Job ID = 9025520 sra ファイルのダウンロード中... Completed: 73858K bytes transferred in 3 seconds (152625K 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 --:--:-- 0 101 5455 0 5455 0 0 715 0 --:--:-- 0:00:07 --:--:-- 4364 100 30246 0 30246 0 0 3507 0 --:--:-- 0:00:08 --:--:-- 13472 100 42723 0 42723 0 0 4683 0 --:--:-- 0:00:09 --:--:-- 15575 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 3183642 spots for /home/okishinya/chipatlas/results/ce10/SRX1388769/SRR2832485.sra Written 3183642 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: 00:00:52 3183642 reads; of these: 3183642 (100.00%) were unpaired; of these: 99414 (3.12%) aligned 0 times 2379946 (74.76%) aligned exactly 1 time 704282 (22.12%) aligned >1 times 96.88% overall alignment rate Time searching: 00:00:52 Overall time: 00:00:52 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] 188693 / 3084228 = 0.0612 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 04:15:06: # Command line: callpeak -t SRX1388769.bam -f BAM -g ce -n SRX1388769.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX1388769.20 # format = BAM # ChIP-seq file = ['SRX1388769.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 04:15:06: # Command line: callpeak -t SRX1388769.bam -f BAM -g ce -n SRX1388769.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX1388769.05 # format = BAM # ChIP-seq file = ['SRX1388769.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 04:15:06: #1 read tag files... INFO @ Sat, 03 Jun 2017 04:15:06: #1 read tag files... INFO @ Sat, 03 Jun 2017 04:15:06: #1 read treatment tags... INFO @ Sat, 03 Jun 2017 04:15:06: # Command line: callpeak -t SRX1388769.bam -f BAM -g ce -n SRX1388769.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX1388769.10 # format = BAM # ChIP-seq file = ['SRX1388769.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 04:15:06: #1 read treatment tags... INFO @ Sat, 03 Jun 2017 04:15:06: #1 read tag files... INFO @ Sat, 03 Jun 2017 04:15:06: #1 read treatment tags... INFO @ Sat, 03 Jun 2017 04:15:13: 1000000 INFO @ Sat, 03 Jun 2017 04:15:13: 1000000 INFO @ Sat, 03 Jun 2017 04:15:13: 1000000 INFO @ Sat, 03 Jun 2017 04:15:19: 2000000 INFO @ Sat, 03 Jun 2017 04:15:19: 2000000 INFO @ Sat, 03 Jun 2017 04:15:20: 2000000 INFO @ Sat, 03 Jun 2017 04:15:25: #1 tag size is determined as 50 bps INFO @ Sat, 03 Jun 2017 04:15:25: #1 tag size = 50 INFO @ Sat, 03 Jun 2017 04:15:25: #1 total tags in treatment: 2895535 INFO @ Sat, 03 Jun 2017 04:15:25: #1 user defined the maximum tags... INFO @ Sat, 03 Jun 2017 04:15:25: #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 04:15:25: #1 tag size is determined as 50 bps INFO @ Sat, 03 Jun 2017 04:15:25: #1 tag size = 50 INFO @ Sat, 03 Jun 2017 04:15:25: #1 total tags in treatment: 2895535 INFO @ Sat, 03 Jun 2017 04:15:25: #1 user defined the maximum tags... INFO @ Sat, 03 Jun 2017 04:15:25: #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 04:15:25: #1 tag size is determined as 50 bps INFO @ Sat, 03 Jun 2017 04:15:25: #1 tag size = 50 INFO @ Sat, 03 Jun 2017 04:15:25: #1 total tags in treatment: 2895535 INFO @ Sat, 03 Jun 2017 04:15:25: #1 user defined the maximum tags... INFO @ Sat, 03 Jun 2017 04:15:25: #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 04:15:26: #1 tags after filtering in treatment: 2895128 INFO @ Sat, 03 Jun 2017 04:15:26: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 03 Jun 2017 04:15:26: #1 finished! INFO @ Sat, 03 Jun 2017 04:15:26: #2 Build Peak Model... INFO @ Sat, 03 Jun 2017 04:15:26: #1 tags after filtering in treatment: 2895128 INFO @ Sat, 03 Jun 2017 04:15:26: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 03 Jun 2017 04:15:26: #1 finished! INFO @ Sat, 03 Jun 2017 04:15:26: #2 Build Peak Model... INFO @ Sat, 03 Jun 2017 04:15:26: #1 tags after filtering in treatment: 2895128 INFO @ Sat, 03 Jun 2017 04:15:26: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 03 Jun 2017 04:15:26: #1 finished! INFO @ Sat, 03 Jun 2017 04:15:26: #2 Build Peak Model... INFO @ Sat, 03 Jun 2017 04:15:26: #2 number of paired peaks: 531 WARNING @ Sat, 03 Jun 2017 04:15:26: Fewer paired peaks (531) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 531 pairs to build model! INFO @ Sat, 03 Jun 2017 04:15:26: start model_add_line... INFO @ Sat, 03 Jun 2017 04:15:26: #2 number of paired peaks: 