Job ID = 10450890 sra ファイルのダウンロード中... Completed: 584653K bytes transferred in 15 seconds (306275K bits/sec), in 1 file. 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 30860817 spots for /home/okishinya/chipatlas/results/dm3/SRX3404030/SRR6303507.sra Written 30860817 spots total rm: cannot remove `[DSE]RX*': No such file or directory rm: cannot remove `[DSE]RR*.fastq': No such file or directory 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: 00:22:09 30860817 reads; of these: 30860817 (100.00%) were unpaired; of these: 922522 (2.99%) aligned 0 times 21688906 (70.28%) aligned exactly 1 time 8249389 (26.73%) aligned >1 times 97.01% overall alignment rate Time searching: 00:22:09 Overall time: 00:22:09 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] 3889018 / 29938295 = 0.1299 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 @ Wed, 07 Feb 2018 13:45:30: # Command line: callpeak -t SRX3404030.bam -f BAM -g dm -n SRX3404030.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX3404030.20 # format = BAM # ChIP-seq file = ['SRX3404030.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 @ Wed, 07 Feb 2018 13:45:30: # Command line: callpeak -t SRX3404030.bam -f BAM -g dm -n SRX3404030.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX3404030.05 # format = BAM # ChIP-seq file = ['SRX3404030.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 @ Wed, 07 Feb 2018 13:45:30: # Command line: callpeak -t SRX3404030.bam -f BAM -g dm -n SRX3404030.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX3404030.10 # format = BAM # ChIP-seq file = ['SRX3404030.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 @ Wed, 07 Feb 2018 13:45:30: #1 read tag files... INFO @ Wed, 07 Feb 2018 13:45:30: #1 read tag files... INFO @ Wed, 07 Feb 2018 13:45:30: #1 read treatment tags... INFO @ Wed, 07 Feb 2018 13:45:30: #1 read tag files... INFO @ Wed, 07 Feb 2018 13:45:30: #1 read treatment tags... INFO @ Wed, 07 Feb 2018 13:45:30: #1 read treatment tags... INFO @ Wed, 07 Feb 2018 13:45:40: 1000000 INFO @ Wed, 07 Feb 2018 13:45:45: 1000000 INFO @ Wed, 07 Feb 2018 13:45:48: 1000000 INFO @ Wed, 07 Feb 2018 13:45:49: 2000000 INFO @ Wed, 07 Feb 2018 13:45:58: 3000000 INFO @ Wed, 07 Feb 2018 13:46:02: 2000000 INFO @ Wed, 07 Feb 2018 13:46:06: 2000000 INFO @ Wed, 07 Feb 2018 13:46:08: 4000000 INFO @ Wed, 07 Feb 2018 13:46:17: 3000000 INFO @ Wed, 07 Feb 2018 13:46:19: 5000000 INFO @ Wed, 07 Feb 2018 13:46:23: 3000000 INFO @ Wed, 07 Feb 2018 13:46:30: 6000000 INFO @ Wed, 07 Feb 2018 13:46:33: 4000000 INFO @ Wed, 07 Feb 2018 13:46:38: 4000000 INFO @ Wed, 07 Feb 2018 13:46:41: 7000000 INFO @ Wed, 07 Feb 2018 13:46:50: 5000000 INFO @ Wed, 07 Feb 2018 13:46:50: 5000000 INFO @ Wed, 07 Feb 2018 13:46:52: 8000000 INFO @ Wed, 07 Feb 2018 13:47:01: 9000000 INFO @ Wed, 07 Feb 2018 13:47:05: 