Job ID = 2590487 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 9,011,846 reads read : 18,023,692 reads written : 9,011,846 reads 0-length : 9,011,846 spots read : 9,007,716 reads read : 18,015,432 reads written : 9,007,716 reads 0-length : 9,007,716 spots read : 9,042,470 reads read : 18,084,940 reads written : 9,042,470 reads 0-length : 9,042,470 spots read : 9,080,127 reads read : 18,160,254 reads written : 9,080,127 reads 0-length : 9,080,127 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: 00:14:10 36142159 reads; of these: 36142159 (100.00%) were unpaired; of these: 1142952 (3.16%) aligned 0 times 25995294 (71.93%) aligned exactly 1 time 9003913 (24.91%) aligned >1 times 96.84% overall alignment rate Time searching: 00:14:11 Overall time: 00:14:11 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] 5173385 / 34999207 = 0.1478 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 22:29:00: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX3981715/SRX3981715.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX3981715/SRX3981715.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX3981715/SRX3981715.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX3981715/SRX3981715.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 22:29:00: #1 read tag files... INFO @ Mon, 12 Aug 2019 22:29:00: #1 read treatment tags... INFO @ Mon, 12 Aug 2019 22:29:01: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX3981715/SRX3981715.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX3981715/SRX3981715.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX3981715/SRX3981715.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX3981715/SRX3981715.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 22:29:01: #1 read tag files... INFO @ Mon, 12 Aug 2019 22:29:01: #1 read treatment tags... INFO @ Mon, 12 Aug 2019 22:29:02: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX3981715/SRX3981715.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX3981715/SRX3981715.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX3981715/SRX3981715.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX3981715/SRX3981715.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 22:29:02: #1 read tag files... INFO @ Mon, 12 Aug 2019 22:29:02: #1 read treatment tags... INFO @ Mon, 12 Aug 2019 22:29:07: 1000000 INFO @ Mon, 12 Aug 2019 22:29:08: 1000000 INFO @ Mon, 12 Aug 2019 22:29:09: 1000000 INFO @ Mon, 12 Aug 2019 22:29:15: 2000000 INFO @ Mon, 12 Aug 2019 22:29:16: 2000000 INFO @ Mon, 12 Aug 2019 22:29:16: 2000000 INFO @ Mon, 12 Aug 2019 22:29:21: 3000000 INFO @ Mon, 12 Aug 2019 22:29:22: 3000000 INFO @ Mon, 12 Aug 2019 22:29:23: 3000000 INFO @ Mon, 12 Aug 2019 22:29:28: 4000000 INFO @ Mon, 12 Aug 2019 22:29:29: 4000000 INFO @ Mon, 12 Aug 2019 22:29:30: 4000000 INFO @ Mon, 12 Aug 2019 22:29:35: 5000000 INFO @ Mon, 12 Aug 2019 22:29:36: 5000000 INFO @ Mon, 12 Aug 2019 22:29:36: 5000000 INFO @ Mon, 12 Aug 2019 22:29:41: 6000000 INFO @ Mon, 12 Aug 2019 22:29:42: 6000000 INFO @ Mon, 12 Aug 2019 22:29:43: 6000000 INFO @ Mon, 12 Aug 2019 22:29:48: 7000000 INFO @ Mon, 12 Aug 2019 22:29:49: 7000000 INFO @ Mon, 12 Aug 2019 22:29:49: 7000000 INFO @ Mon, 12 Aug 2019 22:29:55: 8000000 