Job ID = 2590501 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 12,119,326 reads read : 24,238,652 reads written : 12,119,326 reads 0-length : 12,119,326 spots read : 12,265,875 reads read : 24,531,750 reads written : 12,265,875 reads 0-length : 12,265,875 spots read : 12,323,029 reads read : 24,646,058 reads written : 12,323,029 reads 0-length : 12,323,029 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: 00:12:20 36708230 reads; of these: 36708230 (100.00%) were unpaired; of these: 925804 (2.52%) aligned 0 times 27642330 (75.30%) aligned exactly 1 time 8140096 (22.18%) aligned >1 times 97.48% overall alignment rate Time searching: 00:12:20 Overall time: 00:12:20 マッピングが完了しました。 samtools でBAM に変換中... [samopen] SAM header is present: 15 sequences. [bam_sort_core] merging from 16 files... [bam_rmdupse_core] 12937207 / 35782426 = 0.3616 in library ' ' BAM に変換しました。 Bed ファイルを作成中... BedGraph に変換中... INFO @ Mon, 12 Aug 2019 22:35:44: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX3981728/SRX3981728.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX3981728/SRX3981728.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX3981728/SRX3981728.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX3981728/SRX3981728.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 @ Mon, 12 Aug 2019 22:35:44: #1 read tag files... INFO @ Mon, 12 Aug 2019 22:35:44: #1 read treatment tags... INFO @ Mon, 12 Aug 2019 22:35:45: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX3981728/SRX3981728.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX3981728/SRX3981728.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX3981728/SRX3981728.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX3981728/SRX3981728.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 @ Mon, 12 Aug 2019 22:35:45: #1 read tag files... INFO @ Mon, 12 Aug 2019 22:35:45: #1 read treatment tags... INFO @ Mon, 12 Aug 2019 22:35:46: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX3981728/SRX3981728.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX3981728/SRX3981728.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX3981728/SRX3981728.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX3981728/SRX3981728.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 @ Mon, 12 Aug 2019 22:35:46: #1 read tag files... INFO @ Mon, 12 Aug 2019 22:35:46: #1 read treatment tags... INFO @ Mon, 12 Aug 2019 22:35:51: 1000000 INFO @ Mon, 12 Aug 2019 22:35:54: 1000000 INFO @ Mon, 12 Aug 2019 22:35:55: 1000000 INFO @ Mon, 12 Aug 2019 22:35:58: 2000000 INFO @ Mon, 12 Aug 2019 22:36:03: 2000000 INFO @ Mon, 12 Aug 2019 22:36:04: 2000000 INFO @ Mon, 12 Aug 2019 22:36:05: 3000000 INFO @ Mon, 12 Aug 2019 22:36:11: 4000000 INFO @ Mon, 12 Aug 2019 22:36:12: 3000000 INFO @ Mon, 12 Aug 2019 22:36:12: 3000000 INFO @ Mon, 12 Aug 2019 22:36:18: 5000000 INFO @ Mon, 12 Aug 2019 22:36:20: 4000000 INFO @ Mon, 12 Aug 2019 22:36:21: 4000000 INFO @ Mon, 12 Aug 2019 22:36:24: 6000000 INFO @ Mon, 12 Aug 2019 22:36:29: 5000000 INFO @ Mon, 12 Aug 2019 22:36:30: 5000000 INFO @ Mon, 12 Aug 2019 22:36:31: 7000000 INFO @ Mon, 12 Aug 2019 22:36:37: 8000000 INFO @ Mon, 12 Aug 2019 22:36:37: 6000000 INFO @ Mon, 12 Aug 2019 22:36:38: 6000000 INFO @ Mon, 12 Aug 2019 22:36:43: 9000000 INFO @ Mon, 12 Aug 2019 22:36:46: 7000000 INFO @ Mon, 12 Aug 2019 22:36:47: 7000000 INFO @ Mon, 12 Aug 2019 22:36:50: 10000000 INFO @ Mon, 12 Aug 2019 22:36:54: 8000000 INFO @ Mon, 12 Aug 2019 22:36:55: 8000000 INFO @ Mon, 12 Aug 2019 22:36:56: 11000000 INFO @ Mon, 12 Aug 2019 22:37:02: 9000000 INFO @ Mon, 12 Aug 2019 22:37:03: 12000000 INFO @ Mon, 12 Aug 2019 22:37:03: 9000000 INFO @ Mon, 12 Aug 2019 22:37:09: 13000000 INFO @ Mon, 12 Aug 2019 