Job ID = 8696849 sra ファイルのダウンロード中... Completed: 191138K bytes transferred in 5 seconds (271870K 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 14581 0 14581 0 0 1779 0 --:--:-- 0:00:08 --:--:-- 9885 100 31394 0 31394 0 0 3462 0 --:--:-- 0:00:09 --:--:-- 13376 100 31394 0 31394 0 0 3461 0 --:--:-- 0:00:09 --:--:-- 13370 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 16296767 spots for /home/okishinya/chipatlas/results/dm3/SRX110785/SRR388367.sra Written 16296767 spots total rm: cannot remove `[DSE]RR*.fastq': No such file or directory 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: 00:13:16 16296767 reads; of these: 16296767 (100.00%) were unpaired; of these: 924041 (5.67%) aligned 0 times 8022760 (49.23%) aligned exactly 1 time 7349966 (45.10%) aligned >1 times 94.33% overall alignment rate Time searching: 00:13:16 Overall time: 00:13:16 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_rmdupse_core] 1287235 / 15372726 = 0.0837 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 @ Fri, 10 Mar 2017 12:43:37: # Command line: callpeak -t SRX110785.bam -f BAM -g dm -n SRX110785.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX110785.20 # format = BAM # ChIP-seq file = ['SRX110785.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 @ Fri, 10 Mar 2017 12:43:37: #1 read tag files... INFO @ Fri, 10 Mar 2017 12:43:37: #1 read treatment tags... INFO @ Fri, 10 Mar 2017 12:43:37: # Command line: callpeak -t SRX110785.bam -f BAM -g dm -n SRX110785.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX110785.05 # format = BAM # ChIP-seq file = ['SRX110785.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 @ Fri, 10 Mar 2017 12:43:37: #1 read tag files... INFO @ Fri, 10 Mar 2017 12:43:37: #1 read treatment tags... INFO @ Fri, 10 Mar 2017 12:43:37: # Command line: callpeak -t SRX110785.bam -f BAM -g dm -n SRX110785.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX110785.10 # format = BAM # ChIP-seq file = ['SRX110785.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 @ Fri, 10 Mar 2017 12:43:37: #1 read tag files... INFO @ Fri, 10 Mar 2017 12:43:37: #1 read treatment tags... INFO @ Fri, 10 Mar 2017 12:43:43: 1000000 INFO @ Fri, 10 Mar 2017 12:43:44: 1000000 INFO @ Fri, 10 Mar 2017 12:43:46: 1000000 INFO @ Fri, 10 Mar 2017 12:43:49: 2000000 INFO @ Fri, 10 Mar 2017 12:43:52: 2000000 INFO @ Fri, 10 Mar 2017 12:43:55: 2000000 INFO @ Fri, 10 Mar 2017 12:43:56: 3000000 INFO @ Fri, 10 Mar 2017 12:44:00: 3000000 INFO @ Fri, 10 Mar 2017 12:44:02: 4000000 INFO @ Fri, 10 Mar 2017 12:44:04: 3000000 INFO @ Fri, 10 Mar 2017 12:44:08: 4000000 INFO @ Fri, 10 Mar 2017 12:44:08: 5000000 INFO @ Fri, 10 Mar 2017 12:44:13: 4000000 INFO @ Fri, 10 Mar 2017 12:44:15: 6000000 INFO @ Fri, 10 Mar 2017 12:44:16: 5000000 INFO @ Fri, 10 Mar 2017 12:44:21: 7000000 INFO @ Fri, 10 Mar 2017 12:44:22: 5000000 INFO @ Fri, 10 Mar 2017 12:44:23: 6000000 INFO @ Fri, 10 Mar 2017 12:44:27: 8000000 INFO @ Fri, 10 Mar 2017 12:44:30: 7000000 INFO @ Fri, 10 Mar 2017 12:44:32: 6000000 INFO @ Fri, 10 Mar 2017 12:44:33: 9000000 INFO @ Fri, 10 Mar 2017 12:44:38: 8000000 INFO @ Fri, 10 Mar 2017 12:44:40: 10000000 INFO @ Fri, 10 Mar 2017 12:44:41: 7000000 INFO @ Fri, 10 Mar 2017 12:44:46: 9000000 INFO @ Fri, 10 Mar 2017 12:44:46: 11000000 INFO @ Fri, 10 Mar 2017 12:44:50: 8000000 INFO @ Fri, 10 Mar 2017 12:44:52: 12000000 INFO @ Fri, 10 Mar 2017 12:44:53: 10000000 INFO @ Fri, 10 Mar 2017 12:44:59: 9000000 INFO @ Fri, 10 Mar 2017 12:44:59: 13000000 INFO @ Fri, 10 Mar 2017 12:45:01: 11000000 INFO @ Fri, 10 Mar 2017 12:45:05: 14000000 INFO @ Fri, 10 Mar 2017 12:45:06: #1 tag size is determined as 18 bps INFO @ Fri, 10 Mar 2017 12:45:06: #1 tag size = 18 INFO @ Fri, 10 Mar 2017 12:45:06: #1 total tags in treatment: 14085491 INFO @ Fri, 10 Mar 2017 12:45:06: #1 user defined the maximum tags... INFO @ Fri, 10 Mar 2017 12:45:06: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 10 Mar 2017 12:45:08: 10000000 INFO @ Fri, 10 Mar 2017 12:45:09: #1 tags after filtering in treatment: 14085491 INFO @ Fri, 10 Mar 2017 12:45:09: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 10 Mar 2017 12:45:09: #1 finished! INFO @ Fri, 10 Mar 2017 12:45:09: #2 Build Peak Model... INFO @ Fri, 10 Mar 2017 12:45:10: 12000000 INFO @ Fri, 10 Mar 2017 12:45:12: #2 number of paired peaks: 399 WARNING @ Fri, 10 Mar 2017 12:45:12: Fewer paired peaks (399) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 399 pairs to build model! INFO @ Fri, 10 Mar 2017 12:45:12: start model_add_line... INFO @ Fri, 10 Mar 2017 12:45:17: 11000000 INFO @ Fri, 10 Mar 2017 12:45:18: start X-correlation... INFO @ Fri, 10 Mar 2017 12:45:18: end of X-cor INFO @ Fri, 10 Mar 2017 12:45:18: #2 finished! INFO @ Fri, 10 Mar 2017 12:45:18: #2 predicted fragment length is 63 bps INFO @ Fri, 10 Mar 2017 12:45:18: #2 alternative fragment length(s) may be 4,63,556 bps INFO @ Fri, 10 Mar 2017 12:45:18: #2.2 Generate R script for model : SRX110785.10_model.r INFO @ Fri, 10 Mar 2017 12:45:18: #3 Call peaks... INFO @ Fri, 10 Mar 2017 12:45:18: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 10 Mar 2017 12:45:20: 13000000 INFO @ Fri, 10 Mar 2017 12:45:27: 12000000 INFO @ Fri, 10 Mar 2017 12:45:32: 14000000 INFO @ Fri, 10 Mar 2017 12:45:33: #1 tag size is determined as 18 bps INFO @ Fri, 10 Mar 2017 12:45:33: #1 tag size = 18 INFO @ Fri, 10 Mar 2017 12:45:33: #1 total tags in treatment: 14085491 INFO @ Fri, 10 Mar 2017 12:45:33: #1 user defined the maximum tags... INFO @ Fri, 10 Mar 2017 12:45:33: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 10 Mar 2017 12:45:36: 13000000 INFO @ Fri, 10 Mar 2017 12:45:37: #1 tags after filtering in treatment: 14085491 INFO @ Fri, 10 Mar 2017 12:45:37: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 10 Mar 2017 12:45:37: #1 finished! INFO @ Fri, 10 Mar 2017 12:45:37: #2 Build Peak Model... INFO @ Fri, 10 Mar 2017 12:45:41: #2 number of paired peaks: 399 WARNING @ Fri, 10 Mar 2017 12:45:41: Fewer paired peaks (399) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 399 pairs to build model! INFO @ Fri, 10 Mar 2017 12:45:41: start model_add_line... INFO @ Fri, 10 Mar 2017 12:45:45: 14000000 INFO @ Fri, 10 Mar 2017 12:45:46: start X-correlation... INFO @ Fri, 10 Mar 2017 12:45:46: end of X-cor INFO @ Fri, 10 Mar 2017 12:45:46: #2 finished! INFO @ Fri, 10 Mar 2017 12:45:46: #2 predicted fragment length is 63 bps INFO @ Fri, 10 Mar 2017 12:45:46: #2 alternative fragment length(s) may be 4,63,556 