6000000 INFO @ Wed, 07 Feb 2018 13:47:08: 6000000 INFO @ Wed, 07 Feb 2018 13:47:09: 10000000 INFO @ Wed, 07 Feb 2018 13:47:18: 11000000 INFO @ Wed, 07 Feb 2018 13:47:22: 7000000 INFO @ Wed, 07 Feb 2018 13:47:26: 7000000 INFO @ Wed, 07 Feb 2018 13:47:27: 12000000 INFO @ Wed, 07 Feb 2018 13:47:36: 13000000 INFO @ Wed, 07 Feb 2018 13:47:42: 8000000 INFO @ Wed, 07 Feb 2018 13:47:44: 14000000 INFO @ Wed, 07 Feb 2018 13:47:44: 8000000 INFO @ Wed, 07 Feb 2018 13:47:53: 15000000 INFO @ Wed, 07 Feb 2018 13:48:01: 16000000 INFO @ Wed, 07 Feb 2018 13:48:02: 9000000 INFO @ Wed, 07 Feb 2018 13:48:02: 9000000 INFO @ Wed, 07 Feb 2018 13:48:10: 17000000 INFO @ Wed, 07 Feb 2018 13:48:18: 10000000 INFO @ Wed, 07 Feb 2018 13:48:18: 18000000 INFO @ Wed, 07 Feb 2018 13:48:21: 10000000 INFO @ Wed, 07 Feb 2018 13:48:28: 19000000 INFO @ Wed, 07 Feb 2018 13:48:34: 11000000 INFO @ Wed, 07 Feb 2018 13:48:37: 20000000 INFO @ Wed, 07 Feb 2018 13:48:41: 11000000 INFO @ Wed, 07 Feb 2018 13:48:47: 21000000 INFO @ Wed, 07 Feb 2018 13:48:49: 12000000 INFO @ Wed, 07 Feb 2018 13:48:56: 22000000 INFO @ Wed, 07 Feb 2018 13:49:01: 12000000 INFO @ Wed, 07 Feb 2018 13:49:05: 13000000 INFO @ Wed, 07 Feb 2018 13:49:05: 23000000 INFO @ Wed, 07 Feb 2018 13:49:14: 24000000 INFO @ Wed, 07 Feb 2018 13:49:20: 14000000 INFO @ Wed, 07 Feb 2018 13:49:21: 13000000 INFO @ Wed, 07 Feb 2018 13:49:24: 25000000 INFO @ Wed, 07 Feb 2018 13:49:34: 26000000 INFO @ Wed, 07 Feb 2018 13:49:35: #1 tag size is determined as 51 bps INFO @ Wed, 07 Feb 2018 13:49:35: #1 tag size = 51 INFO @ Wed, 07 Feb 2018 13:49:35: #1 total tags in treatment: 26049277 INFO @ Wed, 07 Feb 2018 13:49:35: #1 user defined the maximum tags... INFO @ Wed, 07 Feb 2018 13:49:35: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Wed, 07 Feb 2018 13:49:35: 15000000 INFO @ Wed, 07 Feb 2018 13:49:35: #1 tags after filtering in treatment: 26049277 INFO @ Wed, 07 Feb 2018 13:49:35: #1 Redundant rate of treatment: 0.00 INFO @ Wed, 07 Feb 2018 13:49:35: #1 finished! INFO @ Wed, 07 Feb 2018 13:49:35: #2 Build Peak Model... INFO @ Wed, 07 Feb 2018 13:49:35: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 07 Feb 2018 13:49:38: #2 number of paired peaks: 398 WARNING @ Wed, 07 Feb 2018 13:49:38: Fewer paired peaks (398) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 398 pairs to build model! INFO @ Wed, 07 Feb 2018 13:49:38: start model_add_line... INFO @ Wed, 07 Feb 2018 13:49:38: start X-correlation... INFO @ Wed, 07 Feb 2018 13:49:38: end of X-cor INFO @ Wed, 07 Feb 2018 13:49:38: #2 finished! INFO @ Wed, 07 Feb 2018 13:49:38: #2 predicted fragment length is 177 bps INFO @ Wed, 07 Feb 2018 13:49:38: #2 alternative fragment length(s) may be 177 bps INFO @ Wed, 07 Feb 2018 13:49:38: #2.2 Generate R script for model : SRX3404030.05_model.r INFO @ Wed, 07 Feb 2018 