Job ID = 9028938 sra ファイルのダウンロード中... Completed: 729012K bytes transferred in 10 seconds (570596K 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 1100 0 --:--:-- 0:00:06 --:--:-- 12379 100 30318 0 30318 0 0 3808 0 --:--:-- 0:00:07 --:--:-- 18772 100 56310 0 56310 0 0 6406 0 --:--:-- 0:00:08 --:--:-- 23030 100 80508 0 80508 0 0 8825 0 --:--:-- 0:00:09 --:--:-- 28990 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 35299435 spots for /home/okishinya/chipatlas/results/ce10/SRX997751/SRR1977498.sra Written 35299435 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: 00:04:41 35299435 reads; of these: 35299435 (100.00%) were unpaired; of these: 27769919 (78.67%) aligned 0 times 5110950 (14.48%) aligned exactly 1 time 2418566 (6.85%) aligned >1 times 21.33% overall alignment rate Time searching: 00:04:41 Overall time: 00:04:41 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] 6719147 / 7529516 = 0.8924 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 12:33:07: # Command line: callpeak -t SRX997751.bam -f BAM -g ce -n SRX997751.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX997751.20 # format = BAM # ChIP-seq file = ['SRX997751.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 12:33:07: #1 read tag files... INFO @ Sat, 03 Jun 2017 12:33:07: #1 read treatment tags... INFO @ Sat, 03 Jun 2017 12:33:07: # Command line: callpeak -t SRX997751.bam -f BAM -g ce -n SRX997751.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX997751.05 # format = BAM # ChIP-seq file = ['SRX997751.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 12:33:07: #1 read tag files... INFO @ Sat, 03 Jun 2017 12:33:07: #1 read treatment tags... INFO @ Sat, 03 Jun 2017 12:33:07: # Command line: callpeak -t SRX997751.bam -f BAM -g ce -n SRX997751.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX997751.10 # format = BAM # ChIP-seq file = ['SRX997751.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 12:33:07: #1 read tag files... INFO @ Sat, 03 Jun 2017 12:33:07: #1 read treatment tags... INFO @ Sat, 03 Jun 2017 12:33:12: #1 tag size is determined as 36 bps INFO @ Sat, 03 Jun 2017 12:33:12: #1 tag size = 36 INFO @ Sat, 03 Jun 2017 12:33:12: #1 total tags in treatment: 810369 INFO @ Sat, 03 Jun 2017 12:33:12: #1 user defined the maximum tags... INFO @ Sat, 03 Jun 2017 12:33:12: #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 12:33:12: #1 tags after filtering in treatment: 808448 INFO @ Sat, 03 Jun 2017 12:33:12: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 03 Jun 2017 12:33:12: #1 finished! INFO @ Sat, 03 Jun 2017 12:33:12: #2 Build Peak Model... INFO @ Sat, 03 Jun 2017 12:33:12: #1 tag size is determined as 36 bps INFO @ Sat, 03 Jun 2017 12:33:12: #1 tag size = 36 INFO @ Sat, 03 Jun 2017 12:33:12: #1 total tags in treatment: 810369 INFO @ Sat, 03 Jun 2017 12:33:12: #1 user defined the maximum tags... INFO @ Sat, 03 Jun 2017 12:33:12: #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 12:33:12: #1 tag size is determined as 36 bps INFO @ Sat, 03 Jun 2017 12:33:12: #1 tag size = 36 INFO @ Sat, 03 Jun 2017 12:33:12: #1 total tags in treatment: 810369 INFO @ Sat, 03 Jun 2017 12:33:12: #1 user defined the maximum tags... INFO @ Sat, 03 Jun 2017 12:33:12: #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 12:33:12: #1 tags after filtering in treatment: 808448 INFO @ Sat, 03 Jun 2017 12:33:12: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 03 Jun 2017 12:33:12: #1 finished! INFO @ Sat, 03 Jun 2017 12:33:12: #2 Build Peak Model... INFO @ Sat, 03 Jun 2017 12:33:12: #1 tags after filtering in treatment: 808448 INFO @ Sat, 03 Jun 2017 12:33:12: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 03 Jun 2017 12:33:12: #1 finished! INFO @ Sat, 03 Jun 2017 12:33:12: #2 Build Peak Model... INFO @ Sat, 03 Jun 2017 12:33:12: #2 number of paired peaks: 1148 INFO @ Sat, 03 Jun 2017 12:33:12: start model_add_line... INFO @ Sat, 03 Jun 2017 12:33:12: #2 number of paired peaks: 1148 INFO @ Sat, 03 Jun 2017 12:33:12: start model_add_line... INFO @ Sat, 03 Jun 2017 