Job ID = 5720784 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... spots read : 24,245,229 reads read : 48,490,458 reads written : 48,490,458 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: 02:18:57 24245229 reads; of these: 24245229 (100.00%) were paired; of these: 6402749 (26.41%) aligned concordantly 0 times 6074510 (25.05%) aligned concordantly exactly 1 time 11767970 (48.54%) aligned concordantly >1 times ---- 6402749 pairs aligned concordantly 0 times; of these: 929509 (14.52%) aligned discordantly 1 time ---- 5473240 pairs aligned 0 times concordantly or discordantly; of these: 10946480 mates make up the pairs; of these: 3855030 (35.22%) aligned 0 times 1002470 (9.16%) aligned exactly 1 time 6088980 (55.63%) aligned >1 times 92.05% overall alignment rate Time searching: 02:18:57 Overall time: 02:18:57 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 20 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] 2480097 / 18684370 = 0.1327 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 04:27:51: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX5246877/SRX5246877.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX5246877/SRX5246877.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX5246877/SRX5246877.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX5246877/SRX5246877.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 04:27:51: #1 read tag files... INFO @ Thu, 16 Apr 2020 04:27:51: #1 read treatment tags... INFO @ Thu, 16 Apr 2020 04:27:59: 1000000 INFO @ Thu, 16 Apr 2020 04:28:06: 2000000 INFO @ Thu, 16 Apr 2020 04:28:13: 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 04:28:20: 4000000 INFO @ Thu, 16 Apr 2020 04:28:21: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX5246877/SRX5246877.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX5246877/SRX5246877.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX5246877/SRX5246877.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX5246877/SRX5246877.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 04:28:21: #1 read tag files... INFO @ Thu, 16 Apr 2020 04:28:21: #1 read treatment tags... INFO @ Thu, 16 Apr 2020 04:28:28: 5000000 INFO @ Thu, 16 Apr 2020 04:28:30: 1000000 INFO @ Thu, 16 Apr 2020 04:28:36: 6000000 INFO @ Thu, 16 Apr 2020 04:28:38: 2000000 INFO @ Thu, 16 Apr 2020 04:28:44: 7000000 INFO @ Thu, 16 Apr 2020 04:28:46: 3000000 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 04:28:51: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX5246877/SRX5246877.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX5246877/SRX5246877.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX5246877/SRX5246877.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX5246877/SRX5246877.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 04:28:51: #1 read tag files... INFO @ Thu, 16 Apr 2020 04:28:51: #1 read treatment tags... INFO @ Thu, 16 Apr 2020 04:28:52: 8000000 INFO @ Thu, 16 Apr 2020 04:28:55: 4000000 INFO @ Thu, 16 Apr 2020 04:29:00: 1000000 INFO @ Thu, 16 Apr 2020 04:29:00: 9000000 INFO @ Thu, 16 Apr 2020 04:29:03: 5000000 INFO @ Thu, 16 Apr 2020 04:29:08: 10000000 INFO @ Thu, 16 Apr 2020 04:29:08: 2000000 INFO @ Thu, 16 Apr 2020 04:29:11: 6000000 INFO @ Thu, 16 Apr 2020 04:29:16: 11000000 INFO @ Thu, 16 Apr 2020 04:29:17: 3000000 INFO @ Thu, 16 Apr 2020 04:29:20: 