Job ID = 1293655 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 23,835,354 reads read : 23,835,354 reads written : 23,835,354 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: 00:06:42 23835354 reads; of these: 23835354 (100.00%) were unpaired; of these: 940054 (3.94%) aligned 0 times 17142021 (71.92%) aligned exactly 1 time 5753279 (24.14%) aligned >1 times 96.06% overall alignment rate Time searching: 00:06:42 Overall time: 00:06:42 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 8 files... [bam_rmdupse_core] 2769172 / 22895300 = 0.1209 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 01:37:00: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX104968/SRX104968.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX104968/SRX104968.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX104968/SRX104968.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX104968/SRX104968.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 01:37:00: #1 read tag files... INFO @ Mon, 03 Jun 2019 01:37:00: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 01:37:00: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX104968/SRX104968.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX104968/SRX104968.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX104968/SRX104968.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX104968/SRX104968.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 01:37:00: #1 read tag files... INFO @ Mon, 03 Jun 2019 01:37:00: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 01:37:00: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX104968/SRX104968.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX104968/SRX104968.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX104968/SRX104968.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX104968/SRX104968.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 01:37:00: #1 read tag files... INFO @ Mon, 03 Jun 2019 01:37:00: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 01:37:07: 1000000 INFO @ Mon, 03 Jun 2019 01:37:08: 1000000 INFO @ Mon, 03 Jun 2019 01:37:09: 1000000 INFO @ Mon, 03 Jun 2019 01:37:14: 2000000 INFO @ Mon, 03 Jun 2019 01:37:15: 2000000 INFO @ Mon, 03 Jun 2019 01:37:18: 2000000 INFO @ Mon, 03 Jun 2019 01:37:20: 3000000 INFO @ Mon, 03 Jun 2019 01:37:22: 3000000 INFO @ Mon, 03 Jun 2019 01:37:26: 3000000 INFO @ Mon, 03 Jun 2019 01:37:27: 4000000 INFO @ Mon, 03 Jun 2019 01:37:29: 4000000 INFO @ Mon, 03 Jun 2019 01:37:33: 5000000 INFO @ Mon, 03 Jun 2019 01:37:34: 4000000 INFO @ Mon, 03 Jun 2019 01:37:36: 5000000 INFO @ Mon, 03 Jun 2019 01:37:40: 6000000 INFO @ Mon, 03 Jun 2019 01:37:42: 5000000 INFO @ Mon, 03 Jun 2019 01:37:44: 6000000 INFO @ Mon, 03 Jun 2019 01:37:46: 7000000 INFO @ Mon, 03 Jun 2019 01:37:51: 6000000 INFO @ Mon, 03 Jun 2019 01:37:51: 7000000 INFO @ Mon, 03 Jun 2019 01:37:53: 8000000 INFO @ Mon, 03 Jun 2019 01:37:58: 8000000 INFO @ Mon, 03 Jun 2019 01:37:59: 7000000 INFO @ Mon, 03 Jun 2019 01:37:59: 9000000 INFO @ Mon, 03 Jun 2019 01:38:05: 9000000 INFO @ Mon, 03 Jun 2019 01:38:06: 10000000 INFO @ Mon, 03 Jun 2019 01:38:07: 8000000 INFO @ Mon, 03 Jun 2019 01:38:12: 11000000 INFO @ Mon, 03 Jun 2019 01:38:13: 10000000 INFO @ Mon, 03 Jun 2019 01:38:15: 9000000 INFO @ Mon, 03 Jun 2019 01:38:19: 12000000 INFO @ Mon, 03 Jun 2019 01:38:21: 11000000 INFO @ Mon, 03 Jun 2019 01:38:24: 10000000 INFO @ Mon, 03 Jun 2019 01:38:25: 13000000 INFO @ Mon, 03 Jun 2019 01:38:28: 12000000 INFO @ Mon, 03 Jun 2019 01:38:31: 14000000 INFO @ Mon, 03 Jun 2019 01:38:32: 11000000 INFO @ Mon, 03 Jun 2019 01:38:35: 13000000 INFO @ Mon, 03 Jun 2019 01:38:38: 15000000 INFO @ Mon, 03 Jun 2019 01:38:40: 12000000 INFO @ Mon, 03 Jun 2019 01:38:43: 14000000 INFO @ Mon, 03 Jun 2019 01:38:44: 16000000 INFO @ Mon, 03 Jun 2019 01:38:48: 13000000 INFO @ Mon, 03 Jun 2019 01:38:50: 15000000 INFO @ Mon, 03 Jun 2019 01:38:51: 17000000 INFO @ Mon, 03 Jun 2019 01:38:56: 14000000 INFO @ Mon, 03 Jun 2019 01:38:57: 18000000 INFO @ Mon, 03 Jun 2019 01:38:58: 16000000 INFO @ Mon, 03 Jun 2019 01:39:04: 19000000 INFO @ Mon, 03 Jun 2019 01:39:04: 15000000 INFO @ Mon, 03 Jun 2019 01:39:05: 17000000 INFO @ Mon, 03 Jun 2019 01:39:10: 20000000 INFO @ Mon, 03 Jun 2019 01:39:11: #1 tag size is determined as 40 bps INFO @ Mon, 03 Jun 2019 01:39:11: #1 tag size = 40 INFO @ Mon, 03 Jun 2019 01:39:11: #1 total tags in treatment: 20126128 INFO @ Mon, 03 Jun 2019 01:39:11: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 01:39:11: #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 01:39:12: #1 tags after filtering in treatment: 20126128 INFO @ Mon, 03 Jun 2019 01:39:12: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 01:39:12: #1 finished! INFO @ Mon, 03 Jun 2019 01:39:12: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 01:39:12: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 01:39:12: 18000000 INFO @ Mon, 03 Jun 2019 01:39:13: 16000000 INFO @ Mon, 03 Jun 2019 01:39:13: #2 number of paired peaks: 670 WARNING @ Mon, 03 Jun 2019 01:39:13: Fewer paired peaks (670) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 670 pairs to build model! INFO @ Mon, 03 Jun 2019 01:39:13: start model_add_line... INFO @ Mon, 03 Jun 2019 01:39:14: start X-correlation... INFO @ Mon, 03 Jun 2019 01:39:14: end of X-cor INFO @ Mon, 03 Jun 2019 01:39:14: #2 finished! INFO @ Mon, 03 Jun 2019 01:39:14: #2 predicted fragment length is 169 bps INFO @ Mon, 03 Jun 2019 01:39:14: #2 alternative fragment length(s) may be 2,169 bps INFO @ Mon, 03 Jun 2019 01:39:14: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX104968/SRX104968.20_model.r INFO @ Mon, 03 Jun 2019 01:39:14: #3 Call peaks... INFO @ Mon, 03 Jun 2019 01:39:14: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 01:39:20: 19000000 INFO @ Mon, 03 Jun 2019 01:39:21: 17000000 INFO @ Mon, 03 Jun 2019 01:39:27: 20000000 INFO @ Mon, 03 Jun 2019 01:39:28: #1 tag size is determined as 40 bps INFO @ Mon, 03 Jun 2019 01:39:28: #1 tag size = 40 INFO @ Mon, 03 Jun 2019 01:39:28: #1 total tags in treatment: 20126128 INFO @ Mon, 03 Jun 2019 01:39:28: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 01:39:28: #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 01:39:29: #1 tags after filtering in treatment: 20126128 INFO @ Mon, 03 Jun 2019 01:39:29: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 01:39:29: #1 finished! INFO @ Mon, 03 Jun 2019 01:39:29: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 01:39:29: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 01:39:29: 18000000 INFO @ Mon, 03 Jun 2019 01:39:30: #2 number of paired peaks: 670 WARNING @ Mon, 03 Jun 2019 01:39:30: Fewer paired peaks (670) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 670 pairs to build model! INFO @ Mon, 03 Jun 2019 01:39:30: start model_add_line... INFO @ Mon, 03 Jun 2019 01:39:31: start X-correlation... INFO @ Mon, 03 Jun 2019 01:39:31: end of X-cor INFO @ Mon, 03 Jun 2019 01:39:31: #2 finished! INFO @ Mon, 03 Jun 2019 01:39:31: #2 predicted fragment length is 169 bps INFO @ Mon, 03 Jun 2019 01:39:31: #2 alternative fragment length(s) may be 2,169 bps INFO @ Mon, 03 Jun 2019 01:39:31: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX104968/SRX104968.05_model.r INFO @ Mon, 03 Jun 2019 01:39:31: #3 Call peaks... INFO @ Mon, 03 Jun 2019 01:39:31: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 01:39:37: 19000000 INFO @ Mon, 03 Jun 2019 01:39:45: 20000000 INFO @ Mon, 03 Jun 2019 01:39:46: #1 tag size is determined as 40 bps INFO @ Mon, 03 Jun 2019 01:39:46: #1 tag size = 40 INFO @ Mon, 03 Jun 2019 01:39:46: #1 total tags in treatment: 20126128 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: 20126128 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 01:39:48: #2 number of paired peaks: 670 WARNING @ Mon, 03 Jun 2019 01:39:48: Fewer paired peaks (670) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 670 pairs to build model! INFO @ Mon, 03 Jun 2019 01:39:48: start model_add_line... 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 169 bps INFO @ Mon, 03 Jun 2019 01:39:49: #2 alternative fragment length(s) may be 2,169 bps INFO @ Mon, 03 Jun 2019 01:39:49: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX104968/SRX104968.10_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 01:40:10: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 01:40:27: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 01:40:35: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX104968/SRX104968.20_peaks.xls INFO @ Mon, 03 Jun 2019 01:40:35: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX104968/SRX104968.20_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 01:40:35: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX104968/SRX104968.20_summits.bed INFO @ Mon, 03 Jun 2019 01:40:35: Done! pass1 - making usageList (13 chroms): 1 millis pass2 - checking and writing primary data (154 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 01:40:45: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 01:40:53: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX104968/SRX104968.05_peaks.xls INFO @ Mon, 03 Jun 2019 01:40:53: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX104968/SRX104968.05_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 01:40:53: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX104968/SRX104968.05_summits.bed INFO @ Mon, 03 Jun 2019 01:40:53: Done! pass1 - making usageList (14 chroms): 2 millis pass2 - checking and writing primary data (1417 records, 4 fields): 7 millis CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 01:41:11: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX104968/SRX104968.10_peaks.xls INFO @ Mon, 03 Jun 2019 01:41:11: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX104968/SRX104968.10_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 01:41:11: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX104968/SRX104968.10_summits.bed INFO @ Mon, 03 Jun 2019 01:41:11: Done! pass1 - making usageList (13 chroms): 1 millis pass2 - checking and writing primary data (436 records, 4 fields): 4 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。