13:49:38: #3 Call peaks... INFO @ Wed, 07 Feb 2018 13:49:38: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 07 Feb 2018 13:49:42: 14000000 INFO @ Wed, 07 Feb 2018 13:49:51: 16000000 INFO @ Wed, 07 Feb 2018 13:50:02: 15000000 INFO @ Wed, 07 Feb 2018 13:50:06: 17000000 INFO @ Wed, 07 Feb 2018 13:50:21: 16000000 INFO @ Wed, 07 Feb 2018 13:50:24: 18000000 INFO @ Wed, 07 Feb 2018 13:50:40: 19000000 INFO @ Wed, 07 Feb 2018 13:50:41: 17000000 INFO @ Wed, 07 Feb 2018 13:50:58: #3 Call peaks for each chromosome... INFO @ Wed, 07 Feb 2018 13:50:59: 18000000 INFO @ Wed, 07 Feb 2018 13:51:00: 20000000 INFO @ Wed, 07 Feb 2018 13:51:19: 19000000 INFO @ Wed, 07 Feb 2018 13:51:21: 21000000 INFO @ Wed, 07 Feb 2018 13:51:39: 20000000 INFO @ Wed, 07 Feb 2018 13:51:39: #4 Write output xls file... SRX3404030.05_peaks.xls INFO @ Wed, 07 Feb 2018 13:51:39: #4 Write peak in narrowPeak format file... SRX3404030.05_peaks.narrowPeak INFO @ Wed, 07 Feb 2018 13:51:39: #4 Write summits bed file... SRX3404030.05_summits.bed INFO @ Wed, 07 Feb 2018 13:51:39: Done! pass1 - making usageList (15 chroms): 3 millis pass2 - checking and writing primary data (5051 records, 4 fields): 11 millis CompletedMACS2peakCalling INFO @ Wed, 07 Feb 2018 13:51:42: 22000000 INFO @ Wed, 07 Feb 2018 13:51:57: 21000000 INFO @ Wed, 07 Feb 2018 13:52:02: 23000000 INFO @ Wed, 07 Feb 2018 13:52:16: 22000000 INFO @ Wed, 07 Feb 2018 13:52:21: 24000000 INFO @ Wed, 07 Feb 2018 13:52:34: 23000000 INFO @ Wed, 07 Feb 2018 13:52:40: 25000000 INFO @ Wed, 07 Feb 2018 13:52:50: 24000000 INFO @ Wed, 07 Feb 2018 13:52:57: 26000000 INFO @ Wed, 07 Feb 2018 13:52:58: #1 tag size is determined as 51 bps INFO @ Wed, 07 Feb 2018 13:52:58: #1 tag size = 51 INFO @ Wed, 07 Feb 2018 13:52:58: #1 total tags in treatment: 26049277 INFO @ Wed, 07 Feb 2018 13:52:58: #1 user defined the maximum tags... INFO @ Wed, 07 Feb 2018 13:52:58: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Wed, 07 Feb 2018 13:52:59: #1 tags after filtering in treatment: 26049277 INFO @ Wed, 07 Feb 2018 13:52:59: #1 Redundant rate of treatment: 0.00 INFO @ Wed, 07 Feb 2018 13:52:59: #1 finished! INFO @ Wed, 07 Feb 2018 13:52:59: #2 Build Peak Model... INFO @ Wed, 07 Feb 2018 13:52:59: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 07 Feb 2018 13:53:01: #2 number of paired peaks: 398 WARNING @ Wed, 07 Feb 2018 13:53:01: Fewer paired peaks (398) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 398 pairs to build model! INFO @ Wed, 07 Feb 2018 13:53:01: start model_add_line... INFO @ Wed, 07 Feb 2018 13:53:02: start X-correlation... INFO @ Wed, 07 Feb 2018 13:53:02: end of X-cor INFO @ Wed, 07 Feb 2018 13:53:02: #2 finished! INFO @ Wed, 07 Feb 2018 13:53:02: #2 predicted fragment length is 177 bps INFO @ Wed, 07 Feb 2018 13:53:02: #2 alternative fragment length(s) may be 