Job ID = 4178460 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 32,124,367 reads read : 64,248,734 reads written : 32,124,367 reads 0-length : 32,124,367 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: 00:08:10 32124367 reads; of these: 32124367 (100.00%) were unpaired; of these: 10727315 (33.39%) aligned 0 times 16158605 (50.30%) aligned exactly 1 time 5238447 (16.31%) aligned >1 times 66.61% overall alignment rate Time searching: 00:08:10 Overall time: 00:08:10 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] 9995256 / 21397052 = 0.4671 in library ' ' BAM に変換しました。 Bed ファイルを作成中... INFO @ Thu, 05 Dec 2019 12:43:35: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX5232776/SRX5232776.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX5232776/SRX5232776.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX5232776/SRX5232776.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX5232776/SRX5232776.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 12:43:35: #1 read tag files... INFO @ Thu, 05 Dec 2019 12:43:35: #1 read treatment tags... INFO @ Thu, 05 Dec 2019 12:43:42: 1000000 INFO @ Thu, 05 Dec 2019 12:43:49: 2000000 INFO @ Thu, 05 Dec 2019 12:43:56: 3000000 INFO @ Thu, 05 Dec 2019 12:44:04: 4000000 INFO @ Thu, 05 Dec 2019 12:44:05: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX5232776/SRX5232776.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX5232776/SRX5232776.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX5232776/SRX5232776.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX5232776/SRX5232776.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 12:44:05: #1 read tag files... INFO @ Thu, 05 Dec 2019 12:44:05: #1 read treatment tags... INFO @ Thu, 05 Dec 2019 12:44:11: 5000000 INFO @ Thu, 05 Dec 2019 12:44:12: 1000000 INFO @ Thu, 05 Dec 2019 12:44:19: 6000000 INFO @ Thu, 05 Dec 2019 12:44:20: 2000000 INFO @ Thu, 05 Dec 2019 12:44:26: 7000000 INFO @ Thu, 05 Dec 2019 12:44:27: 3000000 BedGraph に変換中... INFO @ Thu, 05 Dec 2019 12:44:34: 8000000 INFO @ Thu, 05 Dec 2019 12:44:34: 4000000 INFO @ Thu, 05 Dec 2019 12:44:35: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX5232776/SRX5232776.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX5232776/SRX5232776.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX5232776/SRX5232776.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX5232776/SRX5232776.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 12:44:35: #1 read tag files... INFO @ Thu, 05 Dec 2019 12:44:35: #1 read treatment tags... INFO @ Thu, 05 Dec 2019 12:44:41: 9000000 INFO @ Thu, 05 Dec 2019 12:44:41: 5000000 INFO @ Thu, 05 Dec 2019 12:44:42: 1000000 INFO @ Thu, 05 Dec 2019 12:44:48: 10000000 INFO @ Thu, 05 Dec 2019 12:44:48: 6000000 INFO @ Thu, 05 Dec 2019 12:44:49: 2000000 INFO @ Thu, 05 Dec 2019 12:44:55: 11000000 INFO @ Thu, 05 Dec 2019 12:44:55: 7000000 INFO @ Thu, 05 Dec 2019 12:44:56: 3000000 INFO @ Thu, 05 Dec 2019 12:44:58: #1 tag size is determined as 50 bps INFO @ Thu, 05 Dec 2019 12:44:58: #1 tag size = 50 INFO @ Thu, 05 Dec 2019 12:44:58: #1 total tags in treatment: 11401796 INFO @ Thu, 05 Dec 2019 12:44:58: #1 user defined the maximum tags... INFO @ Thu, 05 Dec 2019 12:44:58: #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 12:44:58: #1 tags after filtering in treatment: 11401796 INFO @ Thu, 05 Dec 2019 12:44:58: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 05 Dec 2019 12:44:58: #1 finished! INFO @ Thu, 05 Dec 2019 12:44:58: #2 Build Peak Model... INFO @ Thu, 05 Dec 2019 12:44:58: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 05 Dec 2019 12:44:59: #2 number of paired peaks: 512 WARNING @ Thu, 05 Dec 2019 12:44:59: Fewer paired peaks (512) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 512 pairs to build model! INFO @ Thu, 05 Dec 2019 12:44:59: start model_add_line... INFO @ Thu, 05 Dec 2019 12:44:59: start X-correlation... INFO @ Thu, 05 Dec 2019 12:44:59: end of X-cor INFO @ Thu, 05 Dec 2019 12:44:59: #2 finished! INFO @ Thu, 05 Dec 2019 12:44:59: #2 predicted fragment length is 117 bps INFO @ Thu, 05 Dec 2019 12:44:59: #2 alternative fragment length(s) may be 117 bps INFO @ Thu, 05 Dec 2019 12:44:59: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX5232776/SRX5232776.05_model.r INFO @ Thu, 05 Dec 2019 12:44:59: #3 Call peaks... INFO @ Thu, 05 Dec 2019 12:44:59: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 05 Dec 2019 12:45:02: 4000000 INFO @ Thu, 05 Dec 2019 12:45:02: 8000000 INFO @ Thu, 05 Dec 2019 12:45:08: 5000000 INFO @ Thu, 05 Dec 2019 12:45:10: 9000000 INFO @ Thu, 05 Dec 2019 12:45:14: 6000000 INFO @ Thu, 05 Dec 2019 12:45:17: 10000000 INFO @ Thu, 05 Dec 2019 12:45:20: 7000000 INFO @ Thu, 05 Dec 2019 12:45:20: #3 Call peaks for each chromosome... INFO @ Thu, 05 Dec 2019 12:45:24: 11000000 INFO @ Thu, 