Job ID = 9028841 sra ファイルのダウンロード中... Completed: 757512K bytes transferred in 9 seconds (637695K 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 --:--:-- 0:00:07 --:--:-- 0 0 0 0 0 0 0 0 0 --:--:-- 0:00:08 --:--:-- 0 0 0 0 0 0 0 0 0 --:--:-- 0:00:09 --:--:-- 0 100 22318 0 22318 0 0 2160 0 --:--:-- 0:00:10 --:--:-- 5724 100 49070 0 49070 0 0 4332 0 --:--:-- 0:00:11 --:--:-- 10022 100 55691 0 55691 0 0 4846 0 --:--:-- 0:00:11 --:--:-- 13727 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 11041327 spots for /home/okishinya/chipatlas/results/ce10/SRX982072/SRR1956550.sra Written 11041327 spots total Written 13062468 spots for /home/okishinya/chipatlas/results/ce10/SRX982072/SRR1956551.sra Written 13062468 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: 00:07:58 24103795 reads; of these: 24103795 (100.00%) were unpaired; of these: 566155 (2.35%) aligned 0 times 18984286 (78.76%) aligned exactly 1 time 4553354 (18.89%) aligned >1 times 97.65% overall alignment rate Time searching: 00:07:58 Overall time: 00:07:58 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 12 files... [bam_rmdupse_core] 4249712 / 23537640 = 0.1805 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 12:14:07: # Command line: callpeak -t SRX982072.bam -f BAM -g ce -n SRX982072.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX982072.10 # format = BAM # ChIP-seq file = ['SRX982072.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 12:14:07: #1 read tag files... INFO @ Sat, 03 Jun 2017 12:14:07: #1 read treatment tags... INFO @ Sat, 03 Jun 2017 12:14:07: # Command line: callpeak -t SRX982072.bam -f BAM -g ce -n SRX982072.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX982072.05 # format = BAM # ChIP-seq file = ['SRX982072.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 12:14:07: #1 read tag files... INFO @ Sat, 03 Jun 2017 12:14:07: #1 read treatment tags... INFO @ Sat, 03 Jun 2017 12:14:07: # Command line: callpeak -t SRX982072.bam -f BAM -g ce -n SRX982072.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX982072.20 # format = BAM # ChIP-seq file = ['SRX982072.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 12:14:07: #1 read tag files... INFO @ Sat, 03 Jun 2017 12:14:07: #1 read treatment tags... INFO @ Sat, 03 Jun 2017 12:14:13: 1000000 INFO @ Sat, 03 Jun 2017 12:14:14: 1000000 INFO @ Sat, 03 Jun 2017 12:14:14: 1000000 INFO @ Sat, 03 Jun 2017 12:14:19: 2000000 INFO @ Sat, 03 Jun 2017 12:14:21: 2000000 INFO @ Sat, 03 Jun 2017 12:14:21: 2000000 INFO @ Sat, 03 Jun 2017 12:14:26: 3000000 INFO @ Sat, 03 Jun 2017 12:14:28: 3000000 INFO @ Sat, 03 Jun 2017 12:14:29: 3000000 INFO @ Sat, 03 Jun 2017 12:14:32: 4000000 INFO @ Sat, 03 Jun 2017 12:14:35: 4000000 INFO @ Sat, 03 Jun 2017 12:14:36: 4000000 INFO @ Sat, 03 Jun 2017 12:14:39: 5000000 INFO @ Sat, 03 Jun 2017 12:14:42: 5000000 INFO @ Sat, 03 Jun 2017 12:14:44: 5000000 INFO @ Sat, 03 Jun 2017 12:14:46: 6000000 INFO @ Sat, 03 Jun 2017 12:14:48: 6000000 INFO @ Sat, 03 Jun 2017 12:14:53: 7000000 INFO @ Sat, 03 Jun 2017 12:14:53: 6000000 INFO @ Sat, 03 Jun 2017 12:14:55: 7000000 INFO @ Sat, 03 Jun 2017 12:14:59: 8000000 INFO @ Sat, 03 Jun 2017 12:15:01: 7000000 INFO @ Sat, 03 Jun 2017 12:15:02: 8000000 INFO @ Sat, 03 Jun 2017 12:15:06: 9000000 INFO @ Sat, 03 Jun 2017 12:15:08: 9000000 INFO @ Sat, 03 Jun 2017 12:15:09: 8000000 INFO @ Sat, 03 Jun 2017 12:15:13: 10000000 INFO @ Sat, 03 Jun 2017 12:15:14: 10000000 INFO @ Sat, 03 Jun 2017 12:15:17: 9000000 INFO @ Sat, 03 Jun 2017 12:15:20: 11000000 INFO @ Sat, 03 Jun 2017 12:15:21: 11000000 INFO @ Sat, 03 Jun 2017 12:15:25: 10000000 INFO @ Sat, 03 Jun 2017 12:15:27: 12000000 INFO @ Sat, 03 Jun 2017 12:15:28: 12000000 INFO @ Sat, 03 Jun 2017 12:15:33: 