From cac6d97996b946e7de05a821a885c75bc2c56003 Mon Sep 17 00:00:00 2001 From: FelixKrueger Date: Wed, 11 Mar 2020 12:57:15 +0000 Subject: [PATCH 1/2] Two file that fail extracting NoHit regex --- data/modules/fastq_screen/failing1_screen.txt | 32 +++++++++++++++++++ data/modules/fastq_screen/failing2_screen.txt | 32 +++++++++++++++++++ 2 files changed, 64 insertions(+) create mode 100644 data/modules/fastq_screen/failing1_screen.txt create mode 100644 data/modules/fastq_screen/failing2_screen.txt diff --git a/data/modules/fastq_screen/failing1_screen.txt b/data/modules/fastq_screen/failing1_screen.txt new file mode 100644 index 00000000..c573f9d9 --- /dev/null +++ b/data/modules/fastq_screen/failing1_screen.txt @@ -0,0 +1,32 @@ +#Fastq_screen version: 0.14.0 #Aligner: bowtie2 #Reads in subset: 100000 +Genome #Reads_processed #Unmapped %Unmapped #One_hit_one_genome %One_hit_one_genome #Multiple_hits_one_genome %Multiple_hits_one_genome #One_hit_multiple_genomes %One_hit_multiple_genomes Multiple_hits_multiple_genomes %Multiple_hits_multiple_genomes +Cat 23 21 91.30 0 0.00 0 0.00 1 4.35 1 4.35 +Chicken 23 22 95.65 0 0.00 0 0.00 0 0.00 1 4.35 +Cow 23 21 91.30 0 0.00 0 0.00 1 4.35 1 4.35 +Drosophila 23 23 100.00 0 0.00 0 0.00 0 0.00 0 0.00 +Human 23 20 86.95 0 0.00 0 0.00 1 4.35 2 8.70 +Mouse 23 0 0.00 5 21.74 4 17.39 4 17.39 10 43.48 +Opossum 23 21 91.30 0 0.00 0 0.00 1 4.35 1 4.35 +Pig 23 20 86.95 0 0.00 0 0.00 2 8.70 1 4.35 +Rat 23 10 43.48 0 0.00 0 0.00 6 26.09 7 30.43 +Zebrafish 23 22 95.65 0 0.00 0 0.00 0 0.00 1 4.35 +Arabidopsis 23 23 100.00 0 0.00 0 0.00 0 0.00 0 0.00 +Grape 23 23 100.00 0 0.00 0 0.00 0 0.00 0 0.00 +Potato 23 23 100.00 0 0.00 0 0.00 0 0.00 0 0.00 +Tomato 23 23 100.00 0 0.00 0 0.00 0 0.00 0 0.00 +Adapters 23 23 100.00 0 0.00 0 0.00 0 0.00 0 0.00 +Brachybacterium 23 23 100.00 0 0.00 0 0.00 0 0.00 0 0.00 +Pseudomonas 23 23 100.00 0 0.00 0 0.00 0 0.00 0 0.00 +Massilia_oculi 23 23 100.00 0 0.00 0 0.00 0 0.00 0 0.00 +Ecoli 23 23 100.00 0 0.00 0 0.00 0 0.00 0 0.00 +Lambda 23 23 100.00 0 0.00 0 0.00 0 0.00 0 0.00 +MT 23 22 95.65 0 0.00 0 0.00 1 4.35 0 0.00 +PhiX 23 23 100.00 0 0.00 0 0.00 0 0.00 0 0.00 +rRNA 23 22 95.65 0 0.00 0 0.00 0 0.00 1 4.35 +Wasp 23 23 100.00 0 0.00 0 0.00 0 0.00 0 0.00 +Vectors 23 23 100.00 0 0.00 0 0.00 0 0.00 0 0.00 +Worm 23 22 95.65 0 0.00 0 0.00 0 0.00 1 4.35 +Yeast 23 23 100.00 0 0.00 0 0.00 0 0.00 0 0.00 +Mycoplasma 23 23 100.00 0 0.00 0 0.00 0 0.00 0 0.00 + +%Hit_no_genomes: 0.00 diff --git a/data/modules/fastq_screen/failing2_screen.txt b/data/modules/fastq_screen/failing2_screen.txt new file mode 100644 index 00000000..74b59d4c --- /dev/null +++ b/data/modules/fastq_screen/failing2_screen.txt @@ -0,0 +1,32 @@ +#Fastq_screen version: 0.14.0 #Aligner: bowtie2 #Reads in subset: 100000 +Genome #Reads_processed #Unmapped %Unmapped #One_hit_one_genome %One_hit_one_genome #Multiple_hits_one_genome %Multiple_hits_one_genome #One_hit_multiple_genomes %One_hit_multiple_genomes Multiple_hits_multiple_genomes %Multiple_hits_multiple_genomes +Cat 154 133 86.37 0 0.00 0 0.00 12 7.79 9 5.84 +Chicken 154 141 91.56 0 0.00 0 0.00 0 0.00 13 8.44 +Cow 154 131 85.06 0 0.00 0 0.00 7 4.55 16 10.39 +Drosophila 154 148 96.10 0 0.00 0 0.00 0 0.00 6 3.90 +Human 154 126 81.82 0 0.00 0 0.00 10 6.49 18 11.69 +Mouse 154 1 0.65 43 27.92 16 10.39 34 22.08 60 38.96 +Opossum 154 138 89.61 0 0.00 0 0.00 3 1.95 13 8.44 +Pig 154 132 85.72 0 0.00 0 0.00 9 5.84 13 8.44 +Rat 154 73 47.40 0 0.00 0 0.00 35 22.73 46 29.87 +Zebrafish 154 142 92.21 0 0.00 0 0.00 2 1.30 10 6.49 +Arabidopsis 154 146 94.81 0 0.00 0 0.00 0 0.00 8 5.19 +Grape 154 147 95.45 0 0.00 0 0.00 1 0.65 6 3.90 +Potato 154 146 94.81 0 0.00 0 0.00 0 0.00 8 5.19 +Tomato 154 146 94.81 0 0.00 0 0.00 0 0.00 8 5.19 +Adapters 154 154 100.00 0 0.00 0 0.00 0 0.00 0 0.00 +Brachybacterium 154 154 100.00 0 0.00 0 0.00 0 0.00 0 0.00 +Pseudomonas 154 154 100.00 0 0.00 0 0.00 0 0.00 0 0.00 +Massilia_oculi 154 154 100.00 0 0.00 0 0.00 0 0.00 0 0.00 +Ecoli 154 154 100.00 0 0.00 0 0.00 0 0.00 0 0.00 +Lambda 154 154 100.00 0 0.00 0 0.00 0 0.00 0 0.00 +MT 154 141 91.56 0 0.00 0 0.00 11 7.14 2 1.30 +PhiX 154 154 100.00 0 0.00 0 0.00 0 0.00 0 0.00 +rRNA 154 148 96.10 0 0.00 0 0.00 2 1.30 4 2.60 +Wasp 154 148 96.10 0 0.00 0 0.00 1 0.65 5 3.25 +Vectors 154 148 96.10 0 0.00 0 0.00 0 0.00 6 3.90 +Worm 154 147 95.45 0 0.00 0 0.00 0 0.00 7 4.55 +Yeast 154 147 95.45 0 0.00 0 0.00 0 0.00 7 4.55 +Mycoplasma 154 154 100.00 0 0.00 0 0.00 0 0.00 0 0.00 + +%Hit_no_genomes: 0.00 From 41ac9def30c13af07c8ef78886babad3f84dd42a Mon Sep 17 00:00:00 2001 From: FelixKrueger Date: Wed, 11 Mar 2020 15:33:22 +0000 Subject: [PATCH 2/2] Better names, moved into v0.14.0 folder --- .../scRNAseq_HISAT_example1_screen.txt} | 0 .../scRNAseq_HISAT_example2_screen.txt} | 0 2 files changed, 0 insertions(+), 0 deletions(-) rename data/modules/fastq_screen/{failing1_screen.txt => v0.14.0/scRNAseq_HISAT_example1_screen.txt} (100%) rename data/modules/fastq_screen/{failing2_screen.txt => v0.14.0/scRNAseq_HISAT_example2_screen.txt} (100%) diff --git a/data/modules/fastq_screen/failing1_screen.txt b/data/modules/fastq_screen/v0.14.0/scRNAseq_HISAT_example1_screen.txt similarity index 100% rename from data/modules/fastq_screen/failing1_screen.txt rename to data/modules/fastq_screen/v0.14.0/scRNAseq_HISAT_example1_screen.txt diff --git a/data/modules/fastq_screen/failing2_screen.txt b/data/modules/fastq_screen/v0.14.0/scRNAseq_HISAT_example2_screen.txt similarity index 100% rename from data/modules/fastq_screen/failing2_screen.txt rename to data/modules/fastq_screen/v0.14.0/scRNAseq_HISAT_example2_screen.txt