Job ID = 9033237 sra ファイルのダウンロード中... Completed: 458823K bytes transferred in 7 seconds (497550K 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 14324 0 14324 0 0 1662 0 --:--:-- 0:00:08 --:--:-- 6537 100 44110 0 44110 0 0 4670 0 --:--:-- 0:00:09 --:--:-- 14605 100 60560 0 60560 0 0 6301 0 --:--:-- 0:00:09 --:--:-- 19008 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 14966969 spots for /home/okishinya/chipatlas/results/dm3/SRX969912/SRR1931628.sra Written 14966969 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: 00:05:06 14966969 reads; of these: 14966969 (100.00%) were unpaired; of these: 414729 (2.77%) aligned 0 times 11611727 (77.58%) aligned exactly 1 time 2940513 (19.65%) aligned >1 times 97.23% overall alignment rate Time searching: 00:05:06 Overall time: 00:05:06 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 8 files... [bam_rmdupse_core] 1411898 / 14552240 = 0.0970 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 @ Sun, 04 Jun 2017 00:17:13: # Command line: callpeak -t SRX969912.bam -f BAM -g dm -n SRX969912.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX969912.05 # format = BAM # ChIP-seq file = ['SRX969912.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 @ Sun, 04 Jun 2017 00:17:13: #1 read tag files... INFO @ Sun, 04 Jun 2017 00:17:13: #1 read treatment tags... INFO @ Sun, 04 Jun 2017 00:17:13: # Command line: callpeak -t SRX969912.bam -f BAM -g dm -n SRX969912.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX969912.10 # format = BAM # ChIP-seq file = ['SRX969912.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 @ Sun, 04 Jun 2017 00:17:13: #1 read tag files... INFO @ Sun, 04 Jun 2017 00:17:13: #1 read treatment tags... INFO @ Sun, 04 Jun 2017 00:17:13: # Command line: callpeak -t SRX969912.bam -f BAM -g dm -n SRX969912.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX969912.20 # format = BAM # ChIP-seq file = ['SRX969912.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 @ Sun, 04 Jun 2017 00:17:13: #1 read tag files... INFO @ Sun, 04 Jun 2017 00:17:13: #1 read treatment tags... INFO @ Sun, 04 Jun 2017 00:17:18: 1000000 INFO @ Sun, 04 Jun 2017 00:17:18: 1000000 INFO @ Sun, 04 Jun 2017 00:17:19: 1000000 INFO @ Sun, 04 Jun 2017 00:17:24: 2000000 INFO @ Sun, 04 Jun 2017 00:17:24: 2000000 INFO @ Sun, 04 Jun 2017 00:17:25: 2000000 INFO @ Sun, 04 Jun 2017 00:17:29: 3000000 INFO @ Sun, 04 Jun 2017 00:17:30: 3000000 INFO @ Sun, 04 Jun 2017 00:17:31: 3000000 INFO @ Sun, 04 Jun 2017 00:17:34: 4000000 INFO @ Sun, 04 Jun 2017 00:17:36: 4000000 INFO @ Sun, 04 Jun 2017 00:17:37: 4000000 INFO @ Sun, 04 Jun 2017 00:17:39: 5000000 INFO @ Sun, 04 Jun 2017 00:17:41: 5000000 INFO @ Sun, 04 Jun 2017 00:17:43: 5000000 INFO @ Sun, 04 Jun 2017 00:17:45: 6000000 INFO @ Sun, 04 Jun 2017 00:17:47: 6000000 INFO @ Sun, 04 Jun 2017 00:17:50: 6000000 INFO @ Sun, 04 Jun 2017 00:17:50: 7000000 INFO @ Sun, 04 Jun 2017 00:17:53: 7000000 INFO @ Sun, 04 Jun 2017 00:17:55: 8000000 INFO @ Sun, 04 Jun 2017 00:17:56: 7000000 INFO @ Sun, 04 Jun 2017 00:17:59: 8000000 INFO @ Sun, 04 Jun 2017 00:18:01: 9000000 INFO @ Sun, 04 Jun 2017 00:18:02: 8000000 INFO @ Sun, 04 Jun 2017 00:18:05: 9000000 