Job ID = 9029405 sra ファイルのダウンロード中... Completed: 1584974K bytes transferred in 14 seconds (877498K 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 17214 0 17214 0 0 2275 0 --:--:-- 0:00:07 --:--:-- 15113 100 30662 0 30662 0 0 3803 0 --:--:-- 0:00:08 --:--:-- 18730 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 38082740 spots for /home/okishinya/chipatlas/results/dm3/SRX1715679/SRR3405220.sra Written 38082740 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: 00:13:39 38082740 reads; of these: 38082740 (100.00%) were unpaired; of these: 729066 (1.91%) aligned 0 times 30193023 (79.28%) aligned exactly 1 time 7160651 (18.80%) aligned >1 times 98.09% overall alignment rate Time searching: 00:13:39 Overall time: 00:13:39 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] 16803832 / 37353674 = 0.4499 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 13:51:41: # Command line: callpeak -t SRX1715679.bam -f BAM -g dm -n SRX1715679.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX1715679.05 # format = BAM # ChIP-seq file = ['SRX1715679.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 13:51:41: #1 read tag files... INFO @ Sat, 03 Jun 2017 13:51:41: #1 read treatment tags... INFO @ Sat, 03 Jun 2017 13:51:41: # Command line: callpeak -t SRX1715679.bam -f BAM -g dm -n SRX1715679.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX1715679.10 # format = BAM # ChIP-seq file = ['SRX1715679.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 13:51:41: #1 read tag files... INFO @ Sat, 03 Jun 2017 13:51:41: #1 read treatment tags... INFO @ Sat, 03 Jun 2017 13:51:41: # Command line: callpeak -t SRX1715679.bam -f BAM -g dm -n SRX1715679.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX1715679.20 # format = BAM # ChIP-seq file = ['SRX1715679.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 13:51:41: #1 read tag files... INFO @ Sat, 03 Jun 2017 13:51:41: #1 read treatment tags... INFO @ Sat, 03 Jun 2017 13:51:47: 1000000 INFO @ Sat, 03 Jun 2017 13:51:47: 1000000 INFO @ Sat, 03 Jun 2017 13:51:47: 1000000 INFO @ Sat, 03 Jun 2017 13:51:53: 2000000 INFO @ Sat, 03 Jun 2017 13:51:53: 2000000 INFO @ Sat, 03 Jun 2017 13:51:53: 2000000 INFO @ Sat, 03 Jun 2017 13:51:59: 3000000 INFO @ Sat, 03 Jun 2017 13:51:59: 3000000 INFO @ Sat, 03 Jun 2017 13:51:59: 3000000 INFO @ Sat, 03 Jun 2017 13:52:05: 4000000 INFO @ Sat, 03 Jun 2017 13:52:05: 4000000 INFO @ Sat, 03 Jun 2017 13:52:05: 4000000 INFO @ Sat, 03 Jun 2017 13:52:11: 5000000 INFO @ Sat, 03 Jun 2017 13:52:12: 5000000 INFO @ Sat, 03 Jun 2017 13:52:12: 5000000 INFO @ Sat, 03 Jun 2017 13:52:16: 6000000 INFO @ Sat, 03 Jun 2017 13:52:18: 6000000 INFO @ Sat, 03 Jun 2017 13:52:18: 6000000 INFO @ Sat, 03 Jun 2017 13:52:22: 7000000 INFO @ Sat, 03 Jun 2017 13:52:24: 7000000 INFO @ Sat, 03 Jun 2017 13:52:24: 7000000 INFO @ Sat, 03 Jun 2017 13:52:28: 8000000 INFO @ Sat, 03 Jun 2017 13:52:30: 8000000 INFO @ Sat, 03 Jun 2017 13:52:30: 8000000 INFO @ Sat, 03 Jun 2017 13:52:34: 9000000 INFO @ Sat, 03 Jun 2017 13:52:37: 9000000 INFO @ Sat, 03 Jun 2017 13:52:37: 9000000 INFO @ Sat, 03 Jun 2017 13:52:39: 10000000 INFO @ Sat, 03 Jun 2017 13:52:43: 10000000 INFO @ Sat, 03 Jun 2017 13:52:43: 10000000 INFO @ Sat, 03 Jun 2017 13:52:45: 11000000 INFO @ Sat, 03 Jun 2017 13:52:49: 11000000 INFO @ Sat, 03 Jun 2017 13:52:49: 11000000 INFO @ Sat, 03 Jun 2017 13:52:51: 12000000 INFO @ Sat, 03 Jun 2017 13:52:55: 