Job ID = 9025547 sra ファイルのダウンロード中... Completed: 1200439K bytes transferred in 14 seconds (698349K 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 --:--:-- 0:00:06 --:--:-- 0 100 30318 0 30318 0 0 3802 0 --:--:-- 0:00:07 --:--:-- 19484 100 77236 0 77236 0 0 8772 0 --:--:-- 0:00:08 --:--:-- 32356 100 79107 0 79107 0 0 8984 0 --:--:-- 0:00:08 --:--:-- 33126 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 56496066 spots for /home/okishinya/chipatlas/results/ce10/SRX1674094/SRR3320140.sra Written 56496066 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: 00:17:08 56496066 reads; of these: 56496066 (100.00%) were unpaired; of these: 1305645 (2.31%) aligned 0 times 49345278 (87.34%) aligned exactly 1 time 5845143 (10.35%) aligned >1 times 97.69% overall alignment rate Time searching: 00:17:08 Overall time: 00:17:08 マッピングが完了しました。 samtools でBAM に変換中... [samopen] SAM header is present: 7 sequences. [bam_sort_core] merging from 24 files... [bam_rmdupse_core] 23268887 / 55190421 = 0.4216 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 04:48:22: # Command line: callpeak -t SRX1674094.bam -f BAM -g ce -n SRX1674094.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX1674094.10 # format = BAM # ChIP-seq file = ['SRX1674094.bam'] # control file = None # effective genome size = 9.00e+07 # 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 04:48:22: #1 read tag files... INFO @ Sat, 03 Jun 2017 04:48:22: #1 read treatment tags... INFO @ Sat, 03 Jun 2017 04:48:22: # Command line: callpeak -t SRX1674094.bam -f BAM -g ce -n SRX1674094.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX1674094.20 # format = BAM # ChIP-seq file = ['SRX1674094.bam'] # control file = None # effective genome size = 9.00e+07 # 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 04:48:22: #1 read tag files... INFO @ Sat, 03 Jun 2017 04:48:22: #1 read treatment tags... INFO @ Sat, 03 Jun 2017 04:48:22: # Command line: callpeak -t SRX1674094.bam -f BAM -g ce -n SRX1674094.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX1674094.05 # format = BAM # ChIP-seq file = ['SRX1674094.bam'] # control file = None # effective genome size = 9.00e+07 # 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 04:48:22: #1 read tag files... INFO @ Sat, 03 Jun 2017 04:48:22: #1 read treatment tags... INFO @ Sat, 03 Jun 2017 04:48:27: 1000000 INFO @ Sat, 03 Jun 2017 04:48:28: 1000000 INFO @ Sat, 03 Jun 2017 04:48:28: 1000000 INFO @ Sat, 03 Jun 2017 04:48:33: 2000000 INFO @ Sat, 03 Jun 2017 04:48:34: 2000000 INFO @ Sat, 03 Jun 2017 04:48:34: 2000000 INFO @ Sat, 03 Jun 2017 04:48:38: 3000000 INFO @ Sat, 03 Jun 2017 04:48:39: 3000000 INFO @ Sat, 03 Jun 2017 04:48:39: 3000000 INFO @ Sat, 03 Jun 2017 04:48:44: 4000000 INFO @ Sat, 03 Jun 2017 04:48:45: 4000000 INFO @ Sat, 03 Jun 2017 04:48:45: 4000000 INFO @ Sat, 03 Jun 2017 04:48:49: 5000000 INFO @ Sat, 03 Jun 2017 04:48:51: 5000000 INFO @ Sat, 03 Jun 2017 04:48:51: 5000000 INFO @ Sat, 03 Jun 2017 04:48:55: 6000000 INFO @ Sat, 03 Jun 2017 04:48:57: 6000000 INFO @ Sat, 03 Jun 2017 