Job ID = 5720781 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... spots read : 27,593,559 reads read : 55,187,118 reads written : 55,187,118 rm: cannot remove ‘[DSE]RR*’: No such file or directory 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: 02:34:37 27593559 reads; of these: 27593559 (100.00%) were paired; of these: 7608659 (27.57%) aligned concordantly 0 times 6736162 (24.41%) aligned concordantly exactly 1 time 13248738 (48.01%) aligned concordantly >1 times ---- 7608659 pairs aligned concordantly 0 times; of these: 1057810 (13.90%) aligned discordantly 1 time ---- 6550849 pairs aligned 0 times concordantly or discordantly; of these: 13101698 mates make up the pairs; of these: 5241013 (40.00%) aligned 0 times 1099772 (8.39%) aligned exactly 1 time 6760913 (51.60%) aligned >1 times 90.50% overall alignment rate Time searching: 02:34:37 Overall time: 02:34:37 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 24 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] 3289583 / 20910269 = 0.1573 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 @ Thu, 16 Apr 2020 04:48:00: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX5246874/SRX5246874.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX5246874/SRX5246874.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX5246874/SRX5246874.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX5246874/SRX5246874.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 @ Thu, 16 Apr 2020 04:48:00: #1 read tag files... INFO @ Thu, 16 Apr 2020 04:48:00: #1 read treatment tags... INFO @ Thu, 16 Apr 2020 04:48:08: 1000000 INFO @ Thu, 16 Apr 2020 04:48:16: 2000000 INFO @ Thu, 16 Apr 2020 04:48:23: 3000000 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 @ Thu, 16 Apr 2020 04:48:30: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX5246874/SRX5246874.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX5246874/SRX5246874.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX5246874/SRX5246874.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX5246874/SRX5246874.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 @ Thu, 16 Apr 2020 04:48:30: #1 read tag files... INFO @ Thu, 16 Apr 2020 04:48:30: #1 read treatment tags... INFO @ Thu, 16 Apr 2020 04:48:31: 4000000 INFO @ Thu, 16 Apr 2020 04:48:38: 1000000 INFO @ Thu, 16 Apr 2020 04:48:39: 5000000 INFO @ Thu, 16 Apr 2020 04:48:45: 2000000 INFO @ Thu, 16 Apr 2020 04:48:47: 6000000 INFO @ Thu, 16 Apr 2020 04:48:53: 3000000 INFO @ Thu, 16 Apr 2020 04:48:55: 7000000 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 @ Thu, 16 Apr 2020 04:49:00: 4000000 INFO @ Thu, 16 Apr 2020 04:49:00: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX5246874/SRX5246874.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX5246874/SRX5246874.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX5246874/SRX5246874.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX5246874/SRX5246874.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 @ Thu, 16 Apr 2020 04:49:00: #1 read tag files... INFO @ Thu, 16 Apr 2020 04:49:00: #1 read treatment tags... INFO @ Thu, 16 Apr 2020 04:49:03: 8000000 INFO @ Thu, 16 Apr 2020 04:49:07: 5000000 INFO @ Thu, 16 Apr 2020 04:49:09: 1000000 INFO @ Thu, 16 Apr 2020 04:49:11: 9000000 INFO @ Thu, 16 Apr 2020 04:49:15: 6000000 INFO @ Thu, 16 Apr 2020 04:49:18: 2000000 INFO @ Thu, 16 Apr 2020 04:49:20: 10000000 INFO @ Thu, 16 Apr 2020 04:49:22: 7000000 INFO @ Thu, 16 Apr 2020 04:49:26: 3000000 INFO @ Thu, 16 Apr 2020 04:49:29: 11000000 