12000000 INFO @ Sat, 03 Jun 2017 13:52:56: 12000000 INFO @ Sat, 03 Jun 2017 13:52:58: 13000000 INFO @ Sat, 03 Jun 2017 13:53:01: 13000000 INFO @ Sat, 03 Jun 2017 13:53:02: 13000000 INFO @ Sat, 03 Jun 2017 13:53:04: 14000000 INFO @ Sat, 03 Jun 2017 13:53:06: 14000000 INFO @ Sat, 03 Jun 2017 13:53:09: 14000000 INFO @ Sat, 03 Jun 2017 13:53:10: 15000000 INFO @ Sat, 03 Jun 2017 13:53:12: 15000000 INFO @ Sat, 03 Jun 2017 13:53:15: 15000000 INFO @ Sat, 03 Jun 2017 13:53:17: 16000000 INFO @ Sat, 03 Jun 2017 13:53:18: 16000000 INFO @ Sat, 03 Jun 2017 13:53:22: 16000000 INFO @ Sat, 03 Jun 2017 13:53:23: 17000000 INFO @ Sat, 03 Jun 2017 13:53:23: 17000000 INFO @ Sat, 03 Jun 2017 13:53:28: 17000000 INFO @ Sat, 03 Jun 2017 13:53:29: 18000000 INFO @ Sat, 03 Jun 2017 13:53:30: 18000000 INFO @ Sat, 03 Jun 2017 13:53:35: 19000000 INFO @ Sat, 03 Jun 2017 13:53:35: 18000000 INFO @ Sat, 03 Jun 2017 13:53:36: 19000000 INFO @ Sat, 03 Jun 2017 13:53:40: 20000000 INFO @ Sat, 03 Jun 2017 13:53:41: 19000000 INFO @ Sat, 03 Jun 2017 13:53:42: 20000000 INFO @ Sat, 03 Jun 2017 13:53:44: #1 tag size is determined as 49 bps INFO @ Sat, 03 Jun 2017 13:53:44: #1 tag size = 49 INFO @ Sat, 03 Jun 2017 13:53:44: #1 total tags in treatment: 20549842 INFO @ Sat, 03 Jun 2017 13:53:44: #1 user defined the maximum tags... INFO @ Sat, 03 Jun 2017 13:53:44: #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 13:53:46: #1 tag size is determined as 49 bps INFO @ Sat, 03 Jun 2017 13:53:46: #1 tag size = 49 INFO @ Sat, 03 Jun 2017 13:53:46: #1 total tags in treatment: 20549842 INFO @ Sat, 03 Jun 2017 13:53:46: #1 user defined the maximum tags... INFO @ Sat, 03 Jun 2017 13:53:46: #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 13:53:48: #1 tags after filtering in treatment: 20541167 INFO @ Sat, 03 Jun 2017 13:53:48: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 03 Jun 2017 13:53:48: #1 finished! INFO @ Sat, 03 Jun 2017 13:53:48: #2 Build Peak Model... INFO @ Sat, 03 Jun 2017 13:53:48: 20000000 INFO @ Sat, 03 Jun 2017 13:53:50: #1 tags after filtering in treatment: 20541167 INFO @ Sat, 03 Jun 2017 13:53:50: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 03 Jun 2017 13:53:50: #1 finished! INFO @ Sat, 03 Jun 2017 13:53:50: #2 Build Peak Model... INFO @ Sat, 03 Jun 2017 13:53:51: #1 tag size is determined as 49 bps INFO @ Sat, 03 Jun 2017 13:53:51: #1 tag size = 49 INFO @ Sat, 03 Jun 2017 13:53:51: #1 total tags in treatment: 20549842 INFO @ Sat, 03 Jun 2017 13:53:51: #1 user defined the maximum tags... INFO @ Sat, 03 Jun 2017 13:53:51: #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 13:53:51: #2 number of paired peaks: 319 WARNING @ Sat, 03 Jun 2017 13:53:51: Fewer paired peaks (319) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 319 pairs to build model! INFO @ Sat, 03 Jun 2017 13:53:51: start model_add_line... INFO @ Sat, 03 Jun 2017 13:53:54: #2 number of paired peaks: 319 WARNING @ Sat, 03 Jun 2017 13:53:54: Fewer paired peaks (319) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 319 pairs to build model! INFO @ Sat, 03 Jun 2017 13:53:54: start model_add_line... INFO @ Sat, 03 Jun 2017 13:53:55: #1 tags after filtering in treatment: 20541167 INFO @ Sat, 03 Jun 2017 13:53:55: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 03 Jun 2017 13:53:55: #1 finished! INFO @ Sat, 03 Jun 2017 13:53:55: #2 Build Peak Model... INFO @ Sat, 03 Jun 2017 13:53:56: