# HG changeset patch # User iuc # Date 1514062675 18000 # Node ID 01237d721a9f8642a382e083034396c62b45475c # Parent 5746cb5cf08d1a303d19c30bcabe188402b9fb7e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit d9175b08720c657b7a4521472450dd5ac6fd9361 diff -r 5746cb5cf08d -r 01237d721a9f multiqc.xml --- a/multiqc.xml Tue Dec 05 05:24:03 2017 -0500 +++ b/multiqc.xml Sat Dec 23 15:57:55 2017 -0500 @@ -1,7 +1,7 @@ aggregate results from bioinformatics analyses into a single report - 1.2 + 1.3 Flexbar + @@ -467,6 +471,9 @@ + + + @@ -727,6 +734,12 @@ + + + + + + @@ -763,6 +776,8 @@ + + @@ -770,6 +785,7 @@ + diff -r 5746cb5cf08d -r 01237d721a9f test-data/aligner_soft_stats.tabular --- a/test-data/aligner_soft_stats.tabular Tue Dec 05 05:24:03 2017 -0500 +++ b/test-data/aligner_soft_stats.tabular Sat Dec 23 15:57:55 2017 -0500 @@ -1,14 +1,16 @@ -Sample Cutadapt_percent_trimmed Kallisto_fragment_length Kallisto_percent_aligned Kallisto_pseudoaligned_reads Bismark_aligned_reads Bismark_percent_aligned Bowtie 2_overall_alignment_rate HISAT2_overall_alignment_rate STAR_uniquely_mapped_percent STAR_uniquely_mapped Tophat_overall_aligned_percent Tophat_aligned_not_multimapped_discordant -HS002-PE-R00059_BD0U5YACXX.RHM066_CGATGT_L002_R1 5.880883098970165 -HS002-PE-R00059_BD0U5YACXX.RHM066_CGATGT_L002_R1_val_1 167.866 83.65114569077758 48531088.0 -HS002-PE-R00059_BD0U5YACXX.RHM066_CGATGT_L002_R2 31.038195169381073 -HS002-PE-R00059_BD0U5YACXX.RHM067_CAGATC_L002_R1 7.7267901650356645 -HS002-PE-R00059_BD0U5YACXX.RHM067_CAGATC_L002_R1_val_1 169.418 84.50278473550448 59280920.0 -HS002-PE-R00059_BD0U5YACXX.RHM067_CAGATC_L002_R2 32.18485266309055 -bismark_SE_report 220558.0 69.71079996207212 -bowtie2_1 98.33 -bowtie2_2 98.31 -hisat2_1 96.15 -hisat2_2 96.15 -star_log 89.0 89.0 -tophat_align 99.5 307733.0 +Sample Cutadapt_percent_trimmed-1 Kallisto_percent_aligned-1-1 Kallisto_pseudoaligned_reads-1 Kallisto_fragment_length-1 Bismark_aligned_reads-1 Bismark_percent_aligned-2 Bowtie 2_overall_alignment_rate-1-1 HiCExplorer_Pairs_considered-1 HiCExplorer_Min_rest_site_distance-1 HiCExplorer_Mapped-1 HiCExplorer_Max_rest_site_distance-1 HiCExplorer_Pairs_used-1 HISAT2_overall_alignment_rate-2 STAR_uniquely_mapped_percent-1 STAR_uniquely_mapped-1 Tophat_overall_aligned_percent-1 Tophat_aligned_not_multimapped_discordant-1 +HS002-PE-R00059_BD0U5YACXX.RHM066_CGATGT_L002_R1 5.880883098970165 +HS002-PE-R00059_BD0U5YACXX.RHM066_CGATGT_L002_R1_val_1 83.65114569077758 48531088.0 167.866 +HS002-PE-R00059_BD0U5YACXX.RHM066_CGATGT_L002_R2 31.038195169381073 +HS002-PE-R00059_BD0U5YACXX.RHM067_CAGATC_L002_R1 7.7267901650356645 +HS002-PE-R00059_BD0U5YACXX.RHM067_CAGATC_L002_R1_val_1 84.50278473550448 59280920.0 169.418 +HS002-PE-R00059_BD0U5YACXX.RHM067_CAGATC_L002_R2 32.18485266309055 +align_0 220558.0 69.71079996207212 +bowtie2_1 98.33 +bowtie2_2 98.31 +hicexplorer_3_small_test 99983.0 303.0 0.08778492343698428 800.0 0.3732734564876029 +hicexplorer_3_small_test_rf 99983.0 152.0 0.08778492343698428 1500.0 0.35940109818669175 +hisat2_1 96.15 +hisat2_2 96.15 +star_log 89.0 89.0 +tophat 99.5 307733.0 diff -r 5746cb5cf08d -r 01237d721a9f test-data/bcftools_stats.tabular --- a/test-data/bcftools_stats.tabular Tue Dec 05 05:24:03 2017 -0500 +++ b/test-data/bcftools_stats.tabular Sat Dec 23 15:57:55 2017 -0500 @@ -1,2 +1,2 @@ -Sample substitution_type_G>T number_of_samples substitution_type_G>C substitution_type_G>A tstv tv_1st_ALT number_of_others number_of_multiallelic_SNP_sites number_of_no-ALTs ts_1st_ALT number_of_MNPs ts number_of_multiallelic_sites number_of_SNPs number_of_indels substitution_type_C>A