Job ID = 2236879 sra ファイルのダウンロード中... Completed: 403970K bytes transferred in 26 seconds (124179K 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 --:--:-- --:--:-- --:--:-- 0 100 6920 0 6920 0 0 11942 0 --:--:-- --:--:-- --:--:-- 17789 100 34725 0 34725 0 0 45154 0 --:--:-- --:--:-- --:--:-- 60077 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 25891064 spots for /home/okishinya/chipatlas/results/ce10/SRX059255/SRR190695.sra Written 25891064 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: 00:04:56 25891064 reads; of these: 25891064 (100.00%) were unpaired; of these: 4473988 (17.28%) aligned 0 times 17611867 (68.02%) aligned exactly 1 time 3805209 (14.70%) aligned >1 times 82.72% overall alignment rate Time searching: 00:04:56 Overall time: 00:04:56 マッピングが完了しました。 samtools でBAM に変換中... [samopen] SAM header is present: 7 sequences. [bam_sort_core] merging from 8 files... [bam_rmdupse_core] 4575617 / 21417076 = 0.2136 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 @ Thu, 30 Apr 2015 11:21:12: # Command line: callpeak -t SRX059255.bam -f BAM -g ce -n SRX059255.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX059255.10 # format = BAM # ChIP-seq file = ['SRX059255.bam'] # control file = None # effective genome size = 9.00e+07 # 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 @ Thu, 30 Apr 2015 11:21:12: #1 read tag files... INFO @ Thu, 30 Apr 2015 11:21:12: #1 read treatment tags... INFO @ Thu, 30 Apr 2015 11:21:12: # Command line: callpeak -t SRX059255.bam -f BAM -g ce -n SRX059255.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX059255.20 # format = BAM # ChIP-seq file = ['SRX059255.bam'] # control file = None # effective genome size = 9.00e+07 # 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 @ Thu, 30 Apr 2015 11:21:12: #1 read tag files... INFO @ Thu, 30 Apr 2015 11:21:12: # Command line: callpeak -t SRX059255.bam -f BAM -g ce -n SRX059255.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX059255.05 # format = BAM # ChIP-seq file = ['SRX059255.bam'] # control file = None # effective genome size = 9.00e+07 # 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 @ Thu, 30 Apr 2015 11:21:12: #1 read treatment tags... INFO @ Thu, 30 Apr 2015 11:21:12: #1 read tag files... INFO @ Thu, 30 Apr 2015 11:21:12: #1 read treatment tags... INFO @ Thu, 30 Apr 2015 11:21:16: 1000000 INFO @ Thu, 30 Apr 2015 11:21:16: 1000000 INFO @ Thu, 30 Apr 2015 11:21:17: 1000000 INFO @ Thu, 30 Apr 2015 11:21:21: 2000000 INFO @ Thu, 30 Apr 2015 11:21:21: 2000000 INFO @ Thu, 30 Apr 2015 11:21:22: 2000000 INFO @ Thu, 30 Apr 2015 11:21:26: 3000000 INFO @ Thu, 30 Apr 2015 11:21:26: 3000000 INFO @ Thu, 30 Apr 2015 11:21:27: 3000000 INFO @ Thu, 30 Apr 2015 11:21:31: 4000000 INFO @ Thu, 30 Apr 2015 11:21:32: 4000000 INFO @ Thu, 30 Apr 2015 11:21:32: 4000000 INFO @ Thu, 30 Apr 2015 11:21:36: 5000000 INFO @ Thu, 30 Apr 2015 11:21:37: 5000000 INFO @ Thu, 30 Apr 2015 11:21:38: 5000000 INFO @ Thu, 30 Apr 2015 11:21:41: 6000000 INFO @ Thu, 30 Apr 2015 11:21:42: 6000000 INFO @ Thu, 30 Apr 2015 11:21:43: 6000000 INFO @ Thu, 30 Apr 2015 11:21:46: 7000000 INFO @ Thu, 30 Apr 2015 11:21:48: 7000000 INFO @ Thu, 30 Apr 2015 11:21:49: 7000000 INFO @ Thu, 30 Apr 2015 11:21:52: 8000000 INFO @ Thu, 30 Apr 2015 11:21:53: 8000000 INFO @ Thu, 30 Apr 2015 11:21:55: 8000000 INFO @ Thu, 30 