11000000 INFO @ Sat, 03 Jun 2017 12:15:34: 13000000 INFO @ Sat, 03 Jun 2017 12:15:35: 13000000 INFO @ Sat, 03 Jun 2017 12:15:40: 12000000 INFO @ Sat, 03 Jun 2017 12:15:41: 14000000 INFO @ Sat, 03 Jun 2017 12:15:41: 14000000 INFO @ Sat, 03 Jun 2017 12:15:47: 15000000 INFO @ Sat, 03 Jun 2017 12:15:48: 15000000 INFO @ Sat, 03 Jun 2017 12:15:48: 13000000 INFO @ Sat, 03 Jun 2017 12:15:54: 16000000 INFO @ Sat, 03 Jun 2017 12:15:55: 16000000 INFO @ Sat, 03 Jun 2017 12:15:56: 14000000 INFO @ Sat, 03 Jun 2017 12:16:00: 17000000 INFO @ Sat, 03 Jun 2017 12:16:02: 17000000 INFO @ Sat, 03 Jun 2017 12:16:04: 15000000 INFO @ Sat, 03 Jun 2017 12:16:06: 18000000 INFO @ Sat, 03 Jun 2017 12:16:09: 18000000 INFO @ Sat, 03 Jun 2017 12:16:12: 16000000 INFO @ Sat, 03 Jun 2017 12:16:13: 19000000 INFO @ Sat, 03 Jun 2017 12:16:15: #1 tag size is determined as 51 bps INFO @ Sat, 03 Jun 2017 12:16:15: #1 tag size = 51 INFO @ Sat, 03 Jun 2017 12:16:15: #1 total tags in treatment: 19287928 INFO @ Sat, 03 Jun 2017 12:16:15: #1 user defined the maximum tags... INFO @ Sat, 03 Jun 2017 12:16:15: #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 12:16:16: 19000000 INFO @ Sat, 03 Jun 2017 12:16:19: #1 tag size is determined as 51 bps INFO @ Sat, 03 Jun 2017 12:16:19: #1 tag size = 51 INFO @ Sat, 03 Jun 2017 12:16:19: #1 total tags in treatment: 19287928 INFO @ Sat, 03 Jun 2017 12:16:19: #1 user defined the maximum tags... INFO @ Sat, 03 Jun 2017 12:16:19: #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 12:16:19: #1 tags after filtering in treatment: 19284878 INFO @ Sat, 03 Jun 2017 12:16:19: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 03 Jun 2017 12:16:19: #1 finished! INFO @ Sat, 03 Jun 2017 12:16:19: #2 Build Peak Model... INFO @ Sat, 03 Jun 2017 12:16:19: 17000000 INFO @ Sat, 03 Jun 2017 12:16:22: #2 number of paired peaks: 294 WARNING @ Sat, 03 Jun 2017 12:16:22: Fewer paired peaks (294) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 294 pairs to build model! INFO @ Sat, 03 Jun 2017 12:16:22: start model_add_line... INFO @ Sat, 03 Jun 2017 12:16:22: #1 tags after filtering in treatment: 19284878 INFO @ Sat, 03 Jun 2017 12:16:22: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 03 Jun 2017 12:16:22: #1 finished! INFO @ Sat, 03 Jun 2017 12:16:22: #2 Build Peak Model... INFO @ Sat, 03 Jun 2017 12:16:26: #2 number of paired peaks: 294 WARNING @ Sat, 03 Jun 2017 12:16:26: Fewer paired peaks (294) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 294 pairs to build model! INFO @ Sat, 03 Jun 2017 12:16:26: start model_add_line... INFO @ Sat, 03 Jun 2017 12:16:27: 18000000 INFO @ Sat, 03 Jun 2017 12:16:29: start X-correlation... INFO @ Sat, 03 Jun 2017 12:16:29: end of X-cor INFO @ Sat, 03 Jun 2017 12:16:29: #2 finished! INFO @ Sat, 03 Jun 2017 12:16:29: #2 predicted fragment length is 51 bps INFO @ Sat, 03 Jun 2017 12:16:29: #2 alternative fragment length(s) may be 2,51 bps INFO @ Sat, 03 Jun 2017 12:16:29: #2.2 Generate R script for model : SRX982072.05_model.r WARNING @ Sat, 03 Jun 2017 12:16:29: #2 Since the d (51) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 03 Jun 2017 12:16:29: #2 You may need to consider one of the other alternative d(s): 2,51 WARNING @ Sat, 03 Jun 2017 12:16:29: #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 12:16:29: #3 Call peaks... INFO @ Sat, 03 Jun 2017 12:16:29: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Jun 2017 12:16:32: start X-correlation... INFO @ Sat, 03 Jun 2017 12:16:32: end of X-cor INFO @ Sat, 03 Jun 2017 12:16:32: #2 finished! INFO @ Sat, 03 Jun 2017 12:16:32: #2 predicted fragment length is 51 bps INFO @ Sat, 03 Jun 2017 12:16:32: #2 alternative fragment length(s) may be 2,51 bps INFO @ Sat, 03 Jun 2017 12:16:32: #2.2 Generate R script for model : SRX982072.10_model.r WARNING @ Sat, 03 Jun 2017 12:16:32: #2 Since the d (51) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 03 Jun 2017 12:16:32: #2 You may need to consider one of the other alternative d(s): 2,51 WARNING @ Sat, 03 Jun 2017 12:16:32: #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 12:16:32: #3 Call peaks... INFO @ Sat, 03 Jun 2017 12:16:32: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Jun 2017 12:16:34: 19000000 INFO @ Sat, 03 Jun 2017 12:16:36: #1 tag size is determined as 51 bps INFO @ Sat, 03 Jun 2017 12:16:36: #1 tag size = 51 INFO @ Sat, 03 Jun 2017 12:16:36: #1 total tags in treatment: 19287928 INFO @ Sat, 03 Jun 2017 12:16:36: #1 user defined the maximum tags... INFO @ Sat, 03 Jun 2017 12:16:36: #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 12:16:40: #1 tags after filtering in treatment: 19284878 INFO @ Sat, 03 Jun 2017 12:16:40: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 03 Jun 2017 12:16:40: #1 finished! INFO @ Sat, 03 Jun 2017 12:16:40: #2 Build Peak Model... INFO @ Sat, 03 Jun 2017 12:16:43: #2 number of paired peaks: 294 WARNING @ Sat, 03 Jun 2017 12:16:43: Fewer paired peaks (294) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 294 pairs to build model! INFO @ Sat, 03 Jun 2017 12:16:43: start model_add_line... INFO @ Sat, 03 Jun 2017 12:16:49: start X-correlation... INFO @ Sat, 03 Jun 2017 12:16:49: end of X-cor INFO @ Sat, 03 Jun 2017 12:16:49: #2 finished! INFO @ Sat, 03 Jun 2017 12:16:49: #2 predicted fragment length is 51 bps INFO @ Sat, 03 Jun 2017 12:16:49: #2 alternative fragment length(s) may be 2,51 bps INFO @ Sat, 03 Jun 2017 12:16:49: #2.2 Generate R script for model : SRX982072.20_model.r WARNING @ Sat, 03 Jun 2017 12:16:49: #2 Since the d (51) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 03 Jun 2017 12:16:49: #2 You may need to consider one of the other alternative d(s): 2,51 WARNING @ Sat, 03 Jun 2017 12:16:49: #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 12:16:49: #3 Call peaks... INFO @ Sat, 03 Jun 2017 12:16:49: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Jun 2017 12:17:56: #3 Call peaks for each chromosome... INFO @ Sat, 03 Jun 2017 12:18:00: #3 Call peaks for each chromosome... INFO @ Sat, 03 Jun 2017 12:18:16: #3 Call peaks for each chromosome... INFO @ Sat, 03 Jun 2017 12:19:05: #4 Write output xls file... SRX982072.05_peaks.xls INFO @ Sat, 03 Jun 2017 12:19:06: #4 Write peak in narrowPeak format file... SRX982072.05_peaks.narrowPeak INFO @ Sat, 03 Jun 2017 12:19:06: #4 Write summits bed file... SRX982072.05_summits.bed INFO @ Sat, 03 Jun 2017 12:19:06: #4 Write output xls file... SRX982072.10_peaks.xls INFO @ Sat, 03 Jun 2017 12:19:06: #4 Write peak in narrowPeak format file... SRX982072.10_peaks.narrowPeak INFO @ Sat, 03 Jun 2017 12:19:06: Done! INFO @ Sat, 03 Jun 2017 12:19:06: #4 Write summits bed file... SRX982072.10_summits.bed INFO @ Sat, 03 Jun 2017 12:19:06: Done! pass1 - making usageList (7 chroms): 0 millis pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (654 records, 4 fields): 3 millis pass2 - checking and writing primary data (2675 records, 4 fields): 5 millis CompletedMACS2peakCalling CompletedMACS2peakCalling INFO @ Sat, 03 Jun 2017 12:19:20: #4 Write output xls file... SRX982072.20_peaks.xls INFO @ Sat, 03 Jun 2017 12:19:20: #4 Write peak in narrowPeak format file... SRX982072.20_peaks.narrowPeak INFO @ Sat, 03 Jun 2017 12:19:20: #4 Write summits bed file... SRX982072.20_summits.bed INFO @ Sat, 03 Jun 2017 12:19:20: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (158 records, 4 fields): 1 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。