/srv/GT/analysis/course_sushi/public/gstore/projects/p1001/o35755_CrisprScreenQC_2025-07-24--16-39-07/scripts/QC_ventricles_100k_1.sh_sushiID1618_2025-07-24--16-39-19_o.log -------------------------------------------------- Job runs on fgcz-h-121 at /scratch/o35755_CrisprScreenQC_2025-07-24--16-39-07_temp609585 Starting CrisprScreenQC CrisprScreenQC_Result o35755_CrisprScreenQC_2025-07-24--16-39-07_temp609585 2025-07-24 16:39:26 EXECUTED CMD: touch mut11_preprocessing.log EXECUTED CMD: fastp --in1 /scratch/o35755_CrisprScreenQC_2025-07-24--16-39-07_temp609585/mut11-subsample_R1.fastq.gz --in2 /scratch/o35755_CrisprScreenQC_2025-07-24--16-39-07_temp609585/mut11-subsample_R2.fastq.gz --out1 trimmed_R1.fastq.gz --out2 trimmed_R2.fastq.gz --thread 1 --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> mut11_preprocessing.log EXECUTED CMD: cat fastp.json >> mut11_preprocessing.log EXECUTED CMD: touch mut22_preprocessing.log EXECUTED CMD: fastp --in1 /scratch/o35755_CrisprScreenQC_2025-07-24--16-39-07_temp609585/mut22-subsample_R1.fastq.gz --in2 /scratch/o35755_CrisprScreenQC_2025-07-24--16-39-07_temp609585/mut22-subsample_R2.fastq.gz --out1 trimmed_R1.fastq.gz --out2 trimmed_R2.fastq.gz --thread 1 --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> mut22_preprocessing.log EXECUTED CMD: cat fastp.json >> mut22_preprocessing.log ezRun tag: ab8b8bb744696ce1f0c18d74d7827aa49a033ee7 ezRun github link: https://github.com/uzh/ezRun/tree/ab8b8bb744696ce1f0c18d74d7827aa49a033ee7 R version 4.5.0 (2025-04-11) 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 LAPACK version 3.11.0 locale: [1] LC_CTYPE=C.UTF-8 LC_NUMERIC=C LC_TIME=C.UTF-8 [4] LC_COLLATE=C.UTF-8 LC_MONETARY=C.UTF-8 LC_MESSAGES=C.UTF-8 [7] LC_PAPER=C.UTF-8 LC_NAME=C LC_ADDRESS=C [10] LC_TELEPHONE=C LC_MEASUREMENT=C.UTF-8 LC_IDENTIFICATION=C time zone: Europe/Zurich tzcode source: system (glibc) attached base packages: [1] grid stats4 stats graphics grDevices utils datasets [8] 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_1.50 qs2_0.1.5 [7] withr_3.0.2 ShortRead_1.66.0 [9] GenomicAlignments_1.44.0 SummarizedExperiment_1.38.1 [11] Biobase_2.68.0 MatrixGenerics_1.20.0 [13] matrixStats_1.5.0 Rsamtools_2.24.0 [15] BiocParallel_1.42.1 seqLogo_1.74.0 [17] Herper_1.18.0 reticulate_1.42.0 [19] ezRun_3.21.1 lubridate_1.9.4 [21] forcats_1.0.0 stringr_1.5.1 [23] dplyr_1.1.4 purrr_1.0.4 [25] readr_2.1.5 tidyr_1.3.1 [27] tibble_3.2.1 ggplot2_3.5.2 [29] tidyverse_2.0.0 GenomicRanges_1.60.0 [31] Biostrings_2.76.0 GenomeInfoDb_1.44.0 [33] XVector_0.48.0 IRanges_2.42.0 [35] S4Vectors_0.46.0 BiocGenerics_0.54.0 [37] generics_0.1.4 data.table_1.17.4 loaded via a namespace (and not attached): [1] tidyselect_1.2.1 viridisLite_0.4.2 farver_2.1.2 [4] bitops_1.0-9 lazyeval_0.2.2 fastmap_1.2.0 [7] stringfish_0.16.0 digest_0.6.37 