7000000 INFO @ Thu, 16 Apr 2020 04:29:24: 12000000 INFO @ Thu, 16 Apr 2020 04:29:25: 4000000 INFO @ Thu, 16 Apr 2020 04:29:28: 8000000 INFO @ Thu, 16 Apr 2020 04:29:33: 13000000 INFO @ Thu, 16 Apr 2020 04:29:34: 5000000 INFO @ Thu, 16 Apr 2020 04:29:36: 9000000 INFO @ Thu, 16 Apr 2020 04:29:41: 14000000 INFO @ Thu, 16 Apr 2020 04:29:42: 6000000 INFO @ Thu, 16 Apr 2020 04:29:45: 10000000 INFO @ Thu, 16 Apr 2020 04:29:49: 15000000 INFO @ Thu, 16 Apr 2020 04:29:51: 7000000 INFO @ Thu, 16 Apr 2020 04:29:53: 11000000 INFO @ Thu, 16 Apr 2020 04:29:58: 16000000 INFO @ Thu, 16 Apr 2020 04:30:00: 8000000 INFO @ Thu, 16 Apr 2020 04:30:02: 12000000 INFO @ Thu, 16 Apr 2020 04:30:06: 17000000 INFO @ Thu, 16 Apr 2020 04:30:08: 9000000 INFO @ Thu, 16 Apr 2020 04:30:10: 13000000 INFO @ Thu, 16 Apr 2020 04:30:14: 18000000 INFO @ Thu, 16 Apr 2020 04:30:17: 10000000 INFO @ Thu, 16 Apr 2020 04:30:19: 14000000 INFO @ Thu, 16 Apr 2020 04:30:23: 19000000 INFO @ Thu, 16 Apr 2020 04:30:25: 11000000 INFO @ Thu, 16 Apr 2020 04:30:28: 15000000 INFO @ Thu, 16 Apr 2020 04:30:31: 20000000 INFO @ Thu, 16 Apr 2020 04:30:33: 12000000 INFO @ Thu, 16 Apr 2020 04:30:36: 16000000 INFO @ Thu, 16 Apr 2020 04:30:40: 21000000 INFO @ Thu, 16 Apr 2020 04:30:42: 13000000 INFO @ Thu, 16 Apr 2020 04:30:45: 17000000 INFO @ Thu, 16 Apr 2020 04:30:48: 22000000 INFO @ Thu, 16 Apr 2020 04:30:51: 14000000 INFO @ Thu, 16 Apr 2020 04:30:54: 18000000 INFO @ Thu, 16 Apr 2020 04:30:56: 23000000 INFO @ Thu, 16 Apr 2020 04:30:59: 15000000 INFO @ Thu, 16 Apr 2020 04:31:03: 19000000 INFO @ Thu, 16 Apr 2020 04:31:05: 24000000 INFO @ Thu, 16 Apr 2020 04:31:08: 16000000 INFO @ Thu, 16 Apr 2020 04:31:13: 20000000 INFO @ Thu, 16 Apr 2020 04:31:15: 25000000 INFO @ Thu, 16 Apr 2020 04:31:18: 17000000 INFO @ Thu, 16 Apr 2020 04:31:22: 21000000 INFO @ Thu, 16 Apr 2020 04:31:24: 26000000 INFO @ Thu, 16 Apr 2020 04:31:27: 18000000 INFO @ Thu, 16 Apr 2020 04:31:32: 22000000 INFO @ Thu, 16 Apr 2020 04:31:33: 27000000 INFO @ Thu, 16 Apr 2020 04:31:37: 19000000 INFO @ Thu, 16 Apr 2020 04:31:41: 23000000 INFO @ Thu, 16 Apr 2020 04:31:42: 28000000 INFO @ Thu, 16 Apr 2020 04:31:46: 20000000 INFO @ Thu, 16 Apr 2020 04:31:50: 24000000 INFO @ Thu, 16 Apr 2020 04:31:51: 29000000 INFO @ Thu, 16 Apr 2020 04:31:55: 21000000 INFO @ Thu, 16 Apr 2020 04:32:00: 25000000 INFO @ Thu, 16 Apr 2020 04:32:00: 30000000 INFO @ Thu, 16 Apr 2020 04:32:04: 22000000 INFO @ Thu, 16 Apr 2020 04:32:09: 26000000 INFO @ Thu, 16 Apr 2020 04:32:09: 31000000 INFO @ Thu, 16 Apr 2020 04:32:13: 23000000 INFO @ Thu, 16 Apr 2020 04:32:18: 32000000 INFO @ Thu, 16 Apr 2020 04:32:18: 27000000 INFO @ Thu, 16 Apr 2020 04:32:22: 24000000 INFO @ Thu, 16 Apr 2020 04:32:26: 33000000 INFO @ Thu, 16 Apr 2020 04:32:27: 28000000 INFO @ Thu, 16 Apr 2020 04:32:31: 25000000 INFO @ Thu, 16 Apr 2020 04:32:35: 34000000 INFO @ Thu, 16 Apr 2020 04:32:36: 29000000 INFO @ Thu, 16 Apr 2020 04:32:40: 26000000 INFO @ Thu, 16 Apr 2020 04:32:43: 35000000 INFO @ Thu, 16 Apr 2020 04:32:45: 30000000 INFO @ Thu, 16 Apr 2020 04:32:48: 27000000 INFO @ Thu, 16 Apr 2020 04:32:52: 36000000 INFO @ Thu, 16 Apr 2020 04:32:54: 31000000 INFO @ Thu, 16 Apr 2020 04:32:57: 28000000 INFO @ Thu, 16 Apr 2020 04:33:01: 37000000 INFO @ Thu, 16 Apr 2020 04:33:03: 32000000 INFO @ Thu, 16 Apr 2020 04:33:06: 29000000 INFO @ Thu, 16 Apr 2020 04:33:10: 