Job ID = 4178561 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 42,749,165 reads read : 85,498,330 reads written : 42,749,165 reads 0-length : 42,749,165 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: 00:11:05 42749165 reads; of these: 42749165 (100.00%) were unpaired; of these: 4292964 (10.04%) aligned 0 times 31689128 (74.13%) aligned exactly 1 time 6767073 (15.83%) aligned >1 times 89.96% overall alignment rate Time searching: 00:11:05 Overall time: 00:11:05 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] 15940400 / 38456201 = 0.4145 in library ' ' BAM に変換しました。 Bed ファイルを作成中... INFO @ Thu, 05 Dec 2019 13:39:16: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX5827833/SRX5827833.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX5827833/SRX5827833.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX5827833/SRX5827833.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX5827833/SRX5827833.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, 05 Dec 2019 13:39:16: #1 read tag files... INFO @ Thu, 05 Dec 2019 13:39:16: #1 read treatment tags... INFO @ Thu, 05 Dec 2019 13:39:21: 1000000 INFO @ Thu, 05 Dec 2019 13:39:27: 2000000 INFO @ Thu, 05 Dec 2019 13:39:33: 3000000 INFO @ Thu, 05 Dec 2019 13:39:39: 4000000 INFO @ Thu, 05 Dec 2019 13:39:44: 5000000 INFO @ Thu, 05 Dec 2019 13:39:46: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX5827833/SRX5827833.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX5827833/SRX5827833.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX5827833/SRX5827833.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX5827833/SRX5827833.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, 05 Dec 2019 13:39:46: #1 read tag files... INFO @ Thu, 05 Dec 2019 13:39:46: #1 read treatment tags... INFO @ Thu, 05 Dec 2019 13:39:50: 6000000 INFO @ Thu, 05 Dec 2019 13:39:52: 1000000 INFO @ Thu, 05 Dec 2019 13:39:56: 7000000 INFO @ Thu, 05 Dec 2019 13:39:59: 2000000 INFO @ Thu, 05 Dec 2019 13:40:02: 8000000 INFO @ Thu, 05 Dec 2019 13:40:06: 3000000 INFO @ Thu, 05 Dec 2019 13:40:08: 9000000 INFO @ Thu, 05 Dec 2019 13:40:12: 4000000 BedGraph に変換中... INFO @ Thu, 05 Dec 2019 13:40:14: 10000000 INFO @ Thu, 05 Dec 2019 13:40:16: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX5827833/SRX5827833.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX5827833/SRX5827833.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX5827833/SRX5827833.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX5827833/SRX5827833.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, 05 Dec 2019 13:40:16: #1 read tag files... INFO @ Thu, 05 Dec 2019 13:40:16: #1 read treatment tags... INFO @ Thu, 05 Dec 2019 13:40:19: 5000000 INFO @ Thu, 05 Dec 2019 13:40:21: 11000000 INFO @ Thu, 05 Dec 2019 13:40:22: 1000000 INFO @ Thu, 05 Dec 2019 13:40:25: 6000000 INFO @ Thu, 05 Dec 2019 13:40:27: 12000000 INFO @ Thu, 05 Dec 2019 13:40:29: 2000000 INFO @ Thu, 05 Dec 2019 13:40:32: 7000000 INFO @ Thu, 05 Dec 2019 13:40:34: 13000000 INFO @ Thu, 05 Dec 2019 13:40:36: 3000000 INFO @ Thu, 05 Dec 2019 13:40:38: 8000000 INFO @ Thu, 05 Dec 2019 13:40:40: 14000000 INFO @ Thu, 05 Dec 2019 13:40:43: 4000000 INFO @ Thu, 05 Dec 2019 13:40:45: 9000000 INFO @ Thu, 05 Dec 2019 13:40:46: 15000000 INFO @ Thu, 05 Dec 2019 13:40:49: 5000000 INFO @ Thu, 05 Dec 2019 13:40:52: 10000000 INFO @ Thu, 05 Dec 2019 13:40:53: 16000000 INFO @ Thu, 05 Dec 2019 13:40:56: 6000000 INFO @ Thu, 05 Dec 2019 13:40:58: 11000000 INFO @ Thu, 05 Dec 2019 13:41:00: 17000000 INFO @ Thu, 05 Dec 2019 13:41:02: 7000000 INFO @ Thu, 05 Dec 2019 13:41:05: 12000000 INFO @ Thu, 05 Dec 2019 13:41:07: 18000000 INFO @ Thu, 05 Dec 2019 13:41:08: 8000000 INFO @ Thu, 05 Dec 2019 13:41:11: 13000000 INFO @ Thu, 05 