Job ID = 14172243 SRX = SRX9281746 Genome = dm3 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... Read 7528067 spots for SRR12813463/SRR12813463.sra Written 7528067 spots for SRR12813463/SRR12813463.sra Read 7479667 spots for SRR12813464/SRR12813464.sra Written 7479667 spots for SRR12813464/SRR12813464.sra Read 7634771 spots for SRR12813465/SRR12813465.sra Written 7634771 spots for SRR12813465/SRR12813465.sra Read 7569262 spots for SRR12813466/SRR12813466.sra Written 7569262 spots for SRR12813466/SRR12813466.sra fastq に変換しました。 bowtie でマッピング中... Your job 14172706 ("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: 00:04:22 30211767 reads; of these: 30211767 (100.00%) were paired; of these: 29178636 (96.58%) aligned concordantly 0 times 788948 (2.61%) aligned concordantly exactly 1 time 244183 (0.81%) aligned concordantly >1 times ---- 29178636 pairs aligned concordantly 0 times; of these: 3891 (0.01%) aligned discordantly 1 time ---- 29174745 pairs aligned 0 times concordantly or discordantly; of these: 58349490 mates make up the pairs; of these: 58158317 (99.67%) aligned 0 times 64152 (0.11%) aligned exactly 1 time 127021 (0.22%) aligned >1 times 3.75% overall alignment rate Time searching: 00:04:23 Overall time: 00:04:23 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] 30814 / 1036221 = 0.0297 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 14:59:39: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX9281746/SRX9281746.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX9281746/SRX9281746.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX9281746/SRX9281746.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX9281746/SRX9281746.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 14:59:39: #1 read tag files... INFO @ Sat, 11 Dec 2021 14:59:39: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 14:59:43: 1000000 INFO @ Sat, 11 Dec 2021 14:59:48: 2000000 INFO @ Sat, 11 Dec 2021 14:59:49: #1 tag size is determined as 39 bps INFO @ Sat, 11 Dec 2021 14:59:49: #1 tag size = 39 INFO @ Sat, 11 Dec 2021 14:59:49: #1 total tags in treatment: 1002407 INFO @ Sat, 11 Dec 2021 14:59:49: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 14:59:49: #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 14:59:49: #1 tags after filtering in treatment: 976592 INFO @ Sat, 11 Dec 2021 14:59:49: #1 Redundant rate of treatment: 0.03 INFO @ Sat, 11 Dec 2021 14:59:49: #1 finished! INFO @ Sat, 11 Dec 2021 14:59:49: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 14:59:49: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 14:59:49: #2 number of paired peaks: 1910 INFO @ Sat, 11 Dec 2021 14:59:49: start model_add_line... INFO @ Sat, 11 Dec 2021 14:59:49: start X-correlation... INFO @ Sat, 11 Dec 2021 14:59:49: end of X-cor INFO @ Sat, 11 Dec 2021 14:59:49: #2 finished! INFO @ Sat, 11 Dec 2021 14:59:49: #2 predicted fragment length is 140 bps INFO @ Sat, 11 Dec 2021 14:59:49: #2 alternative fragment length(s) may be 116,140,266 bps INFO @ Sat, 11 Dec 2021 14:59:49: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX9281746/SRX9281746.05_model.r INFO @ Sat, 11 Dec 2021 14:59:49: #3 Call peaks... INFO @ Sat, 11 Dec 2021 14:59:49: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Dec 2021 14:59:51: #3 Call peaks for each chromosome... INFO @ Sat, 11 Dec 2021 14:59:52: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX9281746/SRX9281746.05_peaks.xls INFO @ Sat, 11 Dec 2021 14:59:52: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX9281746/SRX9281746.05_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 14:59:52: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX9281746/SRX9281746.05_summits.bed INFO @ Sat, 11 Dec 2021 14:59:52: Done! pass1 - making usageList (10 chroms): 0 millis pass2 - checking and writing primary data (198 records, 4 fields): 2 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 15:00:09: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX9281746/SRX9281746.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX9281746/SRX9281746.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX9281746/SRX9281746.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX9281746/SRX9281746.