--trimmed_R1.fastq.gz -k 10 --trim5 4 --trim3 4 --very-sensitive -p 4 --no-unal --no-hd --mm 2> 313095_1-_bowtie2.err | cut -f1,2,3,12 |sed s/AS:i://g >> 313095_1--counts.txt bowtie2 -x /srv/GT/reference/Silva/silva/release_123_1/SILVA_123.1_LSU_SSU -U /scratch/o31309_FastqScreen_2024-12-11--13-20-51_temp1922338/313096_1--trimmed_R1.fastq.gz -k 10 --trim5 4 --trim3 4 --very-sensitive -p 4 --no-unal --no-hd --mm 2> 313096_1-_bowtie2.err | cut -f1,2,3,12 |sed s/AS:i://g >> 313096_1--counts.txt bowtie2 -x /srv/GT/reference/Silva/silva/release_123_1/SILVA_123.1_LSU_SSU -U /scratch/o31309_FastqScreen_2024-12-11--13-20-51_temp1922338/313097_1--trimmed_R1.fastq.gz -k 10 --trim5 4 --trim3 4 --very-sensitive -p 4 --no-unal --no-hd --mm 2> 313097_1-_bowtie2.err | cut -f1,2,3,12 |sed s/AS:i://g >> 313097_1--counts.txt bowtie2 -x /srv/GT/reference/Silva/silva/release_123_1/SILVA_123.1_LSU_SSU -U /scratch/o31309_FastqScreen_2024-12-11--13-20-51_temp1922338/313098_1--trimmed_R1.fastq.gz -k 10 --trim5 4 --trim3 4 --very-sensitive -p 4 --no-unal --no-hd --mm 2> 313098_1-_bowtie2.err | cut -f1,2,3,12 |sed s/AS:i://g >> 313098_1--counts.txt kraken2 --db /srv/GT/databases/kraken2/minikraken_20200917/minikraken_8GB_20200312 /scratch/o31309_FastqScreen_2024-12-11--13-20-51_temp1922338/313091_1--trimmed_R1.fastq.gz --gzip-compressed --threads 4 --report report_313091_1-.kraken >sequences.kraken kraken2 --db /srv/GT/databases/kraken2/minikraken_20200917/minikraken_8GB_20200312 /scratch/o31309_FastqScreen_2024-12-11--13-20-51_temp1922338/313092_1--trimmed_R1.fastq.gz --gzip-compressed --threads 4 --report report_313092_1-.kraken >sequences.kraken kraken2 --db /srv/GT/databases/kraken2/minikraken_20200917/minikraken_8GB_20200312 /scratch/o31309_FastqScreen_2024-12-11--13-20-51_temp1922338/313093_1--trimmed_R1.fastq.gz --gzip-compressed --threads 4 --report report_313093_1-.kraken >sequences.kraken kraken2 --db /srv/GT/databases/kraken2/minikraken_20200917/minikraken_8GB_20200312 /scratch/o31309_FastqScreen_2024-12-11--13-20-51_temp1922338/313094_1--trimmed_R1.fastq.gz --gzip-compressed --threads 4 --report report_313094_1-.kraken >sequences.kraken kraken2 --db /srv/GT/databases/kraken2/minikraken_20200917/minikraken_8GB_20200312 /scratch/o31309_FastqScreen_2024-12-11--13-20-51_temp1922338/313095_1--trimmed_R1.fastq.gz --gzip-compressed --threads 4 --report report_313095_1-.kraken >sequences.kraken kraken2 --db /srv/GT/databases/kraken2/minikraken_20200917/minikraken_8GB_20200312 /scratch/o31309_FastqScreen_2024-12-11--13-20-51_temp1922338/313096_1--trimmed_R1.fastq.gz --gzip-compressed --threads 4 --report report_313096_1-.kraken >sequences.kraken kraken2 --db /srv/GT/databases/kraken2/minikraken_20200917/minikraken_8GB_20200312 /scratch/o31309_FastqScreen_2024-12-11--13-20-51_temp1922338/313097_1--trimmed_R1.fastq.gz --gzip-compressed --threads 4 --report report_313097_1-.kraken >sequences.kraken kraken2 --db /srv/GT/databases/kraken2/minikraken_20200917/minikraken_8GB_20200312 /scratch/o31309_FastqScreen_2024-12-11--13-20-51_temp1922338/313098_1--trimmed_R1.fastq.gz --gzip-compressed --threads 4 --report report_313098_1-.kraken >sequences.kraken ezRun tag: 833ff07eb899d45dbc71b5a40cab95ce4f242d45 ezRun github link: https://github.com/uzh/ezRun/tree/833ff07eb899d45dbc71b5a40cab95ce4f242d45 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 o31309_FastqScreen_2024-12-11--13-20-51_temp1922338 2024-12-11 13:37:53 [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 2024-12-11 13:27:19 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/o31309_FastqScreen_2024-12-11--13-20-51_temp1922338/313091_1--trimmed_R1.fastq.gz -O 313091_1--trimmed_R1.bam -SAMPLE_NAME 313091_1- -LIBRARY_NAME 313091_1- -READ_GROUP_NAME 313091_1- -RUN_DATE 2024-12-11T13:27:18+00:00 -PLATFORM illumina -SEQUENCING_CENTER FGCZ ********** 13:27:20.020 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 INFO 2024-12-11 13:27:20 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/o31309_FastqScreen_2024-12-11--13-20-51_temp1922338/313093_1--trimmed_R1.fastq.gz -O 313093_1--trimmed_R1.bam -SAMPLE_NAME 313093_1- -LIBRARY_NAME 313093_1- -READ_GROUP_NAME 313093_1- -RUN_DATE 2024-12-11T13:27:18+00:00 -PLATFORM illumina -SEQUENCING_CENTER FGCZ ********** [Wed Dec 11 13:27:20 CET 2024] FastqToSam FASTQ=/scratch/o31309_FastqScreen_2024-12-11--13-20-51_temp1922338/313091_1--trimmed_R1.fastq.gz OUTPUT=313091_1--trimmed_R1.bam READ_GROUP_NAME=313091_1- SAMPLE_NAME=313091_1- LIBRARY_NAME=313091_1- PLATFORM=illumina SEQUENCING_CENTER=FGCZ RUN_DATE=2024-12-11T14:27:18+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 INFO 2024-12-11 13:27:20 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/o31309_FastqScreen_2024-12-11--13-20-51_temp1922338/313094_1--trimmed_R1.fastq.gz -O 313094_1--trimmed_R1.bam -SAMPLE_NAME 313094_1- -LIBRARY_NAME 313094_1- -READ_GROUP_NAME 313094_1- -RUN_DATE 2024-12-11T13:27:18+00:00 -PLATFORM illumina -SEQUENCING_CENTER FGCZ ********** INFO 2024-12-11 13:27:20 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/o31309_FastqScreen_2024-12-11--13-20-51_temp1922338/313092_1--trimmed_R1.fastq.gz -O 313092_1--trimmed_R1.bam -SAMPLE_NAME 313092_1- -LIBRARY_NAME 313092_1- -READ_GROUP_NAME 313092_1- -RUN_DATE 2024-12-11T13:27:18+00:00 -PLATFORM illumina -SEQUENCING_CENTER FGCZ ********** 13:27:20.126 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 11 13:27:20 CET 2024] FastqToSam FASTQ=/scratch/o31309_FastqScreen_2024-12-11--13-20-51_temp1922338/313093_1--trimmed_R1.fastq.gz OUTPUT=313093_1--trimmed_R1.bam READ_GROUP_NAME=313093_1- SAMPLE_NAME=313093_1- LIBRARY_NAME=313093_1- PLATFORM=illumina SEQUENCING_CENTER=FGCZ RUN_DATE=2024-12-11T14:27:18+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 13:27:20.170 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 13:27:20.189 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 11 13:27:20 CET 2024] Executing as trxcopy@fgcz-h-166 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 11 13:27:20 CET 2024] FastqToSam FASTQ=/scratch/o31309_FastqScreen_2024-12-11--13-20-51_temp1922338/313092_1--trimmed_R1.fastq.gz OUTPUT=313092_1--trimmed_R1.bam READ_GROUP_NAME=313092_1- SAMPLE_NAME=313092_1- LIBRARY_NAME=313092_1- PLATFORM=illumina