38000000 INFO @ Thu, 16 Apr 2020 04:33:12: 33000000 INFO @ Thu, 16 Apr 2020 04:33:15: 30000000 INFO @ Thu, 16 Apr 2020 04:33:19: 39000000 INFO @ Thu, 16 Apr 2020 04:33:21: 34000000 INFO @ Thu, 16 Apr 2020 04:33:24: 31000000 INFO @ Thu, 16 Apr 2020 04:33:24: #1 tag size is determined as 101 bps INFO @ Thu, 16 Apr 2020 04:33:24: #1 tag size = 101 INFO @ Thu, 16 Apr 2020 04:33:24: #1 total tags in treatment: 15476918 INFO @ Thu, 16 Apr 2020 04:33:24: #1 user defined the maximum tags... INFO @ Thu, 16 Apr 2020 04:33:24: #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 04:33:25: #1 tags after filtering in treatment: 13153782 INFO @ Thu, 16 Apr 2020 04:33:25: #1 Redundant rate of treatment: 0.15 INFO @ Thu, 16 Apr 2020 04:33:25: #1 finished! INFO @ Thu, 16 Apr 2020 04:33:25: #2 Build Peak Model... INFO @ Thu, 16 Apr 2020 04:33:25: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 16 Apr 2020 04:33:26: #2 number of paired peaks: 2974 INFO @ Thu, 16 Apr 2020 04:33:26: start model_add_line... INFO @ Thu, 16 Apr 2020 04:33:26: start X-correlation... INFO @ Thu, 16 Apr 2020 04:33:26: end of X-cor INFO @ Thu, 16 Apr 2020 04:33:26: #2 finished! INFO @ Thu, 16 Apr 2020 04:33:26: #2 predicted fragment length is 220 bps INFO @ Thu, 16 Apr 2020 04:33:26: #2 alternative fragment length(s) may be 220 bps INFO @ Thu, 16 Apr 2020 04:33:26: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX5246877/SRX5246877.05_model.r INFO @ Thu, 16 Apr 2020 04:33:26: #3 Call peaks... INFO @ Thu, 16 Apr 2020 04:33:26: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 16 Apr 2020 04:33:30: 35000000 INFO @ Thu, 16 Apr 2020 04:33:32: 32000000 INFO @ Thu, 16 Apr 2020 04:33:38: 36000000 INFO @ Thu, 16 Apr 2020 04:33:41: 33000000 INFO @ Thu, 16 Apr 2020 04:33:48: 37000000 INFO @ Thu, 16 Apr 2020 04:33:49: 34000000 INFO @ Thu, 16 Apr 2020 04:33:57: 38000000 INFO @ Thu, 16 Apr 2020 04:33:58: 35000000 INFO @ Thu, 16 Apr 2020 04:33:59: #3 Call peaks for each chromosome... INFO @ Thu, 16 Apr 2020 04:34:06: 39000000 INFO @ Thu, 16 Apr 2020 04:34:07: 36000000 INFO @ Thu, 16 Apr 2020 04:34:11: #1 tag size is determined as 101 bps INFO @ Thu, 16 Apr 2020 04:34:11: #1 tag size = 101 INFO @ Thu, 16 Apr 2020 04:34:11: #1 total tags in treatment: 15476918 INFO @ Thu, 16 Apr 2020 04:34:11: #1 user defined the maximum tags... INFO @ Thu, 16 Apr 2020 04:34:11: #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 04:34:12: #1 tags after filtering in treatment: 13153782 INFO @ Thu, 16 Apr 2020 04:34:12: #1 Redundant rate of treatment: 0.15 INFO @ Thu, 16 Apr 2020 04:34:12: #1 finished! INFO @ Thu, 16 Apr 2020 04:34:12: #2 Build Peak Model... INFO @ Thu, 16 Apr 2020 04:34:12: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 16 Apr 2020 04:34:13: #2 number of paired peaks: 2974 INFO @ Thu, 16 Apr 2020 04:34:13: start model_add_line... INFO @ Thu, 16 Apr 2020 04:34:13: start X-correlation... INFO @ Thu, 16 Apr 2020 04:34:13: end of X-cor INFO @ Thu, 16 Apr 2020 04:34:13: #2 finished! INFO @ Thu, 16 Apr 2020 04:34:13: #2 predicted fragment length is 220 bps INFO @ Thu, 16 Apr 2020 04:34:13: #2 alternative fragment length(s) may be 220 bps INFO @ Thu, 16 Apr 2020 04:34:13: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX5246877/SRX5246877.10_model.r INFO @ Thu, 16 Apr 2020 04:34:13: #3 Call peaks... INFO @ Thu, 16 Apr 2020 