substitution_type_C>G substitution_type_A>T substitution_type_A>C number_of_records substitution_type_A>G substitution_type_C>T substitution_type_T>A substitution_type_T>C tstv_1st_ALT substitution_type_T>G tv -Test1 201005.0 1.0 197866.0 763594.0 1.97 1505704.0 73262.0 0.0 0.0 2968539.0 72330.0 2968539.0 0.0 4474244.0 902934.0 196831.0 197211.0 166827.0 190164.0 5522770.0 721395.0 762114.0 166222.0 721436.0 1.97 189578.0 1505704.0 +Sample number_of_records ts_1st_ALT substitution_type_G>C tv substitution_type_A>G substitution_type_A>C number_of_multiallelic_SNP_sites number_of_multiallelic_sites substitution_type_A>T number_of_SNPs number_of_MNPs substitution_type_T>G tstv_1st_ALT tstv number_of_no-ALTs substitution_type_C>G substitution_type_C>T ts number_of_samples substitution_type_T>C substitution_type_G>T substitution_type_T>A substitution_type_C>A number_of_indels tv_1st_ALT number_of_others substitution_type_G>A +Test1 5522770.0 2968539.0 197866.0 1505704.0 721395.0 190164.0 0.0 0.0 166827.0 4474244.0 72330.0 189578.0 1.97 1.97 0.0 197211.0 762114.0 2968539.0 1.0 721436.0 201005.0 166222.0 196831.0 902934.0 1505704.0 73262.0 763594.0 diff -r 5746cb5cf08d -r 01237d721a9f test-data/bismark_stats.tabular --- a/test-data/bismark_stats.tabular Tue Dec 05 05:24:03 2017 -0500 +++ b/test-data/bismark_stats.tabular Sat Dec 23 15:57:55 2017 -0500 @@ -1,2 +1,2 @@ Sample aligned_reads ambig_reads discarded_reads meth_chg meth_chh meth_cpg no_alignments percent_aligned percent_chg_meth percent_chh_meth percent_cpg_meth strand_ctob strand_ctot strand_ob strand_ot total_c total_reads unmeth_chg unmeth_chh unmeth_cpg -bismark_SE_report 220558.0 1904.0 0.0 1358074.0 3449120.0 465068.0 93928.0 69.7107999621 99.8 99.7 98.6 0.0 0.0 112206.0 108352.0 5291918.0 316390.0 2988.0 10269.0 6399.0 +align_0 220558.0 1904.0 0.0 1358074.0 3449120.0 465068.0 93928.0 69.71079996207212 99.8 99.7 98.6 0.0 0.0 112206.0 108352.0 5291918.0 316390.0 2988.0 10269.0 6399.0 diff -r 5746cb5cf08d -r 01237d721a9f test-data/cutadapt_stats.tabular --- a/test-data/cutadapt_stats.tabular Tue Dec 05 05:24:03 2017 -0500 +++ b/test-data/cutadapt_stats.tabular Sat Dec 23 15:57:55 2017 -0500 @@ -1,2 +1,2 @@ -Sample r_trimmed bp_trimmed bp_processed too_short r_processed too_long percent_trimmed -dataset_33 68795 3443775 31955390 0 316390 0 10.7768204362 +Sample too_short percent_trimmed too_long bp_trimmed bp_processed r_trimmed r_processed +dataset_33 0 10.776820436239396 0 3443775 31955390 68795 316390 diff -r 5746cb5cf08d -r 01237d721a9f test-data/fastqc_stats.tabular --- a/test-data/fastqc_stats.tabular Tue Dec 05 05:24:03 2017 -0500 +++ b/test-data/fastqc_stats.tabular Sat Dec 23 15:57:55 2017 -0500 @@ -1,3 +1,3 @@ -Sample adapter_content Sequences flagged as poor quality sequence_duplication_levels avg_sequence_length Encoding kmer_content per_base_sequence_quality sequence_length_distribution Sequence length File type basic_statistics per_sequence_gc_content Total Sequences per_base_n_content per_base_sequence_content overrepresented_sequences %GC total_deduplicated_percentage Filename per_tile_sequence_quality per_sequence_quality_scores -poulet5_1 pass 0.0 warn 101.0 Sanger / Illumina 1.9 warn warn pass 101.0 Conventional base calls pass pass 267849.0 pass fail pass 48.0 63.6940884007 poulet5_1 pass warn -poulet5_2 pass 0.0 warn 101.0 Sanger / Illumina 1.9 warn warn pass 101.0 Conventional base calls pass pass 267849.0 pass fail pass 48.0 63.8266112519 poulet5_2 pass warn +Sample per_base_sequence_quality total_deduplicated_percentage sequence_duplication_levels basic_statistics Filename