Job ID = 9029890 sra ファイルのダウンロード中... Completed: 1065800K bytes transferred in 15 seconds (560065K 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 --:--:-- 0 100 12695 0 12695 0 0 1741 0 --:--:-- 0:00:07 --:--:-- 15653 100 30786 0 30786 0 0 3791 0 --:--:-- 0:00:08 --:--:-- 18771 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 22276144 spots for /home/okishinya/chipatlas/results/dm3/SRX2541752/SRR5234226.sra Written 22276144 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: 00:06:37 22276144 reads; of these: 22276144 (100.00%) were unpaired; of these: 10738177 (48.20%) aligned 0 times 8064957 (36.20%) aligned exactly 1 time 3473010 (15.59%) aligned >1 times 51.80% overall alignment rate Time searching: 00:06:37 Overall time: 00:06:37 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 8 files... [bam_rmdupse_core] 1607638 / 11537967 = 0.1393 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 15:47:35: # Command line: callpeak -t SRX2541752.bam -f BAM -g dm -n SRX2541752.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX2541752.10 # format = BAM # ChIP-seq file = ['SRX2541752.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 15:47:35: #1 read tag files... INFO @ Sat, 03 Jun 2017 15:47:35: #1 read treatment tags... INFO @ Sat, 03 Jun 2017 15:47:35: # Command line: callpeak -t SRX2541752.bam -f BAM -g dm -n SRX2541752.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX2541752.05 # format = BAM # ChIP-seq file = ['SRX2541752.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 15:47:35: #1 read tag files... INFO @ Sat, 03 Jun 2017 15:47:35: #1 read treatment tags... INFO @ Sat, 03 Jun 2017 15:47:35: # Command line: callpeak -t SRX2541752.bam -f BAM -g dm -n SRX2541752.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX2541752.20 # format = BAM # ChIP-seq file = ['SRX2541752.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 15:47:35: #1 read tag files... INFO @ Sat, 03 Jun 2017 15:47:35: #1 read treatment tags... INFO @ Sat, 03 Jun 2017 15:47:42: 1000000 INFO @ Sat, 03 Jun 2017 15:47:42: 1000000 INFO @ Sat, 03 Jun 2017 15:47:43: 1000000 INFO @ Sat, 03 Jun 2017 15:47:50: 2000000 INFO @ Sat, 03 Jun 2017 15:47:50: 2000000 INFO @ Sat, 03 Jun 2017 15:47:52: 2000000 INFO @ Sat, 03 Jun 2017 15:47:57: 3000000 INFO @ Sat, 03 Jun 2017 15:47:57: 3000000 INFO @ Sat, 03 Jun 2017 15:48:00: 3000000 INFO @ Sat, 03 Jun 2017 15:48:05: 4000000 INFO @ Sat, 03 Jun 2017 15:48:06: 4000000 INFO @ Sat, 03 Jun 2017 15:48:10: 4000000 INFO @ Sat, 03 Jun 2017 15:48:12: 5000000 INFO @ Sat, 03 Jun 2017 15:48:15: 5000000 INFO @ Sat, 03 Jun 2017 15:48:19: 5000000 INFO @ Sat, 03 Jun 2017 15:48:20: 6000000 INFO @ Sat, 03 Jun 2017 15:48:24: 6000000 INFO @ Sat, 03 Jun 2017 15:48:27: 7000000 INFO @ Sat, 03 Jun 2017 15:48:28: 6000000 INFO @ Sat, 03 Jun 2017 15:48:33: 7000000 INFO @ Sat, 03 Jun 2017 15:48:35: 8000000 INFO @ Sat, 03 Jun 2017 15:48:36: 7000000 INFO @ Sat, 03 Jun 2017 15:48:41: 8000000 INFO @ Sat, 03 Jun 2017 15:48:42: 9000000 INFO @ Sat, 03 Jun 2017 15:48:45: 8000000 INFO @ Sat, 03 Jun 2017 15:48:49: #1 tag size is determined as 51 bps INFO @ Sat, 03 Jun 2017 15:48:49: #1 tag size = 51 INFO @ Sat, 03 Jun 2017 15:48:49: #1 total tags in treatment: 9930329 INFO @ Sat, 03 Jun 2017 15:48:49: #1 user defined the maximum tags... INFO @ Sat, 03 Jun 2017 15:48:49: #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 15:48:49: 9000000 INFO @ Sat, 03 Jun 2017 15:48:51: #1 tags after filtering in treatment: 9927741 INFO @ Sat, 03 Jun 2017 15:48:51: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 03 Jun 2017 15:48:51: #1 finished! INFO @ Sat, 03 Jun 2017 15:48:51: #2 Build Peak Model... INFO @ Sat, 03 Jun 2017 15:48:53: #2 number of paired peaks: 375 WARNING @ Sat, 03 Jun 2017 15:48:53: Fewer paired peaks (375) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 375 pairs to build model! INFO @ Sat, 03 Jun 2017 15:48:53: start model_add_line... INFO @ Sat, 03 Jun 2017 15:48:54: 9000000 INFO @ Sat, 03 Jun 2017 15:48:56: #1 tag size is determined as 51 bps INFO @ Sat, 03 Jun 2017 15:48:56: #1 tag size = 51 INFO @ Sat, 03 Jun 2017 15:48:56: #1 total tags in treatment: 9930329 INFO @ Sat, 03 Jun 2017 15:48:56: #1 user defined the maximum tags... INFO @ Sat, 03 Jun 2017 15:48:56: #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 15:48:56: start X-correlation... INFO @ Sat, 03 Jun 2017 15:48:56: end of X-cor INFO @ Sat, 