22:37:11: 10000000 INFO @ Mon, 12 Aug 2019 22:37:12: 10000000 INFO @ Mon, 12 Aug 2019 22:37:16: 14000000 INFO @ Mon, 12 Aug 2019 22:37:19: 11000000 INFO @ Mon, 12 Aug 2019 22:37:20: 11000000 INFO @ Mon, 12 Aug 2019 22:37:22: 15000000 INFO @ Mon, 12 Aug 2019 22:37:28: 12000000 INFO @ Mon, 12 Aug 2019 22:37:28: 12000000 INFO @ Mon, 12 Aug 2019 22:37:29: 16000000 INFO @ Mon, 12 Aug 2019 22:37:36: 17000000 INFO @ Mon, 12 Aug 2019 22:37:36: 13000000 INFO @ Mon, 12 Aug 2019 22:37:37: 13000000 INFO @ Mon, 12 Aug 2019 22:37:43: 18000000 INFO @ Mon, 12 Aug 2019 22:37:44: 14000000 INFO @ Mon, 12 Aug 2019 22:37:45: 14000000 INFO @ Mon, 12 Aug 2019 22:37:50: 19000000 INFO @ Mon, 12 Aug 2019 22:37:54: 15000000 INFO @ Mon, 12 Aug 2019 22:37:54: 15000000 INFO @ Mon, 12 Aug 2019 22:37:56: 20000000 INFO @ Mon, 12 Aug 2019 22:38:02: 16000000 INFO @ Mon, 12 Aug 2019 22:38:02: 21000000 INFO @ Mon, 12 Aug 2019 22:38:03: 16000000 INFO @ Mon, 12 Aug 2019 22:38:09: 22000000 INFO @ Mon, 12 Aug 2019 22:38:11: 17000000 INFO @ Mon, 12 Aug 2019 22:38:12: 17000000 INFO @ Mon, 12 Aug 2019 22:38:15: #1 tag size is determined as 51 bps INFO @ Mon, 12 Aug 2019 22:38:15: #1 tag size = 51 INFO @ Mon, 12 Aug 2019 22:38:15: #1 total tags in treatment: 22845219 INFO @ Mon, 12 Aug 2019 22:38:15: #1 user defined the maximum tags... INFO @ Mon, 12 Aug 2019 22:38:15: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Mon, 12 Aug 2019 22:38:15: #1 tags after filtering in treatment: 22845219 INFO @ Mon, 12 Aug 2019 22:38:15: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 12 Aug 2019 22:38:15: #1 finished! INFO @ Mon, 12 Aug 2019 22:38:15: #2 Build Peak Model... INFO @ Mon, 12 Aug 2019 22:38:15: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 12 Aug 2019 22:38:18: #2 number of paired peaks: 4256 INFO @ Mon, 12 Aug 2019 22:38:18: start model_add_line... INFO @ Mon, 12 Aug 2019 22:38:18: start X-correlation... INFO @ Mon, 12 Aug 2019 22:38:18: end of X-cor INFO @ Mon, 12 Aug 2019 22:38:18: #2 finished! INFO @ Mon, 12 Aug 2019 22:38:18: #2 predicted fragment length is 216 bps INFO @ Mon, 12 Aug 2019 22:38:18: #2 alternative fragment length(s) may be 216 bps INFO @ Mon, 12 Aug 2019 22:38:18: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX3981728/SRX3981728.05_model.r INFO @ Mon, 12 Aug 2019 22:38:18: #3 Call peaks... INFO @ Mon, 12 Aug 2019 22:38:18: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 12 Aug 2019 22:38:20: 18000000 INFO @ Mon, 12 Aug 2019 22:38:21: 18000000 INFO @ Mon, 12 Aug 2019 22:38:30: 19000000 INFO @ Mon, 12 Aug 2019 22:38:30: 19000000 INFO @ Mon, 12 Aug 2019 22:38:39: 20000000 INFO @ Mon, 12 Aug 2019 22:38:39: 20000000 INFO @ Mon, 12 Aug 2019 22:38:47: 21000000 INFO @ Mon, 12 Aug 2019 22:38:48: 21000000 INFO @ Mon, 12 Aug 2019 22:38:55: 22000000 INFO @ Mon, 12 Aug 2019 22:38:56: 22000000 INFO @ Mon, 12 Aug 2019 22:39:04: #1 tag size is determined as 51 bps INFO @ Mon, 12 Aug 2019 22:39:04: #1 tag size = 51 INFO @ Mon, 12 Aug 2019 22:39:04: #1 total tags in treatment: 22845219 INFO @ Mon, 12 Aug 2019 22:39:04: #1 user defined the maximum tags... INFO @ Mon, 12 Aug 2019 22:39:04: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Mon, 12 Aug 2019 22:39:04: #1 tags after filtering in treatment: 22845219 INFO @ Mon, 12 Aug 2019 22:39:04: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 12 Aug 2019 22:39:04: #1 finished! INFO @ Mon, 12 Aug 2019 22:39:04: #2 Build Peak Model... INFO @ Mon, 12 Aug 2019 22:39:04: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 12 Aug 2019 22:39:04: #1 tag size is determined as 51 bps INFO @ Mon, 12 Aug 2019 22:39:04: #1 tag size = 51 INFO @ Mon, 12 Aug 2019 22:39:04: #1 total tags in treatment: 22845219 INFO @ Mon, 12 Aug 2019 