Job ID = 9371432 sra ファイルのダウンロード中... Completed: 587603K bytes transferred in 10 seconds (443942K 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 26821883 spots for /home/okishinya/chipatlas/results/dm3/SRX2520633/SRR5206752.sra Written 26821883 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: 00:00:01 Time loading forward index: 00:00:00 Time loading mirror index: 00:00:00 Multiseed full-index search: 00:16:55 26821883 reads; of these: 26821883 (100.00%) were unpaired; of these: 667782 (2.49%) aligned 0 times 20733490 (77.30%) aligned exactly 1 time 5420611 (20.21%) aligned >1 times 97.51% overall alignment rate Time searching: 00:16:56 Overall time: 00:16:56 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] 6802530 / 26154101 = 0.2601 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 14:26:42: # Command line: callpeak -t SRX2520633.bam -f BAM -g dm -n SRX2520633.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX2520633.05 # format = BAM # ChIP-seq file = ['SRX2520633.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 14:26:42: #1 read tag files... INFO @ Fri, 04 Aug 2017 14:26:42: #1 read treatment tags... INFO @ Fri, 04 Aug 2017 14:26:42: # Command line: callpeak -t SRX2520633.bam -f BAM -g dm -n SRX2520633.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX2520633.10 # format = BAM # ChIP-seq file = ['SRX2520633.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 14:26:42: # Command line: callpeak -t SRX2520633.bam -f BAM -g dm -n SRX2520633.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX2520633.20 # format = BAM # ChIP-seq file = ['SRX2520633.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 14:26:42: #1 read tag files... INFO @ Fri, 04 Aug 2017 14:26:42: #1 read tag files... INFO @ Fri, 04 Aug 2017 14:26:42: #1 read treatment tags... INFO @ Fri, 04 Aug 2017 14:26:42: #1 read treatment tags... INFO @ Fri, 04 Aug 2017 14:26:49: 1000000 INFO @ Fri, 04 Aug 2017 14:26:50: 1000000 INFO @ Fri, 04 Aug 2017 14:26:50: 1000000 INFO @ Fri, 04 Aug 2017 14:26:56: 2000000 INFO @ Fri, 04 Aug 2017 14:26:58: 2000000 INFO @ Fri, 04 Aug 2017 14:26:58: 2000000 INFO @ Fri, 04 Aug 2017 14:27:04: 3000000 INFO @ Fri, 04 Aug 2017 14:27:06: 3000000 INFO @ Fri, 04 Aug 2017 14:27:07: 3000000 INFO @ Fri, 04 Aug 2017 14:27:11: 4000000 INFO @ Fri, 04 Aug 2017 14:27:14: 4000000 INFO @ Fri, 04 Aug 2017 14:27:15: 4000000 INFO @ Fri, 04 Aug 2017 14:27:19: 5000000 INFO @ Fri, 04 Aug 2017 14:27:22: 5000000 INFO @ Fri, 04 Aug 2017 14:27:24: 5000000 INFO @ Fri, 04 Aug 2017 14:27:26: 6000000 INFO @ Fri, 04 Aug 2017 14:27:31: 6000000 INFO @ Fri, 04 Aug 2017 14:27:33: 6000000 INFO @ Fri, 04 Aug 2017 14:27:34: 7000000 INFO @ Fri, 04 Aug 2017 14:27:41: 7000000 INFO @ Fri, 04 Aug 2017 14:27:41: 8000000 INFO @ Fri, 04 Aug 2017 14:27:41: 7000000 INFO @ Fri, 04 Aug 2017 14:27:50: 8000000 INFO @ Fri, 04 Aug 2017 14:27:50: 8000000 INFO @ Fri, 04 Aug 2017 14:27:51: 9000000 INFO @ Fri, 04 Aug 2017 14:27:59: 9000000 INFO @ Fri, 04 Aug 2017 14:27:59: 9000000 INFO @ Fri, 04 Aug 2017 14:27:59: 10000000 INFO @ Fri, 04 Aug 2017 14:28:07: 11000000 INFO @ Fri, 04 Aug 2017 14:28:07: 10000000 INFO @ Fri, 04 Aug 2017 14:28:08: 10000000 INFO @ Fri, 04 Aug 2017 14:28:14: 12000000 INFO @ Fri, 04 Aug 2017 14:28:17: 11000000 INFO @ Fri, 04 Aug 2017 14:28:17: 11000000 INFO @ Fri, 04 Aug 2017 14:28:21: 13000000 INFO @ Fri, 04 Aug 2017 14:28:25: 12000000 INFO @ Fri, 04 Aug 2017 