Dec 2019 13:41:14: 19000000 INFO @ Thu, 05 Dec 2019 13:41:15: 9000000 INFO @ Thu, 05 Dec 2019 13:41:18: 14000000 INFO @ Thu, 05 Dec 2019 13:41:20: 20000000 INFO @ Thu, 05 Dec 2019 13:41:21: 10000000 INFO @ Thu, 05 Dec 2019 13:41:24: 15000000 INFO @ Thu, 05 Dec 2019 13:41:27: 21000000 INFO @ Thu, 05 Dec 2019 13:41:28: 11000000 INFO @ Thu, 05 Dec 2019 13:41:30: 16000000 INFO @ Thu, 05 Dec 2019 13:41:33: 22000000 INFO @ Thu, 05 Dec 2019 13:41:34: 12000000 INFO @ Thu, 05 Dec 2019 13:41:37: #1 tag size is determined as 51 bps INFO @ Thu, 05 Dec 2019 13:41:37: #1 tag size = 51 INFO @ Thu, 05 Dec 2019 13:41:37: #1 total tags in treatment: 22515801 INFO @ Thu, 05 Dec 2019 13:41:37: #1 user defined the maximum tags... INFO @ Thu, 05 Dec 2019 13:41:37: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Thu, 05 Dec 2019 13:41:37: 17000000 INFO @ Thu, 05 Dec 2019 13:41:37: #1 tags after filtering in treatment: 22515801 INFO @ Thu, 05 Dec 2019 13:41:37: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 05 Dec 2019 13:41:37: #1 finished! INFO @ Thu, 05 Dec 2019 13:41:37: #2 Build Peak Model... INFO @ Thu, 05 Dec 2019 13:41:37: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 05 Dec 2019 13:41:39: #2 number of paired peaks: 403 WARNING @ Thu, 05 Dec 2019 13:41:39: Fewer paired peaks (403) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 403 pairs to build model! INFO @ Thu, 05 Dec 2019 13:41:39: start model_add_line... INFO @ Thu, 05 Dec 2019 13:41:39: start X-correlation... INFO @ Thu, 05 Dec 2019 13:41:39: end of X-cor INFO @ Thu, 05 Dec 2019 13:41:39: #2 finished! INFO @ Thu, 05 Dec 2019 13:41:39: #2 predicted fragment length is 161 bps INFO @ Thu, 05 Dec 2019 13:41:39: #2 alternative fragment length(s) may be 161 bps INFO @ Thu, 05 Dec 2019 13:41:39: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX5827833/SRX5827833.05_model.r INFO @ Thu, 05 Dec 2019 13:41:39: #3 Call peaks... INFO @ Thu, 05 Dec 2019 13:41:39: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 05 Dec 2019 13:41:40: 13000000 INFO @ Thu, 05 Dec 2019 13:41:44: 18000000 INFO @ Thu, 05 Dec 2019 13:41:46: 14000000 INFO @ Thu, 05 Dec 2019 13:41:50: 19000000 INFO @ Thu, 05 Dec 2019 13:41:52: 15000000 INFO @ Thu, 05 Dec 2019 13:41:56: 20000000 INFO @ Thu, 05 Dec 2019 13:41:58: 16000000 INFO @ Thu, 05 Dec 2019 13:42:02: 21000000 INFO @ Thu, 05 Dec 2019 13:42:04: 17000000 INFO @ Thu, 05 Dec 2019 13:42:08: 22000000 INFO @ Thu, 05 Dec 2019 13:42:11: 18000000 INFO @ Thu, 05 Dec 2019 13:42:12: #1 tag size is determined as 51 bps INFO @ Thu, 05 Dec 2019 13:42:12: #1 tag size = 51 INFO @ Thu, 05 Dec 2019 13:42:12: #1 total tags in treatment: 22515801 INFO @ Thu, 05 Dec 2019 13:42:12: #1 user defined the maximum tags... INFO @ Thu, 05 Dec 2019 13:42:12: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Thu, 05 Dec 2019 13:42:12: #1 tags after filtering in treatment: 22515801 INFO @ Thu, 05 Dec 2019 13:42:12: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 05 Dec 2019 13:42:12: #1 finished! INFO @ Thu, 05 Dec 2019 13:42:12: #2 Build Peak Model... INFO @ Thu, 05 Dec 2019 13:42:12: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 05 Dec 2019 13:42:14: #2 number of paired peaks: 403 WARNING @ Thu, 05 Dec 2019 13:42:14: Fewer paired peaks (403) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 403 pairs to build model! INFO @ Thu, 05 Dec 2019 13:42:14: start model_add_line... INFO @ Thu, 05 Dec 2019 13:42:14: start X-correlation... INFO @ Thu, 05 Dec 2019 13:42:14: end of X-cor INFO @ Thu, 05 Dec 2019 13:42:14: #2 finished! INFO @ Thu, 05 Dec 2019 13:42:14: #2 predicted fragment length is 161 bps INFO @ Thu, 05 Dec 2019 13:42:14: #2 alternative fragment length(s) may be 161 bps INFO @ Thu, 05 Dec 2019 