531 WARNING @ Sat, 03 Jun 2017 04:15:26: Fewer paired peaks (531) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 531 pairs to build model! INFO @ Sat, 03 Jun 2017 04:15:26: start model_add_line... INFO @ Sat, 03 Jun 2017 04:15:27: #2 number of paired peaks: 531 WARNING @ Sat, 03 Jun 2017 04:15:27: Fewer paired peaks (531) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 531 pairs to build model! INFO @ Sat, 03 Jun 2017 04:15:27: start model_add_line... INFO @ Sat, 03 Jun 2017 04:15:29: start X-correlation... INFO @ Sat, 03 Jun 2017 04:15:29: end of X-cor INFO @ Sat, 03 Jun 2017 04:15:29: #2 finished! INFO @ Sat, 03 Jun 2017 04:15:29: #2 predicted fragment length is 52 bps INFO @ Sat, 03 Jun 2017 04:15:29: #2 alternative fragment length(s) may be 52,466 bps INFO @ Sat, 03 Jun 2017 04:15:29: #2.2 Generate R script for model : SRX1388769.10_model.r WARNING @ Sat, 03 Jun 2017 04:15:29: #2 Since the d (52) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 03 Jun 2017 04:15:29: #2 You may need to consider one of the other alternative d(s): 52,466 WARNING @ Sat, 03 Jun 2017 04:15:29: #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 04:15:29: #3 Call peaks... INFO @ Sat, 03 Jun 2017 04:15:29: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Jun 2017 04:15:30: start X-correlation... INFO @ Sat, 03 Jun 2017 04:15:30: end of X-cor INFO @ Sat, 03 Jun 2017 04:15:30: #2 finished! INFO @ Sat, 03 Jun 2017 04:15:30: #2 predicted fragment length is 52 bps INFO @ Sat, 03 Jun 2017 04:15:30: #2 alternative fragment length(s) may be 52,466 bps INFO @ Sat, 03 Jun 2017 04:15:30: #2.2 Generate R script for model : SRX1388769.05_model.r WARNING @ Sat, 03 Jun 2017 04:15:30: #2 Since the d (52) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 03 Jun 2017 04:15:30: #2 You may need to consider one of the other alternative d(s): 52,466 WARNING @ Sat, 03 Jun 2017 04:15:30: #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 04:15:30: #3 Call peaks... INFO @ Sat, 03 Jun 2017 04:15:30: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Jun 2017 04:15:30: start X-correlation... INFO @ Sat, 03 Jun 2017 04:15:30: end of X-cor INFO @ Sat, 03 Jun 2017 04:15:30: #2 finished! INFO @ Sat, 03 Jun 2017 04:15:30: #2 predicted fragment length is 52 bps INFO @ Sat, 03 Jun 2017 04:15:30: #2 alternative fragment length(s) may be 52,466 bps INFO @ Sat, 03 Jun 2017 04:15:30: #2.2 Generate R script for model : SRX1388769.20_model.r WARNING @ Sat, 03 Jun 2017 04:15:30: #2 Since the d (52) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 03 Jun 2017 04:15:30: #2 You may need to consider one of the other alternative d(s): 52,466 WARNING @ Sat, 03 Jun 2017 04:15:30: #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 04:15:30: #3 Call peaks... INFO @ Sat, 03 Jun 2017 04:15:30: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Jun 2017 04:15:46: #3 Call peaks for each chromosome... INFO @ Sat, 03 Jun 2017 04:15:48: #3 Call peaks for each chromosome... INFO @ Sat, 03 Jun 2017 04:15:48: #3 Call peaks for each chromosome... INFO @ Sat, 03 Jun 2017 04:15:58: #4 Write output xls file... SRX1388769.10_peaks.xls INFO @ Sat, 03 Jun 2017 04:15:58: #4 Write peak in narrowPeak format file... SRX1388769.10_peaks.narrowPeak INFO @ Sat, 03 Jun 2017 04:15:58: #4 Write summits bed file... SRX1388769.10_summits.bed INFO @ Sat, 03 Jun 2017 04:15:58: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (268 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Sat, 03 Jun 2017 04:16:00: #4 Write output xls file... SRX1388769.20_peaks.xls INFO @ Sat, 03 Jun 2017 04:16:00: #4 Write peak in narrowPeak format file... SRX1388769.20_peaks.narrowPeak INFO @ Sat, 03 Jun 2017 04:16:00: #4 Write summits bed file... SRX1388769.20_summits.bed INFO @ Sat, 03 Jun 2017 04:16:00: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (114 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Sat, 03 Jun 2017 04:16:00: #4 Write output xls file... SRX1388769.05_peaks.xls INFO @ Sat, 03 Jun 2017 04:16:00: #4 Write peak in narrowPeak format file... SRX1388769.05_peaks.narrowPeak INFO @ Sat, 03 Jun 2017 04:16:00: #4 Write summits bed file... SRX1388769.05_summits.bed INFO @ Sat, 03 Jun 2017 04:16:00: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (432 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。