sequence_length_distribution avg_sequence_length per_sequence_quality_scores per_base_sequence_content adapter_content Total Sequences per_sequence_gc_content File type Encoding per_tile_sequence_quality per_base_n_content kmer_content Sequences flagged as poor quality Sequence length overrepresented_sequences %GC +poulet5_1 warn 63.69408840068983 warn pass poulet5_1 pass 101.0 warn fail pass 267849.0 pass Conventional base calls Sanger / Illumina 1.9 pass pass warn 0.0 101.0 pass 48.0 +poulet5_2 warn 63.826611251945884 warn pass poulet5_2 pass 101.0 warn fail pass 267849.0 pass Conventional base calls Sanger / Illumina 1.9 pass pass warn 0.0 101.0 pass 48.0 diff -r 5746cb5cf08d -r 01237d721a9f test-data/featureCounts_stats.tabular --- a/test-data/featureCounts_stats.tabular Tue Dec 05 05:24:03 2017 -0500 +++ b/test-data/featureCounts_stats.tabular Sat Dec 23 15:57:55 2017 -0500 @@ -1,7 +1,7 @@ -Sample Unassigned_Ambiguity Unassigned_MappingQuality percent_assigned Unassigned_Nonjunction Unassigned_Duplicate Unassigned_Chimera Unassigned_Unmapped Assigned Unassigned_MultiMapping Unassigned_Secondary Unassigned_NoFeatures Unassigned_FragmentLength Total -70: TopHat on data 1, data 4, and data 3: accepted_hits 2333 0 70.8226775535 0 0 0 0 321797 19123 0 111117 0 454370 -75: TopHat on data 1, data 6, and data 5: accepted_hits 3424 0 69.585858033 0 0 0 0 445012 25293 0 165786 0 639515 -80: TopHat on data 1, data 8, and data 7: accepted_hits 3121 0 71.7695776839 0 0 0 0 394981 22580 0 129664 0 550346 -85: TopHat on data 1, data 10, and data 9: accepted_hits 3692 0 72.0245435134 0 0 0 0 437485 19907 0 146327 0 607411 -90: TopHat on data 1, data 12, and data 11: accepted_hits 2782 0 71.3313082644 0 0 0 0 388170 21164 0 132063 0 544179 -95: TopHat on data 1, data 14, and data 13: accepted_hits 3554 0 70.7251710368 0 0 0 0 453929 23533 0 160805 0 641821 +Sample Unassigned_Nonjunction percent_assigned Total Unassigned_FragmentLength Unassigned_MultiMapping Unassigned_NoFeatures Unassigned_Secondary Unassigned_MappingQuality Unassigned_Duplicate Unassigned_Ambiguity Unassigned_Unmapped Assigned Unassigned_Chimera +70: TopHat on data 1, data 4, and data 3: accepted_hits 0 70.82267755353567 454370 0 19123 111117 0 0 0 2333 0 321797 0 +75: TopHat on data 1, data 6, and data 5: accepted_hits 0 69.58585803304067 639515 0 25293 165786 0 0 0 3424 0 445012 0 +80: TopHat on data 1, data 8, and data 7: accepted_hits 0 71.76957768385707 550346 0 22580 129664 0 0 0 3121 0 394981 0 +85: TopHat on data 1, data 10, and data 9: accepted_hits 0 72.02454351337069 607411 0 19907 146327 0 0 0 3692 0 437485 0 +90: TopHat on data 1, data 12, and data 11: accepted_hits 0 71.33130826437625 544179 0 21164 132063 0 0 0 2782 0 388170 0 +95: TopHat on data 1, data 14, and data 13: accepted_hits 0 70.72517103678439 641821 0 23533 160805 0 0 0 3554 0 453929 0 diff -r 5746cb5cf08d -r 01237d721a9f test-data/flexbar_stats.tabular --- a/test-data/flexbar_stats.tabular Tue Dec 05 05:24:03 2017 -0500 +++ b/test-data/flexbar_stats.tabular Sat Dec 23 15:57:55 2017 -0500 @@ -1,2 +1,2 @@ -Sample removed_bases_pct remaining_reads short_prior_to_adapter_removal remaining_bases skipped_due_to_uncalled_bases processed_reads processed_bases removed_bases discarded_reads_overall finally_skipped_short_reads -result_right 45.2606635071 10 0 231 0 13 422 191 3 3 +Sample processed_bases discarded_reads_overall finally_skipped_short_reads skipped_due_to_uncalled_bases removed_bases remaining_bases remaining_reads short_prior_to_adapter_removal removed_bases_pct processed_reads +result_right 422 3 3 0 191 231 10 0 45.26066350710901 13 diff -r 5746cb5cf08d -r 01237d721a9f test-data/gatk_varianteval_stats.tabular --- a/test-data/gatk_varianteval_stats.tabular Tue Dec 05 05:24:03 2017 -0500 +++ b/test-data/gatk_varianteval_stats.tabular Sat Dec 23 15:57:55 2017 -0500 @@ -1,2 +1,2 @@ -Sample deletions insertions known_titv snps symbolic novel_titv complex mnps titv_reference mixed nocalls -gatk_varianteval 0 0 0.0 19199310 0 2.2 0 0 none 0 1330372586 +Sample nocalls mnps novel_titv mixed deletions snps known_titv titv_reference complex symbolic insertions +varianteval_1_gatk_varianteval 1330372586 0 2.2 0 0 19199310 0.0 none 0 0 0 diff -r 5746cb5cf08d -r 01237d721a9f test-data/hicexplorer1.log --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/hicexplorer1.log Sat Dec 23 15:57:55 2017 -0500 @@ -0,0 +1,29 @@ + +File small_test_matrix.h5 +Pairs considered 99983 +Min rest. site distance 303 +Max rest. site distance 800 + +# count (percentage w.r.t. total sequenced reads) +Pairs mappable, unique and high quality 52726 (52.73) +Pairs used 37321 (37.33) +One mate unmapped 8777 (8.78) +One mate not unique 3603 (3.60) +One mate low quality 34877 (34.88) + +# count (percentage w.r.t. mappable, unique and high quality pairs) +dangling end 0 (0.00) +self ligation (removed) 0 (0.00) +One mate not close to rest site 0 (0.00) +same fragment (800 bp) 15393 (29.19) +self circle 0 (0.00) +duplicated pairs 12 (0.02) + +# count (percentage w.r.t. total valid pairs used) +inter chromosomal 5955 (15.96) +short range < 20kb 8853 (23.72) +long range 22513 (60.32) +inward pairs 7145 (19.14) +outward pairs 9731 (26.07) +left pairs 7156 (19.17) +right pairs 7334 (19.65) diff -r 5746cb5cf08d -r 01237d721a9f test-data/hicexplorer2.log --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/hicexplorer2.log Sat Dec 23 15:57:55 2017 -0500 @@ -0,0 +1,29 @@ + +File small_test_rf_matrix.h5 +Pairs considered 99983 +Min rest. site distance 152 +Max rest. site distance 1500 + +# count (percentage w.r.t. total sequenced reads) +Pairs mappable, unique and high quality 52726 (52.73) +Pairs used 35934 (35.94) +One mate unmapped 8777 (8.78) +One mate not unique 3603 (3.60) +One mate low quality 34877 (34.88) + +# count (percentage w.r.t. mappable, unique and high quality pairs) +dangling end 209 (0.40) +self ligation (removed) 5056 (9.59) +One mate not close to rest site 751 (1.42) +same fragment (800 bp) 10146 (19.24) +self circle 618 (1.17) +duplicated pairs 12 (0.02) + +# count (percentage w.r.t. total valid pairs used) +inter chromosomal 5849 (16.28) +short range < 20kb 8071 (22.46) +long range 22014 (61.26) +inward pairs 6977 (19.42) +outward pairs 8907 (24.79) +left pairs 7012 (19.51) +right pairs 7189 (20.01) diff -r 5746cb5cf08d -r 01237d721a9f test-data/hisat2_stats.tabular --- a/test-data/hisat2_stats.tabular Tue Dec 05 05:24:03 2017 -0500 +++ b/test-data/hisat2_stats.tabular Sat Dec 23 15:57:55 2017 -0500 @@ -1,3 +1,3 @@ -Sample overall_alignment_rate unpaired_aligned_none unpaired_aligned_multi unpaired_total unpaired_aligned_one -hisat2_1 96.15 3849 9953 99978 86176 -hisat2_2 96.15 3849 9953 99978 86176 +Sample overall_alignment_rate unpaired_aligned_multi unpaired_aligned_none unpaired_total unpaired_aligned_one +hisat2_1 96.15 9953 3849 99978 86176 +hisat2_2 96.15 9953 3849 99978 86176 diff -r 5746cb5cf08d -r 01237d721a9f test-data/htseq_stats.tabular --- a/test-data/htseq_stats.tabular Tue Dec 05 05:24:03 2017 -0500 +++ b/test-data/htseq_stats.tabular Sat Dec 23 15:57:55 2017 -0500 @@ -1,2 +1,2 @@ -Sample ambiguous percent_assigned too_low_aQual total_count no_feature alignment_not_unique assigned not_aligned -htseq 0 0.0 