Job ID = 9730441 sra ファイルのダウンロード中... Completed: 797529K bytes transferred in 13 seconds (501222K 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 24205473 spots for /home/okishinya/chipatlas/results/dm3/SRX2559029/SRR5253493.sra Written 24205473 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: 00:08:32 24205473 reads; of these: 24205473 (100.00%) were unpaired; of these: 971942 (4.02%) aligned 0 times 18505114 (76.45%) aligned exactly 1 time 4728417 (19.53%) aligned >1 times 95.98% overall alignment rate Time searching: 00:08:32 Overall time: 00:08:32 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] 4353753 / 23233531 = 0.1874 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 @ Sun, 03 Sep 2017 01:10:01: # Command line: callpeak -t SRX2559029.bam -f BAM -g dm -n SRX2559029.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX2559029.20 # format = BAM # ChIP-seq file = ['SRX2559029.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 @ Sun, 03 Sep 2017 01:10:01: # Command line: callpeak -t SRX2559029.bam -f BAM -g dm -n SRX2559029.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX2559029.05 # format = BAM # ChIP-seq file = ['SRX2559029.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 @ Sun, 03 Sep 2017 01:10:01: # Command line: callpeak -t SRX2559029.bam -f BAM -g dm -n SRX2559029.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX2559029.10 # format = BAM # ChIP-seq file = ['SRX2559029.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 @ Sun, 03 Sep 2017 01:10:01: #1 read tag files... INFO @ Sun, 03 Sep 2017 01:10:01: #1 read tag files... INFO @ Sun, 03 Sep 2017 01:10:01: #1 read tag files... INFO @ Sun, 03 Sep 2017 01:10:01: #1 read treatment tags... INFO @ Sun, 03 Sep 2017 01:10:01: #1 read treatment tags... INFO @ Sun, 03 Sep 2017 01:10:01: #1 read treatment tags... INFO @ Sun, 03 Sep 2017 01:10:07: 1000000 INFO @ Sun, 03 Sep 2017 01:10:07: 1000000 INFO @ Sun, 03 Sep 2017 01:10:07: 1000000 INFO @ Sun, 03 Sep 2017 01:10:13: 2000000 INFO @ Sun, 03 Sep 2017 01:10:13: 2000000 INFO @ Sun, 03 Sep 2017 01:10:14: 2000000 INFO @ Sun, 03 Sep 2017 01:10:20: 3000000 INFO @ Sun, 03 Sep 2017 01:10:20: 3000000 INFO @ Sun, 03 Sep 2017 01:10:21: 3000000 INFO @ Sun, 03 Sep 2017 01:10:26: 4000000 INFO @ Sun, 03 Sep 2017 01:10:26: 4000000 INFO @ Sun, 03 Sep 2017 01:10:28: 4000000 INFO @ Sun, 03 Sep 2017 01:10:32: 5000000 INFO @ Sun, 03 Sep 2017 01:10:33: 5000000 INFO @ Sun, 03 Sep 2017 01:10:35: 5000000 INFO @ Sun, 03 Sep 2017 01:10:38: 6000000 INFO @ Sun, 03 Sep 2017 01:10:39: 6000000 INFO @ Sun, 03 Sep 2017 01:10:41: 6000000 INFO @ Sun, 03 Sep 2017 01:10:45: 7000000 INFO @ Sun, 03 Sep 2017 01:10:46: 7000000 INFO @ Sun, 03 Sep 2017 01:10:48: 7000000 INFO @ Sun, 03 Sep 2017 01:10:51: 8000000 INFO @ Sun, 03 Sep 2017 01:10:52: 8000000 INFO @ Sun, 03 Sep 2017 01:10:55: 8000000 INFO @ Sun, 03 Sep 2017 01:10:57: 9000000 INFO @ Sun, 03 Sep 2017 01:10:58: 9000000 INFO @ Sun, 03 Sep 2017 01:11:02: 9000000 INFO @ Sun, 03 Sep 2017 01:11:03: 10000000 INFO @ Sun, 03 Sep 2017 01:11:05: 10000000 INFO @ Sun, 03 Sep 2017 01:11:09: 10000000 INFO @ Sun, 03 Sep 2017 01:11:09: 11000000 INFO @ Sun, 03 Sep 2017 01:11:11: 11000000 INFO @ Sun, 03 Sep 2017 01:11:15: 12000000 INFO @ Sun, 03 Sep 2017 01:11:16: 11000000 INFO @ Sun, 03 Sep 2017 01:11:18: 12000000 INFO @ Sun, 03 Sep 2017 01:11:21: 13000000 INFO @ Sun, 03 Sep 