05 Dec 2019 12:45:26: 8000000 INFO @ Thu, 05 Dec 2019 12:45:27: #1 tag size is determined as 50 bps INFO @ Thu, 05 Dec 2019 12:45:27: #1 tag size = 50 INFO @ Thu, 05 Dec 2019 12:45:27: #1 total tags in treatment: 11401796 INFO @ Thu, 05 Dec 2019 12:45:27: #1 user defined the maximum tags... INFO @ Thu, 05 Dec 2019 12:45:27: #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 12:45:27: #1 tags after filtering in treatment: 11401796 INFO @ Thu, 05 Dec 2019 12:45:27: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 05 Dec 2019 12:45:27: #1 finished! INFO @ Thu, 05 Dec 2019 12:45:27: #2 Build Peak Model... INFO @ Thu, 05 Dec 2019 12:45:27: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 05 Dec 2019 12:45:28: #2 number of paired peaks: 512 WARNING @ Thu, 05 Dec 2019 12:45:28: Fewer paired peaks (512) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 512 pairs to build model! INFO @ Thu, 05 Dec 2019 12:45:28: start model_add_line... INFO @ Thu, 05 Dec 2019 12:45:28: start X-correlation... INFO @ Thu, 05 Dec 2019 12:45:28: end of X-cor INFO @ Thu, 05 Dec 2019 12:45:28: #2 finished! INFO @ Thu, 05 Dec 2019 12:45:28: #2 predicted fragment length is 117 bps INFO @ Thu, 05 Dec 2019 12:45:28: #2 alternative fragment length(s) may be 117 bps INFO @ Thu, 05 Dec 2019 12:45:28: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX5232776/SRX5232776.10_model.r INFO @ Thu, 05 Dec 2019 12:45:30: #3 Call peaks... INFO @ Thu, 05 Dec 2019 12:45:30: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 05 Dec 2019 12:45:32: 9000000 INFO @ Thu, 05 Dec 2019 12:45:33: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX5232776/SRX5232776.05_peaks.xls INFO @ Thu, 05 Dec 2019 12:45:33: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX5232776/SRX5232776.05_peaks.narrowPeak INFO @ Thu, 05 Dec 2019 12:45:33: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX5232776/SRX5232776.05_summits.bed INFO @ Thu, 05 Dec 2019 12:45:33: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (3666 records, 4 fields): 939 millis CompletedMACS2peakCalling INFO @ Thu, 05 Dec 2019 12:45:37: 10000000 INFO @ Thu, 05 Dec 2019 12:45:43: 11000000 INFO @ Thu, 05 Dec 2019 12:45:45: #1 tag size is determined as 50 bps INFO @ Thu, 05 Dec 2019 12:45:45: #1 tag size = 50 INFO @ Thu, 05 Dec 2019 12:45:45: #1 total tags in treatment: 11401796 INFO @ Thu, 05 Dec 2019 12:45:45: #1 user defined the maximum tags... INFO @ Thu, 05 Dec 2019 12:45:45: #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 12:45:46: #1 tags after filtering in treatment: 11401796 INFO @ Thu, 05 Dec 2019 12:45:46: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 05 Dec 2019 12:45:46: #1 finished! INFO @ Thu, 05 Dec 2019 12:45:46: #2 Build Peak Model... INFO @ Thu, 05 Dec 2019 12:45:46: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 05 Dec 2019 12:45:46: #2 number of paired peaks: 512 WARNING @ Thu, 05 Dec 2019 12:45:46: Fewer paired peaks (512) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 512 pairs to build model! INFO @ Thu, 05 Dec 2019 12:45:46: start model_add_line... INFO @ Thu, 05 Dec 2019 12:45:47: start X-correlation... INFO @ Thu, 05 Dec 2019 12:45:47: end of X-cor INFO @ Thu, 05 Dec 2019 12:45:47: #2 finished! INFO @ Thu, 05 Dec 2019 12:45:47: #2 predicted fragment length is 117 bps INFO @ Thu, 05 Dec 2019 12:45:47: #2 alternative fragment length(s) may be 117 bps INFO @ Thu, 05 Dec 2019 12:45:47: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX5232776/SRX5232776.20_model.r INFO @ Thu, 05 Dec 2019 12:45:47: #3 Call peaks... INFO @ Thu, 05 Dec 2019 12:45:47: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 05 Dec 2019 12:45:51: #3 Call peaks for each chromosome... INFO @ Thu, 05 Dec 2019 12:46:04: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX5232776/SRX5232776.10_peaks.xls INFO @ Thu, 05 Dec 2019 12:46:04: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX5232776/SRX5232776.10_peaks.narrowPeak INFO @ Thu, 05 Dec 2019 12:46:04: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX5232776/SRX5232776.10_summits.bed INFO @ Thu, 05 Dec 2019 12:46:04: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (2842 records, 4 fields): 37 millis CompletedMACS2peakCalling INFO @ Thu, 05 Dec 2019 12:46:07: #3 Call peaks for each chromosome... INFO @ Thu, 05 Dec 2019 12:46:20: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX5232776/SRX5232776.20_peaks.xls INFO @ Thu, 05 Dec 2019 12:46:20: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX5232776/SRX5232776.20_peaks.narrowPeak INFO @ Thu, 05 Dec 2019 12:46:20: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX5232776/SRX5232776.20_summits.bed INFO @ Thu, 05 Dec 2019 12:46:20: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (1955 records, 4 fields): 70 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。