Job ID = 14172174 SRX = SRX9281726 Genome = dm3 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... Read 9327950 spots for SRR12813193/SRR12813193.sra Written 9327950 spots for SRR12813193/SRR12813193.sra Read 9198397 spots for SRR12813194/SRR12813194.sra Written 9198397 spots for SRR12813194/SRR12813194.sra Read 9631243 spots for SRR12813195/SRR12813195.sra Written 9631243 spots for SRR12813195/SRR12813195.sra Read 9431528 spots for SRR12813196/SRR12813196.sra Written 9431528 spots for SRR12813196/SRR12813196.sra fastq に変換しました。 bowtie でマッピング中... Your job 14172662 ("srTdm6") has been submitted Time loading reference: 00:00:00 Time loading forward index: 00:00:01 Time loading mirror index: 00:00:00 Multiseed full-index search: 00:06:30 37589118 reads; of these: 37589118 (100.00%) were paired; of these: 36271670 (96.50%) aligned concordantly 0 times 1066243 (2.84%) aligned concordantly exactly 1 time 251205 (0.67%) aligned concordantly >1 times ---- 36271670 pairs aligned concordantly 0 times; of these: 6737 (0.02%) aligned discordantly 1 time ---- 36264933 pairs aligned 0 times concordantly or discordantly; of these: 72529866 mates make up the pairs; of these: 71913845 (99.15%) aligned 0 times 170494 (0.24%) aligned exactly 1 time 445527 (0.61%) aligned >1 times 4.34% overall alignment rate Time searching: 00:06:31 Overall time: 00:06:31 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] 41400 / 1322497 = 0.0313 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 14:49:17: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX9281726/SRX9281726.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX9281726/SRX9281726.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX9281726/SRX9281726.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX9281726/SRX9281726.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 14:49:17: #1 read tag files... INFO @ Sat, 11 Dec 2021 14:49:17: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 14:49:22: 1000000 INFO @ Sat, 11 Dec 2021 14:49:27: 2000000 INFO @ Sat, 11 Dec 2021 14:49:32: 3000000 INFO @ Sat, 11 Dec 2021 14:49:32: #1 tag size is determined as 39 bps INFO @ Sat, 11 Dec 2021 14:49:32: #1 tag size = 39 INFO @ Sat, 11 Dec 2021 14:49:32: #1 total tags in treatment: 1276140 INFO @ Sat, 11 Dec 2021 14:49:32: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 14:49:32: #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 14:49:32: #1 tags after filtering in treatment: 1237119 INFO @ Sat, 11 Dec 2021 14:49:32: #1 Redundant rate of treatment: 0.03 INFO @ Sat, 11 Dec 2021 14:49:32: #1 finished! INFO @ Sat, 11 Dec 2021 14:49:32: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 14:49:32: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 14:49:33: #2 number of paired peaks: 1798 INFO @ Sat, 11 Dec 2021 14:49:33: start model_add_line... INFO @ Sat, 11 Dec 2021 14:49:33: start X-correlation... INFO @ Sat, 11 Dec 2021 14:49:33: end of X-cor INFO @ Sat, 11 Dec 2021 14:49:33: #2 finished! INFO @ Sat, 11 Dec 2021 14:49:33: #2 predicted fragment length is 145 bps INFO @ Sat, 11 Dec 2021 14:49:33: #2 alternative fragment length(s) may be 145 bps INFO @ Sat, 11 Dec 2021 14:49:33: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX9281726/SRX9281726.05_model.r INFO @ Sat, 11 Dec 2021 14:49:33: #3 Call peaks... INFO @ Sat, 11 Dec 2021 14:49:33: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Dec 2021 14:49:35: #3 Call peaks for each chromosome... INFO @ Sat, 11 Dec 2021 14:49:37: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX9281726/SRX9281726.05_peaks.xls INFO @ Sat, 11 Dec 2021 14:49:37: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX9281726/SRX9281726.05_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 14:49:37: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX9281726/SRX9281726.05_summits.bed INFO @ Sat, 11 Dec 2021 14:49:37: Done! pass1 - making usageList (13 chroms): 1 millis pass2 - checking and writing primary data (383 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 14:49:47: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX9281726/SRX9281726.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX9281726/SRX9281726.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX9281726/SRX9281726.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX9281726/SRX9281726.