2017 01:11:23: 12000000 INFO @ Sun, 03 Sep 2017 01:11:24: 13000000 INFO @ Sun, 03 Sep 2017 01:11:27: 14000000 INFO @ Sun, 03 Sep 2017 01:11:29: 13000000 INFO @ Sun, 03 Sep 2017 01:11:30: 14000000 INFO @ Sun, 03 Sep 2017 01:11:34: 15000000 INFO @ Sun, 03 Sep 2017 01:11:36: 14000000 INFO @ Sun, 03 Sep 2017 01:11:37: 15000000 INFO @ Sun, 03 Sep 2017 01:11:40: 16000000 INFO @ Sun, 03 Sep 2017 01:11:43: 15000000 INFO @ Sun, 03 Sep 2017 01:11:43: 16000000 INFO @ Sun, 03 Sep 2017 01:11:46: 17000000 INFO @ Sun, 03 Sep 2017 01:11:50: 17000000 INFO @ Sun, 03 Sep 2017 01:11:50: 16000000 INFO @ Sun, 03 Sep 2017 01:11:52: 18000000 INFO @ Sun, 03 Sep 2017 01:11:56: 18000000 INFO @ Sun, 03 Sep 2017 01:11:57: 17000000 INFO @ Sun, 03 Sep 2017 01:11:58: #1 tag size is determined as 50 bps INFO @ Sun, 03 Sep 2017 01:11:58: #1 tag size = 50 INFO @ Sun, 03 Sep 2017 01:11:58: #1 total tags in treatment: 18879778 INFO @ Sun, 03 Sep 2017 01:11:58: #1 user defined the maximum tags... INFO @ Sun, 03 Sep 2017 01:11:58: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sun, 03 Sep 2017 01:11:58: #1 tags after filtering in treatment: 18879778 INFO @ Sun, 03 Sep 2017 01:11:58: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 03 Sep 2017 01:11:58: #1 finished! INFO @ Sun, 03 Sep 2017 01:11:58: #2 Build Peak Model... INFO @ Sun, 03 Sep 2017 01:11:58: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 03 Sep 2017 01:11:59: #2 number of paired peaks: 970 WARNING @ Sun, 03 Sep 2017 01:11:59: Fewer paired peaks (970) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 970 pairs to build model! INFO @ Sun, 03 Sep 2017 01:11:59: start model_add_line... INFO @ Sun, 03 Sep 2017 01:12:00: start X-correlation... INFO @ Sun, 03 Sep 2017 01:12:00: end of X-cor INFO @ Sun, 03 Sep 2017 01:12:00: #2 finished! INFO @ Sun, 03 Sep 2017 01:12:00: #2 predicted fragment length is 185 bps INFO @ Sun, 03 Sep 2017 01:12:00: #2 alternative fragment length(s) may be 185 bps INFO @ Sun, 03 Sep 2017 01:12:00: #2.2 Generate R script for model : SRX2559029.10_model.r INFO @ Sun, 03 Sep 2017 01:12:00: #3 Call peaks... INFO @ Sun, 03 Sep 2017 01:12:00: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 03 Sep 2017 01:12:02: #1 tag size is determined as 50 bps INFO @ Sun, 03 Sep 2017 01:12:02: #1 tag size = 50 INFO @ Sun, 03 Sep 2017 01:12:02: #1 total tags in treatment: 18879778 INFO @ Sun, 03 Sep 2017 01:12:02: #1 user defined the maximum tags... INFO @ Sun, 03 Sep 2017 01:12:02: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sun, 03 Sep 2017 01:12:02: #1 tags after filtering in treatment: 18879778 INFO @ Sun, 03 Sep 2017 01:12:02: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 03 Sep 2017 01:12:02: #1 finished! INFO @ Sun, 03 Sep 2017 01:12:02: #2 Build Peak Model... INFO @ Sun, 03 Sep 2017 01:12:02: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 03 Sep 2017 01:12:03: 18000000 INFO @ Sun, 03 Sep 2017 01:12:03: #2 number of paired peaks: 970 WARNING @ Sun, 03 Sep 2017 01:12:03: Fewer paired peaks (970) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 970 pairs to build model! INFO @ Sun, 03 Sep 2017 01:12:03: start model_add_line... INFO @ Sun, 03 Sep 2017 01:12:04: start X-correlation... INFO @ Sun, 03 Sep 2017 01:12:04: end of X-cor INFO @ Sun, 03 Sep 2017 01:12:04: #2 finished! INFO @ Sun, 03 Sep 2017 01:12:04: #2 predicted fragment length is 185 