Job ID = 1293637 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 30,131,820 reads read : 30,131,820 reads written : 30,131,820 rm: cannot remove ‘[DSE]RR*’: No such file or directory rm: cannot remove ‘fastqDump_tmp*’: 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: 00:12:45 30131820 reads; of these: 30131820 (100.00%) were unpaired; of these: 750312 (2.49%) aligned 0 times 21526785 (71.44%) aligned exactly 1 time 7854723 (26.07%) aligned >1 times 97.51% overall alignment rate Time searching: 00:12:45 Overall time: 00:12:45 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 12 files... [bam_rmdupse_core] 4841327 / 29381508 = 0.1648 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, 03 Jun 2019 01:36:42: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX1032411/SRX1032411.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX1032411/SRX1032411.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX1032411/SRX1032411.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX1032411/SRX1032411.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, 03 Jun 2019 01:36:42: #1 read tag files... INFO @ Mon, 03 Jun 2019 01:36:42: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 01:36:42: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX1032411/SRX1032411.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX1032411/SRX1032411.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX1032411/SRX1032411.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX1032411/SRX1032411.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, 03 Jun 2019 01:36:42: #1 read tag files... INFO @ Mon, 03 Jun 2019 01:36:42: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 01:36:42: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX1032411/SRX1032411.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX1032411/SRX1032411.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX1032411/SRX1032411.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX1032411/SRX1032411.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, 03 Jun 2019 01:36:42: #1 read tag files... INFO @ Mon, 03 Jun 2019 01:36:42: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 01:36:50: 1000000 INFO @ Mon, 03 Jun 2019 01:36:50: 1000000 INFO @ Mon, 03 Jun 2019 01:36:51: 1000000 INFO @ Mon, 03 Jun 2019 01:36:58: 2000000 INFO @ Mon, 03 Jun 2019 01:36:58: 2000000 INFO @ Mon, 03 Jun 2019 01:36:59: 2000000 INFO @ Mon, 03 Jun 2019 01:37:05: 3000000 INFO @ Mon, 03 Jun 2019 01:37:05: 3000000 INFO @ Mon, 03 Jun 2019 01:37:07: 3000000 INFO @ Mon, 03 Jun 2019 01:37:13: 4000000 INFO @ Mon, 03 Jun 2019 01:37:13: 4000000 INFO @ Mon, 03 Jun 2019 01:37:15: 4000000 INFO @ Mon, 03 Jun 2019 01:37:20: 5000000 INFO @ Mon, 03 Jun 2019 01:37:20: 5000000 INFO @ Mon, 03 Jun 2019 01:37:23: 5000000 INFO @ Mon, 03 Jun 2019 01:37:28: 6000000 INFO @ Mon, 03 Jun 2019 01:37:28: 6000000 INFO @ Mon, 03 Jun 2019 01:37:31: 6000000 INFO @ Mon, 03 Jun 2019 01:37:35: 7000000 INFO @ Mon, 03 Jun 2019 01:37:35: 7000000 INFO @ Mon, 03 Jun 2019 01:37:39: 7000000 INFO @ Mon, 03 Jun 2019 01:37:42: 8000000 INFO @ Mon, 03 Jun 2019 01:37:43: 8000000 INFO @ Mon, 03 Jun 2019 01:37:48: 8000000 INFO @ Mon, 03 Jun 2019 01:37:50: 9000000 INFO @ Mon, 03 Jun 2019 01:37:51: 9000000 INFO @ Mon, 03 Jun 2019 01:37:56: 9000000 INFO @ Mon, 03 Jun 2019 01:37:57: 10000000 INFO @ Mon, 03 Jun 2019 01:37:58: 10000000 INFO @ Mon, 03 Jun 2019 01:38:04: 10000000 INFO @ Mon, 03 Jun 2019 01:38:04: 11000000 INFO @ Mon, 03 Jun 2019 01:38:06: 11000000 INFO @ Mon, 03 Jun 2019 01:38:11: 12000000 INFO @ Mon, 03 Jun 2019 01:38:12: 11000000 INFO @ Mon, 03 Jun 2019 01:38:13: 12000000 INFO @ Mon, 03 Jun 2019 01:38:19: 13000000 INFO @ Mon, 03 Jun 2019 01:38:20: 12000000 INFO @ Mon, 03 Jun 2019 01:38:20: 13000000 INFO @ Mon, 03 Jun 2019 01:38:26: 14000000 INFO @ Mon, 03 Jun 2019 01:38:28: 14000000 INFO @ Mon, 03 Jun 2019 01:38:29: 13000000 INFO @ Mon, 03 Jun 2019 01:38:33: 15000000 INFO @ Mon, 03 Jun 2019 01:38:35: 15000000 INFO @ Mon, 03 Jun 2019 01:38:37: 14000000 INFO @ Mon, 03 Jun 2019 01:38:40: 16000000 INFO @ Mon, 03 Jun 2019 01:38:43: 16000000 INFO @ Mon, 03 Jun 2019 01:38:45: 15000000 INFO @ Mon, 03 Jun 2019 01:38:47: 17000000 INFO @ Mon, 03 Jun 2019 01:38:50: 17000000 INFO @ Mon, 03 Jun 2019 01:38:53: 16000000 INFO @ Mon, 03 Jun 2019 01:38:54: 18000000 INFO @ Mon, 03 Jun 2019 01:38:57: 18000000 INFO @ Mon, 03 Jun 2019 01:39:01: 17000000 INFO @ Mon, 03 Jun 2019 01:39:01: 19000000 INFO @ Mon, 03 Jun 2019 01:39:04: 19000000 INFO @ Mon, 03 Jun 2019 01:39:08: 20000000 INFO @ Mon, 03 Jun 2019 01:39:09: 18000000 INFO @ Mon, 03 Jun 2019 01:39:12: 20000000 INFO @ Mon, 03 Jun 2019 01:39:15: 21000000 INFO @ Mon, 03 Jun 2019 01:39:17: 19000000 INFO @ Mon, 03 Jun 2019 01:39:19: 21000000 INFO @ Mon, 03 Jun 2019 01:39:22: 22000000 INFO @ Mon, 03 Jun 2019 01:39:25: 20000000 INFO @ Mon, 03 Jun 2019 01:39:26: 22000000 INFO @ Mon, 03 Jun 2019 01:39:30: 23000000 INFO @ Mon, 03 Jun 2019 01:39:33: 21000000 INFO @ Mon, 03 Jun 2019 01:39:34: 23000000 INFO @ Mon, 03 Jun 2019 01:39:38: 24000000 INFO @ Mon, 03 Jun 2019 01:39:41: 22000000 INFO @ Mon, 03 Jun 2019 01:39:42: 24000000 INFO @ Mon, 03 Jun 2019 01:39:42: #1 tag size is determined as 51 bps INFO @ Mon, 03 Jun 2019 01:39:42: #1 tag size = 51 INFO @ Mon, 03 Jun 2019 01:39:42: #1 total tags in treatment: 24540181 INFO @ Mon, 03 Jun 2019 01:39:42: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 01:39:42: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Mon, 03 Jun 2019 01:39:43: #1 tags after filtering in treatment: 24540181 INFO @ Mon, 03 Jun 2019 01:39:43: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 01:39:43: #1 finished! INFO @ Mon, 03 Jun 2019 01:39:43: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 01:39:43: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 01:39:45: #2 number of paired peaks: 979 WARNING @ Mon, 03 Jun 2019 01:39:45: Fewer paired peaks (979) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 979 pairs to build model! INFO @ Mon, 03 Jun 2019 01:39:45: start model_add_line... INFO @ Mon, 03 Jun 2019 01:39:45: start X-correlation... INFO @ Mon, 03 Jun 2019 01:39:45: end of X-cor INFO @ Mon, 03 Jun 2019 01:39:45: #2 finished! INFO @ Mon, 03 Jun 2019 01:39:45: #2 predicted fragment length is 117 bps INFO @ Mon, 03 Jun 2019 01:39:45: #2 alternative fragment length(s) may be 4,117 bps INFO @ Mon, 03 Jun 2019 01:39:45: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX1032411/SRX1032411.20_model.r INFO @ Mon, 03 Jun 2019 01:39:45: #3 Call peaks... INFO @ Mon, 03 Jun 2019 01:39:45: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 01:39:46: #1 tag size is determined as 51 bps INFO @ Mon, 03 Jun 2019 01:39:46: #1 tag size = 51 INFO @ Mon, 03 Jun 2019 01:39:46: #1 total tags in treatment: 24540181 INFO @ Mon, 03 Jun 2019 01:39:46: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 01:39:46: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Mon, 03 Jun 2019 01:39:47: #1 tags after filtering in treatment: 24540181 INFO @ Mon, 03 Jun 2019 01:39:47: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 01:39:47: #1 finished! INFO @ Mon, 03 Jun 2019 01:39:47: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 01:39:47: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 01:39:49: #2 number of paired peaks: 979 WARNING @ Mon, 03 Jun 2019 01:39:49: Fewer paired peaks (979) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 979 pairs to build model! INFO @ Mon, 03 Jun 2019 01:39:49: start model_add_line... INFO @ Mon, 03 Jun 2019 01:39:49: 23000000 INFO @ Mon, 03 Jun 2019 01:39:49: start X-correlation... INFO @ Mon, 03 Jun 