Job ID = 1293642 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 23,833,167 reads read : 23,833,167 reads written : 23,833,167 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: 00:09:16 23833167 reads; of these: 23833167 (100.00%) were unpaired; of these: 612969 (2.57%) aligned 0 times 17668728 (74.14%) aligned exactly 1 time 5551470 (23.29%) aligned >1 times 97.43% overall alignment rate Time searching: 00:09:16 Overall time: 00:09:16 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] 3580916 / 23220198 = 0.1542 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 01:32:47: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX1032415/SRX1032415.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX1032415/SRX1032415.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX1032415/SRX1032415.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX1032415/SRX1032415.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 01:32:47: #1 read tag files... INFO @ Mon, 03 Jun 2019 01:32:47: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 01:32:47: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX1032415/SRX1032415.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX1032415/SRX1032415.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX1032415/SRX1032415.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX1032415/SRX1032415.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 01:32:47: #1 read tag files... INFO @ Mon, 03 Jun 2019 01:32:47: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 01:32:47: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX1032415/SRX1032415.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX1032415/SRX1032415.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX1032415/SRX1032415.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX1032415/SRX1032415.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 01:32:47: #1 read tag files... INFO @ Mon, 03 Jun 2019 01:32:47: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 01:32:54: 1000000 INFO @ Mon, 03 Jun 2019 01:32:56: 1000000 INFO @ Mon, 03 Jun 2019 01:32:56: 1000000 INFO @ Mon, 03 Jun 2019 01:33:01: 2000000 INFO @ Mon, 03 Jun 2019 01:33:04: 2000000 INFO @ Mon, 03 Jun 2019 01:33:05: 2000000 INFO @ Mon, 03 Jun 2019 01:33:07: 3000000 INFO @ Mon, 03 Jun 2019 01:33:13: 3000000 INFO @ Mon, 03 Jun 2019 01:33:13: 3000000 INFO @ Mon, 03 Jun 2019 01:33:14: 4000000 INFO @ Mon, 03 Jun 2019 01:33:20: 5000000 INFO @ Mon, 03 Jun 2019 01:33:22: 4000000 INFO @ Mon, 03 Jun 2019 01:33:22: 4000000 INFO @ Mon, 03 Jun 2019 01:33:27: 6000000 INFO @ Mon, 03 Jun 2019 01:33:31: 5000000 INFO @ Mon, 03 Jun 2019 01:33:31: 5000000 INFO @ Mon, 03 Jun 2019 01:33:34: 7000000 INFO @ Mon, 03 Jun 2019 01:33:40: 6000000 INFO @ Mon, 03 Jun 2019 01:33:40: 6000000 INFO @ Mon, 03 Jun 2019 01:33:40: 8000000 INFO @ Mon, 03 Jun 2019 01:33:47: 9000000 INFO @ Mon, 03 Jun 2019 01:33:48: 7000000 INFO @ Mon, 03 Jun 2019 01:33:48: 7000000 INFO @ Mon, 03 Jun 2019 01:33:53: 10000000 INFO @ Mon, 03 Jun 2019 01:33:57: 8000000 INFO @ Mon, 03 Jun 2019 01:33:57: 8000000 INFO @ Mon, 03 Jun 2019 01:34:00: 11000000 INFO @ Mon, 03 Jun 2019 01:34:06: 9000000 INFO @ Mon, 03 Jun 2019 01:34:06: 9000000 INFO @ Mon, 03 Jun 2019 01:34:06: 12000000 INFO @ Mon, 03 Jun 2019 01:34:13: 13000000 INFO @ Mon, 03 Jun 2019 01:34:15: 10000000 INFO @ Mon, 03 Jun 2019 01:34:15: 10000000 INFO @ Mon, 03 Jun 2019 01:34:19: 14000000 INFO @ Mon, 03 Jun 2019 01:34:24: 11000000 INFO @ Mon, 03 Jun 2019 01:34:24: 11000000 INFO @ Mon, 03 Jun 2019 01:34:26: 15000000 