Job ID = 9029232 sra ファイルのダウンロード中... Completed: 607286K bytes transferred in 12 seconds (391660K 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 14324 0 14324 0 0 1955 0 --:--:-- 0:00:07 --:--:-- 13839 100 59205 0 59205 0 0 7114 0 --:--:-- 0:00:08 --:--:-- 29136 100 102k 0 102k 0 0 11727 0 --:--:-- 0:00:08 --:--:-- 39089 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 27471470 spots for /home/okishinya/chipatlas/results/dm3/SRX1433372/SRR2919837.sra Written 27471470 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: 00:11:36 27471470 reads; of these: 27471470 (100.00%) were unpaired; of these: 1693780 (6.17%) aligned 0 times 19108763 (69.56%) aligned exactly 1 time 6668927 (24.28%) aligned >1 times 93.83% overall alignment rate Time searching: 00:11:36 Overall time: 00:11:36 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 12 files... [bam_rmdupse_core] 8385996 / 25777690 = 0.3253 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 13:11:00: # Command line: callpeak -t SRX1433372.bam -f BAM -g dm -n SRX1433372.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX1433372.10 # format = BAM # ChIP-seq file = ['SRX1433372.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 13:11:00: #1 read tag files... INFO @ Sat, 03 Jun 2017 13:11:00: # Command line: callpeak -t SRX1433372.bam -f BAM -g dm -n SRX1433372.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX1433372.20 # format = BAM # ChIP-seq file = ['SRX1433372.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 13:11:00: #1 read treatment tags... INFO @ Sat, 03 Jun 2017 13:11:00: #1 read tag files... INFO @ Sat, 03 Jun 2017 13:11:00: #1 read treatment tags... INFO @ Sat, 03 Jun 2017 13:11:00: # Command line: callpeak -t SRX1433372.bam -f BAM -g dm -n SRX1433372.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX1433372.05 # format = BAM # ChIP-seq file = ['SRX1433372.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 13:11:00: #1 read tag files... INFO @ Sat, 03 Jun 2017 13:11:00: #1 read treatment tags... INFO @ Sat, 03 Jun 2017 13:11:08: 1000000 INFO @ Sat, 03 Jun 2017 13:11:08: 1000000 INFO @ Sat, 03 Jun 2017 13:11:08: 1000000 INFO @ Sat, 03 Jun 2017 13:11:15: 2000000 INFO @ Sat, 03 Jun 2017 13:11:15: 2000000 INFO @ Sat, 03 Jun 2017 13:11:17: 2000000 INFO @ Sat, 03 Jun 2017 13:11:23: 3000000 INFO @ Sat, 03 Jun 2017 13:11:23: 3000000 INFO @ Sat, 03 Jun 2017 13:11:24: 3000000 INFO @ Sat, 03 Jun 2017 13:11:30: 4000000 INFO @ Sat, 03 Jun 2017 13:11:30: 4000000 INFO @ Sat, 03 Jun 2017 13:11:32: 4000000 INFO @ Sat, 03 Jun 2017 13:11:36: 5000000 INFO @ Sat, 03 Jun 2017 13:11:36: 5000000 INFO @ Sat, 03 Jun 2017 13:11:38: 5000000 INFO @ Sat, 03 Jun 2017 13:11:42: 6000000 INFO @ Sat, 03 Jun 2017 13:11:43: 6000000 INFO @ Sat, 03 Jun 2017 13:11:44: 6000000 INFO @ Sat, 03 Jun 2017 13:11:49: 7000000 INFO @ Sat, 03 Jun 2017 13:11:49: 7000000 INFO @ Sat, 03 Jun 2017 13:11:50: 7000000 INFO @ Sat, 03 Jun 2017 13:11:55: 8000000 INFO @ Sat, 03 Jun 2017 13:11:55: 8000000 INFO @ Sat, 03 Jun 2017 13:11:56: 8000000 INFO @ Sat, 03 Jun 2017 13:12:01: 9000000 INFO @ Sat, 03 Jun 2017 13:12:01: 9000000 INFO @ Sat, 03 Jun 2017 13:12:03: 9000000 INFO @ Sat, 03 Jun 2017 13:12:09: 10000000 INFO @ Sat, 03 Jun 2017 13:12:09: 10000000 INFO @ Sat, 03 Jun 2017 13:12:10: 10000000 INFO @ Sat, 03 Jun 2017 13:12:16: 11000000 INFO @ Sat, 03 Jun 2017 13:12:17: 11000000 INFO @ Sat, 03 Jun 2017 13:12:18: 11000000 INFO @ Sat, 03 Jun 2017 13:12:24: 12000000 INFO @ Sat, 03 Jun 2017 13:12:25: 12000000 INFO @ Sat, 03 Jun 2017 13:12:27: 12000000 INFO @ Sat, 03 Jun 2017 13:12:32: 13000000 INFO @ Sat, 03 Jun 2017 13:12:33: 13000000 INFO @ Sat, 03 Jun 2017 13:12:35: 13000000 INFO @ Sat, 03 Jun 2017 13:12:40: 14000000 INFO @ Sat, 03 Jun 2017 13:12:41: 14000000 INFO @ Sat, 03 Jun 2017 13:12:44: 14000000 INFO @ Sat, 03 Jun 2017 13:12:49: 15000000 INFO @ Sat, 03 Jun 2017 13:12:50: 15000000 INFO @ Sat, 03 Jun 2017 13:12:52: 15000000 INFO @ Sat, 03 Jun 2017 13:12:57: 16000000 INFO @ Sat, 03 Jun 2017 13:12:58: 16000000 INFO @ Sat, 03 Jun 2017 13:13:00: 16000000 INFO @ Sat, 03 Jun 2017 13:13:04: 17000000 INFO @ Sat, 03 Jun 2017 13:13:05: 17000000 INFO @ Sat, 03 Jun 2017 13:13:07: #1 tag size is determined as 50 bps INFO @ Sat, 03 Jun 2017 13:13:07: #1 tag size = 50 INFO @ Sat, 03 Jun 2017 13:13:07: #1 total tags in treatment: 17391694 INFO @ Sat, 03 Jun 2017 13:13:07: #1 user defined the maximum tags... INFO @ Sat, 03 Jun 2017 13:13:07: #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 13:13:08: 17000000 INFO @ Sat, 03 Jun 2017 13:13:08: #1 tag size is determined as 50 bps INFO @ Sat, 03 Jun 2017 13:13:08: #1 tag size = 50 INFO @ Sat, 03 Jun 2017 13:13:08: #1 total tags in treatment: 17391694 INFO @ Sat, 03 Jun 2017 13:13:08: #1 user defined the maximum tags... INFO @ Sat, 03 Jun 2017 13:13:08: #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 13:13:10: #1 tags after filtering in treatment: 17387159 INFO @ Sat, 03 Jun 2017 13:13:10: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 03 Jun 2017 13:13:10: #1 finished! INFO @ Sat, 03 Jun 2017 13:13:10: #2 Build Peak Model... INFO @ Sat, 03 Jun 2017 13:13:11: #1 tag size is determined as 50 bps INFO @ Sat, 03 Jun 2017 13:13:11: #1 tag size = 50 INFO @ Sat, 03 Jun 2017 13:13:11: #1 total tags in treatment: 17391694 INFO @ Sat, 03 Jun 2017 13:13:11: #1 user defined the maximum tags... INFO @ Sat, 03 Jun 2017 13:13:11: #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 13:13:12: #1 tags after filtering in treatment: 17387159 INFO @ Sat, 03 Jun 2017 13:13:12: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 03 Jun 2017 13:13:12: #1 finished! INFO @ Sat, 03 Jun 2017 13:13:12: #2 Build Peak Model... INFO @ Sat, 03 Jun 2017 13:13:13: #2 number of paired peaks: 586 WARNING @ Sat, 03 Jun 2017 13:13:13: Fewer paired peaks (586) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 586 pairs to build model! INFO @ Sat, 03 Jun 2017 13:13:13: start model_add_line... INFO @ Sat, 03 Jun 2017 13:13:14: #1 tags after filtering in treatment: 17387159 INFO @ Sat, 03 Jun 2017 13:13:14: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 03 Jun 2017 13:13:14: #1 finished! INFO @ Sat, 03 Jun 2017 13:13:14: #2 Build Peak Model... INFO @ Sat, 03 Jun 2017 13:13:15: #2 number of paired peaks: 586 WARNING @ Sat, 03 Jun 2017 13:13:15: Fewer paired peaks (586) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 586 pairs to build model! INFO @ Sat, 03 Jun 2017 13:13:15: start model_add_line... INFO @ Sat, 03 Jun 2017 13:13:18: #2 number of paired peaks: 586 WARNING @ Sat, 03 Jun 2017 13:13:18: Fewer