Job ID = 9028913 sra ファイルのダウンロード中... Completed: 469285K bytes transferred in 6 seconds (581961K bits/sec), in 2 files, 3 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 --:--:-- 0:00:06 --:--:-- 0 100 12695 0 12695 0 0 1666 0 --:--:-- 0:00:07 --:--:-- 10237 100 37486 0 37486 0 0 4351 0 --:--:-- 0:00:08 --:--:-- 16772 100 57950 0 57950 0 0 6422 0 --:--:-- 0:00:09 --:--:-- 21925 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 8335869 spots for /home/okishinya/chipatlas/results/ce10/SRX982105/SRR1956593.sra Written 8335869 spots total Written 8998757 spots for /home/okishinya/chipatlas/results/ce10/SRX982105/SRR1956594.sra Written 8998757 spots total 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: 00:04:15 17334626 reads; of these: 17334626 (100.00%) were unpaired; of these: 2050865 (11.83%) aligned 0 times 12804316 (73.87%) aligned exactly 1 time 2479445 (14.30%) aligned >1 times 88.17% overall alignment rate Time searching: 00:04:15 Overall time: 00:04:15 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] 1495503 / 15283761 = 0.0978 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 12:30:08: # Command line: callpeak -t SRX982105.bam -f BAM -g ce -n SRX982105.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX982105.10 # format = BAM # ChIP-seq file = ['SRX982105.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 @ Sat, 03 Jun 2017 12:30:08: #1 read tag files... INFO @ Sat, 03 Jun 2017 12:30:08: #1 read treatment tags... INFO @ Sat, 03 Jun 2017 12:30:08: # Command line: callpeak -t SRX982105.bam -f BAM -g ce -n SRX982105.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX982105.05 # format = BAM # ChIP-seq file = ['SRX982105.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 @ Sat, 03 Jun 2017 12:30:08: #1 read tag files... INFO @ Sat, 03 Jun 2017 12:30:08: #1 read treatment tags... INFO @ Sat, 03 Jun 2017 12:30:08: # Command line: callpeak -t SRX982105.bam -f BAM -g ce -n SRX982105.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX982105.20 # format = BAM # ChIP-seq file = ['SRX982105.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 @ Sat, 03 Jun 2017 12:30:08: #1 read tag files... INFO @ Sat, 03 Jun 2017 12:30:08: #1 read treatment tags... INFO @ Sat, 03 Jun 2017 12:30:14: 1000000 INFO @ Sat, 03 Jun 2017 12:30:14: 1000000 INFO @ Sat, 03 Jun 2017 12:30:15: 1000000 INFO @ Sat, 03 Jun 2017 12:30:20: 2000000 INFO @ Sat, 03 Jun 2017 12:30:20: 2000000 INFO @ Sat, 03 Jun 2017 12:30:22: 2000000 INFO @ Sat, 03 Jun 2017 12:30:26: 3000000 INFO @ Sat, 03 Jun 2017 12:30:26: 3000000 INFO @ Sat, 03 Jun 2017 12:30:29: 3000000 INFO @ Sat, 03 Jun 2017 12:30:32: 4000000 INFO @ Sat, 03 Jun 2017 12:30:32: 4000000 INFO @ Sat, 03 Jun 2017 12:30:36: 4000000 INFO @ Sat, 03 Jun 2017 12:30:38: 5000000 INFO @ Sat, 03 Jun 2017 12:30:38: 5000000 INFO @ Sat, 03 Jun 2017 12:30:42: 5000000 INFO @ Sat, 03 Jun 2017 12:30:44: 6000000 INFO @ Sat, 03 Jun 2017 12:30:45: 6000000 INFO @ Sat, 03 Jun 2017 12:30:49: 6000000 INFO @ Sat, 03 Jun 2017 12:30:51: 7000000 INFO @ Sat, 03 Jun 2017 12:30:51: 7000000 INFO @ Sat, 03 Jun 2017 12:30:56: 7000000 INFO @ Sat, 03 Jun 2017 12:30:57: 8000000 INFO @ Sat, 03 Jun 2017 12:30:58: 8000000 INFO @ Sat, 03 Jun 2017 12:31:03: 8000000 INFO @ Sat, 03 Jun 2017 12:31:04: 9000000 INFO @ Sat, 03 Jun 2017 12:31:05: 9000000 INFO @ Sat, 03 Jun 2017 12:31:10: 10000000 INFO @ Sat, 03 Jun 2017 12:31:10: 9000000 INFO @ Sat, 03 Jun 2017 12:31:11: 10000000 INFO @ Sat, 