Job ID = 2590475 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 6,954,252 reads read : 13,908,504 reads written : 6,954,252 reads 0-length : 6,954,252 spots read : 6,944,475 reads read : 13,888,950 reads written : 6,944,475 reads 0-length : 6,944,475 spots read : 6,977,943 reads read : 13,955,886 reads written : 6,977,943 reads 0-length : 6,977,943 spots read : 7,005,644 reads read : 14,011,288 reads written : 7,005,644 reads 0-length : 7,005,644 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: 00:10:36 27882314 reads; of these: 27882314 (100.00%) were unpaired; of these: 1181051 (4.24%) aligned 0 times 19522388 (70.02%) aligned exactly 1 time 7178875 (25.75%) aligned >1 times 95.76% overall alignment rate Time searching: 00:10:36 Overall time: 00:10:36 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] 3208897 / 26701263 = 0.1202 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 22:18:34: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX3981705/SRX3981705.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX3981705/SRX3981705.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX3981705/SRX3981705.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX3981705/SRX3981705.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 22:18:34: #1 read tag files... INFO @ Mon, 12 Aug 2019 22:18:34: #1 read treatment tags... INFO @ Mon, 12 Aug 2019 22:18:35: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX3981705/SRX3981705.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX3981705/SRX3981705.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX3981705/SRX3981705.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX3981705/SRX3981705.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 22:18:35: #1 read tag files... INFO @ Mon, 12 Aug 2019 22:18:35: #1 read treatment tags... INFO @ Mon, 12 Aug 2019 22:18:36: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX3981705/SRX3981705.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX3981705/SRX3981705.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX3981705/SRX3981705.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX3981705/SRX3981705.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 22:18:36: #1 read tag files... INFO @ Mon, 12 Aug 2019 22:18:36: #1 read treatment tags... INFO @ Mon, 12 Aug 2019 22:18:41: 1000000 INFO @ Mon, 12 Aug 2019 22:18:42: 1000000 INFO @ Mon, 12 Aug 2019 22:18:44: 1000000 INFO @ Mon, 12 Aug 2019 22:18:48: 2000000 INFO @ Mon, 12 Aug 2019 22:18:49: 2000000 INFO @ Mon, 12 Aug 2019 22:18:52: 2000000 INFO @ Mon, 12 Aug 2019 22:18:55: 3000000 INFO @ Mon, 12 Aug 2019 22:18:56: 3000000 INFO @ Mon, 12 Aug 2019 22:18:59: 3000000 INFO @ Mon, 12 Aug 2019 22:19:02: 4000000 INFO @ Mon, 12 Aug 2019 22:19:03: 4000000 INFO @ Mon, 12 Aug 2019 22:19:07: 4000000 INFO @ Mon, 12 Aug 2019 22:19:08: 5000000 INFO @ Mon, 12 Aug 2019 22:19:10: 5000000 INFO @ Mon, 12 Aug 2019 22:19:14: 5000000 INFO @ Mon, 12 Aug 2019 22:19:15: 6000000 INFO @ Mon, 12 Aug 2019 22:19:17: 6000000 INFO @ Mon, 12 Aug 2019 22:19:22: 6000000 INFO @ Mon, 12 Aug 2019 22:19:22: 7000000 INFO @ Mon, 12 Aug 2019 22:19:24: 7000000 INFO @ Mon, 12 Aug 2019 22:19:29: 8000000 INFO @ Mon, 12 Aug 2019 22:19:29: 7000000 INFO @ Mon, 12 Aug 2019 22:19:31: 8000000 INFO @ Mon, 12 Aug 2019 22:19:36: 9000000 INFO @ Mon, 12 Aug 2019 22:19:37: 8000000 INFO @ Mon, 12 Aug 2019 22:19:38: 9000000 INFO @ Mon, 12 Aug 2019 22:19:43: 10000000 INFO @ Mon, 12 Aug 2019 22:19:44: 9000000 INFO @ Mon, 12 Aug 2019 22:19:45: 10000000 INFO @ Mon, 12 Aug 2019 22:19:49: 11000000 INFO @ Mon, 12 Aug 2019 22:19:51: 11000000 INFO @ Mon, 12 Aug 2019 22:19:52: 10000000 INFO @ Mon, 12 Aug 2019 22:19:56: 12000000 INFO @ Mon, 12 Aug 2019 22:19:58: 12000000 INFO @ Mon, 12 Aug 2019 22:19:59: 11000000 INFO @ Mon, 12 Aug 2019 22:20:03: 13000000 INFO @ Mon, 12 Aug 2019 22:20:05: 13000000 INFO @ Mon, 12 Aug 2019 22:20:07: 12000000 INFO @ Mon, 12 Aug 2019 22:20:10: 14000000 INFO @ Mon, 12 Aug 2019 22:20:12: 14000000 INFO @ Mon, 12 Aug 2019 22:20:14: 13000000 INFO @ Mon, 12 Aug 2019 22:20:17: 15000000 INFO @ Mon, 12 Aug 2019 22:20:19: 