INFO @ Mon, 03 Jun 2019 01:34:32: 12000000 INFO @ Mon, 03 Jun 2019 01:34:32: 16000000 INFO @ Mon, 03 Jun 2019 01:34:32: 12000000 INFO @ Mon, 03 Jun 2019 01:34:39: 17000000 INFO @ Mon, 03 Jun 2019 01:34:41: 13000000 INFO @ Mon, 03 Jun 2019 01:34:41: 13000000 INFO @ Mon, 03 Jun 2019 01:34:45: 18000000 INFO @ Mon, 03 Jun 2019 01:34:49: 14000000 INFO @ Mon, 03 Jun 2019 01:34:49: 14000000 INFO @ Mon, 03 Jun 2019 01:34:52: 19000000 INFO @ Mon, 03 Jun 2019 01:34:56: #1 tag size is determined as 51 bps INFO @ Mon, 03 Jun 2019 01:34:56: #1 tag size = 51 INFO @ Mon, 03 Jun 2019 01:34:56: #1 total tags in treatment: 19639282 INFO @ Mon, 03 Jun 2019 01:34:56: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 01:34:56: #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 01:34:56: #1 tags after filtering in treatment: 19639282 INFO @ Mon, 03 Jun 2019 01:34:56: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 01:34:56: #1 finished! INFO @ Mon, 03 Jun 2019 01:34:56: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 01:34:56: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 01:34:57: 15000000 INFO @ Mon, 03 Jun 2019 01:34:58: 15000000 INFO @ Mon, 03 Jun 2019 01:34:58: #2 number of paired peaks: 227 WARNING @ Mon, 03 Jun 2019 01:34:58: Fewer paired peaks (227) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 227 pairs to build model! INFO @ Mon, 03 Jun 2019 01:34:58: start model_add_line... INFO @ Mon, 03 Jun 2019 01:34:58: start X-correlation... INFO @ Mon, 03 Jun 2019 01:34:58: end of X-cor INFO @ Mon, 03 Jun 2019 01:34:58: #2 finished! INFO @ Mon, 03 Jun 2019 01:34:58: #2 predicted fragment length is 121 bps INFO @ Mon, 03 Jun 2019 01:34:58: #2 alternative fragment length(s) may be 121 bps INFO @ Mon, 03 Jun 2019 01:34:58: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX1032415/SRX1032415.10_model.r INFO @ Mon, 03 Jun 2019 01:34:58: #3 Call peaks... INFO @ Mon, 03 Jun 2019 01:34:58: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 01:35:06: 16000000 INFO @ Mon, 03 Jun 2019 01:35:06: 16000000 INFO @ Mon, 03 Jun 2019 01:35:14: 17000000 INFO @ Mon, 03 Jun 2019 01:35:15: 17000000 INFO @ Mon, 03 Jun 2019 01:35:23: 18000000 INFO @ Mon, 03 Jun 2019 01:35:23: 18000000 INFO @ Mon, 03 Jun 2019 01:35:31: 19000000 INFO @ Mon, 03 Jun 2019 01:35:31: 19000000 INFO @ Mon, 03 Jun 2019 01:35:37: #1 tag size is determined as 51 bps INFO @ Mon, 03 Jun 2019 01:35:37: #1 tag size = 51 INFO @ Mon, 03 Jun 2019 01:35:37: #1 total tags in treatment: 19639282 INFO @ Mon, 03 Jun 2019 01:35:37: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 01:35:37: #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 01:35:37: #1 tag size is determined as 51 bps INFO @ Mon, 03 Jun 2019 01:35:37: #1 tag size = 51 INFO @ Mon, 03 Jun 2019 01:35:37: #1 total tags in treatment: 19639282 INFO @ Mon, 03 Jun 2019 01:35:37: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 01:35:37: #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 01:35:37: #1 tags after filtering in treatment: 19639282 INFO @ Mon, 03 Jun 2019 01:35:37: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 01:35:37: #1 finished! INFO @ Mon, 03 Jun 2019 01:35:37: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 01:35:37: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 01:35:37: #1 tags after filtering in treatment: 19639282 INFO @ Mon, 03 Jun 2019 01:35:37: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 01:35:37: #1 finished! INFO @ Mon, 03 Jun 2019 01:35:37: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 