Apr 2015 11:21:57: 9000000 INFO @ Thu, 30 Apr 2015 11:21:59: 9000000 INFO @ Thu, 30 Apr 2015 11:22:00: 9000000 INFO @ Thu, 30 Apr 2015 11:22:02: 10000000 INFO @ Thu, 30 Apr 2015 11:22:04: 10000000 INFO @ Thu, 30 Apr 2015 11:22:06: 10000000 INFO @ Thu, 30 Apr 2015 11:22:08: 11000000 INFO @ Thu, 30 Apr 2015 11:22:09: 11000000 INFO @ Thu, 30 Apr 2015 11:22:11: 11000000 INFO @ Thu, 30 Apr 2015 11:22:13: 12000000 INFO @ Thu, 30 Apr 2015 11:22:15: 12000000 INFO @ Thu, 30 Apr 2015 11:22:17: 12000000 INFO @ Thu, 30 Apr 2015 11:22:18: 13000000 INFO @ Thu, 30 Apr 2015 11:22:20: 13000000 INFO @ Thu, 30 Apr 2015 11:22:22: 13000000 INFO @ Thu, 30 Apr 2015 11:22:23: 14000000 INFO @ Thu, 30 Apr 2015 11:22:26: 14000000 INFO @ Thu, 30 Apr 2015 11:22:28: 14000000 INFO @ Thu, 30 Apr 2015 11:22:28: 15000000 INFO @ Thu, 30 Apr 2015 11:22:31: 15000000 INFO @ Thu, 30 Apr 2015 11:22:33: 15000000 INFO @ Thu, 30 Apr 2015 11:22:33: 16000000 INFO @ Thu, 30 Apr 2015 11:22:36: 16000000 INFO @ Thu, 30 Apr 2015 11:22:38: #1 tag size is determined as 36 bps INFO @ Thu, 30 Apr 2015 11:22:38: #1 tag size = 36 INFO @ Thu, 30 Apr 2015 11:22:38: #1 total tags in treatment: 16841459 INFO @ Thu, 30 Apr 2015 11:22:38: #1 user defined the maximum tags... INFO @ Thu, 30 Apr 2015 11:22:38: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Thu, 30 Apr 2015 11:22:39: 16000000 INFO @ Thu, 30 Apr 2015 11:22:41: #1 tag size is determined as 36 bps INFO @ Thu, 30 Apr 2015 11:22:41: #1 tag size = 36 INFO @ Thu, 30 Apr 2015 11:22:41: #1 total tags in treatment: 16841459 INFO @ Thu, 30 Apr 2015 11:22:41: #1 user defined the maximum tags... INFO @ Thu, 30 Apr 2015 11:22:41: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Thu, 30 Apr 2015 11:22:41: #1 tags after filtering in treatment: 16839346 INFO @ Thu, 30 Apr 2015 11:22:41: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 30 Apr 2015 11:22:41: #1 finished! INFO @ Thu, 30 Apr 2015 11:22:41: #2 Build Peak Model... INFO @ Thu, 30 Apr 2015 11:22:43: #1 tag size is determined as 36 bps INFO @ Thu, 30 Apr 2015 11:22:43: #1 tag size = 36 INFO @ Thu, 30 Apr 2015 11:22:43: #1 total tags in treatment: 16841459 INFO @ Thu, 30 Apr 2015 11:22:43: #1 user defined the maximum tags... INFO @ Thu, 30 Apr 2015 11:22:43: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Thu, 30 Apr 2015 11:22:44: #2 number of paired peaks: 750 WARNING @ Thu, 30 Apr 2015 11:22:44: Fewer paired peaks (750) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 750 pairs to build model! INFO @ Thu, 30 Apr 2015 11:22:44: start model_add_line... INFO @ Thu, 30 Apr 2015 11:22:44: #1 tags after filtering in treatment: 16839346 INFO @ Thu, 30 Apr 2015 11:22:44: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 30 Apr 2015 11:22:44: #1 finished! INFO @ Thu, 30 Apr 2015 11:22:44: #2 Build Peak Model... INFO @ Thu, 30 Apr 2015 11:22:46: #1 tags after filtering in treatment: 16839346 INFO @ Thu, 30 Apr 2015 11:22:46: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 30 Apr 2015 11:22:46: #1 finished! INFO @ Thu, 30 Apr 2015 11:22:46: #2 Build Peak Model... INFO @ Thu, 30 Apr 2015 11:22:47: #2 number of paired peaks: 750 WARNING @ Thu, 30 Apr 2015 11:22:47: Fewer paired peaks (750) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 750 pairs to build model! INFO @ Thu, 30 Apr 2015 11:22:47: start