Job ID = 14171636 SRX = SRX9986104 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... fastq に変換しました。 bowtie でマッピング中... Time loading reference: 00:00:00 Time loading forward index: 00:00:00 Time loading mirror index: 00:00:00 Multiseed full-index search: 00:08:42 25873067 reads; of these: 25873067 (100.00%) were unpaired; of these: 1664248 (6.43%) aligned 0 times 14925179 (57.69%) aligned exactly 1 time 9283640 (35.88%) aligned >1 times 93.57% overall alignment rate Time searching: 00:08:42 Overall time: 00:08:42 マッピングが完了しました。 samtools でBAM に変換中... [samopen] SAM header is present: 1870 sequences. [bam_sort_core] merging from 12 files... [bam_rmdupse_core] 8297227 / 24208819 = 0.3427 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 12:28:48: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX9986104/SRX9986104.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX9986104/SRX9986104.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX9986104/SRX9986104.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX9986104/SRX9986104.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 12:28:48: #1 read tag files... INFO @ Sat, 11 Dec 2021 12:28:48: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 12:28:55: 1000000 INFO @ Sat, 11 Dec 2021 12:29:03: 2000000 INFO @ Sat, 11 Dec 2021 12:29:10: 3000000 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 12:29:17: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX9986104/SRX9986104.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX9986104/SRX9986104.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX9986104/SRX9986104.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX9986104/SRX9986104.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 12:29:17: #1 read tag files... INFO @ Sat, 11 Dec 2021 12:29:17: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 12:29:17: 4000000 INFO @ Sat, 11 Dec 2021 12:29:25: 1000000 INFO @ Sat, 11 Dec 2021 12:29:25: 5000000 INFO @ Sat, 11 Dec 2021 12:29:32: 2000000 INFO @ Sat, 11 Dec 2021 12:29:32: 6000000 INFO @ Sat, 11 Dec 2021 12:29:39: 3000000 INFO @ Sat, 11 Dec 2021 12:29:39: 7000000 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 12:29:46: 4000000 INFO @ Sat, 11 Dec 2021 12:29:46: 8000000 INFO @ Sat, 11 Dec 2021 12:29:47: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX9986104/SRX9986104.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX9986104/SRX9986104.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX9986104/SRX9986104.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX9986104/SRX9986104.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 12:29:47: #1 read tag files... INFO @ Sat, 11 Dec 2021 12:29:47: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 12:29:53: 5000000 INFO @ Sat, 11 Dec 2021 12:29:54: 9000000 INFO @ Sat, 11 Dec 2021 12:29:56: 1000000 INFO @ Sat, 11 Dec 2021 12:30:00: 6000000 INFO @ Sat, 11 Dec 2021 12:30:01: 10000000 INFO @ Sat, 11 Dec 2021 12:30:06: 2000000 INFO @ Sat, 11 Dec 2021 12:30:08: 7000000 INFO @ Sat, 11 Dec 2021 12:30:08: 11000000 INFO @ Sat, 11 Dec 2021 12:30:15: 8000000 INFO @ Sat, 11 Dec 2021 12:30:15: 12000000 INFO @ Sat, 11 Dec 2021 12:30:16: 3000000 INFO @ Sat, 11 Dec 2021 12:30:23: 9000000 INFO @ Sat, 11 Dec 2021 12:30:23: 13000000 INFO @ Sat, 11 Dec 2021 12:30:25: 4000000 INFO @ Sat, 11 Dec 2021 12:30:30: 10000000 INFO @ Sat, 11 Dec 2021 12:30:31: 14000000 INFO @ Sat, 11 Dec 2021 12:30:35: 5000000 INFO @ Sat, 11 Dec 2021 12:30:38: 11000000 INFO @ Sat, 11 Dec 2021 12:30:39: 15000000 INFO @ Sat, 11 Dec 2021 12:30:44: 6000000 INFO @ Sat, 11 Dec 2021 12:30:45: 12000000 INFO @ Sat, 11 Dec 2021 12:30:46: #1 tag size is determined as 50 bps INFO @ Sat, 11 Dec 2021 12:30:46: #1 tag size = 50 INFO @ Sat, 11 Dec 2021 12:30:46: #1 total tags in treatment: 15911592 INFO @ Sat, 11 Dec 2021 12:30:46: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 12:30:46: #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 12:30:47: #1 tags after filtering in treatment: 15911521 INFO @ Sat, 11 Dec 2021 12:30:47: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 11 Dec 2021 12:30:47: #1 finished! INFO @ Sat, 11 Dec 2021 12:30:47: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 12:30:47: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 12:30:48: #2 number of paired peaks: 705 WARNING @ Sat, 11 Dec 2021 12:30:48: Fewer paired peaks (705) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 705 pairs to build model! INFO @ Sat, 11 Dec 2021 12:30:48: start model_add_line... INFO @ Sat, 11 Dec 2021 12:30:49: start X-correlation... INFO @ Sat, 11 Dec 2021 12:30:49: end of X-cor INFO @ Sat, 11 Dec 2021 12:30:49: #2 finished! INFO @ Sat, 11 Dec 2021 12:30:49: #2 predicted fragment length is 173 bps INFO @ Sat, 11 Dec 2021 12:30:49: #2 alternative fragment length(s) may be 4,173 bps INFO @ Sat, 11 Dec 2021 12:30:49: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX9986104/SRX9986104.05_model.r INFO @ Sat, 11 Dec 2021 12:30:49: #3 Call peaks... INFO @ Sat, 11 Dec 2021 12:30:49: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Dec 2021 12:30:52: 13000000 INFO @ Sat, 11 Dec 2021 12:30:53: 7000000 INFO @ Sat, 11 Dec 2021 12:31:00: 14000000 INFO @ Sat, 11 Dec 2021 12:31:03: 8000000 INFO @ Sat, 11 Dec 2021 12:31:07: 15000000 INFO @ Sat, 11 Dec 2021 12:31:12: 9000000 INFO @ Sat, 11 Dec 2021 12:31:14: #1 tag size is determined as 50 bps INFO @ Sat, 11 Dec 2021 12:31:14: #1 tag size = 50 INFO @ Sat, 11 Dec 2021 12:31:14: #1 total tags in treatment: 15911592 INFO @ Sat, 11 Dec 2021 12:31:14: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 12:31:14: #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 12:31:15: #1 tags after filtering in treatment: 15911521 INFO @ Sat, 11 Dec 2021 12:31:15: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 11 Dec 2021 12:31:15: #1 finished! INFO @ Sat, 11 Dec 2021 12:31:15: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 12:31:15: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 12:31:17: #2 number of paired peaks: 705 WARNING @ Sat, 11 Dec 2021 12:31:17: Fewer paired peaks (705) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 705 pairs to build model! INFO @ Sat, 11 Dec 2021 12:31:17: start model_add_line... INFO @ Sat, 11 Dec 2021 12:31:17: start X-correlation... INFO @ Sat, 11 Dec 2021 12:31:17: end of X-cor INFO @ Sat, 11 Dec 2021 12:31:17: #2 finished! INFO @ Sat, 11 Dec 2021 12:31:17: #2 predicted fragment length is 173 bps INFO @ Sat, 11 Dec 2021 12:31:17: #2 alternative fragment length(s) may be 4,173 bps INFO @ Sat, 11 Dec 2021 12:31:17: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX9986104/SRX9986104.10_model.r INFO @ Sat, 11 Dec 2021 12:31:17: #3 Call peaks... INFO @ Sat, 11 Dec 2021 12:31:17: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Dec 2021 12:31:21: 10000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 11 Dec 2021 12:31:30: 11000000 INFO @ Sat, 11 Dec 2021 12:31:37: #3 Call peaks for each chromosome... INFO @ Sat, 11 Dec 2021 12:31:39: 12000000 INFO @ Sat, 11 Dec 2021 12:31:47: 13000000 INFO @ Sat, 11 Dec 2021 12:31:57: 14000000 INFO @ Sat, 11 Dec 2021 12:32:00: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX9986104/SRX9986104.05_peaks.xls INFO @ Sat, 11 Dec 2021 12:32:00: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX9986104/SRX9986104.05_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 12:32:00: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX9986104/SRX9986104.05_summits.bed INFO @ Sat, 11 Dec 2021 12:32:00: Done! pass1 - making usageList (679 chroms): 6 millis pass2 - checking and writing primary data (18731 records, 4 fields): 48 millis CompletedMACS2peakCalling INFO @ Sat, 11 Dec 2021 12:32:05: #3 Call peaks for each chromosome... INFO @ Sat, 11 Dec 2021 12:32:05: 15000000 BigWig に変換しました。 INFO @ Sat, 11 Dec 2021 12:32:14: #1 tag size is determined as 50 bps INFO @ Sat, 11 Dec 2021 12:32:14: #1 tag size = 50 INFO @ Sat, 11 Dec 2021 12:32:14: #1 total tags in treatment: 15911592 INFO @ Sat, 11 Dec 2021 12:32:14: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 12:32:14: #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 12:32:15: #1 tags after filtering in treatment: 15911521 INFO @ Sat, 11 Dec 2021 12:32:15: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 11 Dec 2021 12:32:15: #1 finished! INFO @ Sat, 11 Dec 2021 12:32:15: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 12:32:15: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 12:32:16: #2 number of paired peaks: 705 WARNING @ Sat, 11 Dec 2021 12:32:16: Fewer paired peaks (705) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 705 pairs to build model! INFO @ Sat, 11 Dec 2021 12:32:16: start model_add_line... INFO @ Sat, 11 Dec 2021 12:32:17: start X-correlation... INFO @ Sat, 11 Dec 2021 12:32:17: end of X-cor INFO @ Sat, 11 Dec 2021 12:32:17: #2 finished! INFO @ Sat, 11 Dec 2021 12:32:17: #2 predicted fragment length is 173 bps INFO @ Sat, 11 Dec 2021 12:32:17: #2 alternative fragment length(s) may be 4,173 bps INFO @ Sat, 11 Dec 2021 12:32:17: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX9986104/SRX9986104.20_model.r INFO @ Sat, 11 Dec 2021 12:32:17: #3 Call peaks... INFO @ Sat, 11 Dec 2021 12:32:17: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Dec 2021 12:32:27: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX9986104/SRX9986104.10_peaks.xls INFO @ Sat, 11 Dec 2021 12:32:27: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX9986104/SRX9986104.10_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 12:32:27: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX9986104/SRX9986104.10_summits.bed INFO @ Sat, 11 Dec 2021 12:32:27: Done! pass1 - making usageList (585 chroms): 5 millis pass2 - checking and writing primary data (5792 records, 4 fields): 34 millis CompletedMACS2peakCalling INFO @ Sat, 11 Dec 2021 12:33:05: #3 Call peaks for each chromosome... INFO @ Sat, 11 Dec 2021 12:33:27: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX9986104/SRX9986104.20_peaks.xls INFO @ Sat, 11 Dec 2021 12:33:27: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX9986104/SRX9986104.20_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 12:33:27: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX9986104/SRX9986104.20_summits.bed INFO @ Sat, 11 Dec 2021 12:33:27: Done! pass1 - making usageList (465 chroms): 1 millis pass2 - checking and writing primary data (1394 records, 4 fields): 22 millis CompletedMACS2peakCalling