Job ID = 9028910 sra ファイルのダウンロード中... Completed: 378285K bytes transferred in 6 seconds (494992K 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 --:--:-- 0 100 14324 0 14324 0 0 1933 0 --:--:-- 0:00:07 --:--:-- 14601 100 38318 0 38318 0 0 4559 0 --:--:-- 0:00:08 --:--:-- 19391 100 54703 0 54703 0 0 6144 0 --:--:-- 0:00:08 --:--:-- 22120 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 6657936 spots for /home/okishinya/chipatlas/results/ce10/SRX982104/SRR1956591.sra Written 6657936 spots total Written 7293418 spots for /home/okishinya/chipatlas/results/ce10/SRX982104/SRR1956592.sra Written 7293418 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: 00:03:37 13951354 reads; of these: 13951354 (100.00%) were unpaired; of these: 1665412 (11.94%) aligned 0 times 10195204 (73.08%) aligned exactly 1 time 2090738 (14.99%) aligned >1 times 88.06% overall alignment rate Time searching: 00:03:37 Overall time: 00:03:37 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] 918868 / 12285942 = 0.0748 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 12:27:17: # Command line: callpeak -t SRX982104.bam -f BAM -g ce -n SRX982104.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX982104.10 # format = BAM # ChIP-seq file = ['SRX982104.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 12:27:17: #1 read tag files... INFO @ Sat, 03 Jun 2017 12:27:17: #1 read treatment tags... INFO @ Sat, 03 Jun 2017 12:27:17: # Command line: callpeak -t SRX982104.bam -f BAM -g ce -n SRX982104.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX982104.05 # format = BAM # ChIP-seq file = ['SRX982104.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 12:27:17: #1 read tag files... INFO @ Sat, 03 Jun 2017 12:27:17: #1 read treatment tags... INFO @ Sat, 03 Jun 2017 12:27:17: # Command line: callpeak -t SRX982104.bam -f BAM -g ce -n SRX982104.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX982104.20 # format = BAM # ChIP-seq file = ['SRX982104.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 12:27:17: #1 read tag files... INFO @ Sat, 03 Jun 2017 12:27:17: #1 read treatment tags... INFO @ Sat, 03 Jun 2017 12:27:23: 1000000 INFO @ Sat, 03 Jun 2017 12:27:24: 1000000 INFO @ Sat, 03 Jun 2017 12:27:24: 1000000 INFO @ Sat, 03 Jun 2017 12:27:30: 2000000 INFO @ Sat, 03 Jun 2017 12:27:30: 2000000 INFO @ Sat, 03 Jun 2017 12:27:30: 2000000 INFO @ Sat, 03 Jun 2017 12:27:38: 3000000 INFO @ Sat, 03 Jun 2017 12:27:39: 3000000 INFO @ Sat, 03 Jun 2017 12:27:39: 3000000 INFO @ Sat, 03 Jun 2017 12:27:46: 4000000 INFO @ Sat, 03 Jun 2017 12:27:47: 4000000 INFO @ Sat, 03 Jun 2017 12:27:48: 4000000 INFO @ Sat, 03 Jun 2017 12:27:54: 5000000 INFO @ Sat, 03 Jun 2017 12:27:56: 5000000 INFO @ Sat, 03 Jun 2017 12:27:56: 5000000 INFO @ Sat, 03 Jun 2017 12:28:02: 6000000 INFO @ Sat, 03 Jun 2017 12:28:05: 6000000 INFO @ Sat, 03 Jun 2017 12:28:05: 6000000 INFO @ Sat, 03 Jun 2017 12:28:11: 7000000 INFO @ Sat, 03 Jun 2017 12:28:13: 7000000 INFO @ Sat, 03 Jun 2017 12:28:13: 7000000 INFO @ Sat, 03 Jun 2017 12:28:19: 8000000 INFO @ Sat, 03 Jun 2017 12:28:22: 8000000 INFO @ Sat, 03 Jun 2017 12:28:22: 8000000 INFO @ Sat, 03 Jun 2017 12:28:27: 9000000 INFO @ Sat, 03 Jun 2017 12:28:31: 9000000 INFO @ Sat, 03 Jun 2017 12:28:31: 9000000 INFO @ Sat, 03 Jun 2017 12:28:35: 10000000 INFO @ Sat, 03 Jun 2017 12:28:39: 