03 Jun 2017 12:31:17: 11000000 INFO @ Sat, 03 Jun 2017 12:31:17: 10000000 INFO @ Sat, 03 Jun 2017 12:31:18: 11000000 INFO @ Sat, 03 Jun 2017 12:31:23: 12000000 INFO @ Sat, 03 Jun 2017 12:31:24: 11000000 INFO @ Sat, 03 Jun 2017 12:31:25: 12000000 INFO @ Sat, 03 Jun 2017 12:31:30: 13000000 INFO @ Sat, 03 Jun 2017 12:31:31: 12000000 INFO @ Sat, 03 Jun 2017 12:31:31: 13000000 INFO @ Sat, 03 Jun 2017 12:31:35: #1 tag size is determined as 51 bps INFO @ Sat, 03 Jun 2017 12:31:35: #1 tag size = 51 INFO @ Sat, 03 Jun 2017 12:31:35: #1 total tags in treatment: 13788258 INFO @ Sat, 03 Jun 2017 12:31:35: #1 user defined the maximum tags... INFO @ Sat, 03 Jun 2017 12:31:35: #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 12:31:36: #1 tag size is determined as 51 bps INFO @ Sat, 03 Jun 2017 12:31:36: #1 tag size = 51 INFO @ Sat, 03 Jun 2017 12:31:36: #1 total tags in treatment: 13788258 INFO @ Sat, 03 Jun 2017 12:31:36: #1 user defined the maximum tags... INFO @ Sat, 03 Jun 2017 12:31:36: #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 12:31:38: #1 tags after filtering in treatment: 13783714 INFO @ Sat, 03 Jun 2017 12:31:38: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 03 Jun 2017 12:31:38: #1 finished! INFO @ Sat, 03 Jun 2017 12:31:38: #2 Build Peak Model... INFO @ Sat, 03 Jun 2017 12:31:38: 13000000 INFO @ Sat, 03 Jun 2017 12:31:39: #1 tags after filtering in treatment: 13783714 INFO @ Sat, 03 Jun 2017 12:31:39: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 03 Jun 2017 12:31:39: #1 finished! INFO @ Sat, 03 Jun 2017 12:31:39: #2 Build Peak Model... INFO @ Sat, 03 Jun 2017 12:31:40: #2 number of paired peaks: 267 WARNING @ Sat, 03 Jun 2017 12:31:40: Fewer paired peaks (267) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 267 pairs to build model! INFO @ Sat, 03 Jun 2017 12:31:40: start model_add_line... INFO @ Sat, 03 Jun 2017 12:31:41: #2 number of paired peaks: 267 WARNING @ Sat, 03 Jun 2017 12:31:41: Fewer paired peaks (267) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 267 pairs to build model! INFO @ Sat, 03 Jun 2017 12:31:41: start model_add_line... INFO @ Sat, 03 Jun 2017 12:31:44: #1 tag size is determined as 51 bps INFO @ Sat, 03 Jun 2017 12:31:44: #1 tag size = 51 INFO @ Sat, 03 Jun 2017 12:31:44: #1 total tags in treatment: 13788258 INFO @ Sat, 03 Jun 2017 12:31:44: #1 user defined the maximum tags... INFO @ Sat, 03 Jun 2017 12:31:44: #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 12:31:45: start X-correlation... INFO @ Sat, 03 Jun 2017 12:31:45: end of X-cor INFO @ Sat, 03 Jun 2017 12:31:45: #2 finished! INFO @ Sat, 03 Jun 2017 12:31:45: #2 predicted fragment length is 49 bps INFO @ Sat, 03 Jun 2017 12:31:45: #2 alternative fragment length(s) may be 2,49 bps INFO @ Sat, 03 Jun 2017 12:31:45: #2.2 Generate R script for model : SRX982105.05_model.r WARNING @ Sat, 03 Jun 2017 12:31:45: #2 Since the d (49) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 03 Jun 2017 12:31:45: #2 You may need to consider one of the other alternative d(s): 2,49 WARNING @ Sat, 03 Jun 2017 12:31:45: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sat, 03 Jun 2017 12:31:45: #3 Call peaks... INFO @ Sat, 03 Jun 2017 12:31:45: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Jun 2017 12:31:46: #1 tags after filtering in treatment: 13783714 INFO @ Sat, 03 Jun 2017 12:31:46: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 03 Jun 2017 12:31:46: #1 finished! INFO @ Sat, 03 Jun 2017 12:31:46: #2 Build Peak Model... INFO @ Sat, 03 Jun 2017 12:31:46: start X-correlation... INFO @ Sat, 03 Jun 2017 12:31:46: end of X-cor INFO @ Sat, 03 Jun 2017 12:31:46: #2 finished! INFO @ Sat, 03 Jun 2017 12:31:46: #2 predicted fragment length is 49 bps INFO @ Sat, 03 Jun 2017 12:31:46: #2 alternative fragment length(s) may be 2,49 bps INFO @ Sat, 03 Jun 2017 12:31:46: #2.2 Generate R script for model : SRX982105.10_model.r WARNING @ Sat, 03 Jun 2017 12:31:46: #2 Since the d (49) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 03 Jun 2017 12:31:46: #2 You may need to consider one of the other alternative d(s): 2,49 WARNING @ Sat, 03 Jun 2017 12:31:46: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sat, 03 Jun 2017 12:31:46: #3 Call peaks... INFO @ Sat, 03 Jun 2017 12:31:46: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Jun 2017 12:31:48: #2 number of paired peaks: 267 WARNING @ Sat, 03 Jun 2017 12:31:48: Fewer paired peaks (267) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 267 pairs to build model! INFO @ Sat, 03 Jun 2017 12:31:48: start model_add_line... INFO @ Sat, 03 Jun 2017 12:31:53: start X-correlation... INFO @ Sat, 03 Jun 2017 12:31:53: end of X-cor INFO @ Sat, 03 Jun 2017 12:31:53: #2 finished! INFO @ Sat, 03 Jun 2017 12:31:53: #2 predicted fragment length is 49 bps INFO @ Sat, 03 Jun 2017 12:31:53: #2 alternative fragment length(s) may be 2,49 bps INFO @ Sat, 03 Jun 2017 12:31:53: #2.2 Generate R script for model : SRX982105.20_model.r WARNING @ Sat, 03 Jun 2017 12:31:53: #2 Since the d (49) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 03 Jun 2017 12:31:53: #2 You may need to consider one of the other alternative d(s): 2,49 WARNING @ Sat, 03 Jun 2017 12:31:53: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sat, 03 Jun 2017 12:31:53: #3 Call peaks... INFO @ Sat, 03 Jun 2017 12:31:53: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Jun 2017 12:32:52: #3 Call peaks for each chromosome... INFO @ Sat, 03 Jun 2017 12:32:58: #3 Call peaks for each chromosome... INFO @ Sat, 03 Jun 2017 12:33:01: #3 Call peaks for each chromosome... INFO @ Sat, 03 Jun 2017 12:33:40: #4 Write output xls file... SRX982105.05_peaks.xls INFO @ Sat, 03 Jun 2017 12:33:40: #4 Write peak in narrowPeak format file... SRX982105.05_peaks.narrowPeak INFO @ Sat, 03 Jun 2017 12:33:40: #4 Write summits bed file... SRX982105.05_summits.bed INFO @ Sat, 03 Jun 2017 12:33:40: Done! pass1 - making usageList (7 chroms): 0 millis pass2 - checking and writing primary data (645 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Sat, 03 Jun 2017 12:33:49: #4 Write output xls file... SRX982105.20_peaks.xls INFO @ Sat, 03 Jun 2017 12:33:49: #4 Write peak in narrowPeak format file... SRX982105.20_peaks.narrowPeak INFO @ Sat, 03 Jun 2017 12:33:49: #4 Write summits bed file... SRX982105.20_summits.bed INFO @ Sat, 03 Jun 2017 12:33:49: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (168 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Sat, 03 Jun 2017 12:33:50: #4 Write output xls file... SRX982105.10_peaks.xls INFO @ Sat, 03 Jun 2017 12:33:50: #4 Write peak in narrowPeak format file... SRX982105.10_peaks.narrowPeak INFO @ Sat, 03 Jun 2017 12:33:50: #4 Write summits bed file... SRX982105.10_summits.bed INFO @ Sat, 03 Jun 2017 12:33:50: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (416 records, 4 fields): 2 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。