Job ID = 14172382 SRX = SRX9281770 Genome = dm3 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... Read 1805117 spots for SRR12813289/SRR12813289.sra Written 1805117 spots for SRR12813289/SRR12813289.sra Read 1790728 spots for SRR12813290/SRR12813290.sra Written 1790728 spots for SRR12813290/SRR12813290.sra Read 1833851 spots for SRR12813291/SRR12813291.sra Written 1833851 spots for SRR12813291/SRR12813291.sra Read 1817772 spots for SRR12813292/SRR12813292.sra Written 1817772 spots for SRR12813292/SRR12813292.sra fastq に変換しました。 bowtie でマッピング中... Your job 14172801 ("srTdm6") has been submitted Time loading reference: 00:00:00 Time loading forward index: 00:00:00 Time loading mirror index: 00:00:01 Multiseed full-index search: 00:01:07 7247468 reads; of these: 7247468 (100.00%) were paired; of these: 7063863 (97.47%) aligned concordantly 0 times 133181 (1.84%) aligned concordantly exactly 1 time 50424 (0.70%) aligned concordantly >1 times ---- 7063863 pairs aligned concordantly 0 times; of these: 258 (0.00%) aligned discordantly 1 time ---- 7063605 pairs aligned 0 times concordantly or discordantly; of these: 14127210 mates make up the pairs; of these: 14088135 (99.72%) aligned 0 times 12025 (0.09%) aligned exactly 1 time 27050 (0.19%) aligned >1 times 2.81% overall alignment rate Time searching: 00:01:08 Overall time: 00:01:08 マッピングが完了しました。 samtools でBAM に変換中... [samopen] SAM header is present: 15 sequences. [bam_rmdup_core] processing reference chr2L... [bam_rmdup_core] processing reference chr2LHet... [bam_rmdup_core] processing reference chr2R... [bam_rmdup_core] processing reference chr2RHet... [bam_rmdup_core] processing reference chr3L... [bam_rmdup_core] processing reference chr3LHet... [bam_rmdup_core] processing reference chr3R... [bam_rmdup_core] processing reference chr3RHet... [bam_rmdup_core] processing reference chr4... [bam_rmdup_core] processing reference chrM... [bam_rmdup_core] processing reference chrU... [bam_rmdup_core] processing reference chrUextra... [bam_rmdup_core] processing reference chrX... [bam_rmdup_core] processing reference chrXHet... [bam_rmdup_core] processing reference chrYHet... [bam_rmdup_core] 3695 / 183727 = 0.0201 in library ' ' BAM に変換しました。 Bed ファイルを作成中... WARNING: Skipping mount /opt/pkg/singularity/3.8.3/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Sat, 11 Dec 2021 15:14:11: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX9281770/SRX9281770.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX9281770/SRX9281770.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX9281770/SRX9281770.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX9281770/SRX9281770.bam'] # control file = None # effective genome size = 1.20e+08 # band width = 300 # model fold = [5, 50] # qvalue cutoff = 1.00e-05 # Larger dataset will be scaled towards smaller dataset. # Range for calculating regional lambda is: 10000 bps # Broad region calling is off # Paired-End mode is off INFO @ Sat, 11 Dec 2021 15:14:11: #1 read tag files... INFO @ Sat, 11 Dec 2021 15:14:11: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 15:14:13: #1 tag size is determined as 39 bps INFO @ Sat, 11 Dec 2021 15:14:13: #1 tag size = 39 INFO @ Sat, 11 Dec 2021 15:14:13: #1 total tags in treatment: 179915 INFO @ Sat, 11 Dec 2021 15:14:13: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 15:14:13: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 11 Dec 2021 15:14:13: #1 tags after filtering in treatment: 178231 INFO @ Sat, 11 Dec 2021 15:14:13: #1 Redundant rate of treatment: 0.01 INFO @ Sat, 11 Dec 2021 15:14:13: #1 finished! INFO @ Sat, 11 Dec 2021 15:14:13: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 15:14:13: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 15:14:13: #2 number of paired peaks: 2232 INFO @ Sat, 11 Dec 2021 15:14:13: start model_add_line... INFO @ Sat, 11 Dec 2021 15:14:13: start X-correlation... INFO @ Sat, 11 Dec 2021 15:14:13: end of X-cor INFO @ Sat, 11 Dec 2021 15:14:13: #2 finished! INFO @ Sat, 11 Dec 2021 15:14:13: #2 predicted fragment length is 279 bps INFO @ Sat, 11 Dec 2021 15:14:13: #2 alternative fragment length(s) may be 201,247,279 bps INFO @ Sat, 11 Dec 2021 15:14:13: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX9281770/SRX9281770.05_model.r INFO @ Sat, 11 Dec 2021 15:14:13: #3 Call peaks... INFO @ Sat, 11 Dec 2021 15:14:13: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Dec 2021 15:14:14: #3 Call peaks for each chromosome... INFO @ Sat, 11 Dec 2021 15:14:14: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX9281770/SRX9281770.05_peaks.xls INFO @ Sat, 11 Dec 2021 15:14:14: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX9281770/SRX9281770.05_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 15:14:14: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX9281770/SRX9281770.05_summits.bed INFO @ Sat, 11 Dec 2021 15:14:14: Done! pass1 - making usageList (4 chroms): 1 millis pass2 - checking and writing primary data (48 records, 4 fields): 31 millis CompletedMACS2peakCalling WARNING: Skipping mount /opt/pkg/singularity/3.8.3/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Sat, 11 Dec 2021 15:14:41: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX9281770/SRX9281770.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX9281770/SRX9281770.