01:35:37: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 01:35:39: #2 number of paired peaks: 227 WARNING @ Mon, 03 Jun 2019 01:35:39: Fewer paired peaks (227) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 227 pairs to build model! INFO @ Mon, 03 Jun 2019 01:35:39: start model_add_line... INFO @ Mon, 03 Jun 2019 01:35:39: start X-correlation... INFO @ Mon, 03 Jun 2019 01:35:39: end of X-cor INFO @ Mon, 03 Jun 2019 01:35:39: #2 finished! INFO @ Mon, 03 Jun 2019 01:35:39: #2 predicted fragment length is 121 bps INFO @ Mon, 03 Jun 2019 01:35:39: #2 alternative fragment length(s) may be 121 bps INFO @ Mon, 03 Jun 2019 01:35:39: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX1032415/SRX1032415.20_model.r INFO @ Mon, 03 Jun 2019 01:35:39: #3 Call peaks... INFO @ Mon, 03 Jun 2019 01:35:39: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 01:35:39: #2 number of paired peaks: 227 WARNING @ Mon, 03 Jun 2019 01:35:39: Fewer paired peaks (227) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 227 pairs to build model! INFO @ Mon, 03 Jun 2019 01:35:39: start model_add_line... INFO @ Mon, 03 Jun 2019 01:35:39: start X-correlation... INFO @ Mon, 03 Jun 2019 01:35:39: end of X-cor INFO @ Mon, 03 Jun 2019 01:35:39: #2 finished! INFO @ Mon, 03 Jun 2019 01:35:39: #2 predicted fragment length is 121 bps INFO @ Mon, 03 Jun 2019 01:35:39: #2 alternative fragment length(s) may be 121 bps INFO @ Mon, 03 Jun 2019 01:35:39: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX1032415/SRX1032415.05_model.r INFO @ Mon, 03 Jun 2019 01:35:39: #3 Call peaks... INFO @ Mon, 03 Jun 2019 01:35:39: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 01:35:49: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 01:36:14: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX1032415/SRX1032415.10_peaks.xls INFO @ Mon, 03 Jun 2019 01:36:14: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX1032415/SRX1032415.10_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 01:36:14: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX1032415/SRX1032415.10_summits.bed INFO @ Mon, 03 Jun 2019 01:36:14: Done! pass1 - making usageList (15 chroms): 3 millis pass2 - checking and writing primary data (4492 records, 4 fields): 11 millis CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 01:36:31: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 01:36:31: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 01:36:56: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX1032415/SRX1032415.20_peaks.xls INFO @ Mon, 03 Jun 2019 01:36:56: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX1032415/SRX1032415.20_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 01:36:56: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX1032415/SRX1032415.20_summits.bed INFO @ Mon, 03 Jun 2019 01:36:56: Done! INFO @ Mon, 03 Jun 2019 01:36:56: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX1032415/SRX1032415.05_peaks.xls INFO @ Mon, 03 Jun 2019 01:36:56: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX1032415/SRX1032415.05_peaks.narrowPeak pass1 - making usageList (15 chroms): 1 millis INFO @ Mon, 03 Jun 2019 01:36:56: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX1032415/SRX1032415.05_summits.bed pass2 - checking and writing primary data (2582 records, 4 fields): 24 millis CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 01:36:56: Done! pass1 - making usageList (15 chroms): 2 millis pass2 - checking and writing primary data (7144 records, 4 fields): 10 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。