SEQUENCING_CENTER=FGCZ RUN_DATE=2024-12-11T14:27:18+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 11 13:27:20 CET 2024] FastqToSam FASTQ=/scratch/o31309_FastqScreen_2024-12-11--13-20-51_temp1922338/313094_1--trimmed_R1.fastq.gz OUTPUT=313094_1--trimmed_R1.bam READ_GROUP_NAME=313094_1- SAMPLE_NAME=313094_1- LIBRARY_NAME=313094_1- PLATFORM=illumina SEQUENCING_CENTER=FGCZ RUN_DATE=2024-12-11T14:27:18+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 11 13:27:20 CET 2024] Executing as trxcopy@fgcz-h-166 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 2024-12-11 13:27:20 FastqToSam Auto-detected quality format as: Standard. [Wed Dec 11 13:27:20 CET 2024] Executing as trxcopy@fgcz-h-166 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 2024-12-11 13:27:20 FastqToSam Auto-detected quality format as: Standard. [Wed Dec 11 13:27:20 CET 2024] Executing as trxcopy@fgcz-h-166 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 2024-12-11 13:27:20 FastqToSam Auto-detected quality format as: Standard. INFO 2024-12-11 13:27:20 FastqToSam Auto-detected quality format as: Standard. INFO 2024-12-11 13:27:20 FastqToSam Processed 95977 fastq reads INFO 2024-12-11 13:27:20 FastqToSam Processed 96069 fastq reads INFO 2024-12-11 13:27:20 FastqToSam Processed 96044 fastq reads INFO 2024-12-11 13:27:20 FastqToSam Processed 96130 fastq reads [Wed Dec 11 13:27:21 CET 2024] picard.sam.FastqToSam done. Elapsed time: 0.02 minutes. Runtime.totalMemory()=1082130432 [Wed Dec 11 13:27:21 CET 2024] picard.sam.FastqToSam done. Elapsed time: 0.02 minutes. Runtime.totalMemory()=1082130432 [Wed Dec 11 13:27:21 CET 2024] picard.sam.FastqToSam done. Elapsed time: 0.02 minutes. Runtime.totalMemory()=1082130432 [Wed Dec 11 13:27:21 CET 2024] picard.sam.FastqToSam done. Elapsed time: 0.02 minutes. Runtime.totalMemory()=1082130432 INFO 2024-12-11 13:27:22 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/o31309_FastqScreen_2024-12-11--13-20-51_temp1922338/313095_1--trimmed_R1.fastq.gz -O 313095_1--trimmed_R1.bam -SAMPLE_NAME 313095_1- -LIBRARY_NAME 313095_1- -READ_GROUP_NAME 313095_1- -RUN_DATE 2024-12-11T13:27:18+00:00 -PLATFORM illumina -SEQUENCING_CENTER FGCZ ********** 13:27:22.344 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 11 13:27:22 CET 2024] FastqToSam FASTQ=/scratch/o31309_FastqScreen_2024-12-11--13-20-51_temp1922338/313095_1--trimmed_R1.fastq.gz OUTPUT=313095_1--trimmed_R1.bam READ_GROUP_NAME=313095_1- SAMPLE_NAME=313095_1- LIBRARY_NAME=313095_1- PLATFORM=illumina SEQUENCING_CENTER=FGCZ RUN_DATE=2024-12-11T14:27:18+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 11 13:27:22 CET 2024] Executing as trxcopy@fgcz-h-166 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 2024-12-11 13:27:22 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/o31309_FastqScreen_2024-12-11--13-20-51_temp1922338/313096_1--trimmed_R1.fastq.gz -O 313096_1--trimmed_R1.bam -SAMPLE_NAME 313096_1- -LIBRARY_NAME 313096_1- -READ_GROUP_NAME 313096_1- -RUN_DATE 2024-12-11T13:27:18+00:00 -PLATFORM illumina -SEQUENCING_CENTER FGCZ ********** INFO 2024-12-11 13:27:22 