INFO @ Mon, 12 Aug 2019 22:29:56: 8000000 INFO @ Mon, 12 Aug 2019 22:29:56: 8000000 INFO @ Mon, 12 Aug 2019 22:30:01: 9000000 INFO @ Mon, 12 Aug 2019 22:30:02: 9000000 INFO @ Mon, 12 Aug 2019 22:30:03: 9000000 INFO @ Mon, 12 Aug 2019 22:30:08: 10000000 INFO @ Mon, 12 Aug 2019 22:30:09: 10000000 INFO @ Mon, 12 Aug 2019 22:30:09: 10000000 INFO @ Mon, 12 Aug 2019 22:30:15: 11000000 INFO @ Mon, 12 Aug 2019 22:30:16: 11000000 INFO @ Mon, 12 Aug 2019 22:30:16: 11000000 INFO @ Mon, 12 Aug 2019 22:30:21: 12000000 INFO @ Mon, 12 Aug 2019 22:30:22: 12000000 INFO @ Mon, 12 Aug 2019 22:30:23: 12000000 INFO @ Mon, 12 Aug 2019 22:30:28: 13000000 INFO @ Mon, 12 Aug 2019 22:30:29: 13000000 INFO @ Mon, 12 Aug 2019 22:30:29: 13000000 INFO @ Mon, 12 Aug 2019 22:30:35: 14000000 INFO @ Mon, 12 Aug 2019 22:30:36: 14000000 INFO @ Mon, 12 Aug 2019 22:30:36: 14000000 INFO @ Mon, 12 Aug 2019 22:30:41: 15000000 INFO @ Mon, 12 Aug 2019 22:30:43: 15000000 INFO @ Mon, 12 Aug 2019 22:30:43: 15000000 INFO @ Mon, 12 Aug 2019 22:30:48: 16000000 INFO @ Mon, 12 Aug 2019 22:30:49: 16000000 INFO @ Mon, 12 Aug 2019 22:30:49: 16000000 INFO @ Mon, 12 Aug 2019 22:30:55: 17000000 INFO @ Mon, 12 Aug 2019 22:30:56: 17000000 INFO @ Mon, 12 Aug 2019 22:30:56: 17000000 INFO @ Mon, 12 Aug 2019 22:31:01: 18000000 INFO @ Mon, 12 Aug 2019 22:31:02: 18000000 INFO @ Mon, 12 Aug 2019 22:31:03: 18000000 INFO @ Mon, 12 Aug 2019 22:31:08: 19000000 INFO @ Mon, 12 Aug 2019 22:31:09: 19000000 INFO @ Mon, 12 Aug 2019 22:31:09: 19000000 INFO @ Mon, 12 Aug 2019 22:31:15: 20000000 INFO @ Mon, 12 Aug 2019 22:31:16: 20000000 INFO @ Mon, 12 Aug 2019 22:31:16: 20000000 INFO @ Mon, 12 Aug 2019 22:31:21: 21000000 INFO @ Mon, 12 Aug 2019 22:31:23: 21000000 INFO @ Mon, 12 Aug 2019 22:31:23: 21000000 INFO @ Mon, 12 Aug 2019 22:31:28: 22000000 INFO @ Mon, 12 Aug 2019 22:31:29: 22000000 INFO @ Mon, 12 Aug 2019 22:31:29: 22000000 INFO @ Mon, 12 Aug 2019 22:31:34: 23000000 INFO @ Mon, 12 Aug 2019 22:31:36: 23000000 INFO @ Mon, 12 Aug 2019 22:31:36: 23000000 INFO @ Mon, 12 Aug 2019 22:31:41: 24000000 INFO @ Mon, 12 Aug 2019 22:31:42: 24000000 INFO @ Mon, 12 Aug 2019 22:31:43: 24000000 INFO @ Mon, 12 Aug 2019 22:31:48: 25000000 INFO @ Mon, 12 Aug 2019 22:31:49: 25000000 INFO @ Mon, 12 Aug 2019 22:31:49: 25000000 INFO @ Mon, 12 Aug 2019 22:31:54: 26000000 INFO @ Mon, 12 Aug 2019 22:31:56: 26000000 INFO @ Mon, 12 Aug 2019 22:31:56: 26000000 INFO @ Mon, 12 Aug 2019 22:32:01: 27000000 INFO @ Mon, 12 Aug 2019 22:32:02: 27000000 INFO @ Mon, 12 Aug 2019 22:32:03: 27000000 INFO @ Mon, 12 Aug 2019 22:32:08: 28000000 INFO @ Mon, 12 Aug 2019 22:32:09: 28000000 INFO @ Mon, 12 Aug 2019 22:32:09: 28000000 INFO @ Mon, 12 Aug 2019 22:32:14: 29000000 INFO @ Mon, 12 Aug 2019 22:32:15: 29000000 INFO @ Mon, 12 Aug 2019 22:32:16: 29000000 INFO @ Mon, 12 Aug 2019 22:32:20: #1 tag size is determined as 51 bps INFO @ Mon, 12 Aug 2019 22:32:20: #1 tag size = 51 INFO @ Mon, 12 Aug 2019 22:32:20: #1 total tags in treatment: 29825822 INFO @ Mon, 12 Aug 2019 22:32:20: #1 user defined the maximum tags... INFO @ Mon, 12 Aug 2019 22:32:20: #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 22:32:21: #1 tags after filtering in treatment: 29825822 INFO @ Mon, 12 Aug 2019 