INFO @ Thu, 16 Apr 2020 04:49:30: 8000000 INFO @ Thu, 16 Apr 2020 04:49:35: 4000000 INFO @ Thu, 16 Apr 2020 04:49:37: 9000000 INFO @ Thu, 16 Apr 2020 04:49:38: 12000000 INFO @ Thu, 16 Apr 2020 04:49:44: 5000000 INFO @ Thu, 16 Apr 2020 04:49:45: 10000000 INFO @ Thu, 16 Apr 2020 04:49:46: 13000000 INFO @ Thu, 16 Apr 2020 04:49:52: 11000000 INFO @ Thu, 16 Apr 2020 04:49:52: 6000000 INFO @ Thu, 16 Apr 2020 04:49:55: 14000000 INFO @ Thu, 16 Apr 2020 04:49:59: 12000000 INFO @ Thu, 16 Apr 2020 04:50:01: 7000000 INFO @ Thu, 16 Apr 2020 04:50:04: 15000000 INFO @ Thu, 16 Apr 2020 04:50:07: 13000000 INFO @ Thu, 16 Apr 2020 04:50:10: 8000000 INFO @ Thu, 16 Apr 2020 04:50:13: 16000000 INFO @ Thu, 16 Apr 2020 04:50:14: 14000000 INFO @ Thu, 16 Apr 2020 04:50:19: 9000000 INFO @ Thu, 16 Apr 2020 04:50:22: 15000000 INFO @ Thu, 16 Apr 2020 04:50:22: 17000000 INFO @ Thu, 16 Apr 2020 04:50:27: 10000000 INFO @ Thu, 16 Apr 2020 04:50:29: 16000000 INFO @ Thu, 16 Apr 2020 04:50:31: 18000000 INFO @ Thu, 16 Apr 2020 04:50:36: 11000000 INFO @ Thu, 16 Apr 2020 04:50:37: 17000000 INFO @ Thu, 16 Apr 2020 04:50:40: 19000000 INFO @ Thu, 16 Apr 2020 04:50:44: 18000000 INFO @ Thu, 16 Apr 2020 04:50:45: 12000000 INFO @ Thu, 16 Apr 2020 04:50:49: 20000000 INFO @ Thu, 16 Apr 2020 04:50:52: 19000000 INFO @ Thu, 16 Apr 2020 04:50:53: 13000000 INFO @ Thu, 16 Apr 2020 04:50:58: 21000000 INFO @ Thu, 16 Apr 2020 04:50:59: 20000000 INFO @ Thu, 16 Apr 2020 04:51:02: 14000000 INFO @ Thu, 16 Apr 2020 04:51:07: 21000000 INFO @ Thu, 16 Apr 2020 04:51:08: 22000000 INFO @ Thu, 16 Apr 2020 04:51:10: 15000000 INFO @ Thu, 16 Apr 2020 04:51:15: 22000000 INFO @ Thu, 16 Apr 2020 04:51:17: 23000000 INFO @ Thu, 16 Apr 2020 04:51:19: 16000000 INFO @ Thu, 16 Apr 2020 04:51:22: 23000000 INFO @ Thu, 16 Apr 2020 04:51:25: 24000000 INFO @ Thu, 16 Apr 2020 04:51:27: 17000000 INFO @ Thu, 16 Apr 2020 04:51:30: 24000000 INFO @ Thu, 16 Apr 2020 04:51:35: 25000000 INFO @ Thu, 16 Apr 2020 04:51:35: 18000000 INFO @ Thu, 16 Apr 2020 04:51:37: 25000000 INFO @ Thu, 16 Apr 2020 04:51:44: 26000000 INFO @ Thu, 16 Apr 2020 04:51:44: 19000000 INFO @ Thu, 16 Apr 2020 04:51:45: 26000000 INFO @ Thu, 16 Apr 2020 04:51:52: 20000000 INFO @ Thu, 16 Apr 2020 04:51:53: 27000000 INFO @ Thu, 16 Apr 2020 04:51:53: 27000000 INFO @ Thu, 16 Apr 2020 04:52:01: 21000000 INFO @ Thu, 16 Apr 2020 04:52:03: 28000000 INFO @ Thu, 16 Apr 2020 04:52:03: 28000000 INFO @ Thu, 16 Apr 2020 04:52:10: 22000000 INFO @ Thu, 16 Apr 2020 04:52:13: 29000000 INFO @ Thu, 16 Apr 2020 04:52:13: 29000000 INFO @ Thu, 16 Apr 2020 04:52:18: 23000000 INFO @ Thu, 16 Apr 2020 04:52:21: 30000000 INFO @ Thu, 16 Apr 2020 04:52:22: 30000000 INFO @ Thu, 16 Apr 2020 04:52:27: 24000000 INFO @ Thu, 16 Apr 2020 04:52:28: 31000000 INFO @ Thu, 16 Apr 2020 04:52:31: 31000000 INFO @ Thu, 16 Apr 2020 04:52:36: 25000000 INFO @ Thu, 16 Apr 2020 04:52:36: 32000000 INFO @ Thu, 16 Apr 2020 04:52:40: 32000000 INFO @ Thu, 16 Apr 2020 04:52:43: 33000000 INFO @ Thu, 16 Apr 2020 04:52:45: 26000000 INFO @ Thu, 16 Apr 2020 04:52:48: 33000000 INFO @ Thu, 16 Apr 2020 04:52:51: 34000000 INFO @ Thu, 16 Apr 2020 04:52:53: 27000000 INFO @ Thu, 16 Apr 2020 04:52:56: 34000000 INFO @ Thu, 16 Apr 2020 04:52:58: 35000000 INFO @ Thu, 16 Apr 2020 04:53:02: 28000000 INFO @ Thu, 16 Apr 2020 04:53:04: 35000000 INFO @ Thu, 16 Apr 2020 04:53:06: 36000000 INFO @ Thu, 16 Apr 2020 04:53:11: 29000000 INFO @ Thu, 16 Apr 2020 04:53:13: 36000000 INFO @ Thu, 16 Apr 2020 04:53:13: 37000000 INFO @ Thu, 16 Apr 2020 04:53:20: 30000000 INFO @ Thu, 16 Apr 2020 04:53:21: 38000000 INFO @ Thu, 16 Apr 2020 04:53:21: 37000000 INFO @ Thu, 16 Apr 2020 04:53:28: 39000000 INFO @ Thu, 16 Apr 2020 04:53:28: 31000000 INFO @ Thu, 16 Apr 2020 04:53:30: 38000000 INFO @ Thu, 16 Apr 2020 04:53:36: 40000000 INFO @ Thu, 16 Apr 2020 04:53:37: 32000000 INFO @ Thu, 16 Apr 2020 04:53:38: 39000000 INFO @ Thu, 16 Apr 2020 04:53:44: 41000000 INFO @ Thu, 16 Apr 2020 04:53:45: 33000000 INFO @ Thu, 16 Apr 2020 04:53:47: 40000000 INFO @ Thu, 16 Apr 2020 04:53:52: 42000000 INFO @ Thu, 16 Apr 2020 04:53:54: 34000000 INFO @ Thu, 16 Apr 2020 04:53:56: 41000000 INFO @ Thu, 16 Apr 2020 04:53:59: 43000000 INFO @ Thu, 16 Apr 2020 04:54:02: #1 tag size is determined as 101 bps INFO @ Thu, 16 Apr 2020 04:54:02: #1 tag size = 101 INFO @ Thu, 16 Apr 2020 04:54:02: #1 total tags in treatment: 16841353 INFO @ Thu, 16 Apr 2020 04:54:02: #1 user defined the maximum tags... INFO @ Thu, 16 Apr 2020 04:54:02: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Thu, 16 Apr 2020 04:54:02: #1 tags after filtering in treatment: 14016559 INFO @ Thu, 16 Apr 2020 04:54:02: #1 Redundant rate of treatment: 0.17 INFO @ Thu, 16 Apr 2020 04:54:02: #1 finished! INFO @ Thu, 16 Apr 2020 04:54:02: #2 Build Peak Model... INFO @ Thu, 16 Apr 2020 04:54:02: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 16 Apr 2020 04:54:02: 35000000 INFO @ Thu, 16 Apr 2020 04:54:03: #2 number of paired peaks: 3333 INFO @ Thu, 16 Apr 2020 04:54:03: start model_add_line... INFO @ Thu, 16 Apr 2020 04:54:04: start X-correlation... INFO @ Thu, 16 Apr 2020 04:54:04: end of X-cor INFO @ Thu, 16 Apr 2020 04:54:04: #2 finished! INFO @ Thu, 16 Apr 2020 04:54:04: #2 predicted fragment length is 217 bps INFO @ Thu, 16 Apr 2020 04:54:04: #2 alternative fragment length(s) may be 217 bps INFO @ Thu, 16 Apr 2020 04:54:04: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX5246874/SRX5246874.10_model.r INFO @ Thu, 16 Apr 2020 04:54:04: #3 Call peaks... INFO @ Thu, 16 Apr 2020 04:54:04: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 16 Apr 2020 04:54:04: 42000000 INFO @ Thu, 16 Apr 2020 04:54:11: 36000000 INFO @ Thu, 16 Apr 2020 04:54:13: 43000000 INFO @ Thu, 16 Apr 2020 04:54:16: #1 tag size is determined as 101 bps INFO @ Thu, 16 Apr 2020 04:54:16: #1 tag size = 101 INFO @ Thu, 16 Apr 2020 04:54:16: #1 total tags in treatment: 16841353 INFO @ Thu, 16 Apr 2020 04:54:16: #1 user defined the maximum tags... INFO @ Thu, 16 Apr 2020 04:54:16: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Thu, 16 Apr 2020 04:54:16: #1 tags after filtering in treatment: 14016559 INFO @ Thu, 16 Apr 2020 04:54:16: #1 Redundant rate of treatment: 0.17 INFO @ Thu, 16 Apr 2020 04:54:16: #1 finished! INFO @ Thu, 16 Apr 2020 04:54:16: #2 Build Peak Model... INFO @ Thu, 16 Apr 2020 04:54:16: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 16 Apr 2020 04:54:17: #2 number of paired peaks: 3333 INFO @ Thu, 16 Apr 2020 04:54:17: start model_add_line... INFO @ Thu, 16 Apr 2020 04:54:17: start X-correlation... INFO @ Thu, 16 Apr 2020 04:54:17: end of X-cor INFO @ Thu, 16 Apr 2020 04:54:17: #2 finished! INFO @ Thu, 16 Apr 2020 04:54:17: #2 predicted fragment length is 217 bps INFO @ Thu, 16 Apr 2020 04:54:17: #2 alternative fragment length(s) may be 217 bps INFO @ Thu, 16 Apr 2020 04:54:17: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX5246874/SRX5246874.05_model.r INFO @ Thu, 16 Apr 2020 04:54:17: #3 Call peaks... INFO @ Thu, 16 Apr 2020 04:54:17: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 16 Apr 2020 04:54:20: 37000000 INFO @ Thu, 16 Apr 2020 04:54:28: 38000000 INFO @ Thu, 16 Apr 2020 04:54:36: 39000000 INFO @ Thu, 16 Apr 2020 04:54:40: #3 Call peaks for each chromosome... INFO @ Thu, 16 Apr 2020 04:54:44: 40000000 INFO @ Thu, 16 Apr 2020 04:54:52: 41000000 INFO @ Thu, 16 Apr 2020 04:54:53: #3 Call peaks for each chromosome... BedGraph に変換しました。 