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/o31309_FastqScreen_2024-12-11--13-20-51_temp1922338/313098_1--trimmed_R1.fastq.gz -O 313098_1--trimmed_R1.bam -SAMPLE_NAME 313098_1- -LIBRARY_NAME 313098_1- -READ_GROUP_NAME 313098_1- -RUN_DATE 2024-12-11T13:27:18+00:00 -PLATFORM illumina -SEQUENCING_CENTER FGCZ ********** INFO 2024-12-11 13:27:22 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/o31309_FastqScreen_2024-12-11--13-20-51_temp1922338/313097_1--trimmed_R1.fastq.gz -O 313097_1--trimmed_R1.bam -SAMPLE_NAME 313097_1- -LIBRARY_NAME 313097_1- -READ_GROUP_NAME 313097_1- -RUN_DATE 2024-12-11T13:27:18+00:00 -PLATFORM illumina -SEQUENCING_CENTER FGCZ ********** INFO 2024-12-11 13:27:22 FastqToSam Auto-detected quality format as: Standard. 13:27:22.604 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 13:27:22.616 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 13:27:22.628 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 11 13:27:22 CET 2024] FastqToSam FASTQ=/scratch/o31309_FastqScreen_2024-12-11--13-20-51_temp1922338/313098_1--trimmed_R1.fastq.gz OUTPUT=313098_1--trimmed_R1.bam READ_GROUP_NAME=313098_1- SAMPLE_NAME=313098_1- LIBRARY_NAME=313098_1- PLATFORM=illumina SEQUENCING_CENTER=FGCZ RUN_DATE=2024-12-11T14:27:18+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 11 13:27:22 CET 2024] FastqToSam FASTQ=/scratch/o31309_FastqScreen_2024-12-11--13-20-51_temp1922338/313097_1--trimmed_R1.fastq.gz OUTPUT=313097_1--trimmed_R1.bam READ_GROUP_NAME=313097_1- SAMPLE_NAME=313097_1- LIBRARY_NAME=313097_1- PLATFORM=illumina SEQUENCING_CENTER=FGCZ RUN_DATE=2024-12-11T14:27:18+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 11 13:27:22 CET 2024] FastqToSam FASTQ=/scratch/o31309_FastqScreen_2024-12-11--13-20-51_temp1922338/313096_1--trimmed_R1.fastq.gz OUTPUT=313096_1--trimmed_R1.bam READ_GROUP_NAME=313096_1- SAMPLE_NAME=313096_1- LIBRARY_NAME=313096_1- PLATFORM=illumina SEQUENCING_CENTER=FGCZ RUN_DATE=2024-12-11T14:27:18+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 11 13:27:22 CET 2024] Executing as trxcopy@fgcz-h-166 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 11 13:27:22 CET 2024] Executing as trxcopy@fgcz-h-166 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 11 13:27:22 CET 2024] Executing as trxcopy@fgcz-h-166 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 2024-12-11 13:27:22 FastqToSam Auto-detected quality format as: Standard. INFO 2024-12-11 13:27:22 FastqToSam Processed 96028 fastq reads INFO 2024-12-11 13:27:22 FastqToSam Auto-detected quality format as: Standard. INFO 2024-12-11 13:27:22 FastqToSam Auto-detected quality format as: Standard. INFO 2024-12-11 13:27:23 FastqToSam Processed 96049 fastq reads INFO 2024-12-11 13:27:23 FastqToSam Processed 96013 fastq reads INFO 2024-12-11 13:27:23 FastqToSam Processed 96452 fastq reads [Wed Dec 11 13:27:23 CET 2024] picard.sam.FastqToSam done. Elapsed time: 0.03 minutes. Runtime.totalMemory()=1082130432 [Wed Dec 11 13:27:24 CET 2024] picard.sam.FastqToSam done. Elapsed time: 0.03 minutes. Runtime.totalMemory()=1082130432 [Wed Dec 11 13:27:24 CET 2024] picard.sam.FastqToSam done. Elapsed time: 0.03 