Job ID = 14171137 SRX = SRX10000638 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: 00:09:20 40716539 reads; of these: 40716539 (100.00%) were unpaired; of these: 9070370 (22.28%) aligned 0 times 23172045 (56.91%) aligned exactly 1 time 8474124 (20.81%) aligned >1 times 77.72% overall alignment rate Time searching: 00:09:20 Overall time: 00:09:20 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 16 files... [bam_rmdupse_core] 8147395 / 31646169 = 0.2575 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 09:57:57: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX10000638/SRX10000638.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX10000638/SRX10000638.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX10000638/SRX10000638.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX10000638/SRX10000638.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 09:57:57: #1 read tag files... INFO @ Sat, 11 Dec 2021 09:57:57: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 09:58:03: 1000000 INFO @ Sat, 11 Dec 2021 09:58:10: 2000000 INFO @ Sat, 11 Dec 2021 09:58:17: 3000000 INFO @ Sat, 11 Dec 2021 09:58:24: 4000000 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 09:58:27: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX10000638/SRX10000638.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX10000638/SRX10000638.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX10000638/SRX10000638.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX10000638/SRX10000638.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 09:58:27: #1 read tag files... INFO @ Sat, 11 Dec 2021 09:58:27: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 09:58:30: 5000000 INFO @ Sat, 11 Dec 2021 09:58:32: 1000000 INFO @ Sat, 11 Dec 2021 09:58:37: 6000000 INFO @ Sat, 11 Dec 2021 09:58:37: 2000000 INFO @ Sat, 11 Dec 2021 09:58:43: 3000000 INFO @ Sat, 11 Dec 2021 09:58:43: 7000000 INFO @ Sat, 11 Dec 2021 09:58:49: 4000000 INFO @ Sat, 11 Dec 2021 09:58:50: 8000000 INFO @ Sat, 11 Dec 2021 09:58:54: 5000000 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 09:58:57: 9000000 INFO @ Sat, 11 Dec 2021 09:58:57: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX10000638/SRX10000638.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX10000638/SRX10000638.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX10000638/SRX10000638.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX10000638/SRX10000638.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 09:58:57: #1 read tag files... INFO @ Sat, 11 Dec 2021 09:58:57: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 09:59:00: 6000000 INFO @ Sat, 11 Dec 2021 09:59:03: 1000000 INFO @ Sat, 11 Dec 2021 09:59:03: 10000000 INFO @ Sat, 11 Dec 2021 09:59:05: 7000000 INFO @ Sat, 11 Dec 2021 09:59:09: 2000000 INFO @ Sat, 11 Dec 2021 09:59:10: 11000000 INFO @ Sat, 11 Dec 2021 09:59:11: 8000000 INFO @ Sat, 11 Dec 2021 09:59:14: 3000000 INFO @ Sat, 11 Dec 2021 09:59:16: 9000000 INFO @ Sat, 11 Dec 2021 09:59:17: 12000000 INFO @ Sat, 11 Dec 2021 09:59:20: 4000000 INFO @ Sat, 11 Dec 2021 09:59:22: 10000000 INFO @ Sat, 11 Dec 2021 09:59:25: 13000000 INFO @ Sat, 11 Dec 2021 09:59:26: 5000000 INFO @ Sat, 11 Dec 2021 09:59:28: 11000000 INFO @ Sat, 11 Dec 2021 09:59:31: 6000000 INFO @ Sat, 11 Dec 2021 09:59:32: 14000000 INFO @ Sat, 11 Dec 2021 09:59:33: 12000000 INFO @ Sat, 11 Dec 2021 09:59:37: 7000000 INFO @ Sat, 11 Dec 2021 09:59:38: 15000000 INFO @ Sat, 11 Dec 2021 09:59:39: 13000000 INFO @ Sat, 11 Dec 2021 09:59:42: 8000000 INFO @ Sat, 11 Dec 2021 09:59:44: 14000000 INFO @ Sat, 11 Dec 2021 09:59:45: 16000000 INFO @ Sat, 11 Dec 2021 09:59:48: 9000000 INFO @ Sat, 11 Dec 2021 09:59:50: 15000000 INFO @ Sat, 11 Dec 2021 09:59:52: 17000000 INFO @ Sat, 11 Dec 2021 09:59:54: 10000000 