Job ID = 9029600 sra ファイルのダウンロード中... Completed: 1343397K bytes transferred in 13 seconds (787629K bits/sec), in 1 file, 2 directories. % Total % Received % Xferd Average Speed Time Time Time Current Dload Upload Total Spent Left Speed 0 0 0 0 0 0 0 0 --:--:-- 0:00:06 --:--:-- 0 0 0 0 0 0 0 0 0 --:--:-- 0:00:07 --:--:-- 0 100 21558 0 21558 0 0 2717 0 --:--:-- 0:00:07 --:--:-- 16100 100 68296 0 68296 0 0 7650 0 --:--:-- 0:00:08 --:--:-- 29261 100 70167 0 70167 0 0 7859 0 --:--:-- 0:00:08 --:--:-- 30050 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 40997558 spots for /home/okishinya/chipatlas/results/dm3/SRX1872289/SRR3712750.sra Written 40997558 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: 00:12:06 40997558 reads; of these: 40997558 (100.00%) were unpaired; of these: 4919262 (12.00%) aligned 0 times 31384745 (76.55%) aligned exactly 1 time 4693551 (11.45%) aligned >1 times 88.00% overall alignment rate Time searching: 00:12:06 Overall time: 00:12:06 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] 6045967 / 36078296 = 0.1676 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 @ Sat, 03 Jun 2017 14:43:07: # Command line: callpeak -t SRX1872289.bam -f BAM -g dm -n SRX1872289.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX1872289.10 # format = BAM # ChIP-seq file = ['SRX1872289.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 INFO @ Sat, 03 Jun 2017 14:43:07: #1 read tag files... INFO @ Sat, 03 Jun 2017 14:43:07: #1 read treatment tags... INFO @ Sat, 03 Jun 2017 14:43:07: # Command line: callpeak -t SRX1872289.bam -f BAM -g dm -n SRX1872289.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX1872289.20 # format = BAM # ChIP-seq file = ['SRX1872289.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 INFO @ Sat, 03 Jun 2017 14:43:07: #1 read tag files... INFO @ Sat, 03 Jun 2017 14:43:07: #1 read treatment tags... INFO @ Sat, 03 Jun 2017 14:43:07: # Command line: callpeak -t SRX1872289.bam -f BAM -g dm -n SRX1872289.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX1872289.05 # format = BAM # ChIP-seq file = ['SRX1872289.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 INFO @ Sat, 03 Jun 2017 14:43:07: #1 read tag files... INFO @ Sat, 03 Jun 2017 14:43:07: #1 read treatment tags... INFO @ Sat, 03 Jun 2017 14:43:14: 1000000 INFO @ Sat, 03 Jun 2017 14:43:14: 1000000 INFO @ Sat, 03 Jun 2017 14:43:14: 1000000 INFO @ Sat, 03 Jun 2017 14:43:21: 2000000 INFO @ Sat, 03 Jun 2017 14:43:21: 2000000 INFO @ Sat, 03 Jun 2017 14:43:21: 2000000 INFO @ Sat, 03 Jun 2017 14:43:27: 3000000 INFO @ Sat, 03 Jun 2017 14:43:27: 3000000 INFO @ Sat, 03 Jun 2017 14:43:27: 3000000 INFO @ Sat, 03 Jun 2017 14:43:34: 4000000 INFO @ Sat, 03 Jun 2017 14:43:34: 4000000 INFO @ Sat, 03 Jun 2017 14:43:34: 4000000 INFO @ Sat, 03 Jun 2017 14:43:40: 5000000 INFO @ Sat, 03 Jun 2017 14:43:40: 5000000 INFO @ Sat, 03 Jun 2017 14:43:40: 5000000 INFO @ Sat, 03 Jun 2017 14:43:47: 6000000 INFO @ Sat, 03 Jun 2017 14:43:47: 6000000 