minutes. Runtime.totalMemory()=1082130432 [Wed Dec 11 13:27:24 CET 2024] picard.sam.FastqToSam done. Elapsed time: 0.03 minutes. Runtime.totalMemory()=1082130432 INFO 2024-12-11 13:27:26 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 313091_1--trimmed_R1.bam -I 313092_1--trimmed_R1.bam -I 313093_1--trimmed_R1.bam -I 313094_1--trimmed_R1.bam -I 313095_1--trimmed_R1.bam -I 313096_1--trimmed_R1.bam -I 313097_1--trimmed_R1.bam -I 313098_1--trimmed_R1.bam -O refseqResult/allSamples_unmapped.bam -USE_THREADING true -SORT_ORDER queryname ********** 13:27:26.489 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 11 13:27:26 CET 2024] MergeSamFiles INPUT=[313091_1--trimmed_R1.bam, 313092_1--trimmed_R1.bam, 313093_1--trimmed_R1.bam, 313094_1--trimmed_R1.bam, 313095_1--trimmed_R1.bam, 313096_1--trimmed_R1.bam, 313097_1--trimmed_R1.bam, 313098_1--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 11 13:27:26 CET 2024] Executing as trxcopy@fgcz-h-166 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 2024-12-11 13:27:26 MergeSamFiles Input files are in same order as output so sorting to temp directory is not needed. INFO 2024-12-11 13:27:29 MergeSamFiles Finished reading inputs. [Wed Dec 11 13:27:29 CET 2024] picard.sam.MergeSamFiles done. Elapsed time: 0.06 minutes. Runtime.totalMemory()=1082130432 [M::bam2fq_mainloop] discarded 0 singletons [M::bam2fq_mainloop] processed 768762 reads No reads aligned to RefSeq Loading database information... done. 95977 sequences (9.59 Mbp) processed in 0.241s (23939.7 Kseq/m, 2392.60 Mbp/m). 62297 sequences classified (64.91%) 33680 sequences unclassified (35.09%) Loading database information... done. 96130 sequences (9.61 Mbp) processed in 0.184s (31304.4 Kseq/m, 3128.32 Mbp/m). 62947 sequences classified (65.48%) 33183 sequences unclassified (34.52%) Loading database information... done. 96069 sequences (9.60 Mbp) processed in 0.187s (30795.6 Kseq/m, 3078.03 Mbp/m). 62083 sequences classified (64.62%) 33986 sequences unclassified (35.38%) Loading database information... done. 96044 sequences (9.60 Mbp) processed in 0.185s (31125.7 Kseq/m, 3110.90 Mbp/m). 62020 sequences classified (64.57%) 34024 sequences unclassified (35.43%) Loading database information... done. 96028 sequences (9.59 Mbp) processed in 0.205s (28140.1 Kseq/m, 2811.65 Mbp/m). 62408 sequences classified (64.99%) 33620 sequences unclassified (35.01%) Loading database information... done. 96013 sequences (9.59 Mbp) processed in 0.196s (29444.2 Kseq/m, 2942.19 Mbp/m). 61841 sequences classified (64.41%) 34172 sequences unclassified (35.59%) Loading database information... done. 96049 sequences (9.60 Mbp) processed in 0.248s (23198.6 Kseq/m, 2318.52 Mbp/m). 62310 sequences classified (64.87%) 33739 sequences unclassified (35.13%) Loading database information... done. 96452 sequences (9.64 Mbp) processed in 0.187s (30947.2 Kseq/m, 3093.69 Mbp/m). 62550 sequences classified (64.85%) 33902 sequences unclassified (35.15%) slurmstepd-fgcz-h-166: error: Detected 1 oom-kill event(s) in StepId=12893.batch. Some of your processes may have been killed by the cgroup out-of-memory handler.