bps INFO @ Fri, 10 Mar 2017 12:45:46: #2.2 Generate R script for model : SRX110785.20_model.r INFO @ Fri, 10 Mar 2017 12:45:46: #3 Call peaks... INFO @ Fri, 10 Mar 2017 12:45:46: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 10 Mar 2017 12:45:46: #1 tag size is determined as 18 bps INFO @ Fri, 10 Mar 2017 12:45:46: #1 tag size = 18 INFO @ Fri, 10 Mar 2017 12:45:46: #1 total tags in treatment: 14085491 INFO @ Fri, 10 Mar 2017 12:45:46: #1 user defined the maximum tags... INFO @ Fri, 10 Mar 2017 12:45:46: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 10 Mar 2017 12:45:50: #1 tags after filtering in treatment: 14085491 INFO @ Fri, 10 Mar 2017 12:45:50: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 10 Mar 2017 12:45:50: #1 finished! INFO @ Fri, 10 Mar 2017 12:45:50: #2 Build Peak Model... INFO @ Fri, 10 Mar 2017 12:45:53: #2 number of paired peaks: 399 WARNING @ Fri, 10 Mar 2017 12:45:53: Fewer paired peaks (399) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 399 pairs to build model! INFO @ Fri, 10 Mar 2017 12:45:53: start model_add_line... INFO @ Fri, 10 Mar 2017 12:45:58: start X-correlation... INFO @ Fri, 10 Mar 2017 12:45:58: end of X-cor INFO @ Fri, 10 Mar 2017 12:45:58: #2 finished! INFO @ Fri, 10 Mar 2017 12:45:58: #2 predicted fragment length is 63 bps INFO @ Fri, 10 Mar 2017 12:45:58: #2 alternative fragment length(s) may be 4,63,556 bps INFO @ Fri, 10 Mar 2017 12:45:58: #2.2 Generate R script for model : SRX110785.05_model.r INFO @ Fri, 10 Mar 2017 12:45:58: #3 Call peaks... INFO @ Fri, 10 Mar 2017 12:45:58: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 10 Mar 2017 12:46:55: #3 Call peaks for each chromosome... INFO @ Fri, 10 Mar 2017 12:47:17: #3 Call peaks for each chromosome... INFO @ Fri, 10 Mar 2017 12:47:29: #3 Call peaks for each chromosome... INFO @ Fri, 10 Mar 2017 12:48:07: #4 Write output xls file... SRX110785.10_peaks.xls INFO @ Fri, 10 Mar 2017 12:48:07: #4 Write peak in narrowPeak format file... SRX110785.10_peaks.narrowPeak INFO @ Fri, 10 Mar 2017 12:48:07: #4 Write summits bed file... SRX110785.10_summits.bed INFO @ Fri, 10 Mar 2017 12:48:07: Done! pass1 - making usageList (11 chroms): 1 millis pass2 - checking and writing primary data (1850 records, 4 fields): 7 millis CompletedMACS2peakCalling INFO @ Fri, 10 Mar 2017 12:48:23: #4 Write output xls file... SRX110785.20_peaks.xls INFO @ Fri, 10 Mar 2017 12:48:23: #4 Write peak in narrowPeak format file... SRX110785.20_peaks.narrowPeak INFO @ Fri, 10 Mar 2017 12:48:23: #4 Write summits bed file... SRX110785.20_summits.bed INFO @ Fri, 10 Mar 2017 12:48:23: Done! pass1 - making usageList (10 chroms): 1 millis pass2 - checking and writing primary data (416 records, 4 fields): 5288 millis CompletedMACS2peakCalling INFO @ Fri, 10 Mar 2017 12:48:42: #4 Write output xls file... SRX110785.05_peaks.xls INFO @ Fri, 10 Mar 2017 12:48:42: #4 Write peak in narrowPeak format file... SRX110785.05_peaks.narrowPeak INFO @ Fri, 10 Mar 2017 12:48:43: #4 Write summits bed file... SRX110785.05_summits.bed INFO @ Fri, 10 Mar 2017 12:48:43: Done! pass1 - making usageList (13 chroms): 2 millis pass2 - checking and writing primary data (5549 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。