Job ID = 9371913 sra ファイルのダウンロード中... Completed: 930153K bytes transferred in 34 seconds (223233K bits/sec), in 1 file, 2 directories. sra ファイルのダウンロードが完了しました。 Read layout: SINGLE fastq に変換中... Written 37598583 spots for /home/okishinya/chipatlas/results/dm3/SRX2520637/SRR5206756.sra Written 37598583 spots total rm: cannot remove `[DSE]RR*.fastq': そのようなファイルやディレクトリはありません 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: 00:14:11 37598583 reads; of these: 37598583 (100.00%) were unpaired; of these: 7717550 (20.53%) aligned 0 times 21259396 (56.54%) aligned exactly 1 time 8621637 (22.93%) aligned >1 times 79.47% 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] 10530294 / 29881033 = 0.3524 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 @ Fri, 04 Aug 2017 15:12:04: # Command line: callpeak -t SRX2520637.bam -f BAM -g dm -n SRX2520637.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX2520637.10 # format = BAM # ChIP-seq file = ['SRX2520637.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 @ Fri, 04 Aug 2017 15:12:04: # Command line: callpeak -t SRX2520637.bam -f BAM -g dm -n SRX2520637.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX2520637.20 # format = BAM # ChIP-seq file = ['SRX2520637.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 @ Fri, 04 Aug 2017 15:12:04: # Command line: callpeak -t SRX2520637.bam -f BAM -g dm -n SRX2520637.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX2520637.05 # format = BAM # ChIP-seq file = ['SRX2520637.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 @ Fri, 04 Aug 2017 15:12:04: #1 read tag files... INFO @ Fri, 04 Aug 2017 15:12:04: #1 read tag files... INFO @ Fri, 04 Aug 2017 15:12:04: #1 read tag files... INFO @ Fri, 04 Aug 2017 15:12:04: #1 read treatment tags... INFO @ Fri, 04 Aug 2017 15:12:04: #1 read treatment tags... INFO @ Fri, 04 Aug 2017 15:12:04: #1 read treatment tags... INFO @ Fri, 04 Aug 2017 15:12:11: 1000000 INFO @ Fri, 04 Aug 2017 15:12:11: 1000000 INFO @ Fri, 04 Aug 2017 15:12:11: 1000000 INFO @ Fri, 04 Aug 2017 15:12:18: 2000000 INFO @ Fri, 04 Aug 2017 15:12:19: 2000000 INFO @ Fri, 04 Aug 2017 15:12:19: 2000000 INFO @ Fri, 04 Aug 2017 15:12:26: 3000000 INFO @ Fri, 04 Aug 2017 15:12:26: 3000000 INFO @ Fri, 04 Aug 2017 15:12:26: 3000000 INFO @ Fri, 04 Aug 2017 15:12:33: 4000000 INFO @ Fri, 04 Aug 2017 15:12:33: 4000000 INFO @ Fri, 04 Aug 2017 15:12:33: 4000000 INFO @ Fri, 04 Aug 2017 15:12:40: 5000000 INFO @ Fri, 04 Aug 2017 15:12:41: 5000000 INFO @ Fri, 04 Aug 2017 15:12:41: 5000000 INFO @ Fri, 04 Aug 2017 15:12:48: 6000000 INFO @ Fri, 04 Aug 2017 15:12:48: 6000000 INFO @ Fri, 04 Aug 2017 15:12:49: 6000000 INFO @ Fri, 04 Aug 2017 15:12:56: 7000000 INFO @ Fri, 04 Aug 2017 15:12:56: 7000000 INFO @ Fri, 04 Aug 2017 15:12:57: 7000000 INFO @ Fri, 04 Aug 2017 15:13:03: 8000000 INFO @ Fri, 04 Aug 2017 15:13:04: 8000000 INFO @ Fri, 04 Aug 2017 15:13:05: 8000000 INFO @ Fri, 04 Aug 2017 15:13:11: 9000000 INFO @ Fri, 04 Aug 2017 15:13:12: 9000000 INFO @ Fri, 04 Aug 2017 15:13:13: 9000000 INFO @ Fri, 04 Aug 2017 15:13:18: 10000000 INFO @ Fri, 04 Aug 2017 15:13:20: 10000000 INFO @ Fri, 04 Aug 2017 15:13:21: 10000000 INFO @ Fri, 04 Aug 2017 15:13:26: 11000000 INFO @ Fri, 04 Aug 2017 15:13:28: 11000000 INFO @ Fri, 04 Aug 2017 15:13:29: 11000000 INFO @ Fri, 04 Aug 2017 15:13:33: 12000000 INFO @ Fri, 04 Aug 2017 15:13:36: 12000000 INFO @ Fri, 04 Aug 2017 15:13:37: 12000000 INFO @ Fri, 04 Aug 2017 