INFO @ Sat, 03 Jun 2017 14:43:47: 6000000 INFO @ Sat, 03 Jun 2017 14:43:54: 7000000 INFO @ Sat, 03 Jun 2017 14:43:54: 7000000 INFO @ Sat, 03 Jun 2017 14:43:54: 7000000 INFO @ Sat, 03 Jun 2017 14:44:01: 8000000 INFO @ Sat, 03 Jun 2017 14:44:01: 8000000 INFO @ Sat, 03 Jun 2017 14:44:01: 8000000 INFO @ Sat, 03 Jun 2017 14:44:08: 9000000 INFO @ Sat, 03 Jun 2017 14:44:08: 9000000 INFO @ Sat, 03 Jun 2017 14:44:08: 9000000 INFO @ Sat, 03 Jun 2017 14:44:16: 10000000 INFO @ Sat, 03 Jun 2017 14:44:16: 10000000 INFO @ Sat, 03 Jun 2017 14:44:16: 10000000 INFO @ Sat, 03 Jun 2017 14:44:23: 11000000 INFO @ Sat, 03 Jun 2017 14:44:23: 11000000 INFO @ Sat, 03 Jun 2017 14:44:23: 11000000 INFO @ Sat, 03 Jun 2017 14:44:30: 12000000 INFO @ Sat, 03 Jun 2017 14:44:30: 12000000 INFO @ Sat, 03 Jun 2017 14:44:31: 12000000 INFO @ Sat, 03 Jun 2017 14:44:37: 13000000 INFO @ Sat, 03 Jun 2017 14:44:37: 13000000 INFO @ Sat, 03 Jun 2017 14:44:40: 13000000 INFO @ Sat, 03 Jun 2017 14:44:44: 14000000 INFO @ Sat, 03 Jun 2017 14:44:44: 14000000 INFO @ Sat, 03 Jun 2017 14:44:48: 14000000 INFO @ Sat, 03 Jun 2017 14:44:50: 15000000 INFO @ Sat, 03 Jun 2017 14:44:50: 15000000 INFO @ Sat, 03 Jun 2017 14:44:57: 15000000 INFO @ Sat, 03 Jun 2017 14:44:57: 16000000 INFO @ Sat, 03 Jun 2017 14:44:57: 16000000 INFO @ Sat, 03 Jun 2017 14:45:04: 17000000 INFO @ Sat, 03 Jun 2017 14:45:04: 17000000 INFO @ Sat, 03 Jun 2017 14:45:05: 16000000 INFO @ Sat, 03 Jun 2017 14:45:11: 18000000 INFO @ Sat, 03 Jun 2017 14:45:11: 18000000 INFO @ Sat, 03 Jun 2017 14:45:14: 17000000 INFO @ Sat, 03 Jun 2017 14:45:18: 19000000 INFO @ Sat, 03 Jun 2017 14:45:18: 19000000 INFO @ Sat, 03 Jun 2017 14:45:22: 18000000 INFO @ Sat, 03 Jun 2017 14:45:25: 20000000 INFO @ Sat, 03 Jun 2017 14:45:25: 20000000 INFO @ Sat, 03 Jun 2017 14:45:30: 19000000 INFO @ Sat, 03 Jun 2017 14:45:31: 21000000 INFO @ Sat, 03 Jun 2017 14:45:31: 21000000 INFO @ Sat, 03 Jun 2017 14:45:38: 22000000 INFO @ Sat, 03 Jun 2017 14:45:38: 22000000 INFO @ Sat, 03 Jun 2017 14:45:38: 20000000 INFO @ Sat, 03 Jun 2017 14:45:45: 23000000 INFO @ Sat, 03 Jun 2017 14:45:45: 23000000 INFO @ Sat, 03 Jun 2017 14:45:46: 21000000 INFO @ Sat, 03 Jun 2017 14:45:51: 24000000 INFO @ Sat, 03 Jun 2017 14:45:51: 24000000 INFO @ Sat, 03 Jun 2017 14:45:51: 22000000 INFO @ Sat, 03 Jun 2017 14:45:57: 25000000 INFO @ Sat, 03 Jun 2017 14:45:58: 25000000 INFO @ Sat, 03 Jun 2017 14:45:58: 23000000 INFO @ Sat, 03 Jun 2017 14:46:05: 26000000 INFO @ Sat, 03 Jun 2017 14:46:05: 26000000 INFO @ Sat, 03 Jun 2017 14:46:05: 24000000 INFO @ Sat, 03 Jun 2017 14:46:12: 27000000 INFO @ Sat, 03 Jun 2017 14:46:13: 27000000 INFO @ Sat, 03 Jun 2017 14:46:13: 25000000 INFO @ Sat, 03 Jun 2017 14:46:20: 28000000 INFO @ Sat, 03 Jun 2017 14:46:20: 28000000 INFO @ Sat, 03 Jun 2017 14:46:20: 26000000 INFO @ Sat, 03 Jun 2017 14:46:27: 29000000 INFO @ Sat, 03 Jun 2017 14:46:27: 29000000 INFO @ Sat, 03 Jun 2017 14:46:29: 27000000 INFO @ Sat, 03 Jun 2017 14:46:34: 30000000 INFO @ Sat, 03 Jun 2017 