Job ID = 14171637 SRX = SRX9986103 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: 00:00:01 Time loading mirror index: 00:00:00 Multiseed full-index search: 00:08:54 30277999 reads; of these: 30277999 (100.00%) were unpaired; of these: 1753168 (5.79%) aligned 0 times 18494959 (61.08%) aligned exactly 1 time 10029872 (33.13%) aligned >1 times 94.21% overall alignment rate Time searching: 00:08:55 Overall time: 00:08:55 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] 10199727 / 28524831 = 0.3576 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 12:29:41: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX9986103/SRX9986103.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX9986103/SRX9986103.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX9986103/SRX9986103.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX9986103/SRX9986103.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 12:29:41: #1 read tag files... INFO @ Sat, 11 Dec 2021 12:29:41: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 12:29:48: 1000000 INFO @ Sat, 11 Dec 2021 12:29:55: 2000000 INFO @ Sat, 11 Dec 2021 12:30:02: 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 12:30:09: 4000000 INFO @ Sat, 11 Dec 2021 12:30:11: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX9986103/SRX9986103.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX9986103/SRX9986103.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX9986103/SRX9986103.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX9986103/SRX9986103.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 12:30:11: #1 read tag files... INFO @ Sat, 11 Dec 2021 12:30:11: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 12:30:15: 5000000 INFO @ Sat, 11 Dec 2021 12:30:18: 1000000 INFO @ Sat, 11 Dec 2021 12:30:23: 6000000 INFO @ Sat, 11 Dec 2021 12:30:25: 2000000 INFO @ Sat, 11 Dec 2021 12:30:30: 7000000 INFO @ Sat, 11 Dec 2021 12:30:32: 3000000 INFO @ Sat, 11 Dec 2021 12:30:37: 8000000 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 12:30:39: 4000000 INFO @ Sat, 11 Dec 2021 12:30:41: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX9986103/SRX9986103.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX9986103/SRX9986103.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX9986103/SRX9986103.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX9986103/SRX9986103.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 12:30:41: #1 read tag files... INFO @ Sat, 11 Dec 2021 12:30:41: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 12:30:44: 9000000 INFO @ Sat, 11 Dec 2021 12:30:46: 5000000 INFO @ Sat, 11 Dec 2021 12:30:48: 1000000 INFO @ Sat, 11 Dec 2021 12:30:51: 10000000 INFO @ Sat, 11 Dec 2021 12:30:54: 6000000 INFO @ Sat, 11 Dec 2021 12:30:55: 2000000 INFO @ Sat, 11 Dec 2021 12:30:58: 11000000 INFO @ Sat, 11 Dec 2021 12:31:01: 7000000 INFO @ Sat, 11 Dec 2021 12:31:02: 3000000 INFO @ Sat, 11 Dec 2021 12:31:06: 12000000 INFO @ Sat, 11 Dec 2021 12:31:08: 8000000 INFO @ Sat, 11 Dec 2021 12:31:09: 4000000 INFO @ Sat, 11 Dec 2021 12:31:13: 13000000 INFO @ Sat, 11 Dec 2021 12:31:16: 9000000 INFO @ Sat, 11 Dec 2021 12:31:16: 5000000 INFO @ Sat, 11 Dec 2021 12:31:20: 14000000 INFO @ Sat, 11 Dec 2021 12:31:23: 10000000 INFO @ Sat, 11 Dec 2021 12:31:24: 6000000 INFO @ Sat, 11 Dec 2021 12:31:27: 15000000 INFO @ Sat, 11 Dec 2021 12:31:31: 7000000 INFO @ Sat, 11 Dec 2021 12:31:31: 11000000 INFO @ Sat, 11 Dec 2021 12:31:35: 16000000 INFO @ Sat, 11 Dec 2021 12:31:38: 8000000 INFO @ Sat, 11 Dec 2021 12:31:38: 12000000 INFO @ Sat, 11 Dec 2021 12:31:43: 