timechange_0.3.0 [10] lifecycle_1.0.4 pwalign_1.4.0 statmod_1.5.0 [13] magrittr_2.0.3 compiler_4.5.0 rlang_1.1.6 [16] sass_0.4.10 tools_4.5.0 yaml_2.3.10 [19] htmlwidgets_1.6.4 S4Arrays_1.8.0 interp_1.1-6 [22] DelayedArray_0.34.1 xml2_1.3.8 RColorBrewer_1.1-3 [25] abind_1.4-8 hwriter_1.3.2.1 latticeExtra_0.6-30 [28] scales_1.4.0 dichromat_2.0-0.1 cli_3.6.5 [31] rmarkdown_2.29 crayon_1.5.3 RcppParallel_5.1.10 [34] rstudioapi_0.17.1 httr_1.4.7 tzdb_0.5.0 [37] rjson_0.2.23 cachem_1.1.0 parallel_4.5.0 [40] vctrs_0.6.5 Matrix_1.7-3 jsonlite_2.0.0 [43] hms_1.1.3 crosstalk_1.2.1 systemfonts_1.2.3 [46] jpeg_0.1-11 limma_3.64.1 jquerylib_0.1.4 [49] glue_1.8.0 codetools_0.2-20 stringi_1.8.7 [52] gtable_0.3.6 deldir_2.0-4 UCSC.utils_1.4.0 [55] pillar_1.10.2 GenomeInfoDbData_1.2.14 R6_2.6.1 [58] textshaping_1.0.1 evaluate_1.0.3 lattice_0.22-7 [61] png_0.1-8 bslib_0.9.0 Rcpp_1.0.14 [64] svglite_2.2.1 SparseArray_1.8.0 xfun_0.52 [67] pkgconfig_2.0.3 Finished CrisprScreenQC CrisprScreenQC_Result o35755_CrisprScreenQC_2025-07-24--16-39-07_temp609585 2025-07-24 16:41:10 [1] "Success" ___STDOUT_END___ /srv/GT/analysis/course_sushi/public/gstore/projects/p1001/o35755_CrisprScreenQC_2025-07-24--16-39-07/scripts/QC_ventricles_100k_1.sh_sushiID1618_2025-07-24--16-39-19_e.log -------------------------------------------------- Loading required package: data.table Loading required package: Biostrings Loading required package: BiocGenerics Loading required package: generics Attaching package: ‘generics’ The following objects are masked from ‘package:base’: as.difftime, as.factor, as.ordered, intersect, is.element, setdiff, setequal, union 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, is.unsorted, lapply, Map, mapply, match, mget, order, paste, pmax, pmax.int, pmin, pmin.int, Position, rank, rbind, Reduce, rownames, sapply, saveRDS, table, tapply, 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 3.5.2 ✔ tibble 3.2.1 ✔ lubridate 1.9.4 ✔ tidyr 1.3.1 ✔ purrr 1.0.4 ── 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: Herper Loading required package: reticulate Attaching package: ‘Herper’ The following object is masked from ‘package:reticulate’: conda_search 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 INFO @ Thu, 24 Jul 2025 16:40:22: Parameters: /misc/ngseq12/miniforge3/envs/gi_mageck/bin/mageck count -l GEML_Mageck_mergedRefs.csv --fastq /scratch/o35755_CrisprScreenQC_2025-07-24--16-39-07_temp609585/mut11-trimmed_R1.fastq.gz -n mut11 INFO @ Thu, 24 Jul 2025 16:40:22: Welcome to MAGeCK v0.5.9.5. Command: count INFO @ Thu, 24 Jul 2025 16:40:22: Header line of the library file detected; skip the first line ... INFO @ Thu, 24 Jul 2025 16:40:25: Loading 1435762 predefined sgRNAs. WARNING @ Thu, 24 Jul 2025 16:40:25: There are 596131 sgRNAs with duplicated sequences. INFO @ Thu, 24 Jul 