03 Jun 2017 15:48:56: #2 finished! INFO @ Sat, 03 Jun 2017 15:48:56: #2 predicted fragment length is 116 bps INFO @ Sat, 03 Jun 2017 15:48:56: #2 alternative fragment length(s) may be 116 bps INFO @ Sat, 03 Jun 2017 15:48:56: #2.2 Generate R script for model : SRX2541752.05_model.r INFO @ Sat, 03 Jun 2017 15:48:56: #3 Call peaks... INFO @ Sat, 03 Jun 2017 15:48:56: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Jun 2017 15:48:58: #1 tags after filtering in treatment: 9927741 INFO @ Sat, 03 Jun 2017 15:48:58: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 03 Jun 2017 15:48:58: #1 finished! INFO @ Sat, 03 Jun 2017 15:48:58: #2 Build Peak Model... INFO @ Sat, 03 Jun 2017 15:49:00: #1 tag size is determined as 51 bps INFO @ Sat, 03 Jun 2017 15:49:00: #1 tag size = 51 INFO @ Sat, 03 Jun 2017 15:49:00: #1 total tags in treatment: 9930329 INFO @ Sat, 03 Jun 2017 15:49:00: #1 user defined the maximum tags... INFO @ Sat, 03 Jun 2017 15:49:00: #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 15:49:00: #2 number of paired peaks: 375 WARNING @ Sat, 03 Jun 2017 15:49:00: Fewer paired peaks (375) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 375 pairs to build model! INFO @ Sat, 03 Jun 2017 15:49:00: start model_add_line... INFO @ Sat, 03 Jun 2017 15:49:02: #1 tags after filtering in treatment: 9927741 INFO @ Sat, 03 Jun 2017 15:49:02: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 03 Jun 2017 15:49:02: #1 finished! INFO @ Sat, 03 Jun 2017 15:49:02: #2 Build Peak Model... INFO @ Sat, 03 Jun 2017 15:49:03: start X-correlation... INFO @ Sat, 03 Jun 2017 15:49:03: end of X-cor INFO @ Sat, 03 Jun 2017 15:49:03: #2 finished! INFO @ Sat, 03 Jun 2017 15:49:03: #2 predicted fragment length is 116 bps INFO @ Sat, 03 Jun 2017 15:49:03: #2 alternative fragment length(s) may be 116 bps INFO @ Sat, 03 Jun 2017 15:49:03: #2.2 Generate R script for model : SRX2541752.10_model.r INFO @ Sat, 03 Jun 2017 15:49:03: #3 Call peaks... INFO @ Sat, 03 Jun 2017 15:49:03: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Jun 2017 15:49:04: #2 number of paired peaks: 375 WARNING @ Sat, 03 Jun 2017 15:49:04: Fewer paired peaks (375) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 375 pairs to build model! INFO @ Sat, 03 Jun 2017 15:49:04: start model_add_line... INFO @ Sat, 03 Jun 2017 15:49:07: start X-correlation... INFO @ Sat, 03 Jun 2017 15:49:07: end of X-cor INFO @ Sat, 03 Jun 2017 15:49:07: #2 finished! INFO @ Sat, 03 Jun 2017 15:49:07: #2 predicted fragment length is 116 bps INFO @ Sat, 03 Jun 2017 15:49:07: #2 alternative fragment length(s) may be 116 bps INFO @ Sat, 03 Jun 2017 15:49:07: #2.2 Generate R script for model : SRX2541752.20_model.r INFO @ Sat, 03 Jun 2017 15:49:07: #3 Call peaks... INFO @ Sat, 03 Jun 2017 15:49:07: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Jun 2017 15:49:53: #3 Call peaks for each chromosome... INFO @ Sat, 03 Jun 2017 15:50:02: #3 Call peaks for each chromosome... INFO @ Sat, 03 Jun 2017 15:50:03: #3 Call peaks for each chromosome... INFO @ Sat, 03 Jun 2017 15:50:35: #4 Write output xls file... SRX2541752.05_peaks.xls INFO @ Sat, 03 Jun 2017 15:50:35: #4 Write peak in narrowPeak format file... SRX2541752.05_peaks.narrowPeak INFO @ Sat, 03 Jun 2017 15:50:35: #4 Write summits bed file... SRX2541752.05_summits.bed INFO @ Sat, 03 Jun 2017 15:50:35: Done! pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (2490 records, 4 fields): 5 millis CompletedMACS2peakCalling INFO @ Sat, 03 Jun 2017 15:50:43: #4 Write output xls file... SRX2541752.10_peaks.xls INFO @ Sat, 03 Jun 2017 15:50:43: #4 Write peak in narrowPeak format file... SRX2541752.10_peaks.narrowPeak INFO @ Sat, 03 Jun 2017 15:50:43: #4 Write summits bed file... SRX2541752.10_summits.bed INFO @ Sat, 03 Jun 2017 15:50:43: Done! pass1 - making usageList (13 chroms): 1 millis pass2 - checking and writing primary data (1670 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Sat, 03 Jun 2017 15:50:44: #4 Write output xls file... SRX2541752.20_peaks.xls INFO @ Sat, 03 Jun 2017 15:50:44: #4 Write peak in narrowPeak format file... SRX2541752.20_peaks.narrowPeak INFO @ Sat, 03 Jun 2017 15:50:44: #4 Write summits bed file... SRX2541752.20_summits.bed INFO @ Sat, 03 Jun 2017 15:50:44: Done! pass1 - making usageList (10 chroms): 1 millis pass2 - checking and writing primary data (1002 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。