Job ID = 2590480 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 8,544,944 reads read : 17,089,888 reads written : 8,544,944 reads 0-length : 8,544,944 spots read : 8,536,420 reads read : 17,072,840 reads written : 8,536,420 reads 0-length : 8,536,420 spots read : 8,580,355 reads read : 17,160,710 reads written : 8,580,355 reads 0-length : 8,580,355 spots read : 8,614,260 reads read : 17,228,520 reads written : 8,614,260 reads 0-length : 8,614,260 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: 00:12:28 34275979 reads; of these: 34275979 (100.00%) were unpaired; of these: 1180428 (3.44%) aligned 0 times 24377058 (71.12%) aligned exactly 1 time 8718493 (25.44%) aligned >1 times 96.56% overall alignment rate Time searching: 00:12:28 Overall time: 00:12:28 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] 4655724 / 33095551 = 0.1407 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, 12 Aug 2019 22:25:02: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX3981710/SRX3981710.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX3981710/SRX3981710.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX3981710/SRX3981710.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX3981710/SRX3981710.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, 12 Aug 2019 22:25:02: #1 read tag files... INFO @ Mon, 12 Aug 2019 22:25:02: #1 read treatment tags... INFO @ Mon, 12 Aug 2019 22:25:03: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX3981710/SRX3981710.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX3981710/SRX3981710.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX3981710/SRX3981710.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX3981710/SRX3981710.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, 12 Aug 2019 22:25:03: #1 read tag files... INFO @ Mon, 12 Aug 2019 22:25:03: #1 read treatment tags... INFO @ Mon, 12 Aug 2019 22:25:04: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX3981710/SRX3981710.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX3981710/SRX3981710.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX3981710/SRX3981710.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX3981710/SRX3981710.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, 12 Aug 2019 22:25:04: #1 read tag files... INFO @ Mon, 12 Aug 2019 22:25:04: #1 read treatment tags... INFO @ Mon, 12 Aug 2019 22:25:11: 1000000 INFO @ Mon, 12 Aug 2019 22:25:12: 1000000 INFO @ Mon, 12 Aug 2019 22:25:13: 1000000 INFO @ Mon, 12 Aug 2019 22:25:19: 2000000 INFO @ Mon, 12 Aug 2019 22:25:20: 2000000 INFO @ Mon, 12 Aug 2019 22:25:21: 2000000 INFO @ Mon, 12 Aug 2019 22:25:27: 3000000 INFO @ Mon, 12 Aug 2019 22:25:28: 3000000 INFO @ Mon, 12 Aug 2019 22:25:30: 3000000 INFO @ Mon, 12 Aug 2019 22:25:35: 4000000 INFO @ Mon, 12 Aug 2019 22:25:36: 4000000 INFO @ Mon, 12 Aug 2019 22:25:39: 4000000 INFO @ Mon, 12 Aug 2019 22:25:43: 5000000 INFO @ Mon, 12 Aug 2019 22:25:45: 5000000 INFO @ Mon, 12 Aug 2019 22:25:47: 5000000 INFO @ Mon, 12 Aug 2019 22:25:51: 6000000 INFO @ Mon, 12 Aug 2019 22:25:52: 6000000 INFO @ Mon, 12 Aug 2019 22:25:56: 6000000 INFO @ Mon, 12 Aug 2019 22:25:59: 7000000 INFO @ Mon, 12 Aug 2019 22:26:00: 7000000 INFO @ Mon, 12 Aug 2019 22:26:04: 7000000 INFO @ Mon, 12 Aug 2019 22:26:07: 8000000 INFO @ Mon, 