INFO @ Sun, 04 Jun 2017 00:18:06: 10000000 INFO @ Sun, 04 Jun 2017 00:18:08: 9000000 INFO @ Sun, 04 Jun 2017 00:18:10: 10000000 INFO @ Sun, 04 Jun 2017 00:18:11: 11000000 INFO @ Sun, 04 Jun 2017 00:18:14: 10000000 INFO @ Sun, 04 Jun 2017 00:18:16: 11000000 INFO @ Sun, 04 Jun 2017 00:18:16: 12000000 INFO @ Sun, 04 Jun 2017 00:18:20: 11000000 INFO @ Sun, 04 Jun 2017 00:18:21: 12000000 INFO @ Sun, 04 Jun 2017 00:18:22: 13000000 INFO @ Sun, 04 Jun 2017 00:18:23: #1 tag size is determined as 50 bps INFO @ Sun, 04 Jun 2017 00:18:23: #1 tag size = 50 INFO @ Sun, 04 Jun 2017 00:18:23: #1 total tags in treatment: 13140342 INFO @ Sun, 04 Jun 2017 00:18:23: #1 user defined the maximum tags... INFO @ Sun, 04 Jun 2017 00:18:23: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sun, 04 Jun 2017 00:18:25: #1 tags after filtering in treatment: 13137942 INFO @ Sun, 04 Jun 2017 00:18:25: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 04 Jun 2017 00:18:25: #1 finished! INFO @ Sun, 04 Jun 2017 00:18:25: #2 Build Peak Model... INFO @ Sun, 04 Jun 2017 00:18:25: 12000000 INFO @ Sun, 04 Jun 2017 00:18:27: 13000000 INFO @ Sun, 04 Jun 2017 00:18:28: #2 number of paired peaks: 122 WARNING @ Sun, 04 Jun 2017 00:18:28: Fewer paired peaks (122) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 122 pairs to build model! INFO @ Sun, 04 Jun 2017 00:18:28: start model_add_line... INFO @ Sun, 04 Jun 2017 00:18:28: #1 tag size is determined as 50 bps INFO @ Sun, 04 Jun 2017 00:18:28: #1 tag size = 50 INFO @ Sun, 04 Jun 2017 00:18:28: #1 total tags in treatment: 13140342 INFO @ Sun, 04 Jun 2017 00:18:28: #1 user defined the maximum tags... INFO @ Sun, 04 Jun 2017 00:18:28: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sun, 04 Jun 2017 00:18:30: start X-correlation... INFO @ Sun, 04 Jun 2017 00:18:30: end of X-cor INFO @ Sun, 04 Jun 2017 00:18:30: #2 finished! INFO @ Sun, 04 Jun 2017 00:18:30: #2 predicted fragment length is 115 bps INFO @ Sun, 04 Jun 2017 00:18:30: #2 alternative fragment length(s) may be 115 bps INFO @ Sun, 04 Jun 2017 00:18:30: #2.2 Generate R script for model : SRX969912.05_model.r INFO @ Sun, 04 Jun 2017 00:18:30: #3 Call peaks... INFO @ Sun, 04 Jun 2017 00:18:30: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 04 Jun 2017 00:18:31: 13000000 INFO @ Sun, 04 Jun 2017 00:18:31: #1 tags after filtering in treatment: 13137942 INFO @ Sun, 04 Jun 2017 00:18:31: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 04 Jun 2017 00:18:31: #1 finished! INFO @ Sun, 04 Jun 2017 00:18:31: #2 Build Peak Model... INFO @ Sun, 04 Jun 2017 00:18:32: #1 tag size is determined as 50 bps INFO @ Sun, 04 Jun 2017 00:18:32: #1 tag size = 50 INFO @ Sun, 04 Jun 2017 00:18:32: #1 total tags in treatment: 13140342 INFO @ Sun, 04 Jun 2017 00:18:32: #1 user defined the maximum tags... INFO @ Sun, 04 Jun 2017 00:18:32: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sun, 04 Jun 2017 00:18:33: #2 number of paired peaks: 122 WARNING @ Sun, 04 Jun 2017 00:18:33: Fewer paired peaks (122) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 122 pairs to build model! INFO @ Sun, 04 Jun 2017 00:18:33: start model_add_line... INFO @ Sun, 04 Jun 2017 