17000000 INFO @ Sat, 11 Dec 2021 12:31:45: 9000000 INFO @ Sat, 11 Dec 2021 12:31:45: 13000000 INFO @ Sat, 11 Dec 2021 12:31:50: 18000000 INFO @ Sat, 11 Dec 2021 12:31:52: 10000000 INFO @ Sat, 11 Dec 2021 12:31:53: 14000000 INFO @ Sat, 11 Dec 2021 12:31:53: #1 tag size is determined as 50 bps INFO @ Sat, 11 Dec 2021 12:31:53: #1 tag size = 50 INFO @ Sat, 11 Dec 2021 12:31:53: #1 total tags in treatment: 18325104 INFO @ Sat, 11 Dec 2021 12:31:53: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 12:31:53: #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 12:31:54: #1 tags after filtering in treatment: 18325019 INFO @ Sat, 11 Dec 2021 12:31:54: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 11 Dec 2021 12:31:54: #1 finished! INFO @ Sat, 11 Dec 2021 12:31:54: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 12:31:54: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 12:31:55: #2 number of paired peaks: 474 WARNING @ Sat, 11 Dec 2021 12:31:55: Fewer paired peaks (474) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 474 pairs to build model! INFO @ Sat, 11 Dec 2021 12:31:55: start model_add_line... INFO @ Sat, 11 Dec 2021 12:31:55: start X-correlation... INFO @ Sat, 11 Dec 2021 12:31:55: end of X-cor INFO @ Sat, 11 Dec 2021 12:31:55: #2 finished! INFO @ Sat, 11 Dec 2021 12:31:55: #2 predicted fragment length is 157 bps INFO @ Sat, 11 Dec 2021 12:31:55: #2 alternative fragment length(s) may be 4,157 bps INFO @ Sat, 11 Dec 2021 12:31:55: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX9986103/SRX9986103.05_model.r INFO @ Sat, 11 Dec 2021 12:31:55: #3 Call peaks... INFO @ Sat, 11 Dec 2021 12:31:55: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Dec 2021 12:31:59: 11000000 INFO @ Sat, 11 Dec 2021 12:32:00: 15000000 INFO @ Sat, 11 Dec 2021 12:32:06: 12000000 INFO @ Sat, 11 Dec 2021 12:32:08: 16000000 INFO @ Sat, 11 Dec 2021 12:32:14: 13000000 INFO @ Sat, 11 Dec 2021 12:32:15: 17000000 INFO @ Sat, 11 Dec 2021 12:32:21: 14000000 INFO @ Sat, 11 Dec 2021 12:32:23: 18000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 11 Dec 2021 12:32:26: #1 tag size is determined as 50 bps INFO @ Sat, 11 Dec 2021 12:32:26: #1 tag size = 50 INFO @ Sat, 11 Dec 2021 12:32:26: #1 total tags in treatment: 18325104 INFO @ Sat, 11 Dec 2021 12:32:26: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 12:32:26: #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 12:32:27: #1 tags after filtering in treatment: 18325019 INFO @ Sat, 11 Dec 2021 12:32:27: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 11 Dec 2021 12:32:27: #1 finished! INFO @ Sat, 11 Dec 2021 12:32:27: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 12:32:27: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 12:32:28: #2 number of paired peaks: 474 WARNING @ Sat, 11 Dec 2021 12:32:28: Fewer paired peaks (474) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 474 pairs to build model! INFO @ Sat, 11 Dec 2021 12:32:28: start model_add_line... INFO @ Sat, 11 Dec 2021 12:32:28: start X-correlation... INFO @ Sat, 11 Dec 2021 12:32:28: end of X-cor INFO @ Sat, 11 Dec 2021 12:32:28: #2 finished! INFO @ Sat, 11 Dec 2021 12:32:28: #2 predicted fragment length is 157 bps INFO @ Sat, 11 Dec 2021 12:32:28: #2 alternative fragment length(s) may be 4,157 bps INFO @ Sat, 11 Dec 2021 12:32:28: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX9986103/SRX9986103.10_model.r INFO @ Sat, 11 Dec 2021 12:32:28: #3 Call peaks... INFO @ Sat, 11 Dec 2021 12:32:28: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Dec 2021 12:32:29: 