12 Aug 2019 22:26:08: 8000000 INFO @ Mon, 12 Aug 2019 22:26:12: 8000000 INFO @ Mon, 12 Aug 2019 22:26:15: 9000000 INFO @ Mon, 12 Aug 2019 22:26:17: 9000000 INFO @ Mon, 12 Aug 2019 22:26:20: 9000000 INFO @ Mon, 12 Aug 2019 22:26:23: 10000000 INFO @ Mon, 12 Aug 2019 22:26:26: 10000000 INFO @ Mon, 12 Aug 2019 22:26:28: 10000000 INFO @ Mon, 12 Aug 2019 22:26:31: 11000000 INFO @ Mon, 12 Aug 2019 22:26:34: 11000000 INFO @ Mon, 12 Aug 2019 22:26:35: 11000000 INFO @ Mon, 12 Aug 2019 22:26:39: 12000000 INFO @ Mon, 12 Aug 2019 22:26:43: 12000000 INFO @ Mon, 12 Aug 2019 22:26:43: 12000000 INFO @ Mon, 12 Aug 2019 22:26:47: 13000000 INFO @ Mon, 12 Aug 2019 22:26:51: 13000000 INFO @ Mon, 12 Aug 2019 22:26:52: 13000000 INFO @ Mon, 12 Aug 2019 22:26:55: 14000000 INFO @ Mon, 12 Aug 2019 22:26:59: 14000000 INFO @ Mon, 12 Aug 2019 22:27:01: 14000000 INFO @ Mon, 12 Aug 2019 22:27:03: 15000000 INFO @ Mon, 12 Aug 2019 22:27:07: 15000000 INFO @ Mon, 12 Aug 2019 22:27:09: 15000000 INFO @ Mon, 12 Aug 2019 22:27:11: 16000000 INFO @ Mon, 12 Aug 2019 22:27:15: 16000000 INFO @ Mon, 12 Aug 2019 22:27:17: 16000000 INFO @ Mon, 12 Aug 2019 22:27:19: 17000000 INFO @ Mon, 12 Aug 2019 22:27:23: 17000000 INFO @ Mon, 12 Aug 2019 22:27:25: 17000000 INFO @ Mon, 12 Aug 2019 22:27:27: 18000000 INFO @ Mon, 12 Aug 2019 22:27:31: 18000000 INFO @ Mon, 12 Aug 2019 22:27:33: 18000000 INFO @ Mon, 12 Aug 2019 22:27:35: 19000000 INFO @ Mon, 12 Aug 2019 22:27:39: 19000000 INFO @ Mon, 12 Aug 2019 22:27:41: 19000000 INFO @ Mon, 12 Aug 2019 22:27:43: 20000000 INFO @ Mon, 12 Aug 2019 22:27:47: 20000000 INFO @ Mon, 12 Aug 2019 22:27:49: 20000000 INFO @ Mon, 12 Aug 2019 22:27:51: 21000000 INFO @ Mon, 12 Aug 2019 22:27:55: 21000000 INFO @ Mon, 12 Aug 2019 22:27:57: 21000000 INFO @ Mon, 12 Aug 2019 22:27:59: 22000000 INFO @ Mon, 12 Aug 2019 22:28:03: 22000000 INFO @ Mon, 12 Aug 2019 22:28:05: 22000000 INFO @ Mon, 12 Aug 2019 22:28:07: 23000000 INFO @ Mon, 12 Aug 2019 22:28:11: 23000000 INFO @ Mon, 12 Aug 2019 22:28:13: 23000000 INFO @ Mon, 12 Aug 2019 22:28:15: 24000000 INFO @ Mon, 12 Aug 2019 22:28:19: 24000000 INFO @ Mon, 12 Aug 2019 22:28:21: 24000000 INFO @ Mon, 12 Aug 2019 22:28:23: 25000000 INFO @ Mon, 12 Aug 2019 22:28:27: 25000000 INFO @ Mon, 12 Aug 2019 22:28:29: 25000000 INFO @ Mon, 12 Aug 2019 22:28:31: 26000000 INFO @ Mon, 12 Aug 2019 22:28:35: 26000000 INFO @ Mon, 12 Aug 2019 22:28:37: 26000000 INFO @ Mon, 12 Aug 2019 22:28:39: 27000000 INFO @ Mon, 12 Aug 2019 22:28:43: 27000000 INFO @ Mon, 12 Aug 2019 22:28:45: 27000000 INFO @ Mon, 12 Aug 2019 22:28:47: 28000000 INFO @ Mon, 12 Aug 2019 22:28:50: #1 tag size is determined as 51 bps INFO @ Mon, 12 Aug 2019 22:28:50: #1 tag size = 51 INFO @ Mon, 12 Aug 2019 22:28:50: #1 total tags in treatment: 28439827 INFO @ Mon, 12 Aug 2019 22:28:50: #1 user defined the maximum tags... INFO @ Mon, 12 Aug 2019 22:28:50: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Mon, 12 Aug 2019 22:28:51: 28000000 INFO @ Mon, 12 Aug 2019 22:28:51: #1 tags after filtering in treatment: 28439827 INFO @ Mon, 12 Aug 2019 22:28:51: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 12 Aug 2019 22:28:51: #1 finished! INFO @ Mon, 12 Aug 2019 22:28:51: #2 Build Peak Model... INFO @ Mon, 12 Aug 2019 22:28:51: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 