10000000 INFO @ Sat, 03 Jun 2017 12:28:39: 10000000 INFO @ Sat, 03 Jun 2017 12:28:43: 11000000 INFO @ Sat, 03 Jun 2017 12:28:46: #1 tag size is determined as 51 bps INFO @ Sat, 03 Jun 2017 12:28:46: #1 tag size = 51 INFO @ Sat, 03 Jun 2017 12:28:46: #1 total tags in treatment: 11367074 INFO @ Sat, 03 Jun 2017 12:28:46: #1 user defined the maximum tags... INFO @ Sat, 03 Jun 2017 12:28:46: #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 12:28:48: #1 tags after filtering in treatment: 11363610 INFO @ Sat, 03 Jun 2017 12:28:48: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 03 Jun 2017 12:28:48: #1 finished! INFO @ Sat, 03 Jun 2017 12:28:48: #2 Build Peak Model... INFO @ Sat, 03 Jun 2017 12:28:48: 11000000 INFO @ Sat, 03 Jun 2017 12:28:48: 11000000 INFO @ Sat, 03 Jun 2017 12:28:50: #2 number of paired peaks: 306 WARNING @ Sat, 03 Jun 2017 12:28:50: Fewer paired peaks (306) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 306 pairs to build model! INFO @ Sat, 03 Jun 2017 12:28:50: start model_add_line... INFO @ Sat, 03 Jun 2017 12:28:51: #1 tag size is determined as 51 bps INFO @ Sat, 03 Jun 2017 12:28:51: #1 tag size = 51 INFO @ Sat, 03 Jun 2017 12:28:51: #1 total tags in treatment: 11367074 INFO @ Sat, 03 Jun 2017 12:28:51: #1 user defined the maximum tags... INFO @ Sat, 03 Jun 2017 12:28:51: #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 12:28:51: #1 tag size is determined as 51 bps INFO @ Sat, 03 Jun 2017 12:28:51: #1 tag size = 51 INFO @ Sat, 03 Jun 2017 12:28:51: #1 total tags in treatment: 11367074 INFO @ Sat, 03 Jun 2017 12:28:51: #1 user defined the maximum tags... INFO @ Sat, 03 Jun 2017 12:28:51: #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 12:28:53: #1 tags after filtering in treatment: 11363610 INFO @ Sat, 03 Jun 2017 12:28:53: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 03 Jun 2017 12:28:53: #1 finished! INFO @ Sat, 03 Jun 2017 12:28:53: #2 Build Peak Model... INFO @ Sat, 03 Jun 2017 12:28:53: #1 tags after filtering in treatment: 11363610 INFO @ Sat, 03 Jun 2017 12:28:53: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 03 Jun 2017 12:28:53: #1 finished! INFO @ Sat, 03 Jun 2017 12:28:53: #2 Build Peak Model... INFO @ Sat, 03 Jun 2017 12:28:54: start X-correlation... INFO @ Sat, 03 Jun 2017 12:28:54: end of X-cor INFO @ Sat, 03 Jun 2017 12:28:54: #2 finished! INFO @ Sat, 03 Jun 2017 12:28:54: #2 predicted fragment length is 46 bps INFO @ Sat, 03 Jun 2017 12:28:54: #2 alternative fragment length(s) may be 3,46,548 bps INFO @ Sat, 03 Jun 2017 12:28:54: #2.2 Generate R script for model : SRX982104.20_model.r WARNING @ Sat, 03 Jun 2017 12:28:54: #2 Since the d (46) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 03 Jun 2017 12:28:54: #2 You may need to consider one of the other alternative d(s): 3,46,548 WARNING @ Sat, 03 Jun 2017 12:28:54: #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 12:28:54: #3 Call peaks... INFO @ Sat, 03 Jun 2017 12:28:54: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Jun 2017 12:28:55: #2 number of paired peaks: 306 WARNING @ Sat, 03 Jun 2017 12:28:55: Fewer paired peaks (306) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 306 pairs to build model! INFO @ Sat, 03 Jun 2017 12:28:55: start model_add_line... INFO @ Sat, 03 Jun 2017 12:28:55: #2 number of