Job ID = 9028918 sra ファイルのダウンロード中... Completed: 353201K bytes transferred in 6 seconds (456061K 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 --:--:-- 0 100 7663 0 7663 0 0 1088 0 --:--:-- 0:00:07 --:--:-- 11936 100 38318 0 38318 0 0 4767 0 --:--:-- 0:00:08 --:--:-- 23393 100 51471 0 51471 0 0 6274 0 --:--:-- 0:00:08 --:--:-- 28515 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 15198859 spots for /home/okishinya/chipatlas/results/ce10/SRX982108/SRR1956598.sra Written 15198859 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: 00:03:53 15198859 reads; of these: 15198859 (100.00%) were unpaired; of these: 1341137 (8.82%) aligned 0 times 11521179 (75.80%) aligned exactly 1 time 2336543 (15.37%) aligned >1 times 91.18% overall alignment rate Time searching: 00:03:53 Overall time: 00:03:53 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] 1139609 / 13857722 = 0.0822 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 12:30:12: # Command line: callpeak -t SRX982108.bam -f BAM -g ce -n SRX982108.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX982108.20 # format = BAM # ChIP-seq file = ['SRX982108.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 12:30:12: #1 read tag files... INFO @ Sat, 03 Jun 2017 12:30:12: #1 read treatment tags... INFO @ Sat, 03 Jun 2017 12:30:12: # Command line: callpeak -t SRX982108.bam -f BAM -g ce -n SRX982108.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX982108.05 # format = BAM # ChIP-seq file = ['SRX982108.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 12:30:12: #1 read tag files... INFO @ Sat, 03 Jun 2017 12:30:12: #1 read treatment tags... INFO @ Sat, 03 Jun 2017 12:30:12: # Command line: callpeak -t SRX982108.bam -f BAM -g ce -n SRX982108.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX982108.10 # format = BAM # ChIP-seq file = ['SRX982108.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 12:30:12: #1 read tag files... INFO @ Sat, 03 Jun 2017 12:30:12: #1 read treatment tags... INFO @ Sat, 03 Jun 2017 12:30:18: 1000000 INFO @ Sat, 03 Jun 2017 12:30:18: 1000000 INFO @ Sat, 03 Jun 2017 12:30:19: 1000000 INFO @ Sat, 03 Jun 2017 12:30:24: 2000000 INFO @ Sat, 03 Jun 2017 12:30:24: 2000000 INFO @ Sat, 03 Jun 2017 12:30:25: 2000000 INFO @ Sat, 03 Jun 2017 12:30:30: 3000000 INFO @ Sat, 03 Jun 2017 12:30:30: 3000000 INFO @ Sat, 03 Jun 2017 12:30:32: 3000000 INFO @ Sat, 03 Jun 2017 12:30:36: 4000000 INFO @ Sat, 03 Jun 2017 12:30:36: 4000000 INFO @ Sat, 03 Jun 2017 12:30:39: 4000000 INFO @ Sat, 03 Jun 2017 12:30:42: 5000000 INFO @ Sat, 03 Jun 2017 12:30:42: 5000000 INFO @ Sat, 03 Jun 2017 12:30:45: 5000000 INFO @ Sat, 03 Jun 2017 12:30:48: 6000000 INFO @ Sat, 03 Jun 2017 12:30:48: 6000000 INFO @ Sat, 03 Jun 2017 12:30:52: 6000000 INFO @ Sat, 03 Jun 2017 12:30:53: 7000000 INFO @ Sat, 03 Jun 2017 12:30:53: 7000000 INFO @ Sat, 03 Jun 2017 12:30:58: 7000000 INFO @ Sat, 03 Jun 2017 12:30:58: 8000000 INFO @ Sat, 03 Jun 2017 12:30:58: 8000000 INFO @ Sat, 03 Jun 2017 12:31:03: 8000000 INFO @ Sat, 03 Jun 2017 12:31:03: 9000000 INFO @ Sat, 03 Jun 2017 12:31:03: 9000000 INFO @ Sat, 03 Jun 2017 12:31:08: 9000000 INFO @ Sat, 03 Jun 2017 12:31:08: 10000000 INFO @ Sat, 03 Jun 2017 12:31:09: 10000000 INFO @ Sat, 03 Jun 2017 12:31:13: 10000000 INFO @ Sat, 03 Jun 2017 12:31:14: 11000000 