Job ID = 2590472 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 6,433,868 reads read : 12,867,736 reads written : 6,433,868 reads 0-length : 6,433,868 spots read : 6,416,684 reads read : 12,833,368 reads written : 6,416,684 reads 0-length : 6,416,684 spots read : 6,439,493 reads read : 12,878,986 reads written : 6,439,493 reads 0-length : 6,439,493 spots read : 6,474,761 reads read : 12,949,522 reads written : 6,474,761 reads 0-length : 6,474,761 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: 00:10:05 25764806 reads; of these: 25764806 (100.00%) were unpaired; of these: 1486020 (5.77%) aligned 0 times 17131789 (66.49%) aligned exactly 1 time 7146997 (27.74%) aligned >1 times 94.23% overall alignment rate Time searching: 00:10:05 Overall time: 00:10:05 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 12 files... [bam_rmdupse_core] 3703263 / 24278786 = 0.1525 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 22:15:54: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX3981703/SRX3981703.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX3981703/SRX3981703.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX3981703/SRX3981703.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX3981703/SRX3981703.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 22:15:54: #1 read tag files... INFO @ Mon, 12 Aug 2019 22:15:54: #1 read treatment tags... INFO @ Mon, 12 Aug 2019 22:15:55: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX3981703/SRX3981703.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX3981703/SRX3981703.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX3981703/SRX3981703.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX3981703/SRX3981703.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 22:15:55: #1 read tag files... INFO @ Mon, 12 Aug 2019 22:15:55: #1 read treatment tags... INFO @ Mon, 12 Aug 2019 22:15:56: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX3981703/SRX3981703.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX3981703/SRX3981703.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX3981703/SRX3981703.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX3981703/SRX3981703.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 22:15:56: #1 read tag files... INFO @ Mon, 12 Aug 2019 22:15:56: #1 read treatment tags... INFO @ Mon, 12 Aug 2019 22:16:02: 1000000 INFO @ Mon, 12 Aug 2019 22:16:04: 1000000 INFO @ Mon, 12 Aug 2019 22:16:04: 1000000 INFO @ Mon, 12 Aug 2019 22:16:09: 2000000 INFO @ Mon, 12 Aug 2019 22:16:12: 2000000 INFO @ Mon, 12 Aug 2019 22:16:13: 2000000 INFO @ Mon, 12 Aug 2019 22:16:16: 3000000 INFO @ Mon, 12 Aug 2019 22:16:20: 3000000 INFO @ Mon, 12 Aug 2019 22:16:22: 3000000 INFO @ Mon, 12 Aug 2019 22:16:23: 4000000 INFO @ Mon, 12 Aug 2019 22:16:27: 4000000 INFO @ Mon, 12 Aug 2019 22:16:30: 5000000 INFO @ Mon, 12 Aug 2019 22:16:32: 4000000 INFO @ Mon, 12 Aug 2019 22:16:35: 5000000 INFO @ Mon, 12 Aug 2019 22:16:37: 6000000 INFO @ Mon, 12 Aug 2019 22:16:41: 5000000 INFO @ Mon, 12 Aug 2019 22:16:43: 6000000 INFO @ Mon, 12 Aug 2019 22:16:44: 7000000 INFO @ Mon, 12 Aug 2019 22:16:50: 6000000 INFO @ Mon, 12 Aug 2019 22:16:50: 7000000 INFO @ Mon, 12 Aug 2019 22:16:51: 8000000 INFO @ Mon, 12 Aug 2019 22:16:58: 8000000 INFO @ Mon, 12 Aug 2019 22:16:58: 9000000 INFO @ Mon, 12 Aug 2019 22:16:59: 7000000 INFO @ Mon, 12 Aug 2019 22:17:05: 10000000 INFO @ Mon, 12 Aug 2019 22:17:06: 9000000 INFO @ Mon, 12 Aug 2019 22:17:08: 8000000 INFO @ Mon, 12 Aug 2019 22:17:12: 11000000 INFO @ Mon, 12 Aug 2019 22:17:14: 10000000 INFO @ Mon, 12 Aug 2019 22:17:17: 9000000 INFO @ Mon, 12 Aug 2019 22:17:19: 12000000 INFO @ Mon, 12 Aug 2019 22:17:22: 11000000 INFO @ Mon, 12 Aug 2019 22:17:26: 13000000 INFO @ Mon, 12 Aug 2019 22:17:27: 10000000 INFO @ Mon, 12 Aug 2019 22:17:29: 12000000 INFO @ Mon, 12 Aug 2019 22:17:33: 14000000 INFO @ Mon, 12 Aug 2019 22:17:36: 11000000 INFO @ Mon, 12 Aug 2019 22:17:37: 13000000 INFO @ Mon, 12 Aug 2019 22:17:40: 