04:48:57: 6000000 INFO @ Sat, 03 Jun 2017 04:49:00: 7000000 INFO @ Sat, 03 Jun 2017 04:49:03: 7000000 INFO @ Sat, 03 Jun 2017 04:49:03: 7000000 INFO @ Sat, 03 Jun 2017 04:49:05: 8000000 INFO @ Sat, 03 Jun 2017 04:49:09: 8000000 INFO @ Sat, 03 Jun 2017 04:49:09: 8000000 INFO @ Sat, 03 Jun 2017 04:49:10: 9000000 INFO @ Sat, 03 Jun 2017 04:49:15: 9000000 INFO @ Sat, 03 Jun 2017 04:49:15: 9000000 INFO @ Sat, 03 Jun 2017 04:49:15: 10000000 INFO @ Sat, 03 Jun 2017 04:49:20: 11000000 INFO @ Sat, 03 Jun 2017 04:49:21: 10000000 INFO @ Sat, 03 Jun 2017 04:49:21: 10000000 INFO @ Sat, 03 Jun 2017 04:49:26: 12000000 INFO @ Sat, 03 Jun 2017 04:49:27: 11000000 INFO @ Sat, 03 Jun 2017 04:49:27: 11000000 INFO @ Sat, 03 Jun 2017 04:49:31: 13000000 INFO @ Sat, 03 Jun 2017 04:49:33: 12000000 INFO @ Sat, 03 Jun 2017 04:49:33: 12000000 INFO @ Sat, 03 Jun 2017 04:49:37: 14000000 INFO @ Sat, 03 Jun 2017 04:49:39: 13000000 INFO @ Sat, 03 Jun 2017 04:49:39: 13000000 INFO @ Sat, 03 Jun 2017 04:49:42: 15000000 INFO @ Sat, 03 Jun 2017 04:49:45: 14000000 INFO @ Sat, 03 Jun 2017 04:49:45: 14000000 INFO @ Sat, 03 Jun 2017 04:49:47: 16000000 INFO @ Sat, 03 Jun 2017 04:49:50: 15000000 INFO @ Sat, 03 Jun 2017 04:49:50: 15000000 INFO @ Sat, 03 Jun 2017 04:49:52: 17000000 INFO @ Sat, 03 Jun 2017 04:49:56: 16000000 INFO @ Sat, 03 Jun 2017 04:49:56: 16000000 INFO @ Sat, 03 Jun 2017 04:49:58: 18000000 INFO @ Sat, 03 Jun 2017 04:50:01: 17000000 INFO @ Sat, 03 Jun 2017 04:50:01: 17000000 INFO @ Sat, 03 Jun 2017 04:50:03: 19000000 INFO @ Sat, 03 Jun 2017 04:50:07: 18000000 INFO @ Sat, 03 Jun 2017 04:50:07: 18000000 INFO @ Sat, 03 Jun 2017 04:50:08: 20000000 INFO @ Sat, 03 Jun 2017 04:50:12: 19000000 INFO @ Sat, 03 Jun 2017 04:50:13: 19000000 INFO @ Sat, 03 Jun 2017 04:50:14: 21000000 INFO @ Sat, 03 Jun 2017 04:50:18: 20000000 INFO @ Sat, 03 Jun 2017 04:50:18: 20000000 INFO @ Sat, 03 Jun 2017 04:50:19: 22000000 INFO @ Sat, 03 Jun 2017 04:50:23: 21000000 INFO @ Sat, 03 Jun 2017 04:50:24: 21000000 INFO @ Sat, 03 Jun 2017 04:50:24: 23000000 INFO @ Sat, 03 Jun 2017 04:50:29: 22000000 INFO @ Sat, 03 Jun 2017 04:50:30: 24000000 INFO @ Sat, 03 Jun 2017 04:50:30: 22000000 INFO @ Sat, 03 Jun 2017 04:50:36: 25000000 INFO @ Sat, 03 Jun 2017 04:50:36: 23000000 INFO @ Sat, 03 Jun 2017 04:50:37: 23000000 INFO @ Sat, 03 Jun 2017 04:50:42: 26000000 INFO @ Sat, 03 Jun 2017 04:50:44: 24000000 INFO @ Sat, 03 Jun 2017 04:50:44: 24000000 INFO @ Sat, 03 Jun 2017 04:50:49: 27000000 INFO @ Sat, 03 Jun 2017 04:50:51: 25000000 INFO @ Sat, 03 Jun 2017 04:50:52: 25000000 INFO @ Sat, 03 Jun 2017 04:50:55: 28000000 INFO @ Sat, 03 Jun 2017 04:50:58: 26000000 INFO @ Sat, 03 Jun 2017 04:50:59: 26000000 INFO @ Sat, 03 Jun 2017 04:51:01: 29000000 INFO @ Sat, 03 Jun 2017 04:51:06: 27000000 INFO @ Sat, 03 Jun 2017 04:51:07: 27000000 INFO @ Sat, 03 Jun 2017 04:51:08: 30000000 INFO @ Sat, 03 Jun 2017 04:51:14: 28000000 INFO @ Sat, 03 Jun 2017 04:51:14: 31000000 INFO @ Sat, 03 Jun 2017 04:51:15: 28000000 INFO @ Sat, 03 Jun 2017 04:51:21: #1 tag size is determined as 51 bps INFO @ Sat, 03 Jun 2017 04:51:21: #1 tag size = 51 INFO @ Sat, 03 Jun 2017 04:51:21: #1 total tags in treatment: 31921534 INFO @ Sat, 03 Jun 2017 04:51:21: #1 user defined the maximum tags... INFO @ Sat, 03 Jun 2017 04:51:21: #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 04:51:21: 29000000 INFO @ Sat, 03 Jun 2017 04:51:22: 29000000 INFO @ Sat, 03 Jun 2017 04:51:27: #1 tags after filtering in treatment: 31862965 INFO @ Sat, 03 Jun 2017 04:51:27: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 03 Jun 2017 04:51:27: #1 finished! INFO @ Sat, 03 Jun 2017 04:51:27: #2 Build Peak Model... INFO @ Sat, 03 Jun 2017 04:51:29: 30000000 INFO @ Sat, 03 Jun 2017 04:51:30: 30000000 INFO @ Sat, 03 Jun 2017 04:51:32: #2 number of paired peaks: 137 WARNING @ Sat, 03 Jun 2017 04:51:32: Fewer paired peaks (137) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 137 pairs to build model! INFO @ Sat, 03 Jun 2017 04:51:32: start model_add_line... INFO @ Sat, 03 Jun 2017 04:51:37: 31000000 INFO @ Sat, 03 Jun 2017 04:51:38: start X-correlation... INFO @ Sat, 03 Jun 2017 04:51:38: end of X-cor INFO @ Sat, 03 Jun 2017 04:51:38: #2 finished! INFO @ Sat, 03 Jun 2017 04:51:38: #2 predicted fragment length is 182 bps INFO @ Sat, 03 Jun 2017 04:51:38: #2 alternative fragment length(s) may be 2,88,102,129,147,182,237,258,314,336,342,351,372,387,415,419,518,584 bps INFO @ Sat, 03 Jun 2017 04:51:38: #2.2 Generate R script for model : SRX1674094.20_model.r INFO @ Sat, 03 Jun 2017 04:51:38: #3 Call peaks... INFO @ Sat, 03 Jun 2017 04:51:38: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Jun 2017 04:51:38: 31000000 INFO @ Sat, 03 Jun 2017 04:51:45: #1 tag size is determined as 51 bps INFO @ Sat, 03 Jun 2017 04:51:45: #1 tag size = 51 INFO @ Sat, 03 Jun 2017 04:51:45: #1 total tags in treatment: 31921534 INFO @ Sat, 03 Jun 2017 04:51:45: #1 user defined the maximum tags... INFO @ Sat, 03 Jun 2017 04:51:45: #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 04:51:46: #1 tag size is determined as 51 bps INFO @ Sat, 03 Jun 2017 04:51:46: #1 tag size = 51 INFO @ Sat, 03 Jun 2017 04:51:46: #1 total tags in treatment: 31921534 INFO @ Sat, 03 Jun 2017 04:51:46: #1 user defined the maximum tags... INFO @ Sat, 03 Jun 2017 04:51:46: #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 04:51:50: #1 tags after filtering in treatment: 31862965 INFO @ Sat, 03 Jun 2017 04:51:50: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 03 Jun 2017 04:51:50: #1 finished! INFO @ Sat, 03 Jun 2017 04:51:50: #2 Build Peak Model... INFO @ Sat, 03 Jun 2017 04:51:52: #1 tags after filtering in treatment: 31862965 INFO @ Sat, 03 Jun 2017 04:51:52: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 03 Jun 2017 04:51:52: #1 finished! INFO @ Sat, 03 Jun 2017 04:51:52: #2 Build Peak Model... INFO @ Sat, 03 Jun 2017 04:51:56: #2 number of paired peaks: 137 WARNING @ Sat, 03 Jun 2017 04:51:56: Fewer paired peaks (137) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 137 pairs to build model! INFO @ Sat, 03 Jun 2017 04:51:56: start model_add_line... INFO @ Sat, 03 Jun 2017 04:51:57: #2 number of paired peaks: 137 WARNING @ Sat, 03 Jun 2017 04:51:57: Fewer paired peaks (137) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 137 pairs to build model! INFO @ Sat, 03 Jun 2017 04:51:57: start model_add_line... INFO @ Sat, 03 Jun 2017 04:52:01: start X-correlation... INFO @ Sat, 03 Jun 2017 04:52:01: end of X-cor INFO @ Sat, 03 Jun 2017 04:52:01: #2 finished! INFO @ Sat, 03 Jun 2017 04:52:01: #2 predicted fragment length is 182 bps INFO @ Sat, 03 Jun 2017 04:52:01: #2 alternative fragment length(s) may be 2,88,102,129,147,182,237,258,314,336,342,351,372,387,415,419,518,584 bps INFO @ Sat, 03 Jun 2017 04:52:01: #2.2 Generate R script for model : SRX1674094.05_model.r INFO @ Sat, 03 Jun 2017 04:52:01: #3 Call peaks... INFO @ Sat, 03 Jun 2017 04:52:01: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Jun 2017 04:52:02: start X-correlation... INFO @ Sat, 03 Jun 2017 04:52:02: end of X-cor INFO @ Sat, 03 Jun 2017 04:52:02: #2 finished! INFO @ Sat, 03 Jun 2017 04:52:02: #2 predicted fragment length is 182 bps INFO @ Sat, 03 Jun 2017 04:52:02: #2 alternative fragment length(s) may be 2,88,102,129,147,182,237,258,314,336,342,351,372,387,415,419,518,584 bps INFO @ Sat, 03 Jun 2017 04:52:02: #2.2 Generate R script for model : SRX1674094.10_model.r INFO @ Sat, 03 Jun 2017 04:52:02: #3 Call peaks... INFO @ Sat, 03 Jun 2017 04:52:02: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Jun 2017 04:54:12: #3 Call peaks for each chromosome... INFO @ Sat, 03 Jun 2017 04:54:38: #3 Call peaks for each chromosome... INFO @ Sat, 03 Jun 2017 04:54:42: #3 Call peaks for each chromosome... INFO @ Sat, 03 Jun 2017 04:55:55: #4 Write output xls file... SRX1674094.20_peaks.xls INFO @ Sat, 03 Jun 2017 04:55:55: #4 Write peak in narrowPeak format file... SRX1674094.20_peaks.narrowPeak INFO @ Sat, 03 Jun 2017 04:55:55: #4 Write summits bed file... SRX1674094.20_summits.bed INFO @ Sat, 03 Jun 2017 04:55:55: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (3576 records, 4 fields): 6 millis CompletedMACS2peakCalling INFO @ Sat, 03 Jun 2017 04:56:29: #4 Write output xls file... SRX1674094.10_peaks.xls INFO @ Sat, 03 Jun 2017 04:56:29: #4 Write peak in narrowPeak format file... SRX1674094.10_peaks.narrowPeak INFO @ Sat, 03 Jun 2017 04:56:29: #4 Write summits bed file... SRX1674094.10_summits.bed INFO @ Sat, 03 Jun 2017 04:56:30: Done! pass1 - making usageList (6 chroms): 2 millis pass2 - checking and writing primary data (6728 records, 4 fields): 9 millis CompletedMACS2peakCalling INFO @ Sat, 03 Jun 2017 04:56:50: #4 Write output xls file... SRX1674094.05_peaks.xls INFO @ Sat, 03 Jun 2017 04:56:50: #4 Write peak in narrowPeak format file... SRX1674094.05_peaks.narrowPeak INFO @ Sat, 03 Jun 2017 04:56:50: #4 Write summits bed file... SRX1674094.05_summits.bed INFO @ Sat, 03 Jun 2017 04:56:50: Done! pass1 - making usageList (7 chroms): 2 millis pass2 - checking and writing primary data (10125 records, 4 fields): 13 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。