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 15:00:09: #1 read tag files... INFO @ Sat, 11 Dec 2021 15:00:09: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 15:00:13: 1000000 INFO @ Sat, 11 Dec 2021 15:00:18: 2000000 INFO @ Sat, 11 Dec 2021 15:00:19: #1 tag size is determined as 39 bps INFO @ Sat, 11 Dec 2021 15:00:19: #1 tag size = 39 INFO @ Sat, 11 Dec 2021 15:00:19: #1 total tags in treatment: 1002407 INFO @ Sat, 11 Dec 2021 15:00:19: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 15:00:19: #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 15:00:19: #1 tags after filtering in treatment: 976592 INFO @ Sat, 11 Dec 2021 15:00:19: #1 Redundant rate of treatment: 0.03 INFO @ Sat, 11 Dec 2021 15:00:19: #1 finished! INFO @ Sat, 11 Dec 2021 15:00:19: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 15:00:19: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 15:00:19: #2 number of paired peaks: 1910 INFO @ Sat, 11 Dec 2021 15:00:19: start model_add_line... INFO @ Sat, 11 Dec 2021 15:00:19: start X-correlation... INFO @ Sat, 11 Dec 2021 15:00:19: end of X-cor INFO @ Sat, 11 Dec 2021 15:00:19: #2 finished! INFO @ Sat, 11 Dec 2021 15:00:19: #2 predicted fragment length is 140 bps INFO @ Sat, 11 Dec 2021 15:00:19: #2 alternative fragment length(s) may be 116,140,266 bps INFO @ Sat, 11 Dec 2021 15:00:19: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX9281746/SRX9281746.10_model.r INFO @ Sat, 11 Dec 2021 15:00:19: #3 Call peaks... INFO @ Sat, 11 Dec 2021 15:00:19: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Dec 2021 15:00:21: #3 Call peaks for each chromosome... INFO @ Sat, 11 Dec 2021 15:00:22: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX9281746/SRX9281746.10_peaks.xls INFO @ Sat, 11 Dec 2021 15:00:22: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX9281746/SRX9281746.10_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 15:00:22: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX9281746/SRX9281746.10_summits.bed INFO @ Sat, 11 Dec 2021 15:00:22: Done! pass1 - making usageList (8 chroms): 0 millis pass2 - checking and writing primary data (107 records, 4 fields): 2 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 INFO @ Sat, 11 Dec 2021 15:00:39: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX9281746/SRX9281746.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX9281746/SRX9281746.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX9281746/SRX9281746.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX9281746/SRX9281746.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 15:00:39: #1 read tag files... INFO @ Sat, 11 Dec 2021 15:00:39: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 15:00:43: 1000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 11 Dec 2021 15:00:48: 2000000 INFO @ Sat, 11 Dec 2021 15:00:49: #1 tag size is determined as 39 bps INFO @ Sat, 11 Dec 2021 15:00:49: #1 tag size = 39 INFO @ Sat, 11 Dec 2021 15:00:49: #1 total tags in treatment: 1002407 INFO @ Sat, 11 Dec 2021 15:00:49: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 15:00:49: #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 15:00:49: #1 tags after filtering in treatment: 976592 INFO @ Sat, 11 Dec 2021 15:00:49: #1 Redundant rate of treatment: 0.03 INFO @ Sat, 11 Dec 2021 15:00:49: #1 finished! INFO @ Sat, 11 Dec 2021 15:00:49: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 15:00:49: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 15:00:49: #2 number of paired peaks: 1910 INFO @ Sat, 11 Dec 2021 15:00:49: start model_add_line... INFO @ Sat, 11 Dec 2021 15:00:49: start X-correlation... INFO @ Sat, 11 Dec 2021 15:00:49: end of X-cor INFO @ Sat, 11 Dec 2021 15:00:49: #2 finished! INFO @ Sat, 11 Dec 2021 15:00:49: #2 predicted fragment length is 140 bps INFO @ Sat, 11 Dec 2021 15:00:49: #2 alternative fragment length(s) may be 116,140,266 bps INFO @ Sat, 11 Dec 2021 15:00:49: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX9281746/SRX9281746.20_model.r INFO @ Sat, 11 Dec 2021 15:00:49: #3 Call peaks... INFO @ Sat, 11 Dec 2021 15:00:49: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Sat, 11 Dec 2021 15:00:51: #3 Call peaks for each chromosome... INFO @ Sat, 11 Dec 2021 15:00:53: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX9281746/SRX9281746.20_peaks.xls INFO @ Sat, 11 Dec 2021 15:00:53: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX9281746/SRX9281746.20_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 15:00:53: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX9281746/SRX9281746.20_summits.bed INFO @ Sat, 11 Dec 2021 15:00:53: Done! pass1 - making usageList (5 chroms): 0 millis pass2 - checking and writing primary data (45 records, 4 fields): 1 millis CompletedMACS2peakCalling