Job ID = 16439700 SRX = SRX11499369 Genome = dm3 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... Read 30342919 spots for SRR15192728/SRR15192728.sra Written 30342919 spots for SRR15192728/SRR15192728.sra fastq に変換しました。 bowtie でマッピング中... Your job 16440046 ("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: 00:40:54 30342919 reads; of these: 30342919 (100.00%) were paired; of these: 11536228 (38.02%) aligned concordantly 0 times 17652824 (58.18%) aligned concordantly exactly 1 time 1153867 (3.80%) aligned concordantly >1 times ---- 11536228 pairs aligned concordantly 0 times; of these: 3789310 (32.85%) aligned discordantly 1 time ---- 7746918 pairs aligned 0 times concordantly or discordantly; of these: 15493836 mates make up the pairs; of these: 13738435 (88.67%) aligned 0 times 1252336 (8.08%) aligned exactly 1 time 503065 (3.25%) aligned >1 times 77.36% overall alignment rate Time searching: 00:40:54 Overall time: 00:40:54 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_sort_core] merging from 36 files... [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] 2266483 / 21595149 = 0.1050 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/3.8.7/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Tue, 02 Aug 2022 17:05:11: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX11499369/SRX11499369.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX11499369/SRX11499369.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX11499369/SRX11499369.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX11499369/SRX11499369.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, 02 Aug 2022 17:05:11: #1 read tag files... INFO @ Tue, 02 Aug 2022 17:05:11: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 17:05:17: 1000000 INFO @ Tue, 02 Aug 2022 17:05:24: 2000000 INFO @ Tue, 02 Aug 2022 17:05:31: 3000000 WARNING: Skipping mount /opt/pkg/singularity/3.8.7/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Tue, 02 Aug 2022 17:05:38: 4000000 INFO @ Tue, 02 Aug 2022 17:05:40: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX11499369/SRX11499369.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX11499369/SRX11499369.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX11499369/SRX11499369.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX11499369/SRX11499369.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, 02 Aug 2022 17:05:40: #1 read tag files... INFO @ Tue, 02 Aug 2022 17:05:40: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 17:05:46: 5000000 INFO @ Tue, 02 Aug 2022 17:05:47: 1000000 INFO @ Tue, 02 Aug 2022 17:05:53: 6000000 INFO @ Tue, 02 Aug 2022 17:05:55: 2000000 INFO @ Tue, 02 Aug 2022 17:06:01: 7000000 INFO @ Tue, 02 Aug 2022 17:06:02: 3000000 BedGraph に変換中... WARNING: Skipping mount /opt/pkg/singularity/3.8.7/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Tue, 02 Aug 2022 17:06:08: 8000000 INFO @ Tue, 02 Aug 2022 17:06:09: 4000000 INFO @ Tue, 02 Aug 2022 17:06:10: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX11499369/SRX11499369.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX11499369/SRX11499369.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX11499369/SRX11499369.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX11499369/SRX11499369.