15:13:41: 13000000 INFO @ Fri, 04 Aug 2017 15:13:44: 13000000 INFO @ Fri, 04 Aug 2017 15:13:45: 13000000 INFO @ Fri, 04 Aug 2017 15:13:48: 14000000 INFO @ Fri, 04 Aug 2017 15:13:52: 14000000 INFO @ Fri, 04 Aug 2017 15:13:53: 14000000 INFO @ Fri, 04 Aug 2017 15:13:56: 15000000 INFO @ Fri, 04 Aug 2017 15:14:00: 15000000 INFO @ Fri, 04 Aug 2017 15:14:02: 15000000 INFO @ Fri, 04 Aug 2017 15:14:04: 16000000 INFO @ Fri, 04 Aug 2017 15:14:08: 16000000 INFO @ Fri, 04 Aug 2017 15:14:10: 16000000 INFO @ Fri, 04 Aug 2017 15:14:11: 17000000 INFO @ Fri, 04 Aug 2017 15:14:16: 17000000 INFO @ Fri, 04 Aug 2017 15:14:18: 17000000 INFO @ Fri, 04 Aug 2017 15:14:18: 18000000 INFO @ Fri, 04 Aug 2017 15:14:23: 18000000 INFO @ Fri, 04 Aug 2017 15:14:25: 19000000 INFO @ Fri, 04 Aug 2017 15:14:26: 18000000 INFO @ Fri, 04 Aug 2017 15:14:28: #1 tag size is determined as 50 bps INFO @ Fri, 04 Aug 2017 15:14:28: #1 tag size = 50 INFO @ Fri, 04 Aug 2017 15:14:28: #1 total tags in treatment: 19350739 INFO @ Fri, 04 Aug 2017 15:14:28: #1 user defined the maximum tags... INFO @ Fri, 04 Aug 2017 15:14:28: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 04 Aug 2017 15:14:28: #1 tags after filtering in treatment: 19350739 INFO @ Fri, 04 Aug 2017 15:14:28: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 04 Aug 2017 15:14:28: #1 finished! INFO @ Fri, 04 Aug 2017 15:14:28: #2 Build Peak Model... INFO @ Fri, 04 Aug 2017 15:14:28: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 04 Aug 2017 15:14:30: #2 number of paired peaks: 578 WARNING @ Fri, 04 Aug 2017 15:14:30: Fewer paired peaks (578) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 578 pairs to build model! INFO @ Fri, 04 Aug 2017 15:14:30: start model_add_line... INFO @ Fri, 04 Aug 2017 15:14:30: start X-correlation... INFO @ Fri, 04 Aug 2017 15:14:30: end of X-cor INFO @ Fri, 04 Aug 2017 15:14:30: #2 finished! INFO @ Fri, 04 Aug 2017 15:14:30: #2 predicted fragment length is 128 bps INFO @ Fri, 04 Aug 2017 15:14:30: #2 alternative fragment length(s) may be 128 bps INFO @ Fri, 04 Aug 2017 15:14:30: #2.2 Generate R script for model : SRX2520637.20_model.r INFO @ Fri, 04 Aug 2017 15:14:30: #3 Call peaks... INFO @ Fri, 04 Aug 2017 15:14:30: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 04 Aug 2017 15:14:31: 19000000 INFO @ Fri, 04 Aug 2017 15:14:34: 19000000 INFO @ Fri, 04 Aug 2017 15:14:34: #1 tag size is determined as 50 bps INFO @ Fri, 04 Aug 2017 15:14:34: #1 tag size = 50 INFO @ Fri, 04 Aug 2017 15:14:34: #1 total tags in treatment: 19350739 INFO @ Fri, 04 Aug 2017 15:14:34: #1 user defined the maximum tags... INFO @ Fri, 04 Aug 2017 15:14:34: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 04 Aug 2017 15:14:34: #1 tags after filtering in treatment: 19350739 INFO @ Fri, 04 Aug 2017 15:14:34: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 04 Aug 2017 15:14:34: #1 finished! INFO @ Fri, 04 Aug 2017 15:14:34: #2 Build Peak Model... INFO @ Fri, 04 Aug 2017 15:14:34: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 04 Aug 2017 15:14:36: #2 number of paired peaks: 578 WARNING @ Fri, 04 Aug 2017 15:14:36: Fewer paired peaks (578) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 578 pairs to build model! INFO @ Fri, 04 Aug 2017 15:14:36: start model_add_line... INFO @ Fri, 04 Aug 2017 15:14:36: start X-correlation... INFO @ Fri, 04 Aug 2017 15:14:36: end of X-cor INFO @ Fri, 04 Aug 2017 15:14:36: #2 finished! INFO @ Fri, 04 