2025 16:40:27: Parsing FASTQ file /scratch/o35755_CrisprScreenQC_2025-07-24--16-39-07_temp609585/mut11-trimmed_R1.fastq.gz... INFO @ Thu, 24 Jul 2025 16:40:27: Determining the trim-5 length of FASTQ file /scratch/o35755_CrisprScreenQC_2025-07-24--16-39-07_temp609585/mut11-trimmed_R1.fastq.gz... INFO @ Thu, 24 Jul 2025 16:40:27: Possible gRNA lengths:20,19,18,17,2 INFO @ Thu, 24 Jul 2025 16:40:27: Processing 0M reads ... INFO @ Thu, 24 Jul 2025 16:40:34: Read length:50,42,40,44,38,41,47,49,45,28,39,48,30,43,29,31,46,37,34,33,19,32,36,35,24,18,23,26,21,20,27,22,25 INFO @ Thu, 24 Jul 2025 16:40:34: Total tested reads: 86970, mapped: 5288(0.06080257560078188) WARNING @ Thu, 24 Jul 2025 16:40:34: Only 6.080257560078188 % of the reads can be identified. INFO @ Thu, 24 Jul 2025 16:40:34: --trim-5 test data: (trim_length reads fraction) INFO @ Thu, 24 Jul 2025 16:40:34: 9 246 0.04652042360060514 INFO @ Thu, 24 Jul 2025 16:40:34: 0 236 0.04462934947049924 INFO @ Thu, 24 Jul 2025 16:40:34: 20 213 0.04027987897125567 INFO @ Thu, 24 Jul 2025 16:40:34: 6 203 0.03838880484114977 INFO @ Thu, 24 Jul 2025 16:40:34: 11 198 0.03744326777609682 INFO @ Thu, 24 Jul 2025 16:40:34: 15 195 0.03687594553706505 INFO @ Thu, 24 Jul 2025 16:40:34: 7 192 0.036308623298033284 INFO @ Thu, 24 Jul 2025 16:40:34: 3 189 0.035741301059001515 INFO @ Thu, 24 Jul 2025 16:40:34: 5 186 0.03517397881996974 INFO @ Thu, 24 Jul 2025 16:40:34: 2 183 0.03460665658093797 INFO @ Thu, 24 Jul 2025 16:40:34: 16 181 0.034228441754916794 INFO @ Thu, 24 Jul 2025 16:40:34: 1 177 0.033472012102874434 INFO @ Thu, 24 Jul 2025 16:40:34: 8 175 0.03309379727685325 INFO @ Thu, 24 Jul 2025 16:40:34: 21 168 0.03177004538577912 INFO @ Thu, 24 Jul 2025 16:40:34: 4 164 0.031013615733736764 INFO @ Thu, 24 Jul 2025 16:40:34: 18 164 0.031013615733736764 INFO @ Thu, 24 Jul 2025 16:40:34: 24 160 0.030257186081694403 INFO @ Thu, 24 Jul 2025 16:40:34: 12 160 0.030257186081694403 INFO @ Thu, 24 Jul 2025 16:40:34: 10 159 0.03006807866868381 INFO @ Thu, 24 Jul 2025 16:40:34: 22 158 0.029878971255673223 INFO @ Thu, 24 Jul 2025 16:40:34: 17 157 0.02968986384266263 INFO @ Thu, 24 Jul 2025 16:40:34: 27 155 0.02931164901664145 INFO @ Thu, 24 Jul 2025 16:40:34: 26 153 0.028933434190620274 INFO @ Thu, 24 Jul 2025 16:40:34: 23 153 0.028933434190620274 INFO @ Thu, 24 Jul 2025 16:40:34: 28 141 0.026664145234493192 INFO @ Thu, 24 Jul 2025 16:40:34: 14 139 0.026285930408472012 INFO @ Thu, 24 Jul 2025 16:40:34: 29 132 0.024962178517397883 INFO @ Thu, 24 Jul 2025 16:40:34: 13 132 0.024962178517397883 INFO @ Thu, 24 Jul 2025 16:40:34: 25 131 0.02477307110438729 INFO @ Thu, 24 Jul 2025 16:40:34: 30 128 0.024205748865355523 INFO @ Thu, 24 Jul 2025 16:40:34: 19 126 0.023827534039334342 INFO @ Thu, 24 Jul 2025 16:40:34: 31 34 0.006429652042360061 INFO @ Thu, 24 Jul 2025 16:40:34: Auto determination of trim5 results: 9 INFO @ Thu, 24 Jul 2025 16:40:34: Possible gRNA lengths:20,19,18,17,2 INFO @ Thu, 24 Jul 2025 16:40:34: Processing 0M reads .. INFO @ Thu, 24 Jul 2025 16:40:35: Total: 86970. INFO @ Thu, 24 Jul 2025 16:40:35: Mapped: 335. INFO @ Thu, 24 Jul 2025 16:40:36: Final size factor: 2.0 INFO @ Thu, 24 Jul 2025 16:40:37: Summary of file /scratch/o35755_CrisprScreenQC_2025-07-24--16-39-07_temp609585/mut11-trimmed_R1.fastq.gz: INFO @ Thu, 24 Jul 2025 16:40:37: label sample1 INFO @ Thu, 24 Jul 2025 16:40:37: reads 86970 INFO @ Thu, 24 Jul 2025 16:40:37: mappedreads 335 INFO @ Thu, 24 Jul 2025 16:40:37: totalsgrnas 1435762 INFO @ Thu, 24 Jul 2025 16:40:37: zerosgrnas 1435559 INFO @ Thu, 24 Jul 2025 16:40:37: giniindex 0.9998816676973659 INFO @ Thu, 24 Jul 2025 16:40:37: Loading Rnw template file: /misc/ngseq12/miniforge3/envs/gi_mageck/lib/python3.11/site-packages/mageck/count_report.Rmd. INFO @ Thu, 24 Jul 2025 16:40:37: Loading Rnw template file: /misc/ngseq12/miniforge3/envs/gi_mageck/lib/python3.11/site-packages/mageck/fastq_template.Rnw. INFO @ Thu, 24 Jul 2025 16:40:43: Parameters: /misc/ngseq12/miniforge3/envs/gi_mageck/bin/mageck count -l GEML_Mageck_mergedRefs.csv --fastq /scratch/o35755_CrisprScreenQC_2025-07-24--16-39-07_temp609585/mut22-trimmed_R1.fastq.gz -n mut22 INFO @ Thu, 24 Jul 2025 16:40:43: Welcome to MAGeCK v0.5.9.5. Command: count INFO @ Thu, 24 Jul 2025 16:40:43: Header line of the library file detected; skip the first line ... INFO @ Thu, 24 Jul 2025 16:40:46: Loading 1435762 predefined sgRNAs. WARNING @ Thu, 24 Jul 2025 16:40:46: There are 596131 sgRNAs with duplicated sequences. INFO @ Thu, 24 Jul 2025 16:40:48: Parsing FASTQ file /scratch/o35755_CrisprScreenQC_2025-07-24--16-39-07_temp609585/mut22-trimmed_R1.fastq.gz... INFO @ Thu, 24 Jul 2025 16:40:48: Determining the trim-5 length of FASTQ file /scratch/o35755_CrisprScreenQC_2025-07-24--16-39-07_temp609585/mut22-trimmed_R1.fastq.gz... INFO @ Thu, 24 Jul 2025 16:40:48: Possible gRNA lengths:20,19,18,17,2 INFO @ Thu, 24 Jul 2025 16:40:48: Processing 0M reads ... INFO @ Thu, 24 Jul 2025 16:40:55: Read length:50,42,40,44,38,41,47,49,45,28,39,48,30,43,29,31,46,37,34,33,19,32,36,35,24,18,23,26,21,20,27,22,25 INFO @ Thu, 24 Jul 2025 16:40:55: Total tested reads: 86970, mapped: 5288(0.06080257560078188) WARNING @ Thu, 24 Jul 2025 16:40:55: Only 6.080257560078188 % of the reads can be identified. INFO @ Thu, 24 Jul 2025 16:40:55: --trim-5 test data: (trim_length reads fraction) INFO @ Thu, 24 Jul 2025 16:40:55: 9 246 0.04652042360060514 INFO @ Thu, 24 Jul 2025 16:40:55: 0 236 0.04462934947049924 INFO @ Thu, 24 Jul 2025 16:40:55: 20 213 0.04027987897125567 INFO @ Thu, 24 Jul 2025 16:40:55: 6 203 0.03838880484114977 INFO @ Thu, 24 Jul 2025 16:40:55: 11 198 0.03744326777609682 INFO @ Thu, 24 Jul 2025 16:40:55: 15 195 0.03687594553706505 INFO @ Thu, 24 Jul 2025 16:40:55: 7 192 0.036308623298033284 INFO @ Thu, 24 Jul 2025 16:40:55: 3 189 0.035741301059001515 INFO @ Thu, 24 Jul 2025 16:40:55: 5 186 0.03517397881996974 INFO @ Thu, 24 Jul 2025 16:40:55: 2 183 0.03460665658093797 INFO @ Thu, 24 Jul 2025 16:40:55: 16 181 0.034228441754916794 INFO @ Thu, 24 Jul 2025 16:40:55: 1 177 0.033472012102874434 INFO @ Thu, 24 Jul 2025 16:40:55: 8 175 0.03309379727685325 INFO @ Thu, 24 Jul 2025 16:40:55: 21 168 0.03177004538577912 INFO @ Thu, 24 Jul 2025 16:40:55: 4 164 0.031013615733736764 INFO @ Thu, 24 Jul 2025 16:40:55: 18 164 0.031013615733736764 INFO @ Thu, 24 Jul 2025 16:40:55: 24 160 0.030257186081694403 INFO @ Thu, 24 Jul 2025 16:40:55: 12 160 0.030257186081694403 INFO @ Thu, 24 Jul 2025 16:40:55: 10 159 0.03006807866868381 INFO @ Thu, 24 Jul 2025 16:40:55: 22 158 0.029878971255673223 INFO @ Thu, 24 Jul 2025 16:40:55: 17 157 0.02968986384266263 INFO @ Thu, 24 Jul 2025 16:40:55: 27 155 0.02931164901664145 INFO @ Thu, 24 Jul 2025 16:40:55: 26 153 0.028933434190620274 INFO @ Thu, 24 Jul 2025 16:40:55: 23 153 0.028933434190620274 INFO @ Thu, 24 Jul 2025 16:40:55: 28 141 0.026664145234493192 INFO @ Thu, 24 Jul 2025 16:40:55: 14 139 0.026285930408472012 INFO @ Thu, 24 Jul 2025 16:40:55: 29 132 0.024962178517397883 INFO @ Thu, 24 Jul 2025 16:40:55: 13 132 0.024962178517397883 INFO @ Thu, 24 Jul 2025 16:40:55: 25 131 0.02477307110438729 INFO @ Thu, 24 Jul 2025 16:40:55: 30 128 0.024205748865355523 INFO @ Thu, 24 Jul 2025 16:40:55: 19 126 0.023827534039334342 INFO @ Thu, 24 Jul 2025 16:40:55: 31 34 0.006429652042360061 INFO @ Thu, 24 Jul 2025 16:40:55: Auto determination of trim5 results: 9 INFO @ Thu, 24 Jul 2025 16:40:55: Possible gRNA lengths:20,19,18,17,2 INFO @ Thu, 24 Jul 2025 16:40:55: Processing 0M reads .. INFO @ Thu, 24 Jul 2025 16:40:55: Total: 86970. INFO @ Thu, 24 Jul 2025 16:40:55: Mapped: 335. INFO @ Thu, 24 Jul 2025 16:40:57: Final size factor: 2.0 INFO @ Thu, 24 Jul 2025 16:40:58: Summary of file /scratch/o35755_CrisprScreenQC_2025-07-24--16-39-07_temp609585/mut22-trimmed_R1.fastq.gz: INFO @ Thu, 24 Jul 2025 16:40:58: label sample1 INFO @ Thu, 24 Jul 2025 16:40:58: reads 86970 INFO @ Thu, 24 Jul 2025 16:40:58: mappedreads 335 INFO @ Thu, 24 Jul 2025 16:40:58: totalsgrnas 1435762 INFO @ Thu, 24 Jul 2025 16:40:58: zerosgrnas 1435559 INFO @ Thu, 24 Jul 2025 16:40:58: giniindex 0.9998816676973659 INFO @ Thu, 24 Jul 2025 16:40:58: Loading Rnw template file: /misc/ngseq12/miniforge3/envs/gi_mageck/lib/python3.11/site-packages/mageck/count_report.Rmd. INFO @ Thu, 24 Jul 2025 16:40:58: Loading Rnw template file: /misc/ngseq12/miniforge3/envs/gi_mageck/lib/python3.11/site-packages/mageck/fastq_template.Rnw. Loading required package: qs2 qs2 0.1.5 ___STDERR_END___