0 1355 19 0 0 1336 +Sample alignment_not_unique percent_assigned total_count assigned not_aligned no_feature ambiguous too_low_aQual +htseq 0 0.0 1355 0 1336 19 0 0 diff -r 5746cb5cf08d -r 01237d721a9f test-data/picard_baseContent_stats.tabular --- a/test-data/picard_baseContent_stats.tabular Tue Dec 05 05:24:03 2017 -0500 +++ b/test-data/picard_baseContent_stats.tabular Sat Dec 23 15:57:55 2017 -0500 @@ -1,2 +1,2 @@ -Sample sum_pct_n mean_pct_t sum_pct_g sum_pct_a sum_pct_c mean_pct_a sum_pct_t mean_pct_c cycle_count mean_pct_g -D11_H4K16ac_Rep1_R1_fastq_gz 0.499258 28.1544206133 1590.390797 2251.590365 1545.938026 30.0212048667 2111.581546 20.6125070133 75 21.2052106267 +Sample mean_pct_a mean_pct_g sum_pct_g mean_pct_t sum_pct_a mean_pct_c sum_pct_t sum_pct_c sum_pct_n cycle_count +D11_H4K16ac_Rep1_R1_fastq_gz 30.02120486666666 21.205210626666666 1590.390797 28.154420613333333 2251.5903649999996 20.61250701333334 2111.581546 1545.9380260000005 0.49925800000000015 75 diff -r 5746cb5cf08d -r 01237d721a9f test-data/picard_dups_stats.tabular --- a/test-data/picard_dups_stats.tabular Tue Dec 05 05:24:03 2017 -0500 +++ b/test-data/picard_dups_stats.tabular Sat Dec 23 15:57:55 2017 -0500 @@ -1,2 +1,2 @@ -Sample UNMAPPED_READS ESTIMATED_LIBRARY_SIZE READ_PAIR_OPTICAL_DUPLICATES READ_PAIRS_EXAMINED UNPAIRED_READS_EXAMINED PERCENT_DUPLICATION LIBRARY READ_PAIR_DUPLICATES UNPAIRED_READ_DUPLICATES -dataset_114 0.0 77973949.0 0.0 313405.0 2900.0 0.005582 Unknown Library 629.0 2257.0 +Sample LIBRARY UNPAIRED_READS_EXAMINED ESTIMATED_LIBRARY_SIZE READ_PAIR_DUPLICATES UNPAIRED_READ_DUPLICATES READ_PAIR_OPTICAL_DUPLICATES PERCENT_DUPLICATION UNMAPPED_READS READ_PAIRS_EXAMINED +dataset_114 Unknown Library 2900.0 77973949.0 629.0 2257.0 0.0 0.005582 0.0 313405.0 diff -r 5746cb5cf08d -r 01237d721a9f test-data/post_aligner_soft_stats.tabular --- a/test-data/post_aligner_soft_stats.tabular Tue Dec 05 05:24:03 2017 -0500 +++ b/test-data/post_aligner_soft_stats.tabular Sat Dec 23 15:57:55 2017 -0500 @@ -1,21 +1,21 @@ -Sample QUAST_N50 QUAST_Total_length featureCounts_percent_assigned featureCounts_Assigned Picard_PCT_PF_READS_ALIGNED Prokka_organism Prokka_contigs Prokka_bases Prokka_CDS Bcftools Stats_number_of_records Bcftools Stats_number_of_SNPs Bcftools Stats_number_of_indels Bcftools Stats_tstv Bcftools Stats_number_of_MNPs Bamtools_duplicates_pct Bamtools_mapped_reads_pct Picard_PERCENT_DUPLICATION Picard_summed_median Picard_summed_mean GATK VariantEval_known_titv GATK VariantEval_novel_titv HTSeq Count_percent_assigned HTSeq Count_assigned Picard_PCT_RIBOSOMAL_BASES Picard_PCT_MRNA_BASES Samtools Flagstat_mapped_passed Samtools Stats_error_rate Samtools Stats_non_primary_alignments Samtools Stats_reads_mapped Samtools Stats_reads_mapped_percent Samtools Stats_raw_total_sequences Samblaster_pct_dups +Sample QUAST_N50-2-1 QUAST_Total_length-2-1 featureCounts_Assigned-1 featureCounts_percent_assigned-1-1 Picard_PCT_PF_READS_ALIGNED-1 Prokka_contigs-1 Prokka_bases-1 Prokka_CDS-1 Prokka_organism-1 Bcftools Stats_number_of_SNPs-1 Bcftools Stats_tstv-1 Bcftools Stats_number_of_records-1 Bcftools Stats_number_of_MNPs-1 Bcftools Stats_number_of_indels-1 Bamtools_duplicates_pct-1-1 Bamtools_mapped_reads_pct-1-1 Picard_PERCENT_DUPLICATION-1 Picard_summed_mean-1 Picard_summed_median-1 HTSeq Count_percent_assigned-2 HTSeq Count_assigned-1 Picard_PCT_RIBOSOMAL_BASES-1 Picard_PCT_MRNA_BASES-1 Samtools Flagstat_mapped_passed-1-1 Samtools Stats_reads_mapped_percent-1 Samtools Stats_raw_total_sequences-1-1 Samtools Stats_reads_mapped-1 Samtools Stats_error_rate-1 Samtools Stats_non_primary_alignments-1 