Job ID = 9025962 sra ファイルのダウンロード中... Completed: 912962K bytes transferred in 10 seconds (718466K 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 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 0 0 0 0 0 0 0 0 --:--:-- 0:00:10 --:--:-- 0 100 22317 0 22317 0 0 1961 0 --:--:-- 0:00:11 --:--:-- 4466 100 67893 0 67893 0 0 5486 0 --:--:-- 0:00:12 --:--:-- 13611 100 70712 0 70712 0 0 5713 0 --:--:-- 0:00:12 --:--:-- 17735 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 16712402 spots for /home/okishinya/chipatlas/results/ce10/SRX278068/SRR851118.sra Written 16712402 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: 00:03:35 16712402 reads; of these: 16712402 (100.00%) were unpaired; of these: 12367262 (74.00%) aligned 0 times 3663328 (21.92%) aligned exactly 1 time 681812 (4.08%) aligned >1 times 26.00% overall alignment rate Time searching: 00:03:35 Overall time: 00:03:35 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_rmdupse_core] 448268 / 4345140 = 0.1032 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 05:23:45: # Command line: callpeak -t SRX278068.bam -f BAM -g ce -n SRX278068.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX278068.10 # format = BAM # ChIP-seq file = ['SRX278068.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 05:23:45: #1 read tag files... INFO @ Sat, 03 Jun 2017 05:23:45: #1 read treatment tags... INFO @ Sat, 03 Jun 2017 05:23:45: # Command line: callpeak -t SRX278068.bam -f BAM -g ce -n SRX278068.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX278068.05 # format = BAM # ChIP-seq file = ['SRX278068.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 05:23:45: #1 read tag files... INFO @ Sat, 03 Jun 2017 05:23:45: #1 read treatment tags... INFO @ Sat, 03 Jun 2017 05:23:45: # Command line: callpeak -t SRX278068.bam -f BAM -g ce -n SRX278068.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX278068.20 # format = BAM # ChIP-seq file = ['SRX278068.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 05:23:45: #1 read tag files... INFO @ Sat, 03 Jun 2017 05:23:45: #1 read treatment tags... INFO @ Sat, 03 Jun 2017 05:23:52: 1000000 INFO @ Sat, 03 Jun 2017 05:23:52: 1000000 INFO @ Sat, 03 Jun 2017 05:23:52: 1000000 INFO @ Sat, 03 Jun 2017 05:24:00: 2000000 INFO @ Sat, 03 Jun 2017 05:24:00: 2000000 INFO @ Sat, 03 Jun 2017 05:24:00: 2000000 INFO @ Sat, 03 Jun 2017 05:24:08: 3000000 INFO @ Sat, 03 Jun 2017 05:24:08: 3000000 INFO @ Sat, 03 Jun 2017 05:24:09: 3000000 INFO @ Sat, 03 Jun 2017 05:24:15: #1 tag size is determined as 76 bps INFO @ Sat, 03 Jun 2017 05:24:15: #1 tag size = 76 INFO @ Sat, 03 Jun 2017 05:24:15: #1 total tags in treatment: 3896872 INFO @ Sat, 03 Jun 2017 05:24:15: #1 user defined the maximum tags... INFO @ Sat, 03 Jun 2017 05:24:15: #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 05:24:16: #1 tag size is determined as 76 bps INFO @ Sat, 03 Jun 2017 05:24:16: #1 tag size = 76 INFO @ Sat, 03 Jun 2017 05:24:16: #1 total tags in treatment: 3896872 INFO @ Sat, 03 Jun 2017 05:24:16: #1 user defined the maximum tags... INFO @ Sat, 03 Jun 2017 05:24:16: #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 05:24:16: #1 tag size is determined as 76 bps INFO @ Sat, 03 Jun 2017 05:24:16: #1 tag size = 76 INFO @ Sat, 03 Jun 2017 05:24:16: #1 total tags in treatment: 3896872 INFO @ Sat, 03 Jun 2017 05:24:16: #1 user defined the maximum tags... INFO @ Sat, 03 Jun 2017 05:24:16: #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 05:24:16: #1 tags after filtering in treatment: 3895739 INFO @ Sat, 03 Jun 2017 05:24:16: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 03 Jun 2017 05:24:16: #1 finished! INFO @ Sat, 03 Jun 2017 05:24:16: #2 Build Peak Model... INFO @ Sat, 03 Jun 2017 05:24:17: #1 tags after filtering in treatment: 3895739 INFO @ Sat, 03 Jun 2017 05:24:17: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 03 Jun 2017 05:24:17: #1 finished! INFO @ Sat, 03 Jun 2017 05:24:17: #2 Build Peak Model... INFO @ Sat, 03 Jun 2017 05:24:17: #1 tags after filtering in treatment: 3895739 INFO @ Sat, 03 Jun 2017 05:24:17: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 03 Jun 2017 05:24:17: #1 finished! INFO @ Sat, 03 Jun 2017 05:24:17: #2 Build Peak Model... INFO @ Sat, 03 Jun 2017 05:24:17: #2 number of paired peaks: 373 WARNING @ Sat, 03 Jun 2017 05:24:17: Fewer paired peaks (373) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 373 pairs to build model! INFO @ Sat, 03 Jun 