04:34:13: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 16 Apr 2020 04:34:15: 37000000 INFO @ Thu, 16 Apr 2020 04:34:17: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX5246877/SRX5246877.05_peaks.xls INFO @ Thu, 16 Apr 2020 04:34:17: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX5246877/SRX5246877.05_peaks.narrowPeak INFO @ Thu, 16 Apr 2020 04:34:17: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX5246877/SRX5246877.05_summits.bed INFO @ Thu, 16 Apr 2020 04:34:17: Done! pass1 - making usageList (14 chroms): 2 millis pass2 - checking and writing primary data (15165 records, 4 fields): 14 millis CompletedMACS2peakCalling INFO @ Thu, 16 Apr 2020 04:34:24: 38000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Thu, 16 Apr 2020 04:34:32: 39000000 INFO @ Thu, 16 Apr 2020 04:34:37: #1 tag size is determined as 101 bps INFO @ Thu, 16 Apr 2020 04:34:37: #1 tag size = 101 INFO @ Thu, 16 Apr 2020 04:34:37: #1 total tags in treatment: 15476918 INFO @ Thu, 16 Apr 2020 04:34:37: #1 user defined the maximum tags... INFO @ Thu, 16 Apr 2020 04:34:37: #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 04:34:37: #1 tags after filtering in treatment: 13153782 INFO @ Thu, 16 Apr 2020 04:34:37: #1 Redundant rate of treatment: 0.15 INFO @ Thu, 16 Apr 2020 04:34:37: #1 finished! INFO @ Thu, 16 Apr 2020 04:34:37: #2 Build Peak Model... INFO @ Thu, 16 Apr 2020 04:34:37: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 16 Apr 2020 04:34:38: #2 number of paired peaks: 2974 INFO @ Thu, 16 Apr 2020 04:34:38: start model_add_line... INFO @ Thu, 16 Apr 2020 04:34:38: start X-correlation... INFO @ Thu, 16 Apr 2020 04:34:38: end of X-cor INFO @ Thu, 16 Apr 2020 04:34:38: #2 finished! INFO @ Thu, 16 Apr 2020 04:34:38: #2 predicted fragment length is 220 bps INFO @ Thu, 16 Apr 2020 04:34:38: #2 alternative fragment length(s) may be 220 bps INFO @ Thu, 16 Apr 2020 04:34:38: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX5246877/SRX5246877.20_model.r INFO @ Thu, 16 Apr 2020 04:34:38: #3 Call peaks... INFO @ Thu, 16 Apr 2020 04:34:38: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 16 Apr 2020 04:34:46: #3 Call peaks for each chromosome... INFO @ Thu, 16 Apr 2020 04:35:03: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX5246877/SRX5246877.10_peaks.xls INFO @ Thu, 16 Apr 2020 04:35:03: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX5246877/SRX5246877.10_peaks.narrowPeak INFO @ Thu, 16 Apr 2020 04:35:04: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX5246877/SRX5246877.10_summits.bed INFO @ Thu, 16 Apr 2020 04:35:04: Done! pass1 - making usageList (14 chroms): 2 millis pass2 - checking and writing primary data (10133 records, 4 fields): 10 millis CompletedMACS2peakCalling INFO @ Thu, 16 Apr 2020 04:35:12: #3 Call peaks for each chromosome... BigWig に変換しました。 INFO @ Thu, 16 Apr 2020 04:35:28: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX5246877/SRX5246877.20_peaks.xls INFO @ Thu, 16 Apr 2020 04:35:28: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX5246877/SRX5246877.20_peaks.narrowPeak INFO @ Thu, 16 Apr 2020 04:35:28: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX5246877/SRX5246877.20_summits.bed INFO @ Thu, 16 Apr 2020 04:35:28: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (5673 records, 4 fields): 7 millis CompletedMACS2peakCalling