start X-correlation... INFO @ Sat, 03 Jun 2017 13:53:56: end of X-cor INFO @ Sat, 03 Jun 2017 13:53:56: #2 finished! INFO @ Sat, 03 Jun 2017 13:53:56: #2 predicted fragment length is 104 bps INFO @ Sat, 03 Jun 2017 13:53:56: #2 alternative fragment length(s) may be 104 bps INFO @ Sat, 03 Jun 2017 13:53:56: #2.2 Generate R script for model : SRX1715679.10_model.r INFO @ Sat, 03 Jun 2017 13:53:56: #3 Call peaks... INFO @ Sat, 03 Jun 2017 13:53:56: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Jun 2017 13:53:58: #2 number of paired peaks: 319 WARNING @ Sat, 03 Jun 2017 13:53:58: Fewer paired peaks (319) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 319 pairs to build model! INFO @ Sat, 03 Jun 2017 13:53:58: start model_add_line... INFO @ Sat, 03 Jun 2017 13:53:59: start X-correlation... INFO @ Sat, 03 Jun 2017 13:53:59: end of X-cor INFO @ Sat, 03 Jun 2017 13:53:59: #2 finished! INFO @ Sat, 03 Jun 2017 13:53:59: #2 predicted fragment length is 104 bps INFO @ Sat, 03 Jun 2017 13:53:59: #2 alternative fragment length(s) may be 104 bps INFO @ Sat, 03 Jun 2017 13:53:59: #2.2 Generate R script for model : SRX1715679.20_model.r INFO @ Sat, 03 Jun 2017 13:53:59: #3 Call peaks... INFO @ Sat, 03 Jun 2017 13:53:59: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Jun 2017 13:54:03: start X-correlation... INFO @ Sat, 03 Jun 2017 13:54:03: end of X-cor INFO @ Sat, 03 Jun 2017 13:54:03: #2 finished! INFO @ Sat, 03 Jun 2017 13:54:03: #2 predicted fragment length is 104 bps INFO @ Sat, 03 Jun 2017 13:54:03: #2 alternative fragment length(s) may be 104 bps INFO @ Sat, 03 Jun 2017 13:54:03: #2.2 Generate R script for model : SRX1715679.05_model.r INFO @ Sat, 03 Jun 2017 13:54:03: #3 Call peaks... INFO @ Sat, 03 Jun 2017 13:54:03: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Jun 2017 13:55:36: #3 Call peaks for each chromosome... INFO @ Sat, 03 Jun 2017 13:55:40: #3 Call peaks for each chromosome... INFO @ Sat, 03 Jun 2017 13:55:49: #3 Call peaks for each chromosome... INFO @ Sat, 03 Jun 2017 13:57:00: #4 Write output xls file... SRX1715679.10_peaks.xls INFO @ Sat, 03 Jun 2017 13:57:00: #4 Write peak in narrowPeak format file... SRX1715679.10_peaks.narrowPeak INFO @ Sat, 03 Jun 2017 13:57:00: #4 Write summits bed file... SRX1715679.10_summits.bed INFO @ Sat, 03 Jun 2017 13:57:00: Done! pass1 - making usageList (14 chroms): 2 millis pass2 - checking and writing primary data (6645 records, 4 fields): 9 millis CompletedMACS2peakCalling INFO @ Sat, 03 Jun 2017 13:57:00: #4 Write output xls file... SRX1715679.20_peaks.xls INFO @ Sat, 03 Jun 2017 13:57:00: #4 Write peak in narrowPeak format file... SRX1715679.20_peaks.narrowPeak INFO @ Sat, 03 Jun 2017 13:57:00: #4 Write summits bed file... SRX1715679.20_summits.bed INFO @ Sat, 03 Jun 2017 13:57:00: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (3589 records, 4 fields): 6 millis CompletedMACS2peakCalling INFO @ Sat, 03 Jun 2017 13:57:20: #4 Write output xls file... SRX1715679.05_peaks.xls INFO @ Sat, 03 Jun 2017 13:57:20: #4 Write peak in narrowPeak format file... SRX1715679.05_peaks.narrowPeak INFO @ Sat, 03 Jun 2017 13:57:20: #4 Write summits bed file... SRX1715679.05_summits.bed INFO @ Sat, 03 Jun 2017 13:57:20: Done! pass1 - making usageList (15 chroms): 2 millis pass2 - checking and writing primary data (8674 records, 4 fields): 11 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。