Job ID = 4178475 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 31,616,018 reads read : 31,616,018 reads written : 31,616,018 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: 00:08:29 31616018 reads; of these: 31616018 (100.00%) were unpaired; of these: 658320 (2.08%) aligned 0 times 25973890 (82.15%) aligned exactly 1 time 4983808 (15.76%) aligned >1 times 97.92% overall alignment rate Time searching: 00:08:29 Overall time: 00:08:29 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] 12795512 / 30957698 = 0.4133 in library ' ' BAM に変換しました。 Bed ファイルを作成中... INFO @ Thu, 05 Dec 2019 12:51:10: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX5535379/SRX5535379.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX5535379/SRX5535379.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX5535379/SRX5535379.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX5535379/SRX5535379.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 12:51:10: #1 read tag files... INFO @ Thu, 05 Dec 2019 12:51:10: #1 read treatment tags... INFO @ Thu, 05 Dec 2019 12:51:17: 1000000 INFO @ Thu, 05 Dec 2019 12:51:23: 2000000 INFO @ Thu, 05 Dec 2019 12:51:30: 3000000 INFO @ Thu, 05 Dec 2019 12:51:37: 4000000 INFO @ Thu, 05 Dec 2019 12:51:37: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX5535379/SRX5535379.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX5535379/SRX5535379.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX5535379/SRX5535379.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX5535379/SRX5535379.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 12:51:37: #1 read tag files... INFO @ Thu, 05 Dec 2019 12:51:37: #1 read treatment tags... INFO @ Thu, 05 Dec 2019 12:51:43: 5000000 INFO @ Thu, 05 Dec 2019 12:51:43: 1000000 INFO @ Thu, 05 Dec 2019 12:51:50: 2000000 INFO @ Thu, 05 Dec 2019 12:51:50: 6000000 INFO @ Thu, 05 Dec 2019 12:51:56: 3000000 INFO @ Thu, 05 Dec 2019 12:51:56: 7000000 INFO @ Thu, 05 Dec 2019 12:52:01: 4000000 INFO @ Thu, 05 Dec 2019 12:52:02: 8000000 BedGraph に変換中... INFO @ Thu, 05 Dec 2019 12:52:07: 5000000 INFO @ Thu, 05 Dec 2019 12:52:08: 9000000 INFO @ Thu, 05 Dec 2019 12:52:09: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX5535379/SRX5535379.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX5535379/SRX5535379.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX5535379/SRX5535379.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX5535379/SRX5535379.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 12:52:09: #1 read tag files... INFO @ Thu, 05 Dec 2019 12:52:09: #1 read treatment tags... INFO @ Thu, 05 Dec 2019 12:52:14: 6000000 INFO @ Thu, 05 Dec 2019 12:52:14: 10000000 INFO @ Thu, 05 Dec 2019 12:52:15: 1000000 INFO @ Thu, 05 Dec 2019 12:52:20: 7000000 INFO @ Thu, 05 Dec 2019 12:52:21: 11000000 INFO @ Thu, 05 Dec 2019 12:52:21: 2000000 INFO @ Thu, 05 Dec 2019 12:52:26: 8000000 INFO @ Thu, 05 Dec 2019 12:52:26: 12000000 INFO @ Thu, 05 Dec 2019 12:52:27: 3000000 INFO @ Thu, 05 Dec 2019 12:52:32: 9000000 INFO @ Thu, 05 Dec 2019 12:52:32: 4000000 INFO @ Thu, 05 Dec 2019 12:52:33: 13000000 INFO @ Thu, 05 Dec 2019 12:52:38: 5000000 INFO @ Thu, 05 Dec 2019 12:52:38: 10000000 INFO @ Thu, 05 Dec 2019 12:52:39: 14000000 INFO @ Thu, 05 Dec 2019 12:52:43: 6000000 INFO @ Thu, 05 Dec 2019 12:52:44: 11000000 INFO @ Thu, 05 Dec 2019 12:52:45: 15000000 INFO @ Thu, 05 Dec 2019 12:52:50: 7000000 INFO @ Thu, 05 Dec 2019 12:52:51: 12000000 INFO @ Thu, 05 Dec 2019 12:52:52: 16000000 INFO @ Thu, 05 Dec 2019 12:52:56: 8000000 INFO @ Thu, 05 Dec 2019 12:52:57: 13000000 INFO @ Thu, 05 Dec 2019 12:52:59: 17000000 INFO @ Thu, 05 Dec 2019 12:53:01: 9000000 INFO @ Thu, 05 Dec 2019 12:53:03: 14000000 INFO @ Thu, 05 Dec 2019 12:53:05: 18000000 INFO @ Thu, 05 Dec 2019 12:53:07: #1 tag size is determined as 50 bps INFO @ Thu, 05 Dec 2019 12:53:07: #1 tag size = 50 INFO @ Thu, 05 Dec 2019 12:53:07: #1 total tags in treatment: 18162186 INFO @ Thu, 05 Dec 2019 12:53:07: #1 user defined the maximum tags... INFO @ Thu, 05 Dec 2019 12:53:07: #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 12:53:07: 10000000 INFO @ Thu, 05 Dec 2019 12:53:07: #1 tags after filtering in treatment: 18162186 INFO @ Thu, 05 Dec 2019 12:53:07: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 05 Dec 2019 12:53:07: #1 finished! INFO @ Thu, 05 Dec 2019 12:53:07: #2 Build Peak Model... INFO @ Thu, 05 Dec 2019 12:53:07: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 05 Dec 2019 12:53:08: #2 number of paired peaks: 154 WARNING @ Thu, 05 Dec 2019 12:53:08: Fewer paired peaks (154) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 154 pairs to build model! INFO @ Thu, 05 Dec 2019 12:53:08: start model_add_line... INFO @ Thu, 05 Dec 2019 12:53:09: start X-correlation... INFO @ Thu, 05 Dec 2019 12:53:09: end of X-cor INFO @ Thu, 05 Dec 2019 12:53:09: #2 finished! INFO @ Thu, 05 Dec 2019 12:53:09: #2 predicted fragment length is 132 bps INFO @ Thu, 05 Dec 2019 12:53:09: #2 alternative fragment length(s) may be 48,86,107,132,153,187,208,236,268,293,334,371,402,521,557,581 bps INFO @ Thu, 05 Dec 2019 12:53:09: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX5535379/SRX5535379.05_model.r INFO @ Thu, 05 Dec 2019 12:53:09: #3 Call peaks... INFO @ Thu, 05 Dec 2019 12:53:09: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 05 Dec 2019 12:53:09: 15000000 INFO @ Thu, 05 Dec 2019 12:53:12: 11000000 INFO @ Thu, 05 Dec 2019 12:53:15: 16000000 INFO @ Thu, 05 Dec 2019 12:53:18: 12000000 INFO @ Thu, 05 Dec 2019 12:53:20: 17000000 INFO @ Thu, 05 Dec 2019 12:53:23: 13000000 INFO @ Thu, 05 Dec 2019 12:53:25: 18000000 INFO @ Thu, 05 Dec 2019 12:53:26: #1 tag size is determined as 50 bps INFO @ Thu, 05 Dec 2019 12:53:26: #1 tag size = 50 INFO @ Thu, 05 Dec 2019 12:53:26: #1 total tags in treatment: 18162186 INFO @ Thu, 05 Dec 2019 12:53:26: #1 user defined the maximum tags... INFO @ Thu, 05 Dec 2019 12:53:26: #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 12:53:27: #1 tags after filtering in treatment: 18162186 INFO @ Thu, 05 Dec 2019 12:53:27: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 05 Dec 2019 12:53:27: #1 finished! INFO @ Thu, 05 Dec 2019 12:53:27: #2 Build Peak Model... INFO @ Thu, 05 Dec 2019 12:53:27: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 05 Dec 2019 12:53:28: #2 number of paired peaks: 154 WARNING @ Thu, 05 Dec 2019 12:53:28: Fewer paired peaks (154) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 154 pairs to build model! INFO @ Thu, 05 Dec 2019 12:53:28: start model_add_line... INFO @ Thu, 05 Dec 2019 12:53:28: start X-correlation... INFO @ Thu, 05 Dec 2019 12:53:28: 14000000 INFO @ Thu, 05 Dec 2019 12:53:28: end of X-cor INFO @ Thu, 05 Dec 2019 12:53:28: #2 finished! INFO @ Thu, 05 Dec 2019 12:53:28: #2 predicted fragment length is 132 bps INFO @ Thu, 05 Dec 2019 12:53:28: #2 alternative fragment length(s) may be 48,86,107,132,153,187,208,236,268,293,334,371,402,521,557,581 bps INFO @ Thu, 05 Dec 2019 12:53:28: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX5535379/SRX5535379.10_model.r INFO @ Thu, 05 Dec 2019 12:53:28: #3 Call peaks... INFO @ Thu, 05 Dec 2019 