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, 02 Aug 2022 17:06:10: #1 read tag files... INFO @ Tue, 02 Aug 2022 17:06:10: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 17:06:17: 9000000 INFO @ Tue, 02 Aug 2022 17:06:17: 5000000 INFO @ Tue, 02 Aug 2022 17:06:19: 1000000 INFO @ Tue, 02 Aug 2022 17:06:25: 10000000 INFO @ Tue, 02 Aug 2022 17:06:25: 6000000 INFO @ Tue, 02 Aug 2022 17:06:28: 2000000 INFO @ Tue, 02 Aug 2022 17:06:33: 11000000 INFO @ Tue, 02 Aug 2022 17:06:33: 7000000 INFO @ Tue, 02 Aug 2022 17:06:38: 3000000 INFO @ Tue, 02 Aug 2022 17:06:41: 8000000 INFO @ Tue, 02 Aug 2022 17:06:42: 12000000 INFO @ Tue, 02 Aug 2022 17:06:47: 4000000 INFO @ Tue, 02 Aug 2022 17:06:50: 9000000 INFO @ Tue, 02 Aug 2022 17:06:50: 13000000 INFO @ Tue, 02 Aug 2022 17:06:56: 5000000 INFO @ Tue, 02 Aug 2022 17:06:58: 10000000 INFO @ Tue, 02 Aug 2022 17:06:59: 14000000 INFO @ Tue, 02 Aug 2022 17:07:05: 6000000 INFO @ Tue, 02 Aug 2022 17:07:06: 11000000 INFO @ Tue, 02 Aug 2022 17:07:07: 15000000 INFO @ Tue, 02 Aug 2022 17:07:14: 12000000 INFO @ Tue, 02 Aug 2022 17:07:15: 7000000 INFO @ Tue, 02 Aug 2022 17:07:16: 16000000 INFO @ Tue, 02 Aug 2022 17:07:22: 13000000 INFO @ Tue, 02 Aug 2022 17:07:24: 8000000 INFO @ Tue, 02 Aug 2022 17:07:24: 17000000 INFO @ Tue, 02 Aug 2022 17:07:30: 14000000 INFO @ Tue, 02 Aug 2022 17:07:33: 18000000 INFO @ Tue, 02 Aug 2022 17:07:33: 9000000 INFO @ Tue, 02 Aug 2022 17:07:38: 15000000 INFO @ Tue, 02 Aug 2022 17:07:41: 19000000 INFO @ Tue, 02 Aug 2022 17:07:42: 10000000 INFO @ Tue, 02 Aug 2022 17:07:46: 16000000 INFO @ Tue, 02 Aug 2022 17:07:49: 20000000 INFO @ Tue, 02 Aug 2022 17:07:52: 11000000 INFO @ Tue, 02 Aug 2022 17:07:54: 17000000 INFO @ Tue, 02 Aug 2022 17:07:57: 21000000 INFO @ Tue, 02 Aug 2022 17:08:01: 12000000 INFO @ Tue, 02 Aug 2022 17:08:02: 18000000 INFO @ Tue, 02 Aug 2022 17:08:06: 22000000 INFO @ Tue, 02 Aug 2022 17:08:10: 13000000 INFO @ Tue, 02 Aug 2022 17:08:11: 19000000 INFO @ Tue, 02 Aug 2022 17:08:14: 23000000 INFO @ Tue, 02 Aug 2022 17:08:19: 20000000 INFO @ Tue, 02 Aug 2022 17:08:20: 14000000 INFO @ Tue, 02 Aug 2022 17:08:22: 24000000 INFO @ Tue, 02 Aug 2022 17:08:27: 21000000 INFO @ Tue, 02 Aug 2022 17:08:29: 15000000 INFO @ Tue, 02 Aug 2022 17:08:30: 25000000 INFO @ Tue, 02 Aug 2022 17:08:35: 22000000 INFO @ Tue, 02 Aug 2022 17:08:38: 26000000 INFO @ Tue, 02 Aug 2022 17:08:38: 16000000 INFO @ Tue, 02 Aug 2022 17:08:43: 23000000 INFO @ Tue, 02 Aug 2022 17:08:46: 27000000 INFO @ Tue, 02 Aug 2022 17:08:47: 17000000 INFO @ Tue, 02 Aug 2022 17:08:51: 24000000 INFO @ Tue, 02 Aug 2022 17:08:54: 28000000 INFO @ Tue, 02 Aug 2022 17:08:57: 18000000 INFO @ Tue, 02 Aug 2022 17:08:59: 25000000 INFO @ Tue, 02 Aug 2022 17:09:02: 29000000 INFO @ Tue, 02 Aug 2022 17:09:06: 19000000 INFO @ Tue, 02 Aug 2022 17:09:06: 26000000 INFO @ Tue, 02 Aug 2022 17:09:10: 30000000 INFO @ Tue, 02 Aug 2022 17:09:14: 27000000 INFO @ Tue, 02 Aug 2022 17:09:15: 20000000 INFO @ Tue, 02 Aug 2022 17:09:18: 31000000 INFO @ Tue, 02 Aug 2022 17:09:22: 28000000 INFO @ Tue, 02 Aug 2022 17:09:24: 21000000 INFO @ Tue, 02 Aug 2022 17:09:26: 32000000 INFO @ Tue, 02 Aug 2022 17:09:30: 29000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 02 Aug 2022 17:09:34: 33000000 INFO @ Tue, 02 Aug 2022 17:09:34: 22000000 INFO @ Tue, 02 Aug 2022 17:09:38: 30000000 INFO @ Tue, 02 Aug 2022 17:09:41: 34000000 INFO @ Tue, 02 Aug 2022 17:09:43: 23000000 INFO @ Tue, 02 Aug 2022 17:09:46: 31000000 INFO @ Tue, 02 Aug 2022 17:09:50: 35000000 INFO @ Tue, 02 Aug 2022 17:09:52: 24000000 INFO @ Tue, 02 Aug 2022 17:09:54: 32000000 INFO @ Tue, 02 Aug 2022 17:09:58: 36000000 INFO @ Tue, 02 Aug 2022 17:10:02: 25000000 INFO @ Tue, 02 Aug 2022 17:10:02: 33000000 BigWig に変換しました。 