22:39:04: #1 user defined the maximum tags... INFO @ Mon, 12 Aug 2019 22:39:04: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Mon, 12 Aug 2019 22:39:05: #1 tags after filtering in treatment: 22845219 INFO @ Mon, 12 Aug 2019 22:39:05: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 12 Aug 2019 22:39:05: #1 finished! INFO @ Mon, 12 Aug 2019 22:39:05: #2 Build Peak Model... INFO @ Mon, 12 Aug 2019 22:39:05: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 12 Aug 2019 22:39:07: #2 number of paired peaks: 4256 INFO @ Mon, 12 Aug 2019 22:39:07: start model_add_line... INFO @ Mon, 12 Aug 2019 22:39:07: start X-correlation... INFO @ Mon, 12 Aug 2019 22:39:07: end of X-cor INFO @ Mon, 12 Aug 2019 22:39:07: #2 finished! INFO @ Mon, 12 Aug 2019 22:39:07: #2 predicted fragment length is 216 bps INFO @ Mon, 12 Aug 2019 22:39:07: #2 alternative fragment length(s) may be 216 bps INFO @ Mon, 12 Aug 2019 22:39:07: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX3981728/SRX3981728.10_model.r INFO @ Mon, 12 Aug 2019 22:39:07: #3 Call peaks... INFO @ Mon, 12 Aug 2019 22:39:07: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 12 Aug 2019 22:39:07: #2 number of paired peaks: 4256 INFO @ Mon, 12 Aug 2019 22:39:07: start model_add_line... INFO @ Mon, 12 Aug 2019 22:39:08: start X-correlation... INFO @ Mon, 12 Aug 2019 22:39:08: end of X-cor INFO @ Mon, 12 Aug 2019 22:39:08: #2 finished! INFO @ Mon, 12 Aug 2019 22:39:08: #2 predicted fragment length is 216 bps INFO @ Mon, 12 Aug 2019 22:39:08: #2 alternative fragment length(s) may be 216 bps INFO @ Mon, 12 Aug 2019 22:39:08: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX3981728/SRX3981728.20_model.r INFO @ Mon, 12 Aug 2019 22:39:08: #3 Call peaks... INFO @ Mon, 12 Aug 2019 22:39:08: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 12 Aug 2019 22:39:38: #3 Call peaks for each chromosome... INFO @ Mon, 12 Aug 2019 22:40:05: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX3981728/SRX3981728.05_peaks.xls INFO @ Mon, 12 Aug 2019 22:40:05: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX3981728/SRX3981728.05_peaks.narrowPeak INFO @ Mon, 12 Aug 2019 22:40:05: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX3981728/SRX3981728.05_summits.bed INFO @ Mon, 12 Aug 2019 22:40:06: Done! pass1 - making usageList (15 chroms): 5 millis pass2 - checking and writing primary data (10279 records, 4 fields): 15 millis CompletedMACS2peakCalling INFO @ Mon, 12 Aug 2019 22:40:26: #3 Call peaks for each chromosome... INFO @ Mon, 12 Aug 2019 22:40:29: #3 Call peaks for each chromosome... INFO @ Mon, 12 Aug 2019 22:40:53: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX3981728/SRX3981728.10_peaks.xls INFO @ Mon, 12 Aug 2019 22:40:53: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX3981728/SRX3981728.10_peaks.narrowPeak INFO @ Mon, 12 Aug 2019 22:40:53: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX3981728/SRX3981728.10_summits.bed INFO @ Mon, 12 Aug 2019 22:40:53: Done! pass1 - making usageList (15 chroms): 4 millis pass2 - checking and writing primary data (8266 records, 4 fields): 13 millis CompletedMACS2peakCalling INFO @ Mon, 12 Aug 2019 22:40:57: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX3981728/SRX3981728.20_peaks.xls INFO @ Mon, 12 Aug 2019 22:40:58: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX3981728/SRX3981728.20_peaks.narrowPeak INFO @ Mon, 12 Aug 2019 22:40:58: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX3981728/SRX3981728.20_summits.bed INFO @ Mon, 12 Aug 2019 22:40:58: Done! pass1 - making usageList (15 chroms): 3 millis pass2 - checking and writing primary data (6125 records, 4 fields): 12 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。