INFO @ Sat, 03 Jun 2017 12:31:14: 11000000 INFO @ Sat, 03 Jun 2017 12:31:18: 11000000 INFO @ Sat, 03 Jun 2017 12:31:19: 12000000 INFO @ Sat, 03 Jun 2017 12:31:19: 12000000 INFO @ Sat, 03 Jun 2017 12:31:23: #1 tag size is determined as 51 bps INFO @ Sat, 03 Jun 2017 12:31:23: #1 tag size = 51 INFO @ Sat, 03 Jun 2017 12:31:23: #1 total tags in treatment: 12718113 INFO @ Sat, 03 Jun 2017 12:31:23: #1 user defined the maximum tags... INFO @ Sat, 03 Jun 2017 12:31:23: #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 12:31:24: #1 tag size is determined as 51 bps INFO @ Sat, 03 Jun 2017 12:31:24: #1 tag size = 51 INFO @ Sat, 03 Jun 2017 12:31:24: #1 total tags in treatment: 12718113 INFO @ Sat, 03 Jun 2017 12:31:24: #1 user defined the maximum tags... INFO @ Sat, 03 Jun 2017 12:31:24: #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 12:31:24: 12000000 INFO @ Sat, 03 Jun 2017 12:31:25: #1 tags after filtering in treatment: 12716721 INFO @ Sat, 03 Jun 2017 12:31:25: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 03 Jun 2017 12:31:25: #1 finished! INFO @ Sat, 03 Jun 2017 12:31:25: #2 Build Peak Model... INFO @ Sat, 03 Jun 2017 12:31:26: #1 tags after filtering in treatment: 12716721 INFO @ Sat, 03 Jun 2017 12:31:26: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 03 Jun 2017 12:31:26: #1 finished! INFO @ Sat, 03 Jun 2017 12:31:26: #2 Build Peak Model... INFO @ Sat, 03 Jun 2017 12:31:28: #2 number of paired peaks: 297 WARNING @ Sat, 03 Jun 2017 12:31:28: Fewer paired peaks (297) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 297 pairs to build model! INFO @ Sat, 03 Jun 2017 12:31:28: start model_add_line... INFO @ Sat, 03 Jun 2017 12:31:28: #1 tag size is determined as 51 bps INFO @ Sat, 03 Jun 2017 12:31:28: #1 tag size = 51 INFO @ Sat, 03 Jun 2017 12:31:28: #1 total tags in treatment: 12718113 INFO @ Sat, 03 Jun 2017 12:31:28: #1 user defined the maximum tags... INFO @ Sat, 03 Jun 2017 12:31:28: #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 12:31:28: #2 number of paired peaks: 297 WARNING @ Sat, 03 Jun 2017 12:31:28: Fewer paired peaks (297) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 297 pairs to build model! INFO @ Sat, 03 Jun 2017 12:31:28: start model_add_line... INFO @ Sat, 03 Jun 2017 12:31:30: #1 tags after filtering in treatment: 12716721 INFO @ Sat, 03 Jun 2017 12:31:30: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 03 Jun 2017 12:31:30: #1 finished! INFO @ Sat, 03 Jun 2017 12:31:30: #2 Build Peak Model... INFO @ Sat, 03 Jun 2017 12:31:32: #2 number of paired peaks: 297 WARNING @ Sat, 03 Jun 2017 12:31:32: Fewer paired peaks (297) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 297 pairs to build model! INFO @ Sat, 03 Jun 2017 12:31:32: start model_add_line... INFO @ Sat, 03 Jun 2017 12:31:32: start X-correlation... INFO @ Sat, 03 Jun 2017 12:31:32: end of X-cor INFO @ Sat, 03 Jun 2017 12:31:32: #2 finished! INFO @ Sat, 03 Jun 2017 12:31:32: #2 predicted fragment length is 50 bps INFO @ Sat, 03 Jun 2017 12:31:32: #2 alternative fragment length(s) may be 2,50 bps INFO @ Sat, 03 Jun 2017 12:31:32: #2.2 Generate R script for model : SRX982108.20_model.r WARNING @ Sat, 03 Jun 2017 12:31:32: #2 Since the d (50) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 03 Jun 2017 12:31:32: #2 