BigWig に変換中... INFO @ Thu, 16 Apr 2020 04:54:58: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX5246874/SRX5246874.10_peaks.xls INFO @ Thu, 16 Apr 2020 04:54:58: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX5246874/SRX5246874.10_peaks.narrowPeak INFO @ Thu, 16 Apr 2020 04:54:58: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX5246874/SRX5246874.10_summits.bed INFO @ Thu, 16 Apr 2020 04:54:58: Done! pass1 - making usageList (14 chroms): 2 millis pass2 - checking and writing primary data (10783 records, 4 fields): 11 millis CompletedMACS2peakCalling INFO @ Thu, 16 Apr 2020 04:55:00: 42000000 INFO @ Thu, 16 Apr 2020 04:55:08: 43000000 INFO @ Thu, 16 Apr 2020 04:55:10: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX5246874/SRX5246874.05_peaks.xls INFO @ Thu, 16 Apr 2020 04:55:10: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX5246874/SRX5246874.05_peaks.narrowPeak INFO @ Thu, 16 Apr 2020 04:55:10: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX5246874/SRX5246874.05_summits.bed INFO @ Thu, 16 Apr 2020 04:55:10: Done! pass1 - making usageList (14 chroms): 2 millis pass2 - checking and writing primary data (15418 records, 4 fields): 15 millis CompletedMACS2peakCalling INFO @ Thu, 16 Apr 2020 04:55:11: #1 tag size is determined as 101 bps INFO @ Thu, 16 Apr 2020 04:55:11: #1 tag size = 101 INFO @ Thu, 16 Apr 2020 04:55:11: #1 total tags in treatment: 16841353 INFO @ Thu, 16 Apr 2020 04:55:11: #1 user defined the maximum tags... INFO @ Thu, 16 Apr 2020 04:55:11: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Thu, 16 Apr 2020 04:55:11: #1 tags after filtering in treatment: 14016559 INFO @ Thu, 16 Apr 2020 04:55:11: #1 Redundant rate of treatment: 0.17 INFO @ Thu, 16 Apr 2020 04:55:11: #1 finished! INFO @ Thu, 16 Apr 2020 04:55:11: #2 Build Peak Model... INFO @ Thu, 16 Apr 2020 04:55:11: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 16 Apr 2020 04:55:12: #2 number of paired peaks: 3333 INFO @ Thu, 16 Apr 2020 04:55:12: start model_add_line... INFO @ Thu, 16 Apr 2020 04:55:12: start X-correlation... INFO @ Thu, 16 Apr 2020 04:55:12: end of X-cor INFO @ Thu, 16 Apr 2020 04:55:12: #2 finished! INFO @ Thu, 16 Apr 2020 04:55:12: #2 predicted fragment length is 217 bps INFO @ Thu, 16 Apr 2020 04:55:12: #2 alternative fragment length(s) may be 217 bps INFO @ Thu, 16 Apr 2020 04:55:12: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX5246874/SRX5246874.20_model.r INFO @ Thu, 16 Apr 2020 04:55:12: #3 Call peaks... INFO @ Thu, 16 Apr 2020 04:55:12: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 16 Apr 2020 04:55:48: #3 Call peaks for each chromosome... BigWig に変換しました。 INFO @ Thu, 16 Apr 2020 04:56:06: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX5246874/SRX5246874.20_peaks.xls INFO @ Thu, 16 Apr 2020 04:56:06: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX5246874/SRX5246874.20_peaks.narrowPeak INFO @ Thu, 16 Apr 2020 04:56:06: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX5246874/SRX5246874.20_summits.bed INFO @ Thu, 16 Apr 2020 04:56:06: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (6348 records, 4 fields): 7 millis CompletedMACS2peakCalling