15000000 INFO @ Sat, 11 Dec 2021 12:32:34: #3 Call peaks for each chromosome... INFO @ Sat, 11 Dec 2021 12:32:37: 16000000 INFO @ Sat, 11 Dec 2021 12:32:44: 17000000 INFO @ Sat, 11 Dec 2021 12:32:52: 18000000 INFO @ Sat, 11 Dec 2021 12:32:54: #1 tag size is determined as 50 bps INFO @ Sat, 11 Dec 2021 12:32:54: #1 tag size = 50 INFO @ Sat, 11 Dec 2021 12:32:54: #1 total tags in treatment: 18325104 INFO @ Sat, 11 Dec 2021 12:32:54: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 12:32:54: #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 12:32:55: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX9986103/SRX9986103.05_peaks.xls INFO @ Sat, 11 Dec 2021 12:32:55: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX9986103/SRX9986103.05_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 12:32:55: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX9986103/SRX9986103.05_summits.bed INFO @ Sat, 11 Dec 2021 12:32:55: Done! INFO @ Sat, 11 Dec 2021 12:32:55: #1 tags after filtering in treatment: 18325019 INFO @ Sat, 11 Dec 2021 12:32:55: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 11 Dec 2021 12:32:55: #1 finished! INFO @ Sat, 11 Dec 2021 12:32:55: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 12:32:55: #2 looking for paired plus/minus strand peaks... pass1 - making usageList (666 chroms): 4 millis pass2 - checking and writing primary data (13986 records, 4 fields): 58 millis CompletedMACS2peakCalling INFO @ Sat, 11 Dec 2021 12:32:57: #2 number of paired peaks: 474 WARNING @ Sat, 11 Dec 2021 12:32:57: Fewer paired peaks (474) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 474 pairs to build model! INFO @ Sat, 11 Dec 2021 12:32:57: start model_add_line... INFO @ Sat, 11 Dec 2021 12:32:57: start X-correlation... INFO @ Sat, 11 Dec 2021 12:32:57: end of X-cor INFO @ Sat, 11 Dec 2021 12:32:57: #2 finished! INFO @ Sat, 11 Dec 2021 12:32:57: #2 predicted fragment length is 157 bps INFO @ Sat, 11 Dec 2021 12:32:57: #2 alternative fragment length(s) may be 4,157 bps INFO @ Sat, 11 Dec 2021 12:32:57: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX9986103/SRX9986103.20_model.r INFO @ Sat, 11 Dec 2021 12:32:57: #3 Call peaks... INFO @ Sat, 11 Dec 2021 12:32:57: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Dec 2021 12:33:07: #3 Call peaks for each chromosome... BigWig に変換しました。 INFO @ Sat, 11 Dec 2021 12:33:27: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX9986103/SRX9986103.10_peaks.xls INFO @ Sat, 11 Dec 2021 12:33:27: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX9986103/SRX9986103.10_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 12:33:27: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX9986103/SRX9986103.10_summits.bed INFO @ Sat, 11 Dec 2021 12:33:27: Done! pass1 - making usageList (572 chroms): 14 millis pass2 - checking and writing primary data (3250 records, 4 fields): 40 millis CompletedMACS2peakCalling INFO @ Sat, 11 Dec 2021 12:33:36: #3 Call peaks for each chromosome... INFO @ Sat, 11 Dec 2021 12:33:56: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX9986103/SRX9986103.20_peaks.xls INFO @ Sat, 11 Dec 2021 12:33:56: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX9986103/SRX9986103.20_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 12:33:56: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX9986103/SRX9986103.20_summits.bed INFO @ Sat, 11 Dec 2021 12:33:56: Done! pass1 - making usageList (446 chroms): 1 millis pass2 - checking and writing primary data (1116 records, 4 fields): 29 millis CompletedMACS2peakCalling