14:28:26: 12000000 INFO @ Fri, 04 Aug 2017 14:28:29: 14000000 INFO @ Fri, 04 Aug 2017 14:28:34: 13000000 INFO @ Fri, 04 Aug 2017 14:28:35: 13000000 INFO @ Fri, 04 Aug 2017 14:28:36: 15000000 INFO @ Fri, 04 Aug 2017 14:28:42: 14000000 INFO @ Fri, 04 Aug 2017 14:28:43: 16000000 INFO @ Fri, 04 Aug 2017 14:28:43: 14000000 INFO @ Fri, 04 Aug 2017 14:28:50: 15000000 INFO @ Fri, 04 Aug 2017 14:28:51: 17000000 INFO @ Fri, 04 Aug 2017 14:28:52: 15000000 INFO @ Fri, 04 Aug 2017 14:28:58: 16000000 INFO @ Fri, 04 Aug 2017 14:28:58: 18000000 INFO @ Fri, 04 Aug 2017 14:29:01: 16000000 INFO @ Fri, 04 Aug 2017 14:29:06: 19000000 INFO @ Fri, 04 Aug 2017 14:29:07: 17000000 INFO @ Fri, 04 Aug 2017 14:29:09: #1 tag size is determined as 50 bps INFO @ Fri, 04 Aug 2017 14:29:09: #1 tag size = 50 INFO @ Fri, 04 Aug 2017 14:29:09: #1 total tags in treatment: 19351571 INFO @ Fri, 04 Aug 2017 14:29:09: #1 user defined the maximum tags... INFO @ Fri, 04 Aug 2017 14:29:09: #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 14:29:09: 17000000 INFO @ Fri, 04 Aug 2017 14:29:09: #1 tags after filtering in treatment: 19351571 INFO @ Fri, 04 Aug 2017 14:29:09: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 04 Aug 2017 14:29:09: #1 finished! INFO @ Fri, 04 Aug 2017 14:29:09: #2 Build Peak Model... INFO @ Fri, 04 Aug 2017 14:29:09: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 04 Aug 2017 14:29:11: #2 number of paired peaks: 999 WARNING @ Fri, 04 Aug 2017 14:29:11: Fewer paired peaks (999) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 999 pairs to build model! INFO @ Fri, 04 Aug 2017 14:29:11: start model_add_line... INFO @ Fri, 04 Aug 2017 14:29:12: start X-correlation... INFO @ Fri, 04 Aug 2017 14:29:12: end of X-cor INFO @ Fri, 04 Aug 2017 14:29:12: #2 finished! INFO @ Fri, 04 Aug 2017 14:29:12: #2 predicted fragment length is 118 bps INFO @ Fri, 04 Aug 2017 14:29:12: #2 alternative fragment length(s) may be 4,118 bps INFO @ Fri, 04 Aug 2017 14:29:12: #2.2 Generate R script for model : SRX2520633.20_model.r INFO @ Fri, 04 Aug 2017 14:29:12: #3 Call peaks... INFO @ Fri, 04 Aug 2017 14:29:12: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 04 Aug 2017 14:29:16: 18000000 INFO @ Fri, 04 Aug 2017 14:29:18: 18000000 INFO @ Fri, 04 Aug 2017 14:29:24: 19000000 INFO @ Fri, 04 Aug 2017 14:29:27: 19000000 INFO @ Fri, 04 Aug 2017 14:29:27: #1 tag size is determined as 50 bps INFO @ Fri, 04 Aug 2017 14:29:27: #1 tag size = 50 INFO @ Fri, 04 Aug 2017 14:29:27: #1 total tags in treatment: 19351571 INFO @ Fri, 04 Aug 2017 14:29:27: #1 user defined the maximum tags... INFO @ Fri, 04 Aug 2017 14:29:27: #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 14:29:28: #1 tags after filtering in treatment: 19351571 INFO @ Fri, 04 Aug 2017 14:29:28: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 04 Aug 2017 14:29:28: #1 finished! INFO @ Fri, 04 Aug 2017 14:29:28: #2 Build Peak Model... INFO @ Fri, 04 Aug 2017 14:29:28: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 04 Aug 2017 14:29:29: #2 number of paired peaks: 999 WARNING @ Fri, 04 Aug 2017 14:29:29: Fewer paired peaks (999) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 999 pairs to build model! INFO @ Fri, 04 Aug 2017 14:29:29: start model_add_line... INFO @ Fri, 04 Aug 2017 14:29:30: start X-correlation... INFO @ Fri, 04 Aug 2017 14:29:30: end of X-cor INFO @ Fri, 04 Aug 2017 14:29:30: #2 finished! INFO @ Fri, 04 Aug 