14:46:34: 30000000 INFO @ Sat, 03 Jun 2017 14:46:35: #1 tag size is determined as 50 bps INFO @ Sat, 03 Jun 2017 14:46:35: #1 tag size = 50 INFO @ Sat, 03 Jun 2017 14:46:35: #1 total tags in treatment: 30032329 INFO @ Sat, 03 Jun 2017 14:46:35: #1 user defined the maximum tags... INFO @ Sat, 03 Jun 2017 14:46:35: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 03 Jun 2017 14:46:35: #1 tag size is determined as 50 bps INFO @ Sat, 03 Jun 2017 14:46:35: #1 tag size = 50 INFO @ Sat, 03 Jun 2017 14:46:35: #1 total tags in treatment: 30032329 INFO @ Sat, 03 Jun 2017 14:46:35: #1 user defined the maximum tags... INFO @ Sat, 03 Jun 2017 14:46:35: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 03 Jun 2017 14:46:37: 28000000 INFO @ Sat, 03 Jun 2017 14:46:40: #1 tags after filtering in treatment: 30017441 INFO @ Sat, 03 Jun 2017 14:46:40: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 03 Jun 2017 14:46:40: #1 finished! INFO @ Sat, 03 Jun 2017 14:46:40: #2 Build Peak Model... INFO @ Sat, 03 Jun 2017 14:46:40: #1 tags after filtering in treatment: 30017441 INFO @ Sat, 03 Jun 2017 14:46:40: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 03 Jun 2017 14:46:40: #1 finished! INFO @ Sat, 03 Jun 2017 14:46:40: #2 Build Peak Model... INFO @ Sat, 03 Jun 2017 14:46:45: #2 number of paired peaks: 121 WARNING @ Sat, 03 Jun 2017 14:46:45: Fewer paired peaks (121) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 121 pairs to build model! INFO @ Sat, 03 Jun 2017 14:46:45: start model_add_line... INFO @ Sat, 03 Jun 2017 14:46:45: 29000000 INFO @ Sat, 03 Jun 2017 14:46:45: #2 number of paired peaks: 121 WARNING @ Sat, 03 Jun 2017 14:46:45: Fewer paired peaks (121) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 121 pairs to build model! INFO @ Sat, 03 Jun 2017 14:46:45: start model_add_line... INFO @ Sat, 03 Jun 2017 14:46:49: start X-correlation... INFO @ Sat, 03 Jun 2017 14:46:49: end of X-cor INFO @ Sat, 03 Jun 2017 14:46:49: #2 finished! INFO @ Sat, 03 Jun 2017 14:46:49: #2 predicted fragment length is 212 bps INFO @ Sat, 03 Jun 2017 14:46:49: #2 alternative fragment length(s) may be 4,212,232,250 bps INFO @ Sat, 03 Jun 2017 14:46:49: #2.2 Generate R script for model : SRX1872289.20_model.r INFO @ Sat, 03 Jun 2017 14:46:49: #3 Call peaks... INFO @ Sat, 03 Jun 2017 14:46:49: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Jun 2017 14:46:49: start X-correlation... INFO @ Sat, 03 Jun 2017 14:46:49: end of X-cor INFO @ Sat, 03 Jun 2017 14:46:49: #2 finished! INFO @ Sat, 03 Jun 2017 14:46:49: #2 predicted fragment length is 212 bps INFO @ Sat, 03 Jun 2017 14:46:49: #2 alternative fragment length(s) may be 4,212,232,250 bps INFO @ Sat, 03 Jun 2017 14:46:49: #2.2 Generate R script for model : SRX1872289.10_model.r INFO @ Sat, 03 Jun 2017 14:46:49: #3 Call peaks... INFO @ Sat, 03 Jun 2017 14:46:49: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Jun 2017 14:46:53: 30000000 INFO @ Sat, 03 Jun 2017 14:46:54: #1 tag size