2019 01:39:49: end of X-cor INFO @ Mon, 03 Jun 2019 01:39:49: #2 finished! INFO @ Mon, 03 Jun 2019 01:39:49: #2 predicted fragment length is 117 bps INFO @ Mon, 03 Jun 2019 01:39:49: #2 alternative fragment length(s) may be 4,117 bps INFO @ Mon, 03 Jun 2019 01:39:49: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX1032411/SRX1032411.05_model.r INFO @ Mon, 03 Jun 2019 01:39:49: #3 Call peaks... INFO @ Mon, 03 Jun 2019 01:39:49: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 01:39:57: 24000000 INFO @ Mon, 03 Jun 2019 01:40:02: #1 tag size is determined as 51 bps INFO @ Mon, 03 Jun 2019 01:40:02: #1 tag size = 51 INFO @ Mon, 03 Jun 2019 01:40:02: #1 total tags in treatment: 24540181 INFO @ Mon, 03 Jun 2019 01:40:02: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 01:40:02: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Mon, 03 Jun 2019 01:40:02: #1 tags after filtering in treatment: 24540181 INFO @ Mon, 03 Jun 2019 01:40:02: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 01:40:02: #1 finished! INFO @ Mon, 03 Jun 2019 01:40:02: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 01:40:02: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 01:40:05: #2 number of paired peaks: 979 WARNING @ Mon, 03 Jun 2019 01:40:05: Fewer paired peaks (979) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 979 pairs to build model! INFO @ Mon, 03 Jun 2019 01:40:05: start model_add_line... INFO @ Mon, 03 Jun 2019 01:40:05: start X-correlation... INFO @ Mon, 03 Jun 2019 01:40:05: end of X-cor INFO @ Mon, 03 Jun 2019 01:40:05: #2 finished! INFO @ Mon, 03 Jun 2019 01:40:05: #2 predicted fragment length is 117 bps INFO @ Mon, 03 Jun 2019 01:40:05: #2 alternative fragment length(s) may be 4,117 bps INFO @ Mon, 03 Jun 2019 01:40:05: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX1032411/SRX1032411.10_model.r INFO @ Mon, 03 Jun 2019 01:40:05: #3 Call peaks... INFO @ Mon, 03 Jun 2019 01:40:05: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 01:40:53: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 01:40:58: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 01:41:12: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 01:41:25: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX1032411/SRX1032411.20_peaks.xls INFO @ Mon, 03 Jun 2019 01:41:25: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX1032411/SRX1032411.20_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 01:41:25: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX1032411/SRX1032411.20_summits.bed INFO @ Mon, 03 Jun 2019 01:41:25: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (1195 records, 4 fields): 6 millis CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 01:41:31: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX1032411/SRX1032411.05_peaks.xls INFO @ Mon, 03 Jun 2019 01:41:31: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX1032411/SRX1032411.05_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 01:41:31: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX1032411/SRX1032411.05_summits.bed INFO @ Mon, 03 Jun 2019 01:41:31: Done! pass1 - making usageList (15 chroms): 2 millis pass2 - checking and writing primary data (6069 records, 4 fields): 226 millis CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 01:41:44: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX1032411/SRX1032411.10_peaks.xls INFO @ Mon, 03 Jun 2019 01:41:44: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX1032411/SRX1032411.10_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 01:41:44: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX1032411/SRX1032411.10_summits.bed INFO @ Mon, 03 Jun 2019 01:41:44: Done! pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (2857 records, 4 fields): 1191 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。