12:53:28: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 05 Dec 2019 12:53:33: 15000000 INFO @ Thu, 05 Dec 2019 12:53:39: 16000000 INFO @ Thu, 05 Dec 2019 12:53:44: 17000000 INFO @ Thu, 05 Dec 2019 12:53:46: #3 Call peaks for each chromosome... INFO @ Thu, 05 Dec 2019 12:53:49: 18000000 INFO @ Thu, 05 Dec 2019 12:53:49: #1 tag size is determined as 50 bps INFO @ Thu, 05 Dec 2019 12:53:49: #1 tag size = 50 INFO @ Thu, 05 Dec 2019 12:53:49: #1 total tags in treatment: 18162186 INFO @ Thu, 05 Dec 2019 12:53:49: #1 user defined the maximum tags... INFO @ Thu, 05 Dec 2019 12:53:49: #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 12:53:50: #1 tags after filtering in treatment: 18162186 INFO @ Thu, 05 Dec 2019 12:53:50: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 05 Dec 2019 12:53:50: #1 finished! INFO @ Thu, 05 Dec 2019 12:53:50: #2 Build Peak Model... INFO @ Thu, 05 Dec 2019 12:53:50: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 05 Dec 2019 12:53:51: #2 number of paired peaks: 154 WARNING @ Thu, 05 Dec 2019 12:53:51: Fewer paired peaks (154) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 154 pairs to build model! INFO @ Thu, 05 Dec 2019 12:53:51: start model_add_line... INFO @ Thu, 05 Dec 2019 12:53:51: start X-correlation... INFO @ Thu, 05 Dec 2019 12:53:51: end of X-cor INFO @ Thu, 05 Dec 2019 12:53:51: #2 finished! INFO @ Thu, 05 Dec 2019 12:53:51: #2 predicted fragment length is 132 bps INFO @ Thu, 05 Dec 2019 12:53:51: #2 alternative fragment length(s) may be 48,86,107,132,153,187,208,236,268,293,334,371,402,521,557,581 bps INFO @ Thu, 05 Dec 2019 12:53:51: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX5535379/SRX5535379.20_model.r INFO @ Thu, 05 Dec 2019 12:53:51: #3 Call peaks... INFO @ Thu, 05 Dec 2019 12:53:51: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 05 Dec 2019 12:54:05: #3 Call peaks for each chromosome... INFO @ Thu, 05 Dec 2019 12:54:06: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX5535379/SRX5535379.05_peaks.xls INFO @ Thu, 05 Dec 2019 12:54:06: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX5535379/SRX5535379.05_peaks.narrowPeak INFO @ Thu, 05 Dec 2019 12:54:06: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX5535379/SRX5535379.05_summits.bed INFO @ Thu, 05 Dec 2019 12:54:06: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (3783 records, 4 fields): 7 millis CompletedMACS2peakCalling INFO @ Thu, 05 Dec 2019 12:54:27: #3 Call peaks for each chromosome... INFO @ Thu, 05 Dec 2019 12:54:27: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX5535379/SRX5535379.10_peaks.xls INFO @ Thu, 05 Dec 2019 12:54:27: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX5535379/SRX5535379.10_peaks.narrowPeak INFO @ Thu, 05 Dec 2019 12:54:27: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX5535379/SRX5535379.10_summits.bed INFO @ Thu, 05 Dec 2019 12:54:27: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (944 records, 4 fields): 291 millis CompletedMACS2peakCalling INFO @ Thu, 05 Dec 2019 12:54:48: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX5535379/SRX5535379.20_peaks.xls INFO @ Thu, 05 Dec 2019 12:54:48: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX5535379/SRX5535379.20_peaks.narrowPeak INFO @ Thu, 05 Dec 2019 12:54:48: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX5535379/SRX5535379.20_summits.bed INFO @ Thu, 05 Dec 2019 12:54:48: Done! pass1 - making usageList (11 chroms): 2 millis pass2 - checking and writing primary data (324 records, 4 fields): 2 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。