2017 05:24:17: start model_add_line... INFO @ Sat, 03 Jun 2017 05:24:17: #2 number of paired peaks: 373 WARNING @ Sat, 03 Jun 2017 05:24:17: Fewer paired peaks (373) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 373 pairs to build model! INFO @ Sat, 03 Jun 2017 05:24:17: start model_add_line... INFO @ Sat, 03 Jun 2017 05:24:17: #2 number of paired peaks: 373 WARNING @ Sat, 03 Jun 2017 05:24:17: Fewer paired peaks (373) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 373 pairs to build model! INFO @ Sat, 03 Jun 2017 05:24:17: start model_add_line... INFO @ Sat, 03 Jun 2017 05:24:20: start X-correlation... INFO @ Sat, 03 Jun 2017 05:24:20: end of X-cor INFO @ Sat, 03 Jun 2017 05:24:20: #2 finished! INFO @ Sat, 03 Jun 2017 05:24:20: #2 predicted fragment length is 71 bps INFO @ Sat, 03 Jun 2017 05:24:20: #2 alternative fragment length(s) may be 71,556 bps INFO @ Sat, 03 Jun 2017 05:24:20: #2.2 Generate R script for model : SRX278068.10_model.r WARNING @ Sat, 03 Jun 2017 05:24:20: #2 Since the d (71) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 03 Jun 2017 05:24:20: #2 You may need to consider one of the other alternative d(s): 71,556 WARNING @ Sat, 03 Jun 2017 05:24:20: #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 05:24:20: #3 Call peaks... INFO @ Sat, 03 Jun 2017 05:24:20: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Jun 2017 05:24:20: start X-correlation... INFO @ Sat, 03 Jun 2017 05:24:20: end of X-cor INFO @ Sat, 03 Jun 2017 05:24:20: #2 finished! INFO @ Sat, 03 Jun 2017 05:24:20: #2 predicted fragment length is 71 bps INFO @ Sat, 03 Jun 2017 05:24:20: #2 alternative fragment length(s) may be 71,556 bps INFO @ Sat, 03 Jun 2017 05:24:20: #2.2 Generate R script for model : SRX278068.20_model.r WARNING @ Sat, 03 Jun 2017 05:24:20: #2 Since the d (71) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 03 Jun 2017 05:24:20: #2 You may need to consider one of the other alternative d(s): 71,556 WARNING @ Sat, 03 Jun 2017 05:24:20: #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 05:24:20: #3 Call peaks... INFO @ Sat, 03 Jun 2017 05:24:20: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Jun 2017 05:24:20: start X-correlation... INFO @ Sat, 03 Jun 2017 05:24:20: end of X-cor INFO @ Sat, 03 Jun 2017 05:24:20: #2 finished! INFO @ Sat, 03 Jun 2017 05:24:20: #2 predicted fragment length is 71 bps INFO @ Sat, 03 Jun 2017 05:24:20: #2 alternative fragment length(s) may be 71,556 bps INFO @ Sat, 03 Jun 2017 05:24:20: #2.2 Generate R script for model : SRX278068.05_model.r WARNING @ Sat, 03 Jun 2017 05:24:20: #2 Since the d (71) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 03 Jun 2017 05:24:20: #2 You may need to consider one of the other alternative d(s): 71,556 WARNING @ Sat, 03 Jun 2017 05:24:20: #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 05:24:20: #3 Call peaks... INFO @ Sat, 03 Jun 2017 05:24:20: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Jun 2017 05:24:41: #3 Call peaks for each chromosome... INFO @ Sat, 03 Jun 2017 05:24:42: #3 Call peaks for each chromosome... INFO @ Sat, 03 Jun 2017 05:24:43: #3 Call peaks for each chromosome... INFO @ Sat, 03 Jun 2017 05:24:57: #4 Write output xls file... SRX278068.20_peaks.xls INFO @ Sat, 03 Jun 2017 05:24:57: #4 Write peak in narrowPeak format file... SRX278068.20_peaks.narrowPeak INFO @ Sat, 03 Jun 2017 05:24:57: #4 Write summits bed file... SRX278068.20_summits.bed INFO @ Sat, 03 Jun 2017 05:24:57: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (146 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Sat, 03 Jun 2017 05:24:58: #4 Write output xls file... SRX278068.10_peaks.xls INFO @ Sat, 03 Jun 2017 05:24:58: #4 Write peak in narrowPeak format file... SRX278068.10_peaks.narrowPeak INFO @ Sat, 03 Jun 2017 05:24:58: #4 Write summits bed file... SRX278068.10_summits.bed INFO @ Sat, 03 Jun 2017 05:24:58: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (283 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Sat, 03 Jun 2017 05:24:59: #4 Write output xls file... SRX278068.05_peaks.xls INFO @ Sat, 03 Jun 2017 05:24:59: #4 Write peak in narrowPeak format file... SRX278068.05_peaks.narrowPeak INFO @ Sat, 03 Jun 2017 05:24:59: #4 Write summits bed file... SRX278068.05_summits.bed INFO @ Sat, 03 Jun 2017 05:24:59: Done! pass1 - making usageList (7 chroms): 0 millis pass2 - checking and writing primary data (442 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。