12 Aug 2019 22:28:53: 28000000 INFO @ Mon, 12 Aug 2019 22:28:53: #2 number of paired peaks: 120 WARNING @ Mon, 12 Aug 2019 22:28:53: Fewer paired peaks (120) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 120 pairs to build model! INFO @ Mon, 12 Aug 2019 22:28:53: start model_add_line... INFO @ Mon, 12 Aug 2019 22:28:53: start X-correlation... INFO @ Mon, 12 Aug 2019 22:28:53: end of X-cor INFO @ Mon, 12 Aug 2019 22:28:53: #2 finished! INFO @ Mon, 12 Aug 2019 22:28:53: #2 predicted fragment length is 48 bps INFO @ Mon, 12 Aug 2019 22:28:53: #2 alternative fragment length(s) may be 2,16,48,548,598 bps INFO @ Mon, 12 Aug 2019 22:28:53: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX3981710/SRX3981710.05_model.r WARNING @ Mon, 12 Aug 2019 22:28:53: #2 Since the d (48) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 12 Aug 2019 22:28:53: #2 You may need to consider one of the other alternative d(s): 2,16,48,548,598 WARNING @ Mon, 12 Aug 2019 22:28:53: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Mon, 12 Aug 2019 22:28:53: #3 Call peaks... INFO @ Mon, 12 Aug 2019 22:28:53: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 12 Aug 2019 22:28:54: #1 tag size is determined as 51 bps INFO @ Mon, 12 Aug 2019 22:28:54: #1 tag size = 51 INFO @ Mon, 12 Aug 2019 22:28:54: #1 total tags in treatment: 28439827 INFO @ Mon, 12 Aug 2019 22:28:54: #1 user defined the maximum tags... INFO @ Mon, 12 Aug 2019 22:28:54: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Mon, 12 Aug 2019 22:28:55: #1 tags after filtering in treatment: 28439827 INFO @ Mon, 12 Aug 2019 22:28:55: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 12 Aug 2019 22:28:55: #1 finished! INFO @ Mon, 12 Aug 2019 22:28:55: #2 Build Peak Model... INFO @ Mon, 12 Aug 2019 22:28:55: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 12 Aug 2019 22:28:56: #1 tag size is determined as 51 bps INFO @ Mon, 12 Aug 2019 22:28:56: #1 tag size = 51 INFO @ Mon, 12 Aug 2019 22:28:56: #1 total tags in treatment: 28439827 INFO @ Mon, 12 Aug 2019 22:28:56: #1 user defined the maximum tags... INFO @ Mon, 12 Aug 2019 22:28:56: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Mon, 12 Aug 2019 22:28:57: #1 tags after filtering in treatment: 28439827 INFO @ Mon, 12 Aug 2019 22:28:57: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 12 Aug 2019 22:28:57: #1 finished! INFO @ Mon, 12 Aug 2019 22:28:57: #2 Build Peak Model... INFO @ Mon, 12 Aug 2019 22:28:57: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 12 Aug 2019 22:28:57: #2 number of paired peaks: 120 WARNING @ Mon, 12 Aug 2019 22:28:57: Fewer paired peaks (120) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 120 pairs to build model! INFO @ Mon, 12 Aug 2019 22:28:57: start model_add_line... INFO @ Mon, 12 Aug 2019 22:28:57: start X-correlation... INFO @ Mon, 12 Aug 2019 22:28:57: end of X-cor INFO @ Mon, 12 Aug 2019 22:28:57: #2 finished! INFO @ Mon, 12 Aug 2019 22:28:57: #2 predicted fragment length is 48 bps INFO @ Mon, 12 Aug 2019 22:28:57: #2 alternative fragment length(s) may be 2,16,48,548,598 bps INFO @ Mon, 12 Aug 2019 22:28:57: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX3981710/SRX3981710.20_model.r WARNING @ Mon, 12 Aug 2019 22:28:57: #2 Since the d (48) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 