2017 14:29:30: #2 predicted fragment length is 118 bps INFO @ Fri, 04 Aug 2017 14:29:30: #2 alternative fragment length(s) may be 4,118 bps INFO @ Fri, 04 Aug 2017 14:29:30: #2.2 Generate R script for model : SRX2520633.10_model.r INFO @ Fri, 04 Aug 2017 14:29:30: #3 Call peaks... INFO @ Fri, 04 Aug 2017 14:29:30: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 04 Aug 2017 14:29:30: #1 tag size is determined as 50 bps INFO @ Fri, 04 Aug 2017 14:29:30: #1 tag size = 50 INFO @ Fri, 04 Aug 2017 14:29:30: #1 total tags in treatment: 19351571 INFO @ Fri, 04 Aug 2017 14:29:30: #1 user defined the maximum tags... INFO @ Fri, 04 Aug 2017 14:29:30: #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 14:29:31: #1 tags after filtering in treatment: 19351571 INFO @ Fri, 04 Aug 2017 14:29:31: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 04 Aug 2017 14:29:31: #1 finished! INFO @ Fri, 04 Aug 2017 14:29:31: #2 Build Peak Model... INFO @ Fri, 04 Aug 2017 14:29:31: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 04 Aug 2017 14:29:32: #2 number of paired peaks: 999 WARNING @ Fri, 04 Aug 2017 14:29:32: Fewer paired peaks (999) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 999 pairs to build model! INFO @ Fri, 04 Aug 2017 14:29:32: start model_add_line... INFO @ Fri, 04 Aug 2017 14:29:33: start X-correlation... INFO @ Fri, 04 Aug 2017 14:29:33: end of X-cor INFO @ Fri, 04 Aug 2017 14:29:33: #2 finished! INFO @ Fri, 04 Aug 2017 14:29:33: #2 predicted fragment length is 118 bps INFO @ Fri, 04 Aug 2017 14:29:33: #2 alternative fragment length(s) may be 4,118 bps INFO @ Fri, 04 Aug 2017 14:29:33: #2.2 Generate R script for model : SRX2520633.05_model.r INFO @ Fri, 04 Aug 2017 14:29:33: #3 Call peaks... INFO @ Fri, 04 Aug 2017 14:29:33: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 04 Aug 2017 14:30:08: #3 Call peaks for each chromosome... INFO @ Fri, 04 Aug 2017 14:30:25: #3 Call peaks for each chromosome... INFO @ Fri, 04 Aug 2017 14:30:29: #3 Call peaks for each chromosome... INFO @ Fri, 04 Aug 2017 14:30:39: #4 Write output xls file... SRX2520633.20_peaks.xls INFO @ Fri, 04 Aug 2017 14:30:39: #4 Write peak in narrowPeak format file... SRX2520633.20_peaks.narrowPeak INFO @ Fri, 04 Aug 2017 14:30:39: #4 Write summits bed file... SRX2520633.20_summits.bed INFO @ Fri, 04 Aug 2017 14:30:39: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (1849 records, 4 fields): 7 millis CompletedMACS2peakCalling INFO @ Fri, 04 Aug 2017 14:30:56: #4 Write output xls file... SRX2520633.10_peaks.xls INFO @ Fri, 04 Aug 2017 14:30:56: #4 Write peak in narrowPeak format file... SRX2520633.10_peaks.narrowPeak INFO @ Fri, 04 Aug 2017 14:30:56: #4 Write summits bed file... SRX2520633.10_summits.bed INFO @ Fri, 04 Aug 2017 14:30:56: Done! pass1 - making usageList (15 chroms): 3 millis pass2 - checking and writing primary data (3900 records, 4 fields): 10 millis CompletedMACS2peakCalling INFO @ Fri, 04 Aug 2017 14:31:01: #4 Write output xls file... SRX2520633.05_peaks.xls INFO @ Fri, 04 Aug 2017 14:31:01: #4 Write peak in narrowPeak format file... SRX2520633.05_peaks.narrowPeak INFO @ Fri, 04 Aug 2017 14:31:01: #4 Write summits bed file... SRX2520633.05_summits.bed INFO @ Fri, 04 Aug 2017 14:31:01: Done! pass1 - making usageList (15 chroms): 3 millis pass2 - checking and writing primary data (7353 records, 4 fields): 14 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。