INFO @ Sat, 11 Dec 2021 09:59:55: 16000000 INFO @ Sat, 11 Dec 2021 09:59:59: 18000000 INFO @ Sat, 11 Dec 2021 10:00:00: 11000000 INFO @ Sat, 11 Dec 2021 10:00:01: 17000000 INFO @ Sat, 11 Dec 2021 10:00:05: 12000000 INFO @ Sat, 11 Dec 2021 10:00:06: 19000000 INFO @ Sat, 11 Dec 2021 10:00:06: 18000000 INFO @ Sat, 11 Dec 2021 10:00:11: 13000000 INFO @ Sat, 11 Dec 2021 10:00:12: 19000000 INFO @ Sat, 11 Dec 2021 10:00:13: 20000000 INFO @ Sat, 11 Dec 2021 10:00:16: 14000000 INFO @ Sat, 11 Dec 2021 10:00:18: 20000000 INFO @ Sat, 11 Dec 2021 10:00:21: 21000000 INFO @ Sat, 11 Dec 2021 10:00:22: 15000000 INFO @ Sat, 11 Dec 2021 10:00:23: 21000000 INFO @ Sat, 11 Dec 2021 10:00:28: 16000000 INFO @ Sat, 11 Dec 2021 10:00:28: 22000000 INFO @ Sat, 11 Dec 2021 10:00:29: 22000000 INFO @ Sat, 11 Dec 2021 10:00:33: 17000000 INFO @ Sat, 11 Dec 2021 10:00:36: 23000000 INFO @ Sat, 11 Dec 2021 10:00:36: 23000000 INFO @ Sat, 11 Dec 2021 10:00:39: 18000000 INFO @ Sat, 11 Dec 2021 10:00:39: #1 tag size is determined as 51 bps INFO @ Sat, 11 Dec 2021 10:00:39: #1 tag size = 51 INFO @ Sat, 11 Dec 2021 10:00:39: #1 total tags in treatment: 23498774 INFO @ Sat, 11 Dec 2021 10:00:39: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 10:00:39: #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 10:00:40: #1 tags after filtering in treatment: 23498713 INFO @ Sat, 11 Dec 2021 10:00:40: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 11 Dec 2021 10:00:40: #1 finished! INFO @ Sat, 11 Dec 2021 10:00:40: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 10:00:40: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 10:00:40: #1 tag size is determined as 51 bps INFO @ Sat, 11 Dec 2021 10:00:40: #1 tag size = 51 INFO @ Sat, 11 Dec 2021 10:00:40: #1 total tags in treatment: 23498774 INFO @ Sat, 11 Dec 2021 10:00:40: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 10:00:40: #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 10:00:41: #1 tags after filtering in treatment: 23498713 INFO @ Sat, 11 Dec 2021 10:00:41: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 11 Dec 2021 10:00:41: #1 finished! INFO @ Sat, 11 Dec 2021 10:00:41: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 10:00:41: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 10:00:41: #2 number of paired peaks: 693 WARNING @ Sat, 11 Dec 2021 10:00:41: Fewer paired peaks (693) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 693 pairs to build model! INFO @ Sat, 11 Dec 2021 10:00:41: start model_add_line... INFO @ Sat, 11 Dec 2021 10:00:41: start X-correlation... INFO @ Sat, 11 Dec 2021 10:00:41: end of X-cor INFO @ Sat, 11 Dec 2021 10:00:41: #2 finished! INFO @ Sat, 11 Dec 2021 10:00:41: #2 predicted fragment length is 179 bps INFO @ Sat, 11 Dec 2021 10:00:41: #2 alternative fragment length(s) may be 3,179 bps INFO @ Sat, 11 Dec 2021 10:00:41: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX10000638/SRX10000638.10_model.r INFO @ Sat, 11 Dec 2021 10:00:41: #3 Call peaks... INFO @ Sat, 11 Dec 2021 10:00:41: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Dec 2021 10:00:43: #2 number of paired peaks: 693 WARNING @ Sat, 11 Dec 2021 10:00:43: Fewer paired peaks (693) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 693 pairs to build model! INFO @ Sat, 11 Dec 2021 10:00:43: start model_add_line... INFO @ Sat, 11 Dec 2021 10:00:43: start X-correlation... INFO @ Sat, 11 Dec 2021 10:00:43: end of X-cor INFO @ Sat, 11 Dec 2021 10:00:43: #2 finished! INFO @ Sat, 11 Dec 2021 10:00:43: #2 predicted fragment length is 179 bps INFO @ Sat, 11 Dec 2021 10:00:43: #2 alternative fragment length(s) may be 3,179 bps INFO @ Sat, 11 Dec 2021 10:00:43: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX10000638/SRX10000638.05_model.r INFO @ Sat, 11 Dec 2021 