15000000 INFO @ Mon, 12 Aug 2019 22:20:22: 14000000 INFO @ Mon, 12 Aug 2019 22:20:24: 16000000 INFO @ Mon, 12 Aug 2019 22:20:26: 16000000 INFO @ Mon, 12 Aug 2019 22:20:29: 15000000 INFO @ Mon, 12 Aug 2019 22:20:31: 17000000 INFO @ Mon, 12 Aug 2019 22:20:33: 17000000 INFO @ Mon, 12 Aug 2019 22:20:37: 16000000 INFO @ Mon, 12 Aug 2019 22:20:38: 18000000 INFO @ Mon, 12 Aug 2019 22:20:40: 18000000 INFO @ Mon, 12 Aug 2019 22:20:44: 17000000 INFO @ Mon, 12 Aug 2019 22:20:44: 19000000 INFO @ Mon, 12 Aug 2019 22:20:47: 19000000 INFO @ Mon, 12 Aug 2019 22:20:51: 20000000 INFO @ Mon, 12 Aug 2019 22:20:52: 18000000 INFO @ Mon, 12 Aug 2019 22:20:54: 20000000 INFO @ Mon, 12 Aug 2019 22:20:58: 21000000 INFO @ Mon, 12 Aug 2019 22:20:59: 19000000 INFO @ Mon, 12 Aug 2019 22:21:01: 21000000 INFO @ Mon, 12 Aug 2019 22:21:05: 22000000 INFO @ Mon, 12 Aug 2019 22:21:07: 20000000 INFO @ Mon, 12 Aug 2019 22:21:08: 22000000 INFO @ Mon, 12 Aug 2019 22:21:12: 23000000 INFO @ Mon, 12 Aug 2019 22:21:15: 23000000 INFO @ Mon, 12 Aug 2019 22:21:15: 21000000 INFO @ Mon, 12 Aug 2019 22:21:16: #1 tag size is determined as 51 bps INFO @ Mon, 12 Aug 2019 22:21:16: #1 tag size = 51 INFO @ Mon, 12 Aug 2019 22:21:16: #1 total tags in treatment: 23492366 INFO @ Mon, 12 Aug 2019 22:21:16: #1 user defined the maximum tags... INFO @ Mon, 12 Aug 2019 22:21:16: #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 22:21:16: #1 tags after filtering in treatment: 23492366 INFO @ Mon, 12 Aug 2019 22:21:16: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 12 Aug 2019 22:21:16: #1 finished! INFO @ Mon, 12 Aug 2019 22:21:16: #2 Build Peak Model... INFO @ Mon, 12 Aug 2019 22:21:16: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 12 Aug 2019 22:21:18: #1 tag size is determined as 51 bps INFO @ Mon, 12 Aug 2019 22:21:18: #1 tag size = 51 INFO @ Mon, 12 Aug 2019 22:21:18: #1 total tags in treatment: 23492366 INFO @ Mon, 12 Aug 2019 22:21:18: #1 user defined the maximum tags... INFO @ Mon, 12 Aug 2019 22:21:18: #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 22:21:18: #2 number of paired peaks: 245 WARNING @ Mon, 12 Aug 2019 22:21:18: Fewer paired peaks (245) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 245 pairs to build model! INFO @ Mon, 12 Aug 2019 22:21:18: start model_add_line... INFO @ Mon, 12 Aug 2019 22:21:18: start X-correlation... INFO @ Mon, 12 Aug 2019 22:21:18: end of X-cor INFO @ Mon, 12 Aug 2019 22:21:18: #2 finished! INFO @ Mon, 12 Aug 2019 22:21:18: #2 predicted fragment length is 40 bps INFO @ Mon, 12 Aug 2019 22:21:18: #2 alternative fragment length(s) may be 2,40,50,596 bps INFO @ Mon, 12 Aug 2019 22:21:18: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX3981705/SRX3981705.05_model.r WARNING @ Mon, 12 Aug 2019 22:21:18: #2 Since the d (40) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 12 Aug 2019 22:21:18: #2 You may need to consider one of the other alternative d(s): 2,40,50,596 WARNING @ Mon, 12 Aug 2019 22:21:18: #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 22:21:18: #3 Call peaks... INFO @ Mon, 12 Aug 2019 22:21:18: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 12 Aug 2019 22:21:19: #1 tags after filtering in treatment: 23492366 INFO @ Mon, 12 Aug 2019 22:21:19: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 12 Aug 2019 22:21:19: #1 finished! INFO @ Mon, 12 Aug 2019 22:21:19: #2 Build Peak Model... INFO @ Mon, 12 Aug 2019 22:21:19: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 12 Aug 2019 22:21:21: #2 number of paired peaks: 245 WARNING @ Mon, 12 Aug 2019 22:21:21: Fewer paired peaks (245) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 245 pairs to build model! INFO @ Mon, 12 Aug 2019 22:21:21: start model_add_line... INFO @ Mon, 12 Aug 2019 22:21:21: start X-correlation... INFO @ Mon, 12 Aug 2019 22:21:21: end of X-cor INFO @ Mon, 12 Aug 2019 22:21:21: #2 finished! INFO @ Mon, 12 Aug 2019 22:21:21: #2 predicted fragment length is 40 bps INFO @ Mon, 12 Aug 2019 22:21:21: #2 alternative fragment length(s) may be 2,40,50,596 bps INFO @ Mon, 12 Aug 2019 22:21:21: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX3981705/SRX3981705.10_model.r