15000000 INFO @ Mon, 12 Aug 2019 22:17:45: 14000000 INFO @ Mon, 12 Aug 2019 22:17:45: 12000000 INFO @ Mon, 12 Aug 2019 22:17:47: 16000000 INFO @ Mon, 12 Aug 2019 22:17:52: 15000000 INFO @ Mon, 12 Aug 2019 22:17:54: 13000000 INFO @ Mon, 12 Aug 2019 22:17:54: 17000000 INFO @ Mon, 12 Aug 2019 22:18:00: 16000000 INFO @ Mon, 12 Aug 2019 22:18:01: 18000000 INFO @ Mon, 12 Aug 2019 22:18:03: 14000000 INFO @ Mon, 12 Aug 2019 22:18:07: 17000000 INFO @ Mon, 12 Aug 2019 22:18:08: 19000000 INFO @ Mon, 12 Aug 2019 22:18:12: 15000000 INFO @ Mon, 12 Aug 2019 22:18:15: 18000000 INFO @ Mon, 12 Aug 2019 22:18:16: 20000000 INFO @ Mon, 12 Aug 2019 22:18:20: #1 tag size is determined as 51 bps INFO @ Mon, 12 Aug 2019 22:18:20: #1 tag size = 51 INFO @ Mon, 12 Aug 2019 22:18:20: #1 total tags in treatment: 20575523 INFO @ Mon, 12 Aug 2019 22:18:20: #1 user defined the maximum tags... INFO @ Mon, 12 Aug 2019 22:18:20: #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 22:18:20: #1 tags after filtering in treatment: 20575523 INFO @ Mon, 12 Aug 2019 22:18:20: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 12 Aug 2019 22:18:20: #1 finished! INFO @ Mon, 12 Aug 2019 22:18:20: #2 Build Peak Model... INFO @ Mon, 12 Aug 2019 22:18:20: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 12 Aug 2019 22:18:21: 16000000 INFO @ Mon, 12 Aug 2019 22:18:22: #2 number of paired peaks: 110 WARNING @ Mon, 12 Aug 2019 22:18:22: Fewer paired peaks (110) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 110 pairs to build model! INFO @ Mon, 12 Aug 2019 22:18:22: start model_add_line... INFO @ Mon, 12 Aug 2019 22:18:22: start X-correlation... INFO @ Mon, 12 Aug 2019 22:18:22: end of X-cor INFO @ Mon, 12 Aug 2019 22:18:22: #2 finished! INFO @ Mon, 12 Aug 2019 22:18:22: #2 predicted fragment length is 48 bps INFO @ Mon, 12 Aug 2019 22:18:22: #2 alternative fragment length(s) may be 3,11,33,48,574 bps INFO @ Mon, 12 Aug 2019 22:18:22: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX3981703/SRX3981703.05_model.r WARNING @ Mon, 12 Aug 2019 22:18:22: #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 22:18:22: #2 You may need to consider one of the other alternative d(s): 3,11,33,48,574 WARNING @ Mon, 12 Aug 2019 22:18:22: #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 22:18:22: #3 Call peaks... INFO @ Mon, 12 Aug 2019 22:18:22: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 12 Aug 2019 22:18:23: 19000000 INFO @ Mon, 12 Aug 2019 22:18:30: 17000000 INFO @ Mon, 12 Aug 2019 22:18:30: 20000000 INFO @ Mon, 12 Aug 2019 22:18:35: #1 tag size is determined as 51 bps INFO @ Mon, 12 Aug 2019 22:18:35: #1 tag size = 51 INFO @ Mon, 12 Aug 2019 22:18:35: #1 total tags in treatment: 20575523 INFO @ Mon, 12 Aug 2019 22:18:35: #1 user defined the maximum tags... INFO @ Mon, 12 Aug 2019 22:18:35: #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 22:18:35: #1 tags after filtering in treatment: 20575523 INFO @ Mon, 12 Aug 2019 22:18:35: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 12 Aug 2019 22:18:35: #1 finished! INFO @ Mon, 12 Aug 2019 22:18:35: #2 Build Peak Model... INFO @ Mon, 12 Aug 2019 22:18:35: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 12 Aug 2019 22:18:37: #2 number of paired peaks: 110 WARNING @ Mon, 12 Aug 2019 22:18:37: Fewer paired peaks (110) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 110 pairs to build model! INFO @ Mon, 12 Aug 2019 22:18:37: start model_add_line... INFO @ Mon, 12 Aug 2019 22:18:37: start X-correlation... INFO @ Mon, 12 Aug 2019 22:18:37: end of X-cor INFO @ Mon, 12 Aug 2019 22:18:37: #2 finished! INFO @ Mon, 12 Aug 2019 22:18:37: #2 predicted fragment length is 48 bps INFO @ Mon, 12 Aug 2019 22:18:37: #2 alternative fragment length(s) may be 3,11,33,48,574 bps INFO @ Mon, 12 Aug 2019 22:18:37: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX3981703/SRX3981703.20_model.r WARNING @ Mon, 12 Aug 2019 22:18:37: #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 