22:32:21: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 12 Aug 2019 22:32:21: #1 finished! INFO @ Mon, 12 Aug 2019 22:32:21: #2 Build Peak Model... INFO @ Mon, 12 Aug 2019 22:32:21: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 12 Aug 2019 22:32:21: #1 tag size is determined as 51 bps INFO @ Mon, 12 Aug 2019 22:32:21: #1 tag size = 51 INFO @ Mon, 12 Aug 2019 22:32:21: #1 total tags in treatment: 29825822 INFO @ Mon, 12 Aug 2019 22:32:21: #1 user defined the maximum tags... INFO @ Mon, 12 Aug 2019 22:32:21: #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 22:32:22: #1 tag size is determined as 51 bps INFO @ Mon, 12 Aug 2019 22:32:22: #1 tag size = 51 INFO @ Mon, 12 Aug 2019 22:32:22: #1 total tags in treatment: 29825822 INFO @ Mon, 12 Aug 2019 22:32:22: #1 user defined the maximum tags... INFO @ Mon, 12 Aug 2019 22:32:22: #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 22:32:22: #1 tags after filtering in treatment: 29825822 INFO @ Mon, 12 Aug 2019 22:32:22: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 12 Aug 2019 22:32:22: #1 finished! INFO @ Mon, 12 Aug 2019 22:32:22: #2 Build Peak Model... INFO @ Mon, 12 Aug 2019 22:32:22: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 12 Aug 2019 22:32:22: #1 tags after filtering in treatment: 29825822 INFO @ Mon, 12 Aug 2019 22:32:22: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 12 Aug 2019 22:32:22: #1 finished! INFO @ Mon, 12 Aug 2019 22:32:22: #2 Build Peak Model... INFO @ Mon, 12 Aug 2019 22:32:22: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 12 Aug 2019 22:32:23: #2 number of paired peaks: 166 WARNING @ Mon, 12 Aug 2019 22:32:23: Fewer paired peaks (166) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 166 pairs to build model! INFO @ Mon, 12 Aug 2019 22:32:23: start model_add_line... INFO @ Mon, 12 Aug 2019 22:32:24: start X-correlation... INFO @ Mon, 12 Aug 2019 22:32:24: end of X-cor INFO @ Mon, 12 Aug 2019 22:32:24: #2 finished! INFO @ Mon, 12 Aug 2019 22:32:24: #2 predicted fragment length is 1 bps INFO @ Mon, 12 Aug 2019 22:32:24: #2 alternative fragment length(s) may be 1,42,58,594,596 bps INFO @ Mon, 12 Aug 2019 22:32:24: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX3981715/SRX3981715.05_model.r WARNING @ Mon, 12 Aug 2019 22:32:24: #2 Since the d (1) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 12 Aug 2019 22:32:24: #2 You may need to consider one of the other alternative d(s): 1,42,58,594,596 WARNING @ Mon, 12 Aug 2019 22:32:24: #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 22:32:24: #3 Call peaks... INFO @ Mon, 12 Aug 2019 22:32:24: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 12 Aug 2019 22:32:24: #2 number of paired peaks: 166 WARNING @ Mon, 12 Aug 2019 22:32:24: Fewer paired peaks (166) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 166 pairs to build model! INFO @ Mon, 12 Aug 2019 22:32:24: start model_add_line... INFO @ Mon, 12 Aug 2019 22:32:25: start X-correlation... INFO @ Mon, 12 Aug 2019 22:32:25: end of X-cor INFO @ Mon, 12 Aug 2019 22:32:25: #2 finished! INFO @ Mon, 12 Aug 2019 22:32:25: #2 predicted fragment length is 1 bps INFO @ Mon, 12 Aug 2019 22:32:25: #2 alternative fragment length(s) may be 