WARNING @ Mon, 12 Aug 2019 22:21:21: #2 Since the d (40) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 12 Aug 2019 22:21:21: #2 You may need to consider one of the other alternative d(s): 2,40,50,596 WARNING @ Mon, 12 Aug 2019 22:21:21: #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 22:21:21: #3 Call peaks... INFO @ Mon, 12 Aug 2019 22:21:21: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 12 Aug 2019 22:21:22: 22000000 INFO @ Mon, 12 Aug 2019 22:21:29: 23000000 INFO @ Mon, 12 Aug 2019 22:21:33: #1 tag size is determined as 51 bps INFO @ Mon, 12 Aug 2019 22:21:33: #1 tag size = 51 INFO @ Mon, 12 Aug 2019 22:21:33: #1 total tags in treatment: 23492366 INFO @ Mon, 12 Aug 2019 22:21:33: #1 user defined the maximum tags... INFO @ Mon, 12 Aug 2019 22:21:33: #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 22:21:34: #1 tags after filtering in treatment: 23492366 INFO @ Mon, 12 Aug 2019 22:21:34: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 12 Aug 2019 22:21:34: #1 finished! INFO @ Mon, 12 Aug 2019 22:21:34: #2 Build Peak Model... INFO @ Mon, 12 Aug 2019 22:21:34: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 12 Aug 2019 22:21:36: #2 number of paired peaks: 245 WARNING @ Mon, 12 Aug 2019 22:21:36: Fewer paired peaks (245) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 245 pairs to build model! INFO @ Mon, 12 Aug 2019 22:21:36: start model_add_line... INFO @ Mon, 12 Aug 2019 22:21:36: start X-correlation... INFO @ Mon, 12 Aug 2019 22:21:36: end of X-cor INFO @ Mon, 12 Aug 2019 22:21:36: #2 finished! INFO @ Mon, 12 Aug 2019 22:21:36: #2 predicted fragment length is 40 bps INFO @ Mon, 12 Aug 2019 22:21:36: #2 alternative fragment length(s) may be 2,40,50,596 bps INFO @ Mon, 12 Aug 2019 22:21:36: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX3981705/SRX3981705.20_model.r WARNING @ Mon, 12 Aug 2019 22:21:36: #2 Since the d (40) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 12 Aug 2019 22:21:36: #2 You may need to consider one of the other alternative d(s): 2,40,50,596 WARNING @ Mon, 12 Aug 2019 22:21:36: #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 22:21:36: #3 Call peaks... INFO @ Mon, 12 Aug 2019 22:21:36: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 12 Aug 2019 22:22:15: #3 Call peaks for each chromosome... INFO @ Mon, 12 Aug 2019 22:22:17: #3 Call peaks for each chromosome... INFO @ Mon, 12 Aug 2019 22:22:32: #3 Call peaks for each chromosome... INFO @ Mon, 12 Aug 2019 22:22:41: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX3981705/SRX3981705.05_peaks.xls INFO @ Mon, 12 Aug 2019 22:22:42: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX3981705/SRX3981705.05_peaks.narrowPeak INFO @ Mon, 12 Aug 2019 22:22:42: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX3981705/SRX3981705.05_summits.bed INFO @ Mon, 12 Aug 2019 22:22:42: Done! pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (2648 records, 4 fields): 6 millis CompletedMACS2peakCalling INFO @ Mon, 12 Aug 2019 22:22:44: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX3981705/SRX3981705.10_peaks.xls INFO @ Mon, 12 Aug 2019 22:22:44: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX3981705/SRX3981705.10_peaks.narrowPeak INFO @ Mon, 12 Aug 2019 22:22:44: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX3981705/SRX3981705.10_summits.bed INFO @ Mon, 12 Aug 2019 22:22:44: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (1303 records, 4 fields): 5 millis CompletedMACS2peakCalling INFO @ Mon, 12 Aug 2019 22:22:58: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX3981705/SRX3981705.20_peaks.xls INFO @ Mon, 12 Aug 2019 22:22:58: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX3981705/SRX3981705.20_peaks.narrowPeak INFO @ Mon, 12 Aug 2019 22:22:58: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX3981705/SRX3981705.20_summits.bed INFO @ Mon, 12 Aug 2019 22:22:58: Done! pass1 - making usageList (8 chroms): 1 millis pass2 - checking and writing primary data (393 records, 4 fields): 3 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。