model_add_line... INFO @ Thu, 30 Apr 2015 11:22:49: #2 number of paired peaks: 750 WARNING @ Thu, 30 Apr 2015 11:22:49: Fewer paired peaks (750) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 750 pairs to build model! INFO @ Thu, 30 Apr 2015 11:22:49: start model_add_line... INFO @ Thu, 30 Apr 2015 11:22:55: start X-correlation... INFO @ Thu, 30 Apr 2015 11:22:55: end of X-cor INFO @ Thu, 30 Apr 2015 11:22:55: #2 finished! INFO @ Thu, 30 Apr 2015 11:22:55: #2 predicted fragment length is 88 bps INFO @ Thu, 30 Apr 2015 11:22:55: #2 alternative fragment length(s) may be 4,88 bps INFO @ Thu, 30 Apr 2015 11:22:55: #2.2 Generate R script for model : SRX059255.10_model.r INFO @ Thu, 30 Apr 2015 11:22:55: #3 Call peaks... INFO @ Thu, 30 Apr 2015 11:22:55: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 30 Apr 2015 11:22:59: start X-correlation... INFO @ Thu, 30 Apr 2015 11:22:59: end of X-cor INFO @ Thu, 30 Apr 2015 11:22:59: #2 finished! INFO @ Thu, 30 Apr 2015 11:22:59: #2 predicted fragment length is 88 bps INFO @ Thu, 30 Apr 2015 11:22:59: #2 alternative fragment length(s) may be 4,88 bps INFO @ Thu, 30 Apr 2015 11:22:59: #2.2 Generate R script for model : SRX059255.05_model.r INFO @ Thu, 30 Apr 2015 11:22:59: #3 Call peaks... INFO @ Thu, 30 Apr 2015 11:22:59: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 30 Apr 2015 11:23:00: start X-correlation... INFO @ Thu, 30 Apr 2015 11:23:00: end of X-cor INFO @ Thu, 30 Apr 2015 11:23:00: #2 finished! INFO @ Thu, 30 Apr 2015 11:23:00: #2 predicted fragment length is 88 bps INFO @ Thu, 30 Apr 2015 11:23:00: #2 alternative fragment length(s) may be 4,88 bps INFO @ Thu, 30 Apr 2015 11:23:00: #2.2 Generate R script for model : SRX059255.20_model.r INFO @ Thu, 30 Apr 2015 11:23:00: #3 Call peaks... INFO @ Thu, 30 Apr 2015 11:23:00: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 30 Apr 2015 11:24:16: #3 Call peaks for each chromosome... INFO @ Thu, 30 Apr 2015 11:24:17: #3 Call peaks for each chromosome... INFO @ Thu, 30 Apr 2015 11:24:25: #3 Call peaks for each chromosome... INFO @ Thu, 30 Apr 2015 11:25:19: #4 Write output xls file... SRX059255.05_peaks.xls INFO @ Thu, 30 Apr 2015 11:25:19: #4 Write peak in narrowPeak format file... SRX059255.05_peaks.narrowPeak INFO @ Thu, 30 Apr 2015 11:25:19: #4 Write summits bed file... SRX059255.05_summits.bed INFO @ Thu, 30 Apr 2015 11:25:19: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (5326 records, 4 fields): 7 millis CompletedMACS2peakCalling INFO @ Thu, 30 Apr 2015 11:25:22: #4 Write output xls file... SRX059255.10_peaks.xls INFO @ Thu, 30 Apr 2015 11:25:22: #4 Write peak in narrowPeak format file... SRX059255.10_peaks.narrowPeak INFO @ Thu, 30 Apr 2015 11:25:22: #4 Write summits bed file... SRX059255.10_summits.bed INFO @ Thu, 30 Apr 2015 11:25:22: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (3691 records, 4 fields): 6 millis CompletedMACS2peakCalling INFO @ Thu, 30 Apr 2015 11:25:23: #4 Write output xls file... SRX059255.20_peaks.xls INFO @ Thu, 30 Apr 2015 11:25:23: #4 Write peak in narrowPeak format file... SRX059255.20_peaks.narrowPeak INFO @ Thu, 30 Apr 2015 11:25:23: #4 Write summits bed file... SRX059255.20_summits.bed INFO @ Thu, 30 Apr 2015 11:25:23: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (2354 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。