10:00:43: #3 Call peaks... INFO @ Sat, 11 Dec 2021 10:00:43: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Dec 2021 10:00:44: 19000000 INFO @ Sat, 11 Dec 2021 10:00:50: 20000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 11 Dec 2021 10:00:55: 21000000 INFO @ Sat, 11 Dec 2021 10:01:01: 22000000 INFO @ Sat, 11 Dec 2021 10:01:06: 23000000 INFO @ Sat, 11 Dec 2021 10:01:09: #1 tag size is determined as 51 bps INFO @ Sat, 11 Dec 2021 10:01:09: #1 tag size = 51 INFO @ Sat, 11 Dec 2021 10:01:09: #1 total tags in treatment: 23498774 INFO @ Sat, 11 Dec 2021 10:01:09: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 10:01:09: #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 10:01:10: #1 tags after filtering in treatment: 23498713 INFO @ Sat, 11 Dec 2021 10:01:10: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 11 Dec 2021 10:01:10: #1 finished! INFO @ Sat, 11 Dec 2021 10:01:10: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 10:01:10: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 10:01:11: #2 number of paired peaks: 693 WARNING @ Sat, 11 Dec 2021 10:01:11: Fewer paired peaks (693) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 693 pairs to build model! INFO @ Sat, 11 Dec 2021 10:01:11: start model_add_line... INFO @ Sat, 11 Dec 2021 10:01:11: start X-correlation... INFO @ Sat, 11 Dec 2021 10:01:11: end of X-cor INFO @ Sat, 11 Dec 2021 10:01:11: #2 finished! INFO @ Sat, 11 Dec 2021 10:01:11: #2 predicted fragment length is 179 bps INFO @ Sat, 11 Dec 2021 10:01:11: #2 alternative fragment length(s) may be 3,179 bps INFO @ Sat, 11 Dec 2021 10:01:11: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX10000638/SRX10000638.20_model.r INFO @ Sat, 11 Dec 2021 10:01:11: #3 Call peaks... INFO @ Sat, 11 Dec 2021 10:01:11: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Dec 2021 10:01:33: #3 Call peaks for each chromosome... INFO @ Sat, 11 Dec 2021 10:01:34: #3 Call peaks for each chromosome... BigWig に変換しました。 INFO @ Sat, 11 Dec 2021 10:02:02: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX10000638/SRX10000638.05_peaks.xls INFO @ Sat, 11 Dec 2021 10:02:02: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX10000638/SRX10000638.05_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 10:02:02: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX10000638/SRX10000638.05_summits.bed INFO @ Sat, 11 Dec 2021 10:02:02: Done! INFO @ Sat, 11 Dec 2021 10:02:02: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX10000638/SRX10000638.10_peaks.xls INFO @ Sat, 11 Dec 2021 10:02:02: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX10000638/SRX10000638.10_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 10:02:02: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX10000638/SRX10000638.10_summits.bed INFO @ Sat, 11 Dec 2021 10:02:02: Done! pass1 - making usageList (528 chroms): 2 millis pass2 - checking and writing primary data (4568 records, 4 fields): 21 millis CompletedMACS2peakCalling pass1 - making usageList (672 chroms): 3 millis pass2 - checking and writing primary data (11746 records, 4 fields): 32 millis CompletedMACS2peakCalling INFO @ Sat, 11 Dec 2021 10:02:05: #3 Call peaks for each chromosome... INFO @ Sat, 11 Dec 2021 10:02:35: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX10000638/SRX10000638.20_peaks.xls INFO @ Sat, 11 Dec 2021 10:02:35: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX10000638/SRX10000638.20_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 10:02:35: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX10000638/SRX10000638.20_summits.bed INFO @ Sat, 11 Dec 2021 10:02:35: Done! pass1 - making usageList (306 chroms): 1 millis pass2 - checking and writing primary data (1288 records, 4 fields): 10 millis CompletedMACS2peakCalling