1,42,58,594,596 bps INFO @ Mon, 12 Aug 2019 22:32:25: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX3981715/SRX3981715.20_model.r WARNING @ Mon, 12 Aug 2019 22:32:25: #2 Since the d (1) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 12 Aug 2019 22:32:25: #2 You may need to consider one of the other alternative d(s): 1,42,58,594,596 WARNING @ Mon, 12 Aug 2019 22:32:25: #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 22:32:25: #3 Call peaks... INFO @ Mon, 12 Aug 2019 22:32:25: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 12 Aug 2019 22:32:25: #2 number of paired peaks: 166 WARNING @ Mon, 12 Aug 2019 22:32:25: Fewer paired peaks (166) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 166 pairs to build model! INFO @ Mon, 12 Aug 2019 22:32:25: start model_add_line... INFO @ Mon, 12 Aug 2019 22:32:25: start X-correlation... INFO @ Mon, 12 Aug 2019 22:32:25: end of X-cor INFO @ Mon, 12 Aug 2019 22:32:25: #2 finished! INFO @ Mon, 12 Aug 2019 22:32:25: #2 predicted fragment length is 1 bps INFO @ Mon, 12 Aug 2019 22:32:25: #2 alternative fragment length(s) may be 1,42,58,594,596 bps INFO @ Mon, 12 Aug 2019 22:32:25: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX3981715/SRX3981715.10_model.r WARNING @ Mon, 12 Aug 2019 22:32:25: #2 Since the d (1) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 12 Aug 2019 22:32:25: #2 You may need to consider one of the other alternative d(s): 1,42,58,594,596 WARNING @ Mon, 12 Aug 2019 22:32:25: #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 22:32:25: #3 Call peaks... INFO @ Mon, 12 Aug 2019 22:32:25: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 12 Aug 2019 22:33:27: #3 Call peaks for each chromosome... INFO @ Mon, 12 Aug 2019 22:33:28: #3 Call peaks for each chromosome... INFO @ Mon, 12 Aug 2019 22:33:28: #3 Call peaks for each chromosome... INFO @ Mon, 12 Aug 2019 22:33:56: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX3981715/SRX3981715.05_peaks.xls INFO @ Mon, 12 Aug 2019 22:33:56: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX3981715/SRX3981715.05_peaks.narrowPeak INFO @ Mon, 12 Aug 2019 22:33:56: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX3981715/SRX3981715.05_summits.bed INFO @ Mon, 12 Aug 2019 22:33:56: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling INFO @ Mon, 12 Aug 2019 22:33:57: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX3981715/SRX3981715.20_peaks.xls INFO @ Mon, 12 Aug 2019 22:33:57: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX3981715/SRX3981715.20_peaks.narrowPeak INFO @ Mon, 12 Aug 2019 22:33:57: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX3981715/SRX3981715.20_summits.bed INFO @ Mon, 12 Aug 2019 22:33:57: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling INFO @ Mon, 12 Aug 2019 22:33:57: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX3981715/SRX3981715.10_peaks.xls INFO @ Mon, 12 Aug 2019 22:33:57: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX3981715/SRX3981715.10_peaks.narrowPeak INFO @ Mon, 12 Aug 2019 22:33:57: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX3981715/SRX3981715.10_summits.bed INFO @ Mon, 12 Aug 2019 22:33:57: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。