bps INFO @ Sun, 03 Sep 2017 01:12:04: #2 alternative fragment length(s) may be 185 bps INFO @ Sun, 03 Sep 2017 01:12:04: #2.2 Generate R script for model : SRX2559029.05_model.r INFO @ Sun, 03 Sep 2017 01:12:04: #3 Call peaks... INFO @ Sun, 03 Sep 2017 01:12:04: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 03 Sep 2017 01:12:09: #1 tag size is determined as 50 bps INFO @ Sun, 03 Sep 2017 01:12:09: #1 tag size = 50 INFO @ Sun, 03 Sep 2017 01:12:09: #1 total tags in treatment: 18879778 INFO @ Sun, 03 Sep 2017 01:12:09: #1 user defined the maximum tags... INFO @ Sun, 03 Sep 2017 01:12:09: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sun, 03 Sep 2017 01:12:09: #1 tags after filtering in treatment: 18879778 INFO @ Sun, 03 Sep 2017 01:12:09: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 03 Sep 2017 01:12:09: #1 finished! INFO @ Sun, 03 Sep 2017 01:12:09: #2 Build Peak Model... INFO @ Sun, 03 Sep 2017 01:12:09: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 03 Sep 2017 01:12:11: #2 number of paired peaks: 970 WARNING @ Sun, 03 Sep 2017 01:12:11: Fewer paired peaks (970) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 970 pairs to build model! INFO @ Sun, 03 Sep 2017 01:12:11: start model_add_line... INFO @ Sun, 03 Sep 2017 01:12:11: start X-correlation... INFO @ Sun, 03 Sep 2017 01:12:11: end of X-cor INFO @ Sun, 03 Sep 2017 01:12:11: #2 finished! INFO @ Sun, 03 Sep 2017 01:12:11: #2 predicted fragment length is 185 bps INFO @ Sun, 03 Sep 2017 01:12:11: #2 alternative fragment length(s) may be 185 bps INFO @ Sun, 03 Sep 2017 01:12:11: #2.2 Generate R script for model : SRX2559029.20_model.r INFO @ Sun, 03 Sep 2017 01:12:11: #3 Call peaks... INFO @ Sun, 03 Sep 2017 01:12:11: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 03 Sep 2017 01:12:49: #3 Call peaks for each chromosome... INFO @ Sun, 03 Sep 2017 01:12:51: #3 Call peaks for each chromosome... INFO @ Sun, 03 Sep 2017 01:13:00: #3 Call peaks for each chromosome... INFO @ Sun, 03 Sep 2017 01:13:17: #4 Write output xls file... SRX2559029.10_peaks.xls INFO @ Sun, 03 Sep 2017 01:13:17: #4 Write peak in narrowPeak format file... SRX2559029.10_peaks.narrowPeak INFO @ Sun, 03 Sep 2017 01:13:17: #4 Write summits bed file... SRX2559029.10_summits.bed INFO @ Sun, 03 Sep 2017 01:13:17: Done! pass1 - making usageList (14 chroms): 2 millis pass2 - checking and writing primary data (7100 records, 4 fields): 10 millis CompletedMACS2peakCalling INFO @ Sun, 03 Sep 2017 01:13:18: #4 Write output xls file... SRX2559029.05_peaks.xls INFO @ Sun, 03 Sep 2017 01:13:18: #4 Write peak in narrowPeak format file... SRX2559029.05_peaks.narrowPeak INFO @ Sun, 03 Sep 2017 01:13:18: #4 Write summits bed file... SRX2559029.05_summits.bed INFO @ Sun, 03 Sep 2017 01:13:18: Done! pass1 - making usageList (14 chroms): 3 millis pass2 - checking and writing primary data (10690 records, 4 fields): 13 millis CompletedMACS2peakCalling INFO @ Sun, 03 Sep 2017 01:13:25: #4 Write output xls file... SRX2559029.20_peaks.xls INFO @ Sun, 03 Sep 2017 01:13:25: #4 Write peak in narrowPeak format file... SRX2559029.20_peaks.narrowPeak INFO @ Sun, 03 Sep 2017 01:13:25: #4 Write summits bed file... SRX2559029.20_summits.bed INFO @ Sun, 03 Sep 2017 01:13:25: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (3725 records, 4 fields): 6 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。