INFO @ Tue, 02 Aug 2022 17:10:05: 37000000 INFO @ Tue, 02 Aug 2022 17:10:10: 34000000 INFO @ Tue, 02 Aug 2022 17:10:11: 26000000 INFO @ Tue, 02 Aug 2022 17:10:14: 38000000 INFO @ Tue, 02 Aug 2022 17:10:18: 35000000 INFO @ Tue, 02 Aug 2022 17:10:20: 27000000 INFO @ Tue, 02 Aug 2022 17:10:22: 39000000 INFO @ Tue, 02 Aug 2022 17:10:26: 36000000 INFO @ Tue, 02 Aug 2022 17:10:30: 40000000 INFO @ Tue, 02 Aug 2022 17:10:30: 28000000 INFO @ Tue, 02 Aug 2022 17:10:34: 37000000 INFO @ Tue, 02 Aug 2022 17:10:38: 41000000 INFO @ Tue, 02 Aug 2022 17:10:40: 29000000 INFO @ Tue, 02 Aug 2022 17:10:42: 38000000 INFO @ Tue, 02 Aug 2022 17:10:46: 42000000 INFO @ Tue, 02 Aug 2022 17:10:49: 30000000 INFO @ Tue, 02 Aug 2022 17:10:50: #1 tag size is determined as 144 bps INFO @ Tue, 02 Aug 2022 17:10:50: #1 tag size = 144 INFO @ Tue, 02 Aug 2022 17:10:50: #1 total tags in treatment: 16782888 INFO @ Tue, 02 Aug 2022 17:10:50: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 17:10:50: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 02 Aug 2022 17:10:50: #1 tags after filtering in treatment: 9424733 INFO @ Tue, 02 Aug 2022 17:10:50: #1 Redundant rate of treatment: 0.44 INFO @ Tue, 02 Aug 2022 17:10:50: #1 finished! INFO @ Tue, 02 Aug 2022 17:10:50: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 17:10:50: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 17:10:51: 39000000 INFO @ Tue, 02 Aug 2022 17:10:51: #2 number of paired peaks: 7990 INFO @ Tue, 02 Aug 2022 17:10:51: start model_add_line... INFO @ Tue, 02 Aug 2022 17:10:52: start X-correlation... INFO @ Tue, 02 Aug 2022 17:10:52: end of X-cor INFO @ Tue, 02 Aug 2022 17:10:52: #2 finished! INFO @ Tue, 02 Aug 2022 17:10:52: #2 predicted fragment length is 298 bps INFO @ Tue, 02 Aug 2022 17:10:52: #2 alternative fragment length(s) may be 298 bps INFO @ Tue, 02 Aug 2022 17:10:52: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX11499369/SRX11499369.05_model.r INFO @ Tue, 02 Aug 2022 17:10:52: #3 Call peaks... INFO @ Tue, 02 Aug 2022 17:10:52: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 02 Aug 2022 17:10:58: 31000000 INFO @ Tue, 02 Aug 2022 17:10:59: 40000000 INFO @ Tue, 02 Aug 2022 17:11:07: 32000000 INFO @ Tue, 02 Aug 2022 17:11:08: 41000000 INFO @ Tue, 02 Aug 2022 17:11:16: 42000000 INFO @ Tue, 02 Aug 2022 17:11:17: 33000000 INFO @ Tue, 02 Aug 2022 17:11:19: #1 tag size is determined as 144 bps INFO @ Tue, 02 Aug 2022 17:11:19: #1 tag size = 144 INFO @ Tue, 02 Aug 2022 17:11:19: #1 total tags in treatment: 16782888 INFO @ Tue, 02 Aug 2022 17:11:19: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 17:11:19: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 02 Aug 2022 17:11:19: #1 tags after filtering in treatment: 9424733 INFO @ Tue, 02 Aug 2022 17:11:19: #1 Redundant rate of treatment: 0.44 INFO @ Tue, 02 Aug 2022 17:11:19: #1 finished! INFO @ Tue, 02 Aug 2022 17:11:19: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 17:11:19: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 17:11:21: #2 number of paired peaks: 7990 INFO @ Tue, 02 Aug 2022 17:11:21: start model_add_line... INFO @ Tue, 02 Aug 2022 17:11:21: start X-correlation... INFO @ Tue, 02 Aug 2022 17:11:21: end of X-cor INFO @ Tue, 02 Aug 2022 17:11:21: #2 finished! INFO @ Tue, 02 Aug 2022 17:11:21: #2 predicted fragment length is 298 bps INFO @ Tue, 02 Aug 2022 17:11:21: #2 alternative fragment length(s) may be 298 bps INFO @ Tue, 02 Aug 2022 17:11:21: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX11499369/SRX11499369.10_model.r INFO @ Tue, 02 Aug 2022 17:11:21: #3 Call peaks... INFO @ Tue, 02 Aug 2022 17:11:21: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 