You may need to consider one of the other alternative d(s): 2,50 WARNING @ Sat, 03 Jun 2017 12:31:32: #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 12:31:32: #3 Call peaks... INFO @ Sat, 03 Jun 2017 12:31:32: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Jun 2017 12:31:34: start X-correlation... INFO @ Sat, 03 Jun 2017 12:31:34: end of X-cor INFO @ Sat, 03 Jun 2017 12:31:34: #2 finished! INFO @ Sat, 03 Jun 2017 12:31:34: #2 predicted fragment length is 50 bps INFO @ Sat, 03 Jun 2017 12:31:34: #2 alternative fragment length(s) may be 2,50 bps INFO @ Sat, 03 Jun 2017 12:31:34: #2.2 Generate R script for model : SRX982108.05_model.r WARNING @ Sat, 03 Jun 2017 12:31:34: #2 Since the d (50) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 03 Jun 2017 12:31:34: #2 You may need to consider one of the other alternative d(s): 2,50 WARNING @ Sat, 03 Jun 2017 12:31:34: #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 12:31:34: #3 Call peaks... INFO @ Sat, 03 Jun 2017 12:31:34: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Jun 2017 12:31:38: start X-correlation... INFO @ Sat, 03 Jun 2017 12:31:38: end of X-cor INFO @ Sat, 03 Jun 2017 12:31:38: #2 finished! INFO @ Sat, 03 Jun 2017 12:31:38: #2 predicted fragment length is 50 bps INFO @ Sat, 03 Jun 2017 12:31:38: #2 alternative fragment length(s) may be 2,50 bps INFO @ Sat, 03 Jun 2017 12:31:38: #2.2 Generate R script for model : SRX982108.10_model.r WARNING @ Sat, 03 Jun 2017 12:31:38: #2 Since the d (50) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 03 Jun 2017 12:31:38: #2 You may need to consider one of the other alternative d(s): 2,50 WARNING @ Sat, 03 Jun 2017 12:31:38: #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 12:31:38: #3 Call peaks... INFO @ Sat, 03 Jun 2017 12:31:38: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Jun 2017 12:32:35: #3 Call peaks for each chromosome... INFO @ Sat, 03 Jun 2017 12:32:38: #3 Call peaks for each chromosome... INFO @ Sat, 03 Jun 2017 12:32:50: #3 Call peaks for each chromosome... INFO @ Sat, 03 Jun 2017 12:33:20: #4 Write output xls file... SRX982108.05_peaks.xls INFO @ Sat, 03 Jun 2017 12:33:20: #4 Write peak in narrowPeak format file... SRX982108.05_peaks.narrowPeak INFO @ Sat, 03 Jun 2017 12:33:20: #4 Write summits bed file... SRX982108.05_summits.bed INFO @ Sat, 03 Jun 2017 12:33:20: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (637 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Sat, 03 Jun 2017 12:33:24: #4 Write output xls file... SRX982108.20_peaks.xls INFO @ Sat, 03 Jun 2017 12:33:24: #4 Write peak in narrowPeak format file... SRX982108.20_peaks.narrowPeak INFO @ Sat, 03 Jun 2017 12:33:24: #4 Write summits bed file... SRX982108.20_summits.bed INFO @ Sat, 03 Jun 2017 12:33:24: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (173 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Sat, 03 Jun 2017 12:33:39: #4 Write output xls file... SRX982108.10_peaks.xls INFO @ Sat, 03 Jun 2017 12:33:39: #4 Write peak in narrowPeak format file... SRX982108.10_peaks.narrowPeak INFO @ Sat, 03 Jun 2017 12:33:39: #4 Write summits bed file... SRX982108.10_summits.bed INFO @ Sat, 03 Jun 2017 12:33:39: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (424 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。