13:42:14: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX5827833/SRX5827833.10_model.r INFO @ Thu, 05 Dec 2019 13:42:14: #3 Call peaks... INFO @ Thu, 05 Dec 2019 13:42:14: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 05 Dec 2019 13:42:16: 19000000 INFO @ Thu, 05 Dec 2019 13:42:22: 20000000 INFO @ Thu, 05 Dec 2019 13:42:22: #3 Call peaks for each chromosome... INFO @ Thu, 05 Dec 2019 13:42:27: 21000000 INFO @ Thu, 05 Dec 2019 13:42:33: 22000000 INFO @ Thu, 05 Dec 2019 13:42:36: #1 tag size is determined as 51 bps INFO @ Thu, 05 Dec 2019 13:42:36: #1 tag size = 51 INFO @ Thu, 05 Dec 2019 13:42:36: #1 total tags in treatment: 22515801 INFO @ Thu, 05 Dec 2019 13:42:36: #1 user defined the maximum tags... INFO @ Thu, 05 Dec 2019 13:42:36: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Thu, 05 Dec 2019 13:42:37: #1 tags after filtering in treatment: 22515801 INFO @ Thu, 05 Dec 2019 13:42:37: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 05 Dec 2019 13:42:37: #1 finished! INFO @ Thu, 05 Dec 2019 13:42:37: #2 Build Peak Model... INFO @ Thu, 05 Dec 2019 13:42:37: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 05 Dec 2019 13:42:38: #2 number of paired peaks: 403 WARNING @ Thu, 05 Dec 2019 13:42:38: Fewer paired peaks (403) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 403 pairs to build model! INFO @ Thu, 05 Dec 2019 13:42:38: start model_add_line... INFO @ Thu, 05 Dec 2019 13:42:38: start X-correlation... INFO @ Thu, 05 Dec 2019 13:42:38: end of X-cor INFO @ Thu, 05 Dec 2019 13:42:38: #2 finished! INFO @ Thu, 05 Dec 2019 13:42:38: #2 predicted fragment length is 161 bps INFO @ Thu, 05 Dec 2019 13:42:38: #2 alternative fragment length(s) may be 161 bps INFO @ Thu, 05 Dec 2019 13:42:38: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX5827833/SRX5827833.20_model.r INFO @ Thu, 05 Dec 2019 13:42:38: #3 Call peaks... INFO @ Thu, 05 Dec 2019 13:42:38: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 05 Dec 2019 13:42:44: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX5827833/SRX5827833.05_peaks.xls INFO @ Thu, 05 Dec 2019 13:42:45: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX5827833/SRX5827833.05_peaks.narrowPeak INFO @ Thu, 05 Dec 2019 13:42:45: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX5827833/SRX5827833.05_summits.bed INFO @ Thu, 05 Dec 2019 13:42:45: Done! pass1 - making usageList (15 chroms): 11 millis pass2 - checking and writing primary data (6663 records, 4 fields): 20 millis CompletedMACS2peakCalling INFO @ Thu, 05 Dec 2019 13:42:57: #3 Call peaks for each chromosome... INFO @ Thu, 05 Dec 2019 13:43:19: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX5827833/SRX5827833.10_peaks.xls INFO @ Thu, 05 Dec 2019 13:43:19: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX5827833/SRX5827833.10_peaks.narrowPeak INFO @ Thu, 05 Dec 2019 13:43:19: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX5827833/SRX5827833.10_summits.bed INFO @ Thu, 05 Dec 2019 13:43:19: Done! pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (4245 records, 4 fields): 8 millis CompletedMACS2peakCalling INFO @ Thu, 05 Dec 2019 13:43:21: #3 Call peaks for each chromosome... INFO @ Thu, 05 Dec 2019 13:43:43: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX5827833/SRX5827833.20_peaks.xls INFO @ Thu, 05 Dec 2019 13:43:43: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX5827833/SRX5827833.20_peaks.narrowPeak INFO @ Thu, 05 Dec 2019 13:43:43: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX5827833/SRX5827833.20_summits.bed INFO @ Thu, 05 Dec 2019 13:43:43: Done! pass1 - making usageList (15 chroms): 4 millis pass2 - checking and writing primary data (2460 records, 4 fields): 15 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。