02 Aug 2022 17:11:22: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 17:11:25: 34000000 INFO @ Tue, 02 Aug 2022 17:11:34: 35000000 INFO @ Tue, 02 Aug 2022 17:11:34: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX11499369/SRX11499369.05_peaks.xls INFO @ Tue, 02 Aug 2022 17:11:34: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX11499369/SRX11499369.05_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 17:11:34: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX11499369/SRX11499369.05_summits.bed INFO @ Tue, 02 Aug 2022 17:11:34: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (7779 records, 4 fields): 26 millis CompletedMACS2peakCalling INFO @ Tue, 02 Aug 2022 17:11:42: 36000000 INFO @ Tue, 02 Aug 2022 17:11:50: 37000000 INFO @ Tue, 02 Aug 2022 17:11:51: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 17:11:59: 38000000 INFO @ Tue, 02 Aug 2022 17:12:03: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX11499369/SRX11499369.10_peaks.xls INFO @ Tue, 02 Aug 2022 17:12:03: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX11499369/SRX11499369.10_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 17:12:03: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX11499369/SRX11499369.10_summits.bed INFO @ Tue, 02 Aug 2022 17:12:03: Done! pass1 - making usageList (14 chroms): 2 millis pass2 - checking and writing primary data (7018 records, 4 fields): 46 millis CompletedMACS2peakCalling INFO @ Tue, 02 Aug 2022 17:12:07: 39000000 INFO @ Tue, 02 Aug 2022 17:12:15: 40000000 INFO @ Tue, 02 Aug 2022 17:12:23: 41000000 INFO @ Tue, 02 Aug 2022 17:12:31: 42000000 INFO @ Tue, 02 Aug 2022 17:12:35: #1 tag size is determined as 144 bps INFO @ Tue, 02 Aug 2022 17:12:35: #1 tag size = 144 INFO @ Tue, 02 Aug 2022 17:12:35: #1 total tags in treatment: 16782888 INFO @ Tue, 02 Aug 2022 17:12:35: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 17:12:35: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 02 Aug 2022 17:12:35: #1 tags after filtering in treatment: 9424733 INFO @ Tue, 02 Aug 2022 17:12:35: #1 Redundant rate of treatment: 0.44 INFO @ Tue, 02 Aug 2022 17:12:35: #1 finished! INFO @ Tue, 02 Aug 2022 17:12:35: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 17:12:35: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 17:12:36: #2 number of paired peaks: 7990 INFO @ Tue, 02 Aug 2022 17:12:36: start model_add_line... INFO @ Tue, 02 Aug 2022 17:12:36: start X-correlation... INFO @ Tue, 02 Aug 2022 17:12:36: end of X-cor INFO @ Tue, 02 Aug 2022 17:12:36: #2 finished! INFO @ Tue, 02 Aug 2022 17:12:36: #2 predicted fragment length is 298 bps INFO @ Tue, 02 Aug 2022 17:12:36: #2 alternative fragment length(s) may be 298 bps INFO @ Tue, 02 Aug 2022 17:12:36: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX11499369/SRX11499369.20_model.r INFO @ Tue, 02 Aug 2022 17:12:36: #3 Call peaks... INFO @ Tue, 02 Aug 2022 17:12:36: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 02 Aug 2022 17:13:06: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 17:13:17: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX11499369/SRX11499369.20_peaks.xls INFO @ Tue, 02 Aug 2022 17:13:18: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX11499369/SRX11499369.20_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 17:13:18: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX11499369/SRX11499369.20_summits.bed INFO @ Tue, 02 Aug 2022 17:13:18: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (6209 records, 4 fields): 26 millis CompletedMACS2peakCalling