22:18:37: #2 You may need to consider one of the other alternative d(s): 3,11,33,48,574 WARNING @ Mon, 12 Aug 2019 22:18:37: #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 22:18:37: #3 Call peaks... INFO @ Mon, 12 Aug 2019 22:18:37: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 12 Aug 2019 22:18:39: 18000000 INFO @ Mon, 12 Aug 2019 22:18:48: 19000000 INFO @ Mon, 12 Aug 2019 22:18:57: 20000000 INFO @ Mon, 12 Aug 2019 22:19:02: #1 tag size is determined as 51 bps INFO @ Mon, 12 Aug 2019 22:19:02: #1 tag size = 51 INFO @ Mon, 12 Aug 2019 22:19:02: #1 total tags in treatment: 20575523 INFO @ Mon, 12 Aug 2019 22:19:02: #1 user defined the maximum tags... INFO @ Mon, 12 Aug 2019 22:19:02: #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 22:19:03: #1 tags after filtering in treatment: 20575523 INFO @ Mon, 12 Aug 2019 22:19:03: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 12 Aug 2019 22:19:03: #1 finished! INFO @ Mon, 12 Aug 2019 22:19:03: #2 Build Peak Model... INFO @ Mon, 12 Aug 2019 22:19:03: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 12 Aug 2019 22:19:04: #2 number of paired peaks: 110 WARNING @ Mon, 12 Aug 2019 22:19:04: Fewer paired peaks (110) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 110 pairs to build model! INFO @ Mon, 12 Aug 2019 22:19:04: start model_add_line... INFO @ Mon, 12 Aug 2019 22:19:05: start X-correlation... INFO @ Mon, 12 Aug 2019 22:19:05: end of X-cor INFO @ Mon, 12 Aug 2019 22:19:05: #2 finished! INFO @ Mon, 12 Aug 2019 22:19:05: #2 predicted fragment length is 48 bps INFO @ Mon, 12 Aug 2019 22:19:05: #2 alternative fragment length(s) may be 3,11,33,48,574 bps INFO @ Mon, 12 Aug 2019 22:19:05: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX3981703/SRX3981703.10_model.r WARNING @ Mon, 12 Aug 2019 22:19:05: #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 22:19:05: #2 You may need to consider one of the other alternative d(s): 3,11,33,48,574 WARNING @ Mon, 12 Aug 2019 22:19:05: #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 22:19:05: #3 Call peaks... INFO @ Mon, 12 Aug 2019 22:19:05: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 12 Aug 2019 22:19:14: #3 Call peaks for each chromosome... INFO @ Mon, 12 Aug 2019 22:19:29: #3 Call peaks for each chromosome... INFO @ Mon, 12 Aug 2019 22:19:39: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX3981703/SRX3981703.05_peaks.xls INFO @ Mon, 12 Aug 2019 22:19:39: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX3981703/SRX3981703.05_peaks.narrowPeak INFO @ Mon, 12 Aug 2019 22:19:39: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX3981703/SRX3981703.05_summits.bed INFO @ Mon, 12 Aug 2019 22:19:39: Done! pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (3016 records, 4 fields): 5 millis CompletedMACS2peakCalling INFO @ Mon, 12 Aug 2019 22:19:53: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX3981703/SRX3981703.20_peaks.xls INFO @ Mon, 12 Aug 2019 22:19:54: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX3981703/SRX3981703.20_peaks.narrowPeak INFO @ Mon, 12 Aug 2019 22:19:54: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX3981703/SRX3981703.20_summits.bed INFO @ Mon, 12 Aug 2019 22:19:54: Done! pass1 - making usageList (8 chroms): 2 millis pass2 - checking and writing primary data (816 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Mon, 12 Aug 2019 22:19:57: #3 Call peaks for each chromosome... INFO @ Mon, 12 Aug 2019 22:20:22: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX3981703/SRX3981703.10_peaks.xls INFO @ Mon, 12 Aug 2019 22:20:22: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX3981703/SRX3981703.10_peaks.narrowPeak INFO @ Mon, 12 Aug 2019 22:20:22: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX3981703/SRX3981703.10_summits.bed INFO @ Mon, 12 Aug 2019 22:20:22: Done! pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (1898 records, 4 fields): 7 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。