Job ID = 9026092 sra ファイルのダウンロード中... Completed: 106021K bytes transferred in 3 seconds (217449K 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 --:--:-- 0 100 24453 0 24453 0 0 2683 0 --:--:-- 0:00:09 --:--:-- 9026 100 41400 0 41400 0 0 4382 0 --:--:-- 0:00:09 --:--:-- 13613 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 5779814 spots for /home/okishinya/chipatlas/results/ce10/SRX331139/SRR947370.sra Written 5779814 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: 00:00:01 Time loading mirror index: 00:00:00 Multiseed full-index search: 00:01:04 5779814 reads; of these: 5779814 (100.00%) were unpaired; of these: 59381 (1.03%) aligned 0 times 4788752 (82.85%) aligned exactly 1 time 931681 (16.12%) aligned >1 times 98.97% overall alignment rate Time searching: 00:01:05 Overall time: 00:01:05 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] 349773 / 5720433 = 0.0611 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 05:31:55: # Command line: callpeak -t SRX331139.bam -f BAM -g ce -n SRX331139.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX331139.10 # format = BAM # ChIP-seq file = ['SRX331139.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 05:31:55: #1 read tag files... INFO @ Sat, 03 Jun 2017 05:31:55: #1 read treatment tags... INFO @ Sat, 03 Jun 2017 05:31:55: # Command line: callpeak -t SRX331139.bam -f BAM -g ce -n SRX331139.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX331139.05 # format = BAM # ChIP-seq file = ['SRX331139.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 05:31:55: #1 read tag files... INFO @ Sat, 03 Jun 2017 05:31:55: #1 read treatment tags... INFO @ Sat, 03 Jun 2017 05:31:55: # Command line: callpeak -t SRX331139.bam -f BAM -g ce -n SRX331139.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX331139.20 # format = BAM # ChIP-seq file = ['SRX331139.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 05:31:55: #1 read tag files... INFO @ Sat, 03 Jun 2017 05:31:55: #1 read treatment tags... INFO @ Sat, 03 Jun 2017 05:32:00: 1000000 INFO @ Sat, 03 Jun 2017 05:32:00: 1000000 INFO @ Sat, 03 Jun 2017 05:32:00: 1000000 INFO @ Sat, 03 Jun 2017 05:32:06: 2000000 INFO @ Sat, 03 Jun 2017 05:32:06: 2000000 INFO @ Sat, 03 Jun 2017 05:32:06: 2000000 INFO @ Sat, 03 Jun 2017 05:32:11: 3000000 INFO @ Sat, 03 Jun 2017 05:32:12: 3000000 INFO @ Sat, 03 Jun 2017 05:32:12: 3000000 INFO @ Sat, 03 Jun 2017 05:32:17: 4000000 INFO @ Sat, 03 Jun 2017 05:32:17: 4000000 INFO @ Sat, 03 Jun 2017 05:32:17: 4000000 INFO @ Sat, 03 Jun 2017 05:32:23: 5000000 INFO @ Sat, 03 Jun 2017 05:32:23: 5000000 INFO @ Sat, 03 Jun 2017 05:32:23: 5000000 INFO @ Sat, 03 Jun 2017 05:32:25: #1 tag size is determined as 32 bps INFO @ Sat, 03 Jun 2017 05:32:25: #1 tag size = 32 INFO @ Sat, 03 Jun 2017 05:32:25: #1 total tags in treatment: 5370660 INFO @ Sat, 03 Jun 2017 05:32:25: #1 user defined the maximum tags... INFO @ Sat, 03 Jun 2017 05:32:25: #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 05:32:25: #1 tag size is determined as 32 bps INFO @ Sat, 03 Jun 2017 05:32:25: #1 tag size = 32 INFO @ Sat, 03 Jun 2017 05:32:25: #1 total tags in treatment: 5370660 INFO @ Sat, 03 Jun 2017 05:32:25: #1 user defined the maximum tags... INFO @ Sat, 03 Jun 2017 05:32:25: #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 05:32:25: #1 tag size is determined as 32 bps INFO @ Sat, 03 Jun 2017 05:32:25: #1 tag size = 32 INFO @ Sat, 03 Jun 2017 05:32:25: #1 total tags in treatment: 5370660 INFO @ Sat, 03 Jun 2017 05:32:25: #1 user defined the maximum tags... INFO @ Sat, 03 Jun 2017 05:32:25: #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 05:32:26: #1 tags after filtering in treatment: 5370559 INFO @ Sat, 03 Jun 2017 05:32:26: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 03 Jun 2017 05:32:26: #1 finished! INFO @ Sat, 03 Jun 2017 05:32:26: #2 Build Peak Model... INFO @ Sat, 03 Jun 2017 05:32:26: #1 tags after filtering in treatment: 5370559 INFO @ Sat, 03 Jun 2017 05:32:26: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 03 Jun 2017 05:32:26: #1 finished! INFO @ Sat, 03 Jun 2017 05:32:26: #2 Build Peak Model... INFO @ Sat, 03 Jun 2017 05:32:27: #1 tags after filtering in treatment: 5370559 INFO @ Sat, 03 Jun 2017 05:32:27: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 03 Jun 2017 05:32:27: #1 finished! INFO @ Sat, 03 Jun 2017 05:32:27: #2 Build Peak Model... INFO @ Sat, 03 Jun 2017 05:32:27: #2 number of paired peaks: 360 WARNING @ Sat, 03 Jun 2017 05:32:27: Fewer paired peaks (360) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 360 pairs to build model! INFO @ Sat, 03 Jun 2017 05:32:27: start model_add_line... INFO @ Sat, 03 Jun 2017 05:32:27: #2 number of paired peaks: 360 WARNING @ Sat, 03 Jun 2017 05:32:27: Fewer paired peaks (360) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 360 pairs to build model! INFO @ Sat, 03 Jun 2017 05:32:27: start model_add_line... INFO @ Sat, 03 Jun 2017 05:32:28: #2 number of paired peaks: 360 WARNING @ Sat, 03 Jun 2017 05:32:28: Fewer paired peaks (360) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 360 pairs to build model! INFO @ Sat, 03 Jun 2017 05:32:28: start model_add_line... INFO @ Sat, 03 Jun 2017 05:32:30: start X-correlation... INFO @ Sat, 03 Jun 2017 05:32:30: end of X-cor INFO @ Sat, 03 Jun 2017 05:32:30: #2 finished! INFO @ Sat, 03 Jun 2017 05:32:30: #2 predicted fragment length is 31 bps INFO @ Sat, 03 Jun 2017 05:32:30: #2 alternative fragment length(s) may be 2,31,530 bps INFO @ Sat, 03 Jun 2017 05:32:30: #2.2 Generate R script for model : SRX331139.05_model.r WARNING @ Sat, 03 Jun 2017 05:32:30: #2 Since the d (31) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 03 Jun 2017 05:32:30: #2 You may need to consider one of the other alternative d(s): 2,31,530 WARNING @ Sat, 03 Jun 2017 05:32:30: #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 05:32:30: #3 Call peaks... INFO @ Sat, 03 Jun 2017 05:32:30: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Jun 2017 05:32:30: start X-correlation... INFO @ Sat, 03 Jun 2017 05:32:30: end of X-cor INFO @ Sat, 03 Jun 2017 05:32:30: #2 finished! INFO @ Sat, 03 Jun 2017 05:32:30: #2 predicted fragment length is 31 bps INFO @ Sat, 03 Jun 2017 05:32:30: #2 alternative fragment length(s) may be 2,31,530 bps INFO @ Sat, 03 Jun 2017 05:32:30: #2.2 Generate R script for model : SRX331139.10_model.r WARNING @ Sat, 03 Jun 2017 05:32:30: #2 Since the d (31) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 03 Jun 2017 05:32:30: #2 You may need to consider one of the other alternative d(s): 2,31,530 WARNING @ Sat, 03 Jun 2017 05:32:30: #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 05:32:30: #3 Call peaks... INFO @ Sat, 03 Jun 2017 05:32:30: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Jun 2017 05:32:31: start X-correlation... INFO @ Sat, 03 Jun 2017 05:32:31: end of X-cor INFO @ Sat, 03 Jun 2017 05:32:31: #2 finished! INFO @ Sat, 03 Jun 2017 05:32:31: #2 predicted fragment length is 31 bps INFO @ Sat, 03 Jun 2017 05:32:31: #2 alternative fragment length(s) may be 2,31,530 bps INFO @ Sat, 03 Jun 2017 05:32:31: #2.2 Generate R script for model : SRX331139.20_model.r WARNING @ Sat, 03 Jun 2017 05:32:31: #2 Since the d (31) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 03 Jun 2017 05:32:31: #2 You may need to consider one of the other alternative d(s): 2,31,530 WARNING @ Sat, 03 Jun 2017 05:32:31: #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 05:32:31: #3 Call peaks... INFO @ Sat, 03 Jun 2017 05:32:31: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Jun 2017 05:33:00: #3 Call peaks for each chromosome... INFO @ Sat, 03 Jun 2017 05:33:00: #3 Call peaks for each chromosome... INFO @ Sat, 03 Jun 2017 05:33:01: #3 Call peaks for each chromosome... INFO @ Sat, 03 Jun 2017 05:33:21: #4 Write output xls file... SRX331139.10_peaks.xls INFO @ Sat, 03 Jun 2017 05:33:21: #4 Write peak in narrowPeak format file... SRX331139.10_peaks.narrowPeak INFO @ Sat, 03 Jun 2017 05:33:21: #4 Write summits bed file... SRX331139.10_summits.bed INFO @ Sat, 03 Jun 2017 05:33:21: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (183 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Sat, 03 Jun 2017 05:33:22: #4 Write output xls file... SRX331139.20_peaks.xls INFO @ Sat, 03 Jun 2017 05:33:22: #4 Write peak in narrowPeak format file... SRX331139.20_peaks.narrowPeak INFO @ Sat, 03 Jun 2017 05:33:22: #4 Write summits bed file... SRX331139.20_summits.bed INFO @ Sat, 03 Jun 2017 05:33:22: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (65 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Sat, 03 Jun 2017 05:33:23: #4 Write output xls file... SRX331139.05_peaks.xls INFO @ Sat, 03 Jun 2017 05:33:23: #4 Write peak in narrowPeak format file... SRX331139.05_peaks.narrowPeak INFO @ Sat, 03 Jun 2017 05:33:23: #4 Write summits bed file... SRX331139.05_summits.bed INFO @ Sat, 03 Jun 2017 05:33:23: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (425 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。