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 14:49:47: #1 read tag files... INFO @ Sat, 11 Dec 2021 14:49:47: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 14:49:52: 1000000 INFO @ Sat, 11 Dec 2021 14:49:57: 2000000 INFO @ Sat, 11 Dec 2021 14:50:02: 3000000 INFO @ Sat, 11 Dec 2021 14:50:02: #1 tag size is determined as 39 bps INFO @ Sat, 11 Dec 2021 14:50:02: #1 tag size = 39 INFO @ Sat, 11 Dec 2021 14:50:02: #1 total tags in treatment: 1276140 INFO @ Sat, 11 Dec 2021 14:50:02: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 14:50:02: #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 14:50:02: #1 tags after filtering in treatment: 1237119 INFO @ Sat, 11 Dec 2021 14:50:02: #1 Redundant rate of treatment: 0.03 INFO @ Sat, 11 Dec 2021 14:50:02: #1 finished! INFO @ Sat, 11 Dec 2021 14:50:02: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 14:50:02: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 14:50:03: #2 number of paired peaks: 1798 INFO @ Sat, 11 Dec 2021 14:50:03: start model_add_line... INFO @ Sat, 11 Dec 2021 14:50:03: start X-correlation... INFO @ Sat, 11 Dec 2021 14:50:03: end of X-cor INFO @ Sat, 11 Dec 2021 14:50:03: #2 finished! INFO @ Sat, 11 Dec 2021 14:50:03: #2 predicted fragment length is 145 bps INFO @ Sat, 11 Dec 2021 14:50:03: #2 alternative fragment length(s) may be 145 bps INFO @ Sat, 11 Dec 2021 14:50:03: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX9281726/SRX9281726.10_model.r INFO @ Sat, 11 Dec 2021 14:50:03: #3 Call peaks... INFO @ Sat, 11 Dec 2021 14:50:03: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Dec 2021 14:50:05: #3 Call peaks for each chromosome... INFO @ Sat, 11 Dec 2021 14:50:07: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX9281726/SRX9281726.10_peaks.xls INFO @ Sat, 11 Dec 2021 14:50:07: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX9281726/SRX9281726.10_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 14:50:07: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX9281726/SRX9281726.10_summits.bed INFO @ Sat, 11 Dec 2021 14:50:07: Done! pass1 - making usageList (9 chroms): 0 millis pass2 - checking and writing primary data (206 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 14:50:17: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX9281726/SRX9281726.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX9281726/SRX9281726.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX9281726/SRX9281726.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX9281726/SRX9281726.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 14:50:17: #1 read tag files... INFO @ Sat, 11 Dec 2021 14:50:17: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 14:50:22: 1000000 INFO @ Sat, 11 Dec 2021 14:50:27: 2000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 11 Dec 2021 14:50:33: 3000000 INFO @ Sat, 11 Dec 2021 14:50:34: #1 tag size is determined as 39 bps INFO @ Sat, 11 Dec 2021 14:50:34: #1 tag size = 39 INFO @ Sat, 11 Dec 2021 14:50:34: #1 total tags in treatment: 1276140 INFO @ Sat, 11 Dec 2021 14:50:34: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 14:50:34: #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 14:50:34: #1 tags after filtering in treatment: 1237119 INFO @ Sat, 11 Dec 2021 14:50:34: #1 Redundant rate of treatment: 0.03 INFO @ Sat, 11 Dec 2021 14:50:34: #1 finished! INFO @ Sat, 11 Dec 2021 14:50:34: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 14:50:34: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 14:50:34: #2 number of paired peaks: 1798 INFO @ Sat, 11 Dec 2021 14:50:34: start model_add_line... INFO @ Sat, 11 Dec 2021 14:50:34: start X-correlation... INFO @ Sat, 11 Dec 2021 14:50:34: end of X-cor INFO @ Sat, 11 Dec 2021 14:50:34: #2 finished! INFO @ Sat, 11 Dec 2021 14:50:34: #2 predicted fragment length is 145 bps INFO @ Sat, 11 Dec 2021 14:50:34: #2 alternative fragment length(s) may be 145 bps INFO @ Sat, 11 Dec 2021 14:50:34: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX9281726/SRX9281726.20_model.r INFO @ Sat, 11 Dec 2021 14:50:34: #3 Call peaks... INFO @ Sat, 11 Dec 2021 14:50:34: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Sat, 11 Dec 2021 14:50:36: #3 Call peaks for each chromosome... INFO @ Sat, 11 Dec 2021 14:50:38: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX9281726/SRX9281726.20_peaks.xls INFO @ Sat, 11 Dec 2021 14:50:38: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX9281726/SRX9281726.20_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 14:50:38: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX9281726/SRX9281726.20_summits.bed INFO @ Sat, 11 Dec 2021 14:50:38: Done! pass1 - making usageList (3 chroms): 0 millis pass2 - checking and writing primary data (71 records, 4 fields): 1 millis CompletedMACS2peakCalling