00:18:34: #1 tags after filtering in treatment: 13137942 INFO @ Sun, 04 Jun 2017 00:18:34: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 04 Jun 2017 00:18:34: #1 finished! INFO @ Sun, 04 Jun 2017 00:18:34: #2 Build Peak Model... INFO @ Sun, 04 Jun 2017 00:18:35: start X-correlation... INFO @ Sun, 04 Jun 2017 00:18:35: end of X-cor INFO @ Sun, 04 Jun 2017 00:18:35: #2 finished! INFO @ Sun, 04 Jun 2017 00:18:35: #2 predicted fragment length is 115 bps INFO @ Sun, 04 Jun 2017 00:18:35: #2 alternative fragment length(s) may be 115 bps INFO @ Sun, 04 Jun 2017 00:18:35: #2.2 Generate R script for model : SRX969912.20_model.r INFO @ Sun, 04 Jun 2017 00:18:35: #3 Call peaks... INFO @ Sun, 04 Jun 2017 00:18:35: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 04 Jun 2017 00:18:36: #2 number of paired peaks: 122 WARNING @ Sun, 04 Jun 2017 00:18:36: Fewer paired peaks (122) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 122 pairs to build model! INFO @ Sun, 04 Jun 2017 00:18:36: start model_add_line... INFO @ Sun, 04 Jun 2017 00:18:38: start X-correlation... INFO @ Sun, 04 Jun 2017 00:18:38: end of X-cor INFO @ Sun, 04 Jun 2017 00:18:38: #2 finished! INFO @ Sun, 04 Jun 2017 00:18:38: #2 predicted fragment length is 115 bps INFO @ Sun, 04 Jun 2017 00:18:38: #2 alternative fragment length(s) may be 115 bps INFO @ Sun, 04 Jun 2017 00:18:38: #2.2 Generate R script for model : SRX969912.10_model.r INFO @ Sun, 04 Jun 2017 00:18:38: #3 Call peaks... INFO @ Sun, 04 Jun 2017 00:18:38: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 04 Jun 2017 00:19:43: #3 Call peaks for each chromosome... INFO @ Sun, 04 Jun 2017 00:19:45: #3 Call peaks for each chromosome... INFO @ Sun, 04 Jun 2017 00:19:47: #3 Call peaks for each chromosome... INFO @ Sun, 04 Jun 2017 00:20:35: #4 Write output xls file... SRX969912.05_peaks.xls INFO @ Sun, 04 Jun 2017 00:20:35: #4 Write peak in narrowPeak format file... SRX969912.05_peaks.narrowPeak INFO @ Sun, 04 Jun 2017 00:20:35: #4 Write summits bed file... SRX969912.05_summits.bed INFO @ Sun, 04 Jun 2017 00:20:35: Done! pass1 - making usageList (13 chroms): 1 millis pass2 - checking and writing primary data (2647 records, 4 fields): 6 millis CompletedMACS2peakCalling INFO @ Sun, 04 Jun 2017 00:20:36: #4 Write output xls file... SRX969912.20_peaks.xls INFO @ Sun, 04 Jun 2017 00:20:36: #4 Write peak in narrowPeak format file... SRX969912.20_peaks.narrowPeak INFO @ Sun, 04 Jun 2017 00:20:36: #4 Write summits bed file... SRX969912.20_summits.bed INFO @ Sun, 04 Jun 2017 00:20:36: Done! pass1 - making usageList (11 chroms): 1 millis pass2 - checking and writing primary data (836 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Sun, 04 Jun 2017 00:20:41: #4 Write output xls file... SRX969912.10_peaks.xls INFO @ Sun, 04 Jun 2017 00:20:41: #4 Write peak in narrowPeak format file... SRX969912.10_peaks.narrowPeak INFO @ Sun, 04 Jun 2017 00:20:41: #4 Write summits bed file... SRX969912.10_summits.bed INFO @ Sun, 04 Jun 2017 00:20:41: Done! pass1 - making usageList (11 chroms): 0 millis pass2 - checking and writing primary data (1549 records, 4 fields): 4 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。