paired peaks (586) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 586 pairs to build model! INFO @ Sat, 03 Jun 2017 13:13:18: start model_add_line... INFO @ Sat, 03 Jun 2017 13:13:20: start X-correlation... INFO @ Sat, 03 Jun 2017 13:13:20: end of X-cor INFO @ Sat, 03 Jun 2017 13:13:20: #2 finished! INFO @ Sat, 03 Jun 2017 13:13:20: #2 predicted fragment length is 141 bps INFO @ Sat, 03 Jun 2017 13:13:20: #2 alternative fragment length(s) may be 141 bps INFO @ Sat, 03 Jun 2017 13:13:20: #2.2 Generate R script for model : SRX1433372.20_model.r INFO @ Sat, 03 Jun 2017 13:13:20: #3 Call peaks... INFO @ Sat, 03 Jun 2017 13:13:20: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Jun 2017 13:13:22: start X-correlation... INFO @ Sat, 03 Jun 2017 13:13:22: end of X-cor INFO @ Sat, 03 Jun 2017 13:13:22: #2 finished! INFO @ Sat, 03 Jun 2017 13:13:22: #2 predicted fragment length is 141 bps INFO @ Sat, 03 Jun 2017 13:13:22: #2 alternative fragment length(s) may be 141 bps INFO @ Sat, 03 Jun 2017 13:13:22: #2.2 Generate R script for model : SRX1433372.10_model.r INFO @ Sat, 03 Jun 2017 13:13:22: #3 Call peaks... INFO @ Sat, 03 Jun 2017 13:13:22: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Jun 2017 13:13:25: start X-correlation... INFO @ Sat, 03 Jun 2017 13:13:25: end of X-cor INFO @ Sat, 03 Jun 2017 13:13:25: #2 finished! INFO @ Sat, 03 Jun 2017 13:13:25: #2 predicted fragment length is 141 bps INFO @ Sat, 03 Jun 2017 13:13:25: #2 alternative fragment length(s) may be 141 bps INFO @ Sat, 03 Jun 2017 13:13:25: #2.2 Generate R script for model : SRX1433372.05_model.r INFO @ Sat, 03 Jun 2017 13:13:25: #3 Call peaks... INFO @ Sat, 03 Jun 2017 13:13:25: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Jun 2017 13:14:53: #3 Call peaks for each chromosome... INFO @ Sat, 03 Jun 2017 13:14:54: #3 Call peaks for each chromosome... INFO @ Sat, 03 Jun 2017 13:14:56: #3 Call peaks for each chromosome... INFO @ Sat, 03 Jun 2017 13:16:04: #4 Write output xls file... SRX1433372.10_peaks.xls INFO @ Sat, 03 Jun 2017 13:16:04: #4 Write peak in narrowPeak format file... SRX1433372.10_peaks.narrowPeak INFO @ Sat, 03 Jun 2017 13:16:04: #4 Write summits bed file... SRX1433372.10_summits.bed INFO @ Sat, 03 Jun 2017 13:16:04: Done! pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (3926 records, 4 fields): 6 millis CompletedMACS2peakCalling INFO @ Sat, 03 Jun 2017 13:16:05: #4 Write output xls file... SRX1433372.20_peaks.xls INFO @ Sat, 03 Jun 2017 13:16:05: #4 Write peak in narrowPeak format file... SRX1433372.20_peaks.narrowPeak INFO @ Sat, 03 Jun 2017 13:16:05: #4 Write summits bed file... SRX1433372.20_summits.bed INFO @ Sat, 03 Jun 2017 13:16:05: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (2217 records, 4 fields): 4 millis CompletedMACS2peakCalling INFO @ Sat, 03 Jun 2017 13:16:11: #4 Write output xls file... SRX1433372.05_peaks.xls INFO @ Sat, 03 Jun 2017 13:16:11: #4 Write peak in narrowPeak format file... SRX1433372.05_peaks.narrowPeak INFO @ Sat, 03 Jun 2017 13:16:11: #4 Write summits bed file... SRX1433372.05_summits.bed INFO @ Sat, 03 Jun 2017 13:16:11: Done! pass1 - making usageList (15 chroms): 2 millis pass2 - checking and writing primary data (6088 records, 4 fields): 9 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。