12:33:12: #2 number of paired peaks: 1148 INFO @ Sat, 03 Jun 2017 12:33:12: start model_add_line... INFO @ Sat, 03 Jun 2017 12:33:14: start X-correlation... INFO @ Sat, 03 Jun 2017 12:33:14: end of X-cor INFO @ Sat, 03 Jun 2017 12:33:14: #2 finished! INFO @ Sat, 03 Jun 2017 12:33:14: #2 predicted fragment length is 36 bps INFO @ Sat, 03 Jun 2017 12:33:14: #2 alternative fragment length(s) may be 36,501 bps INFO @ Sat, 03 Jun 2017 12:33:14: #2.2 Generate R script for model : SRX997751.20_model.r WARNING @ Sat, 03 Jun 2017 12:33:14: #2 Since the d (36) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 03 Jun 2017 12:33:14: #2 You may need to consider one of the other alternative d(s): 36,501 WARNING @ Sat, 03 Jun 2017 12:33:14: #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 12:33:14: #3 Call peaks... INFO @ Sat, 03 Jun 2017 12:33:14: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Jun 2017 12:33:14: start X-correlation... INFO @ Sat, 03 Jun 2017 12:33:14: end of X-cor INFO @ Sat, 03 Jun 2017 12:33:14: #2 finished! INFO @ Sat, 03 Jun 2017 12:33:14: #2 predicted fragment length is 36 bps INFO @ Sat, 03 Jun 2017 12:33:14: #2 alternative fragment length(s) may be 36,501 bps INFO @ Sat, 03 Jun 2017 12:33:14: #2.2 Generate R script for model : SRX997751.05_model.r WARNING @ Sat, 03 Jun 2017 12:33:14: #2 Since the d (36) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 03 Jun 2017 12:33:14: #2 You may need to consider one of the other alternative d(s): 36,501 WARNING @ Sat, 03 Jun 2017 12:33:14: #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 12:33:14: #3 Call peaks... INFO @ Sat, 03 Jun 2017 12:33:14: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Jun 2017 12:33:14: start X-correlation... INFO @ Sat, 03 Jun 2017 12:33:14: end of X-cor INFO @ Sat, 03 Jun 2017 12:33:14: #2 finished! INFO @ Sat, 03 Jun 2017 12:33:14: #2 predicted fragment length is 36 bps INFO @ Sat, 03 Jun 2017 12:33:14: #2 alternative fragment length(s) may be 36,501 bps INFO @ Sat, 03 Jun 2017 12:33:14: #2.2 Generate R script for model : SRX997751.10_model.r WARNING @ Sat, 03 Jun 2017 12:33:14: #2 Since the d (36) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 03 Jun 2017 12:33:14: #2 You may need to consider one of the other alternative d(s): 36,501 WARNING @ Sat, 03 Jun 2017 12:33:14: #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 12:33:14: #3 Call peaks... INFO @ Sat, 03 Jun 2017 12:33:14: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Jun 2017 12:33:19: #3 Call peaks for each chromosome... INFO @ Sat, 03 Jun 2017 12:33:19: #3 Call peaks for each chromosome... INFO @ Sat, 03 Jun 2017 12:33:19: #3 Call peaks for each chromosome... BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 03 Jun 2017 12:33:22: #4 Write output xls file... SRX997751.20_peaks.xls INFO @ Sat, 03 Jun 2017 12:33:22: #4 Write peak in narrowPeak format file... SRX997751.20_peaks.narrowPeak INFO @ Sat, 03 Jun 2017 12:33:22: #4 Write summits bed file... SRX997751.20_summits.bed INFO @ Sat, 03 Jun 2017 12:33:22: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (338 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Sat, 03 Jun 2017 12:33:22: #4 Write output xls file... SRX997751.10_peaks.xls INFO @ Sat, 03 Jun 2017 12:33:22: #4 Write peak in narrowPeak format file... SRX997751.10_peaks.narrowPeak INFO @ Sat, 03 Jun 2017 12:33:22: #4 Write summits bed file... SRX997751.10_summits.bed INFO @ Sat, 03 Jun 2017 12:33:22: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (679 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Sat, 03 Jun 2017 12:33:23: #4 Write output xls file... SRX997751.05_peaks.xls INFO @ Sat, 03 Jun 2017 12:33:23: #4 Write peak in narrowPeak format file... SRX997751.05_peaks.narrowPeak INFO @ Sat, 03 Jun 2017 12:33:23: #4 Write summits bed file... SRX997751.05_summits.bed INFO @ Sat, 03 Jun 2017 12:33:23: Done! pass1 - making usageList (7 chroms): 0 millis pass2 - checking and writing primary data (1152 records, 4 fields): 3 millis CompletedMACS2peakCalling BigWig に変換しました。