GATK VariantEval_known_titv-1 GATK VariantEval_novel_titv-1 Samblaster_pct_dups-1 14892_1#15 115136.0 18435361.0 -70: TopHat on data 1, data 4, and data 3: accepted_hits 70.82267755353567 321797 -75: TopHat on data 1, data 6, and data 5: accepted_hits 69.58585803304067 445012 -80: TopHat on data 1, data 8, and data 7: accepted_hits 71.76957768385707 394981 -85: TopHat on data 1, data 10, and data 9: accepted_hits 72.02454351337069 437485 -90: TopHat on data 1, data 12, and data 11: accepted_hits 71.33130826437625 388170 -95: TopHat on data 1, data 14, and data 13: accepted_hits 70.72517103678439 453929 +70: TopHat on data 1, data 4, and data 3: accepted_hits 321797 70.82267755353567 +75: TopHat on data 1, data 6, and data 5: accepted_hits 445012 69.58585803304067 +80: TopHat on data 1, data 8, and data 7: accepted_hits 394981 71.76957768385707 +85: TopHat on data 1, data 10, and data 9: accepted_hits 437485 72.02454351337069 +90: TopHat on data 1, data 12, and data 11: accepted_hits 388170 71.33130826437625 +95: TopHat on data 1, data 14, and data 13: accepted_hits 453929 70.72517103678439 D11_H4K16ac_Rep1_R1_fastq_gz 0.983085 -Sample1 Helicobacter pylori 30 1629978 1548 -Sample2 Escherichia coli 52 162997532523 1548 -Test1 5522770.0 4474244.0 902934.0 1.97 72330.0 +Sample1 30 1629978 1548 Helicobacter pylori +Sample2 52 162997532523 1548 Escherichia coli +Test1 4474244.0 1.97 5522770.0 72330.0 902934.0 bamtools 0.0 93.125 dataset_114 0.005582 -dataset_197 176 271.809759 -gatk_varianteval 0.0 2.2 -htseq 0.0 0 -picard_CollectRnaSeqMetrics_bam 79.62310000000001 -samtools_flagstat 20689039 -samtools_stats 0.004248509 12111.0 641821.0 100.0 641821.0 +dataset_197 271.809759 176 +htseq 0.0 0 +picard_CollectRnaSeqMetrics_bam 79.62310000000001 +samtools_flagstat 20689039 +samtools_stats 100.0 641821.0 641821.0 0.004248509 12111.0 +varianteval_1_gatk_varianteval 0.0 2.2 virtual-normal 1.28 diff -r 5746cb5cf08d -r 01237d721a9f test-data/pre_alignment_soft_stats.tabular --- a/test-data/pre_alignment_soft_stats.tabular Tue Dec 05 05:24:03 2017 -0500 +++ b/test-data/pre_alignment_soft_stats.tabular Sat Dec 23 15:57:55 2017 -0500 @@ -1,7 +1,7 @@ -Sample SortMeRNA_rRNA_pct Trimmomatic_dropped_pct Cutadapt_percent_trimmed FastQC_percent_duplicates FastQC_percent_gc FastQC_avg_sequence_length FastQC_total_sequences FastQC_percent_fails Flexbar_removed_bases_pct -25839_merged 1.09929975002 +Sample SortMeRNA_rRNA_pct-1 Trimmomatic_dropped_pct-1 Cutadapt_percent_trimmed-1 FastQC_percent_gc-1 FastQC_total_sequences-1 FastQC_avg_sequence_length-1 FastQC_percent_duplicates-1 FastQC_percent_fails-1 Flexbar_removed_bases_pct-1 +25839_merged 1.099299750020029 C2 17.98 -dataset_33 10.7768204362 -poulet5_1 36.3059115993 48.0 101.0 267849.0 8.33333333333 -poulet5_2 36.1733887481 48.0 101.0 267849.0 8.33333333333 -result_right 45.2606635071 +dataset_33 10.776820436239396 +poulet5_1 48.0 267849.0 101.0 36.30591159931017 8.333333333333332 +poulet5_2 48.0 267849.0 101.0 36.173388748054116 8.333333333333332 +result_right 45.26066350710901 diff -r 5746cb5cf08d -r 01237d721a9f test-data/prokka_stats.tabular --- a/test-data/prokka_stats.tabular Tue Dec 05 05:24:03 2017 -0500 +++ b/test-data/prokka_stats.tabular Sat Dec 23 15:57:55 2017 -0500 @@ -1,3 +1,3 @@ -Sample contigs tmRNA tRNA repeat_region sig_peptide bases rRNA CDS organism misc_RNA -Sample1 30 1 36 15 88 1629978 2 1548 Helicobacter pylori -Sample2 52 162997532523 2 1548 Escherichia coli 5152 +Sample tRNA CDS rRNA repeat_region bases organism contigs sig_peptide tmRNA misc_RNA +Sample1 36 1548 2 15 1629978 Helicobacter pylori 30 88 1 +Sample2 1548 2 162997532523 Escherichia coli 52 5152 diff -r 5746cb5cf08d -r 01237d721a9f test-data/quast_stats.tabular --- a/test-data/quast_stats.tabular Tue Dec 05 05:24:03 2017 -0500 +++ b/test-data/quast_stats.tabular Sat Dec 23 15:57:55 2017 -0500 @@ -1,2 +1,2 @@ -Sample L50 Duplication ratio GC (%) LG75 # misassemblies # contigs (>= 25000 bp) L75 Total length (>= 10000 bp) # genes # mismatches per 100 kbp # indels per 100 kbp # contigs (>= 5000 bp) Unaligned length Total length # unaligned contigs # local misassemblies Reference GC (%) # N's per 100 kbp Total length (>= 25000 bp) # contigs (>= 0 bp) # genes_partial NGA50 NGA75 Largest contig # contigs # unaligned contigs_partial NG75 # contigs (>= 50000 bp) Total length (>= 0 bp) NG50 # contigs (>= 10000 bp) LGA50 NA75 Total length (>= 5000 bp) Genome fraction (%) LGA75 LG50 N75 Total length (>= 1000 bp) NA50 # contigs (>= 1000 bp) N50 Total length (>= 50000 bp) Largest alignment LA75 LA50 Misassembled contigs length Reference length # misassembled contigs -14892_1#15 48.0 1.016 48.17 106.0 107.0 181.0 100.0 17893099.0 7280.0 262.21 33.75 242.0 88446.0 18435361.0 8.0 132.0 48.21 929.55 17353907.0 545.0 968.0 99244.0 51757.0 435484.0 467.0 59.0 56990.0 123.0 18465341.0 112874.0 215.0 59.0 54365.0 18079934.0 95.482 124.0 50.0 62262.0 18373173.0 102129.0 376.0 115136.0 15112131.0 356982.0 117.0 56.0 4540800.0 18916112.0 82.0 +Sample # mismatches per 100 kbp # misassembled contigs Largest contig # indels per 100 kbp LG75 # local misassemblies Total length (>= 25000 bp) Total length N50 NGA50 Reference GC (%) # contigs (>= 10000 bp) LA75 NG50 # genes_partial # unaligned contigs Total length (>= 50000 bp) LA50 # contigs (>= 25000 bp) NA75 GC (%) LG50 NA50 LGA75 # contigs (>= 0 bp) Largest alignment Total length (>= 0 bp) # genes # misassemblies NGA75 Total length (>= 10000 bp) # contigs (>= 5000 bp) L75 Total length (>= 1000 bp) # unaligned contigs_partial # contigs (>= 50000 bp) Total length (>= 5000 bp) N75 # contigs (>= 1000 bp) LGA50 Duplication ratio Genome fraction (%) NG75 Unaligned length # N's per 100 kbp Misassembled contigs length Reference length L50 # contigs +14892_1#15 262.21 82.0 435484.0 33.75 106.0 132.0 17353907.0 18435361.0 115136.0 99244.0 48.21 215.0 117.0 112874.0 968.0 8.0 15112131.0 56.0 181.0 54365.0 48.17 50.0 102129.0 124.0 545.0 356982.0 18465341.0 7280.0 107.0 51757.0 17893099.0 242.0 100.0 18373173.0 59.0 123.0 18079934.0 62262.0 376.0 59.0 1.016 95.482 56990.0 88446.0 929.55 4540800.0 18916112.0 48.0 467.0 diff -r 5746cb5cf08d -r 01237d721a9f test-data/report_manual_custom_content.html --- a/test-data/report_manual_custom_content.html Tue Dec 05 05:24:03 2017 -0500 +++ b/test-data/report_manual_custom_content.html Sat Dec 23 15:57:55 2017 -0500 @@ -1,4806 +0,0 @@ - - - - - - - - - - - - - -MultiQC Report - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
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is_sorted reads_duplicated -samtools_stats 0.0 0.004248509 1223.0 12111.0 101.0 0.0109064676911 638746.0 641821.0 26.0 719.7 641821.0 0.0 0.0 0.0 641821.0 320981.0 70.0 101.0 99.520894455 64823921.0 64823921.0 64823921.0 0.0 30.0 275405.0 635626.0 317512.0 0.0 1294.0 0.0 0.0 99.0347776093 100.0 100.0 641821.0 0.0 320840.0 1.0 0.0 +Sample insert_size_average reads_mapped_and_paired reads_QC_failed_percent outward_oriented_pairs 1st_fragments bases_duplicated reads_MQ0 bases_mapped maximum_length bases_trimmed reads_duplicated inward_oriented_pairs sequences error_rate insert_size_standard_deviation non-primary_alignments reads_unmapped_percent mismatches reads_mapped_and_paired_percent