paired peaks: 306 WARNING @ Sat, 03 Jun 2017 12:28:55: Fewer paired peaks (306) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 306 pairs to build model! INFO @ Sat, 03 Jun 2017 12:28:55: start model_add_line... INFO @ Sat, 03 Jun 2017 12:29:00: start X-correlation... INFO @ Sat, 03 Jun 2017 12:29:00: end of X-cor INFO @ Sat, 03 Jun 2017 12:29:00: #2 finished! INFO @ Sat, 03 Jun 2017 12:29:00: #2 predicted fragment length is 46 bps INFO @ Sat, 03 Jun 2017 12:29:00: #2 alternative fragment length(s) may be 3,46,548 bps INFO @ Sat, 03 Jun 2017 12:29:00: #2.2 Generate R script for model : SRX982104.05_model.r WARNING @ Sat, 03 Jun 2017 12:29:00: #2 Since the d (46) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 03 Jun 2017 12:29:00: #2 You may need to consider one of the other alternative d(s): 3,46,548 WARNING @ Sat, 03 Jun 2017 12:29:00: #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 12:29:00: #3 Call peaks... INFO @ Sat, 03 Jun 2017 12:29:00: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Jun 2017 12:29:00: start X-correlation... INFO @ Sat, 03 Jun 2017 12:29:00: end of X-cor INFO @ Sat, 03 Jun 2017 12:29:00: #2 finished! INFO @ Sat, 03 Jun 2017 12:29:00: #2 predicted fragment length is 46 bps INFO @ Sat, 03 Jun 2017 12:29:00: #2 alternative fragment length(s) may be 3,46,548 bps INFO @ Sat, 03 Jun 2017 12:29:00: #2.2 Generate R script for model : SRX982104.10_model.r WARNING @ Sat, 03 Jun 2017 12:29:00: #2 Since the d (46) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 03 Jun 2017 12:29:00: #2 You may need to consider one of the other alternative d(s): 3,46,548 WARNING @ Sat, 03 Jun 2017 12:29:00: #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 12:29:00: #3 Call peaks... INFO @ Sat, 03 Jun 2017 12:29:00: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Jun 2017 12:29:54: #3 Call peaks for each chromosome... INFO @ Sat, 03 Jun 2017 12:30:00: #3 Call peaks for each chromosome... INFO @ Sat, 03 Jun 2017 12:30:02: #3 Call peaks for each chromosome... INFO @ Sat, 03 Jun 2017 12:30:39: #4 Write output xls file... SRX982104.20_peaks.xls INFO @ Sat, 03 Jun 2017 12:30:39: #4 Write peak in narrowPeak format file... SRX982104.20_peaks.narrowPeak INFO @ Sat, 03 Jun 2017 12:30:39: #4 Write summits bed file... SRX982104.20_summits.bed INFO @ Sat, 03 Jun 2017 12:30:39: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (158 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Sat, 03 Jun 2017 12:30:43: #4 Write output xls file... SRX982104.05_peaks.xls INFO @ Sat, 03 Jun 2017 12:30:43: #4 Write peak in narrowPeak format file... SRX982104.05_peaks.narrowPeak INFO @ Sat, 03 Jun 2017 12:30:43: #4 Write summits bed file... SRX982104.05_summits.bed INFO @ Sat, 03 Jun 2017 12:30:43: Done! pass1 - making usageList (7 chroms): 0 millis pass2 - checking and writing primary data (639 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Sat, 03 Jun 2017 12:30:44: #4 Write output xls file... SRX982104.10_peaks.xls INFO @ Sat, 03 Jun 2017 12:30:44: #4 Write peak in narrowPeak format file... SRX982104.10_peaks.narrowPeak INFO @ Sat, 03 Jun 2017 12:30:44: #4 Write summits bed file... SRX982104.10_summits.bed INFO @ Sat, 03 Jun 2017 12:30:44: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (412 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。