Job ID = 6626623 SRX = SRX7262539 Genome = dm3 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... Read 41103148 spots for SRR10582169/SRR10582169.sra Written 41103148 spots for SRR10582169/SRR10582169.sra fastq に変換しました。 bowtie でマッピング中... Your job 6626748 ("srTdm6") has been submitted Time loading reference: 00:00:00 Time loading forward index: 00:00:00 Time loading mirror index: 00:00:00 Multiseed full-index search: 00:06:30 41103148 reads; of these: 41103148 (100.00%) were unpaired; of these: 36179600 (88.02%) aligned 0 times 4151733 (10.10%) aligned exactly 1 time 771815 (1.88%) aligned >1 times 11.98% overall alignment rate Time searching: 00:06:30 Overall time: 00:06:30 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_rmdupse_core] 1024398 / 4923548 = 0.2081 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/3.5.2/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Tue, 14 Jul 2020 08:07:43: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX7262539/SRX7262539.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX7262539/SRX7262539.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX7262539/SRX7262539.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX7262539/SRX7262539.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 @ Tue, 14 Jul 2020 08:07:43: #1 read tag files... INFO @ Tue, 14 Jul 2020 08:07:43: #1 read treatment tags... INFO @ Tue, 14 Jul 2020 08:07:49: 1000000 INFO @ Tue, 14 Jul 2020 08:07:54: 2000000 INFO @ Tue, 14 Jul 2020 08:08:00: 3000000 INFO @ Tue, 14 Jul 2020 08:08:05: #1 tag size is determined as 75 bps INFO @ Tue, 14 Jul 2020 08:08:05: #1 tag size = 75 INFO @ Tue, 14 Jul 2020 08:08:05: #1 total tags in treatment: 3899150 INFO @ Tue, 14 Jul 2020 08:08:05: #1 user defined the maximum tags... INFO @ Tue, 14 Jul 2020 08:08:05: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 14 Jul 2020 08:08:05: #1 tags after filtering in treatment: 3899150 INFO @ Tue, 14 Jul 2020 08:08:05: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 14 Jul 2020 08:08:05: #1 finished! INFO @ Tue, 14 Jul 2020 08:08:05: #2 Build Peak Model... INFO @ Tue, 14 Jul 2020 08:08:05: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 14 Jul 2020 08:08:05: #2 number of paired peaks: 9189 INFO @ Tue, 14 Jul 2020 08:08:05: start model_add_line... INFO @ Tue, 14 Jul 2020 08:08:05: start X-correlation... INFO @ Tue, 14 Jul 2020 08:08:05: end of X-cor INFO @ Tue, 14 Jul 2020 08:08:05: #2 finished! INFO @ Tue, 14 Jul 2020 08:08:05: #2 predicted fragment length is 221 bps INFO @ Tue, 14 Jul 2020 08:08:05: #2 alternative fragment length(s) may be 221 bps INFO @ Tue, 14 Jul 2020 08:08:05: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX7262539/SRX7262539.05_model.r INFO @ Tue, 14 Jul 2020 08:08:05: #3 Call peaks... INFO @ Tue, 14 Jul 2020 08:08:05: #3 Pre-compute pvalue-qvalue table... WARNING: Skipping mount /opt/pkg/singularity/3.5.2/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Tue, 14 Jul 2020 08:08:13: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX7262539/SRX7262539.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX7262539/SRX7262539.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX7262539/SRX7262539.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX7262539/SRX7262539.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 @ Tue, 14 Jul 2020 08:08:13: #1 read tag files... INFO @ Tue, 14 Jul 2020 08:08:13: #1 read treatment tags... INFO @ Tue, 14 Jul 2020 08:08:16: #3 Call peaks for each chromosome... INFO @ Tue, 14 Jul 2020 08:08:19: 1000000 INFO @ Tue, 14 Jul 2020 08:08:21: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX7262539/SRX7262539.05_peaks.xls INFO @ Tue, 14 Jul 2020 08:08:21: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX7262539/SRX7262539.05_peaks.narrowPeak INFO @ Tue, 14 Jul 2020 08:08:21: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX7262539/SRX7262539.05_summits.bed INFO @ Tue, 14 Jul 2020 08:08:21: Done! pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (5495 records, 4 fields): 7 millis CompletedMACS2peakCalling INFO @ Tue, 14 Jul 2020 08:08:24: 2000000 INFO @ Tue, 14 Jul 2020 08:08:30: 3000000 INFO @ Tue, 14 Jul 2020 08:08:35: #1 tag size is determined as 75 bps INFO @ Tue, 14 Jul 2020 08:08:35: #1 tag size = 75 INFO @ Tue, 14 Jul 2020 08:08:35: #1 total tags in treatment: 3899150 INFO @ Tue, 14 Jul 2020 08:08:35: #1 user defined the maximum tags... INFO @ Tue, 14 Jul 2020 08:08:35: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 14 Jul 2020 08:08:35: #1 tags after filtering in treatment: 3899150 INFO @ Tue, 14 Jul 2020 08:08:35: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 14 Jul 2020 08:08:35: #1 finished! INFO @ Tue, 14 Jul 2020 08:08:35: #2 Build Peak Model... INFO @ Tue, 14 Jul 2020 08:08:35: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 14 Jul 2020 08:08:36: #2 number of paired peaks: 9189 INFO @ Tue, 14 Jul 2020 08:08:36: start model_add_line... INFO @ Tue, 14 Jul 2020 08:08:36: start X-correlation... INFO @ Tue, 14 Jul 2020 08:08:36: end of X-cor INFO @ Tue, 14 Jul 2020 08:08:36: #2 finished! INFO @ Tue, 14 Jul 2020 08:08:36: #2 predicted fragment length is 221 bps INFO @ Tue, 14 Jul 2020 08:08:36: #2 alternative fragment length(s) may be 221 bps INFO @ Tue, 14 Jul 2020 08:08:36: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX7262539/SRX7262539.10_model.r INFO @ Tue, 14 Jul 2020 08:08:36: #3 Call peaks... INFO @ Tue, 14 Jul 2020 08:08:36: #3 Pre-compute pvalue-qvalue table... BedGraph に変換中... WARNING: Skipping mount /opt/pkg/singularity/3.5.2/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Tue, 14 Jul 2020 08:08:43: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX7262539/SRX7262539.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX7262539/SRX7262539.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX7262539/SRX7262539.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX7262539/SRX7262539.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 @ Tue, 14 Jul 2020 08:08:43: #1 read tag files... INFO @ Tue, 14 Jul 2020 08:08:43: #1 read treatment tags... INFO @ Tue, 14 Jul 2020 08:08:47: #3 Call peaks for each chromosome... INFO @ Tue, 14 Jul 2020 08:08:49: 1000000 INFO @ Tue, 14 Jul 2020 08:08:51: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX7262539/SRX7262539.10_peaks.xls INFO @ Tue, 14 Jul 2020 08:08:51: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX7262539/SRX7262539.10_peaks.narrowPeak INFO @ Tue, 14 Jul 2020 08:08:51: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX7262539/SRX7262539.10_summits.bed INFO @ Tue, 14 Jul 2020 08:08:51: Done! pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (3640 records, 4 fields): 14 millis CompletedMACS2peakCalling INFO @ Tue, 14 Jul 2020 08:08:54: 2000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 14 Jul 2020 08:09:00: 3000000 INFO @ Tue, 14 Jul 2020 08:09:05: #1 tag size is determined as 75 bps INFO @ Tue, 14 Jul 2020 08:09:05: #1 tag size = 75 INFO @ Tue, 14 Jul 2020 08:09:05: #1 total tags in treatment: 3899150 INFO @ Tue, 14 Jul 2020 08:09:05: #1 user defined the maximum tags... INFO @ Tue, 14 Jul 2020 08:09:05: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 14 Jul 2020 08:09:05: #1 tags after filtering in treatment: 3899150 INFO @ Tue, 14 Jul 2020 08:09:05: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 14 Jul 2020 08:09:05: #1 finished! INFO @ Tue, 14 Jul 2020 08:09:05: #2 Build Peak Model... INFO @ Tue, 14 Jul 2020 08:09:05: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 14 Jul 2020 08:09:05: #2 number of paired peaks: 9189 INFO @ Tue, 14 Jul 2020 08:09:05: start model_add_line... INFO @ Tue, 14 Jul 2020 08:09:06: start X-correlation... INFO @ Tue, 14 Jul 2020 08:09:06: end of X-cor INFO @ Tue, 14 Jul 2020 08:09:06: #2 finished! INFO @ Tue, 14 Jul 2020 08:09:06: #2 predicted fragment length is 221 bps INFO @ Tue, 14 Jul 2020 08:09:06: #2 alternative fragment length(s) may be 221 bps INFO @ Tue, 14 Jul 2020 08:09:06: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX7262539/SRX7262539.20_model.r INFO @ Tue, 14 Jul 2020 08:09:06: #3 Call peaks... INFO @ Tue, 14 Jul 2020 08:09:06: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Tue, 14 Jul 2020 08:09:17: #3 Call peaks for each chromosome... INFO @ Tue, 14 Jul 2020 08:09:22: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX7262539/SRX7262539.20_peaks.xls INFO @ Tue, 14 Jul 2020 08:09:22: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX7262539/SRX7262539.20_peaks.narrowPeak INFO @ Tue, 14 Jul 2020 08:09:22: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX7262539/SRX7262539.20_summits.bed INFO @ Tue, 14 Jul 2020 08:09:22: Done! pass1 - making usageList (13 chroms): 1 millis pass2 - checking and writing primary data (2090 records, 4 fields): 4 millis CompletedMACS2peakCalling