12 Aug 2019 22:28:57: #2 You may need to consider one of the other alternative d(s): 2,16,48,548,598 WARNING @ Mon, 12 Aug 2019 22:28:57: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Mon, 12 Aug 2019 22:28:57: #3 Call peaks... INFO @ Mon, 12 Aug 2019 22:28:57: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 12 Aug 2019 22:28:59: #2 number of paired peaks: 120 WARNING @ Mon, 12 Aug 2019 22:28:59: Fewer paired peaks (120) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 120 pairs to build model! INFO @ Mon, 12 Aug 2019 22:28:59: start model_add_line... INFO @ Mon, 12 Aug 2019 22:28:59: start X-correlation... INFO @ Mon, 12 Aug 2019 22:28:59: end of X-cor INFO @ Mon, 12 Aug 2019 22:28:59: #2 finished! INFO @ Mon, 12 Aug 2019 22:28:59: #2 predicted fragment length is 48 bps INFO @ Mon, 12 Aug 2019 22:28:59: #2 alternative fragment length(s) may be 2,16,48,548,598 bps INFO @ Mon, 12 Aug 2019 22:28:59: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX3981710/SRX3981710.10_model.r WARNING @ Mon, 12 Aug 2019 22:28:59: #2 Since the d (48) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 12 Aug 2019 22:28:59: #2 You may need to consider one of the other alternative d(s): 2,16,48,548,598 WARNING @ Mon, 12 Aug 2019 22:28:59: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Mon, 12 Aug 2019 22:28:59: #3 Call peaks... INFO @ Mon, 12 Aug 2019 22:28:59: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 12 Aug 2019 22:29:59: #3 Call peaks for each chromosome... INFO @ Mon, 12 Aug 2019 22:30:03: #3 Call peaks for each chromosome... INFO @ Mon, 12 Aug 2019 22:30:05: #3 Call peaks for each chromosome... INFO @ Mon, 12 Aug 2019 22:30:33: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX3981710/SRX3981710.05_peaks.xls INFO @ Mon, 12 Aug 2019 22:30:33: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX3981710/SRX3981710.05_peaks.narrowPeak INFO @ Mon, 12 Aug 2019 22:30:33: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX3981710/SRX3981710.05_summits.bed INFO @ Mon, 12 Aug 2019 22:30:33: Done! pass1 - making usageList (15 chroms): 2 millis pass2 - checking and writing primary data (2731 records, 4 fields): 8 millis CompletedMACS2peakCalling INFO @ Mon, 12 Aug 2019 22:30:35: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX3981710/SRX3981710.20_peaks.xls INFO @ Mon, 12 Aug 2019 22:30:35: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX3981710/SRX3981710.20_peaks.narrowPeak INFO @ Mon, 12 Aug 2019 22:30:35: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX3981710/SRX3981710.20_summits.bed INFO @ Mon, 12 Aug 2019 22:30:35: Done! pass1 - making usageList (8 chroms): 1 millis pass2 - checking and writing primary data (427 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Mon, 12 Aug 2019 22:30:37: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX3981710/SRX3981710.10_peaks.xls INFO @ Mon, 12 Aug 2019 22:30:37: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX3981710/SRX3981710.10_peaks.narrowPeak INFO @ Mon, 12 Aug 2019 22:30:37: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX3981710/SRX3981710.10_summits.bed INFO @ Mon, 12 Aug 2019 22:30:37: Done! pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (1353 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。