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX9281770/SRX9281770.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX9281770/SRX9281770.bam'] # control file = None # effective genome size = 1.20e+08 # band width = 300 # model fold = [5, 50] # qvalue cutoff = 1.00e-10 # Larger dataset will be scaled towards smaller dataset. # Range for calculating regional lambda is: 10000 bps # Broad region calling is off # Paired-End mode is off INFO @ Sat, 11 Dec 2021 15:14:41: #1 read tag files... INFO @ Sat, 11 Dec 2021 15:14:41: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 15:14:43: #1 tag size is determined as 39 bps INFO @ Sat, 11 Dec 2021 15:14:43: #1 tag size = 39 INFO @ Sat, 11 Dec 2021 15:14:43: #1 total tags in treatment: 179915 INFO @ Sat, 11 Dec 2021 15:14:43: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 15:14:43: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 11 Dec 2021 15:14:43: #1 tags after filtering in treatment: 178231 INFO @ Sat, 11 Dec 2021 15:14:43: #1 Redundant rate of treatment: 0.01 INFO @ Sat, 11 Dec 2021 15:14:43: #1 finished! INFO @ Sat, 11 Dec 2021 15:14:43: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 15:14:43: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 15:14:43: #2 number of paired peaks: 2232 INFO @ Sat, 11 Dec 2021 15:14:43: start model_add_line... INFO @ Sat, 11 Dec 2021 15:14:43: start X-correlation... INFO @ Sat, 11 Dec 2021 15:14:43: end of X-cor INFO @ Sat, 11 Dec 2021 15:14:43: #2 finished! INFO @ Sat, 11 Dec 2021 15:14:43: #2 predicted fragment length is 279 bps INFO @ Sat, 11 Dec 2021 15:14:43: #2 alternative fragment length(s) may be 201,247,279 bps INFO @ Sat, 11 Dec 2021 15:14:43: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX9281770/SRX9281770.10_model.r INFO @ Sat, 11 Dec 2021 15:14:43: #3 Call peaks... INFO @ Sat, 11 Dec 2021 15:14:43: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Dec 2021 15:14:43: #3 Call peaks for each chromosome... INFO @ Sat, 11 Dec 2021 15:14:44: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX9281770/SRX9281770.10_peaks.xls INFO @ Sat, 11 Dec 2021 15:14:44: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX9281770/SRX9281770.10_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 15:14:44: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX9281770/SRX9281770.10_summits.bed INFO @ Sat, 11 Dec 2021 15:14:44: Done! pass1 - making usageList (3 chroms): 1 millis pass2 - checking and writing primary data (25 records, 4 fields): 1 millis CompletedMACS2peakCalling BedGraph に変換中... WARNING: Skipping mount /opt/pkg/singularity/3.8.3/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 11 Dec 2021 15:15:11: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX9281770/SRX9281770.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX9281770/SRX9281770.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX9281770/SRX9281770.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX9281770/SRX9281770.bam'] # control file = None # effective genome size = 1.20e+08 # band width = 300 # model fold = [5, 50] # qvalue cutoff = 1.00e-20 # Larger dataset will be scaled towards smaller dataset. # Range for calculating regional lambda is: 10000 bps # Broad region calling is off # Paired-End mode is off INFO @ Sat, 11 Dec 2021 15:15:11: #1 read tag files... INFO @ Sat, 11 Dec 2021 15:15:11: #1 read treatment tags... BigWig に変換しました。 INFO @ Sat, 11 Dec 2021 15:15:13: #1 tag size is determined as 39 bps INFO @ Sat, 11 Dec 2021 15:15:13: #1 tag size = 39 INFO @ Sat, 11 Dec 2021 15:15:13: #1 total tags in treatment: 179915 INFO @ Sat, 11 Dec 2021 15:15:13: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 15:15:13: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 11 Dec 2021 15:15:13: #1 tags after filtering in treatment: 178231 INFO @ Sat, 11 Dec 2021 15:15:13: #1 Redundant rate of treatment: 0.01 INFO @ Sat, 11 Dec 2021 15:15:13: #1 finished! INFO @ Sat, 11 Dec 2021 15:15:13: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 15:15:13: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 15:15:13: #2 number of paired peaks: 2232 INFO @ Sat, 11 Dec 2021 15:15:13: start model_add_line... INFO @ Sat, 11 Dec 2021 15:15:13: start X-correlation... INFO @ Sat, 11 Dec 2021 15:15:13: end of X-cor INFO @ Sat, 11 Dec 2021 15:15:13: #2 finished! INFO @ Sat, 11 Dec 2021 15:15:13: #2 predicted fragment length is 279 bps INFO @ Sat, 11 Dec 2021 15:15:13: #2 alternative fragment length(s) may be 201,247,279 bps INFO @ Sat, 11 Dec 2021 15:15:13: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX9281770/SRX9281770.20_model.r INFO @ Sat, 11 Dec 2021 15:15:13: #3 Call peaks... INFO @ Sat, 11 Dec 2021 15:15:13: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Dec 2021 15:15:14: #3 Call peaks for each chromosome... INFO @ Sat, 11 Dec 2021 15:15:14: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX9281770/SRX9281770.20_peaks.xls INFO @ Sat, 11 Dec 2021 15:15:14: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX9281770/SRX9281770.20_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 15:15:14: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX9281770/SRX9281770.20_summits.bed INFO @ Sat, 11 Dec 2021 15:15:14: Done! pass1 - making usageList (2 chroms): 0 millis pass2 - checking and writing primary data (11 records, 4 fields): 2 millis CompletedMACS2peakCalling