Aug 2017 15:14:36: #2 predicted fragment length is 128 bps INFO @ Fri, 04 Aug 2017 15:14:36: #2 alternative fragment length(s) may be 128 bps INFO @ Fri, 04 Aug 2017 15:14:36: #2.2 Generate R script for model : SRX2520637.10_model.r INFO @ Fri, 04 Aug 2017 15:14:36: #3 Call peaks... INFO @ Fri, 04 Aug 2017 15:14:36: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 04 Aug 2017 15:14:36: #1 tag size is determined as 50 bps INFO @ Fri, 04 Aug 2017 15:14:36: #1 tag size = 50 INFO @ Fri, 04 Aug 2017 15:14:36: #1 total tags in treatment: 19350739 INFO @ Fri, 04 Aug 2017 15:14:36: #1 user defined the maximum tags... INFO @ Fri, 04 Aug 2017 15:14:36: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 04 Aug 2017 15:14:37: #1 tags after filtering in treatment: 19350739 INFO @ Fri, 04 Aug 2017 15:14:37: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 04 Aug 2017 15:14:37: #1 finished! INFO @ Fri, 04 Aug 2017 15:14:37: #2 Build Peak Model... INFO @ Fri, 04 Aug 2017 15:14:37: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 04 Aug 2017 15:14:38: #2 number of paired peaks: 578 WARNING @ Fri, 04 Aug 2017 15:14:38: Fewer paired peaks (578) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 578 pairs to build model! INFO @ Fri, 04 Aug 2017 15:14:38: start model_add_line... INFO @ Fri, 04 Aug 2017 15:14:38: start X-correlation... INFO @ Fri, 04 Aug 2017 15:14:38: end of X-cor INFO @ Fri, 04 Aug 2017 15:14:38: #2 finished! INFO @ Fri, 04 Aug 2017 15:14:38: #2 predicted fragment length is 128 bps INFO @ Fri, 04 Aug 2017 15:14:38: #2 alternative fragment length(s) may be 128 bps INFO @ Fri, 04 Aug 2017 15:14:38: #2.2 Generate R script for model : SRX2520637.05_model.r INFO @ Fri, 04 Aug 2017 15:14:38: #3 Call peaks... INFO @ Fri, 04 Aug 2017 15:14:38: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 04 Aug 2017 15:15:11: #3 Call peaks for each chromosome... INFO @ Fri, 04 Aug 2017 15:15:19: #3 Call peaks for each chromosome... INFO @ Fri, 04 Aug 2017 15:15:20: #3 Call peaks for each chromosome... INFO @ Fri, 04 Aug 2017 15:15:34: #4 Write output xls file... SRX2520637.20_peaks.xls INFO @ Fri, 04 Aug 2017 15:15:34: #4 Write peak in narrowPeak format file... SRX2520637.20_peaks.narrowPeak INFO @ Fri, 04 Aug 2017 15:15:34: #4 Write summits bed file... SRX2520637.20_summits.bed INFO @ Fri, 04 Aug 2017 15:15:34: Done! pass1 - making usageList (14 chroms): 2 millis pass2 - checking and writing primary data (2467 records, 4 fields): 5 millis CompletedMACS2peakCalling INFO @ Fri, 04 Aug 2017 15:15:42: #4 Write output xls file... SRX2520637.10_peaks.xls INFO @ Fri, 04 Aug 2017 15:15:42: #4 Write peak in narrowPeak format file... SRX2520637.10_peaks.narrowPeak INFO @ Fri, 04 Aug 2017 15:15:42: #4 Write summits bed file... SRX2520637.10_summits.bed INFO @ Fri, 04 Aug 2017 15:15:42: Done! pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (4169 records, 4 fields): 7 millis CompletedMACS2peakCalling INFO @ Fri, 04 Aug 2017 15:15:43: #4 Write output xls file... SRX2520637.05_peaks.xls INFO @ Fri, 04 Aug 2017 15:15:43: #4 Write peak in narrowPeak format file... SRX2520637.05_peaks.narrowPeak INFO @ Fri, 04 Aug 2017 15:15:43: #4 Write summits bed file... SRX2520637.05_summits.bed INFO @ Fri, 04 Aug 2017 15:15:43: Done! pass1 - making usageList (15 chroms): 2 millis pass2 - checking and writing primary data (6239 records, 4 fields): 9 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。