reads_mapped_percent raw_total_sequences reads_mapped pairs_on_different_chromosomes reads_MQ0_percent pairs_with_other_orientation reads_paired_percent total_length reads_unmapped average_length reads_duplicated_percent bases_mapped_(cigar) average_quality reads_properly_paired reads_properly_paired_percent reads_QC_failed last_fragments filtered_sequences reads_paired is_sorted +samtools_stats 719.7 638746.0 0.0 1294.0 320981.0 0.0 70.0 64823921.0 101.0 0.0 0.0 317512.0 641821.0 0.004248509 1223.0 12111.0 0.0 275405.0 99.52089445499603 100.0 641821.0 641821.0 0.0 0.010906467691147531 30.0 100.0 64823921.0 0.0 101.0 0.0 64823921.0 26.0 635626.0 99.03477760933345 0.0 320840.0 0.0 641821.0 1.0 diff -r 5746cb5cf08d -r 01237d721a9f test-data/sortmerna_stats.tabular --- a/test-data/sortmerna_stats.tabular Tue Dec 05 05:24:03 2017 -0500 +++ b/test-data/sortmerna_stats.tabular Sat Dec 23 15:57:55 2017 -0500 @@ -1,2 +1,2 @@ -Sample silva-arc-16s-id95_count silva-euk-28s-id98_pct non_rRNA silva-bac-23s-id98_pct silva-euk-18s-id95_pct silva-bac-23s-id98_count rRNA_pct silva-arc-23s-id98_count rfam-5s-database-id98_pct silva-arc-16s-id95_pct rfam-5s-database-id98_count non_rRNA_pct silva-euk-28s-id98_count rfam-5.8s-database-id98_pct rRNA silva-bac-16s-id90_pct silva-euk-18s-id95_count silva-bac-16s-id90_count total rfam-5.8s-database-id98_count silva-arc-23s-id98_pct -25839_merged 0.0 0.01 4394708 0.24 0.25 10664.5344 1.09929975002 0.0 0.0 0.0 0.0 98.90070025 444.3556 0.0 48848 0.59 11108.89 26216.9804 4443556 0.0 0.0 +Sample non_rRNA silva-euk-18s-id95_count silva-euk-18s-id95_pct rRNA_pct silva-arc-16s-id95_count silva-euk-28s-id98_pct rfam-5.8s-database-id98_pct rRNA silva-bac-16s-id90_count rfam-5s-database-id98_count silva-bac-23s-id98_count silva-bac-23s-id98_pct rfam-5.8s-database-id98_count silva-arc-16s-id95_pct non_rRNA_pct rfam-5s-database-id98_pct silva-arc-23s-id98_count silva-arc-23s-id98_pct total silva-bac-16s-id90_pct silva-euk-28s-id98_count +25839_merged 4394708 11108.89 0.25 1.099299750020029 0.0 0.01 0.0 48848 26216.9804 0.0 10664.534399999999 0.24 0.0 0.0 98.90070024997996 0.0 0.0 0.0 4443556 0.59 444.35560000000004 diff -r 5746cb5cf08d -r 01237d721a9f test-data/star_stats.tabular --- a/test-data/star_stats.tabular Tue Dec 05 05:24:03 2017 -0500 +++ b/test-data/star_stats.tabular Sat Dec 23 15:57:55 2017 -0500 @@ -1,2 +1,2 @@ -Sample uniquely_mapped_percent num_splices num_GCAG_splices insertion_length deletion_length unmapped_tooshort_percent avg_mapped_read_length deletion_rate mismatch_rate avg_input_read_length num_ATAC_splices num_annotated_splices num_GTAG_splices uniquely_mapped multimapped_toomany unmapped_mismatches unmapped_mismatches_percent total_reads unmapped_other insertion_rate unmapped_other_percent multimapped_percent multimapped num_noncanonical_splices unmapped_tooshort multimapped_toomany_percent -star_log 89.0 47.0 0.0 0.0 0.0 10.0 74.8 0.0 1.73 75.0 0.0 0.0 47.0 89.0 0.0 0 0.0 100.0 0 0.0 0.0 1.0 1.0 0.0 10 0.0 +Sample unmapped_tooshort multimapped mismatch_rate num_splices total_reads num_GCAG_splices unmapped_mismatches_percent avg_mapped_read_length num_GTAG_splices deletion_length avg_input_read_length multimapped_percent deletion_rate uniquely_mapped unmapped_tooshort_percent unmapped_mismatches unmapped_other_percent insertion_length multimapped_toomany_percent num_noncanonical_splices unmapped_other multimapped_toomany insertion_rate num_annotated_splices uniquely_mapped_percent num_ATAC_splices +star_log 10 1.0 1.73 47.0 100.0 0.0 0.0 74.8 47.0 0.0 75.0 1.0 0.0 89.0 10.0 0 0.0 0.0 0.0 0.0 0 0.0 0.0 0.0 89.0 0.0