is determined as 50 bps INFO @ Sat, 03 Jun 2017 14:46:54: #1 tag size = 50 INFO @ Sat, 03 Jun 2017 14:46:54: #1 total tags in treatment: 30032329 INFO @ Sat, 03 Jun 2017 14:46:54: #1 user defined the maximum tags... INFO @ Sat, 03 Jun 2017 14:46:54: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 03 Jun 2017 14:46:59: #1 tags after filtering in treatment: 30017441 INFO @ Sat, 03 Jun 2017 14:46:59: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 03 Jun 2017 14:46:59: #1 finished! INFO @ Sat, 03 Jun 2017 14:46:59: #2 Build Peak Model... INFO @ Sat, 03 Jun 2017 14:47:04: #2 number of paired peaks: 121 WARNING @ Sat, 03 Jun 2017 14:47:04: Fewer paired peaks (121) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 121 pairs to build model! INFO @ Sat, 03 Jun 2017 14:47:04: start model_add_line... INFO @ Sat, 03 Jun 2017 14:47:08: start X-correlation... INFO @ Sat, 03 Jun 2017 14:47:08: end of X-cor INFO @ Sat, 03 Jun 2017 14:47:08: #2 finished! INFO @ Sat, 03 Jun 2017 14:47:08: #2 predicted fragment length is 212 bps INFO @ Sat, 03 Jun 2017 14:47:08: #2 alternative fragment length(s) may be 4,212,232,250 bps INFO @ Sat, 03 Jun 2017 14:47:08: #2.2 Generate R script for model : SRX1872289.05_model.r INFO @ Sat, 03 Jun 2017 14:47:08: #3 Call peaks... INFO @ Sat, 03 Jun 2017 14:47:08: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Jun 2017 14:49:17: #3 Call peaks for each chromosome... INFO @ Sat, 03 Jun 2017 14:49:25: #3 Call peaks for each chromosome... INFO @ Sat, 03 Jun 2017 14:49:44: #3 Call peaks for each chromosome... INFO @ Sat, 03 Jun 2017 14:50:52: #4 Write output xls file... SRX1872289.20_peaks.xls INFO @ Sat, 03 Jun 2017 14:50:52: #4 Write peak in narrowPeak format file... SRX1872289.20_peaks.narrowPeak INFO @ Sat, 03 Jun 2017 14:50:52: #4 Write summits bed file... SRX1872289.20_summits.bed INFO @ Sat, 03 Jun 2017 14:50:52: Done! pass1 - making usageList (10 chroms): 1 millis pass2 - checking and writing primary data (203 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Sat, 03 Jun 2017 14:51:08: #4 Write output xls file... SRX1872289.10_peaks.xls INFO @ Sat, 03 Jun 2017 14:51:08: #4 Write peak in narrowPeak format file... SRX1872289.10_peaks.narrowPeak INFO @ Sat, 03 Jun 2017 14:51:08: #4 Write summits bed file... SRX1872289.10_summits.bed INFO @ Sat, 03 Jun 2017 14:51:08: Done! pass1 - making usageList (13 chroms): 0 millis pass2 - checking and writing primary data (529 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Sat, 03 Jun 2017 14:51:36: #4 Write output xls file... SRX1872289.05_peaks.xls INFO @ Sat, 03 Jun 2017 14:51:36: #4 Write peak in narrowPeak format file... SRX1872289.05_peaks.narrowPeak INFO @ Sat, 03 Jun 2017 14:51:36: #4 Write summits bed file... SRX1872289.05_summits.bed INFO @ Sat, 03 Jun 2017 14:51:36: Done! pass1 - making usageList (13 chroms): 1 millis pass2 - checking and writing primary data (1356 records, 4 fields): 3 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。