177 bps INFO @ Wed, 07 Feb 2018 13:53:02: #2.2 Generate R script for model : SRX3404030.20_model.r INFO @ Wed, 07 Feb 2018 13:53:02: #3 Call peaks... INFO @ Wed, 07 Feb 2018 13:53:02: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 07 Feb 2018 13:53:06: 25000000 INFO @ Wed, 07 Feb 2018 13:53:24: 26000000 INFO @ Wed, 07 Feb 2018 13:53:25: #1 tag size is determined as 51 bps INFO @ Wed, 07 Feb 2018 13:53:25: #1 tag size = 51 INFO @ Wed, 07 Feb 2018 13:53:25: #1 total tags in treatment: 26049277 INFO @ Wed, 07 Feb 2018 13:53:25: #1 user defined the maximum tags... INFO @ Wed, 07 Feb 2018 13:53:25: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Wed, 07 Feb 2018 13:53:25: #1 tags after filtering in treatment: 26049277 INFO @ Wed, 07 Feb 2018 13:53:25: #1 Redundant rate of treatment: 0.00 INFO @ Wed, 07 Feb 2018 13:53:25: #1 finished! INFO @ Wed, 07 Feb 2018 13:53:25: #2 Build Peak Model... INFO @ Wed, 07 Feb 2018 13:53:25: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 07 Feb 2018 13:53:28: #2 number of paired peaks: 398 WARNING @ Wed, 07 Feb 2018 13:53:28: Fewer paired peaks (398) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 398 pairs to build model! INFO @ Wed, 07 Feb 2018 13:53:28: start model_add_line... INFO @ Wed, 07 Feb 2018 13:53:28: start X-correlation... INFO @ Wed, 07 Feb 2018 13:53:28: end of X-cor INFO @ Wed, 07 Feb 2018 13:53:28: #2 finished! INFO @ Wed, 07 Feb 2018 13:53:28: #2 predicted fragment length is 177 bps INFO @ Wed, 07 Feb 2018 13:53:28: #2 alternative fragment length(s) may be 177 bps INFO @ Wed, 07 Feb 2018 13:53:28: #2.2 Generate R script for model : SRX3404030.10_model.r INFO @ Wed, 07 Feb 2018 13:53:28: #3 Call peaks... INFO @ Wed, 07 Feb 2018 13:53:28: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 07 Feb 2018 13:54:19: #3 Call peaks for each chromosome... INFO @ Wed, 07 Feb 2018 13:54:45: #3 Call peaks for each chromosome... INFO @ Wed, 07 Feb 2018 13:54:59: #4 Write output xls file... SRX3404030.20_peaks.xls INFO @ Wed, 07 Feb 2018 13:54:59: #4 Write peak in narrowPeak format file... SRX3404030.20_peaks.narrowPeak INFO @ Wed, 07 Feb 2018 13:54:59: #4 Write summits bed file... SRX3404030.20_summits.bed INFO @ Wed, 07 Feb 2018 13:54:59: Done! pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (2572 records, 4 fields): 9 millis CompletedMACS2peakCalling INFO @ Wed, 07 Feb 2018 13:55:26: #4 Write output xls file... SRX3404030.10_peaks.xls INFO @ Wed, 07 Feb 2018 13:55:26: #4 Write peak in narrowPeak format file... SRX3404030.10_peaks.narrowPeak INFO @ Wed, 07 Feb 2018 13:55:26: #4 Write summits bed file... SRX3404030.10_summits.bed INFO @ Wed, 07 Feb 2018 13:55:26: Done! pass1 - making usageList (15 chroms): 2 millis pass2 - checking and writing primary data (3675 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。