Job ID = 9029889 sra ファイルのダウンロード中... Completed: 1133365K bytes transferred in 15 seconds (596057K 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 --:--:-- 0:00:06 --:--:-- 0 100 21558 0 21558 0 0 2821 0 --:--:-- 0:00:07 --:--:-- 16221 100 30786 0 30786 0 0 3861 0 --:--:-- 0:00:07 --:--:-- 18534 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 23743733 spots for /home/okishinya/chipatlas/results/dm3/SRX2541751/SRR5234225.sra Written 23743733 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: 00:00:01 Multiseed full-index search: 00:06:26 23743733 reads; of these: 23743733 (100.00%) were unpaired; of these: 15093901 (63.57%) aligned 0 times 5881455 (24.77%) aligned exactly 1 time 2768377 (11.66%) aligned >1 times 36.43% overall alignment rate Time searching: 00:06:27 Overall time: 00:06:27 マッピングが完了しました。 samtools でBAM に変換中... [samopen] SAM header is present: 15 sequences. [bam_rmdupse_core] 967516 / 8649832 = 0.1119 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 15:46:39: # Command line: callpeak -t SRX2541751.bam -f BAM -g dm -n SRX2541751.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX2541751.20 # format = BAM # ChIP-seq file = ['SRX2541751.bam'] # control file = None # effective genome size = 1.20e+08 # 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 15:46:39: #1 read tag files... INFO @ Sat, 03 Jun 2017 15:46:39: #1 read treatment tags... INFO @ Sat, 03 Jun 2017 15:46:39: # Command line: callpeak -t SRX2541751.bam -f BAM -g dm -n SRX2541751.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX2541751.05 # format = BAM # ChIP-seq file = ['SRX2541751.bam'] # control file = None # effective genome size = 1.20e+08 # 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 15:46:39: #1 read tag files... INFO @ Sat, 03 Jun 2017 15:46:39: #1 read treatment tags... INFO @ Sat, 03 Jun 2017 15:46:39: # Command line: callpeak -t SRX2541751.bam -f BAM -g dm -n SRX2541751.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX2541751.10 # format = BAM # ChIP-seq file = ['SRX2541751.bam'] # control file = None # effective genome size = 1.20e+08 # 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 15:46:39: #1 read tag files... INFO @ Sat, 03 Jun 2017 15:46:39: #1 read treatment tags... INFO @ Sat, 03 Jun 2017 15:46:45: 1000000 INFO @ Sat, 03 Jun 2017 15:46:45: 1000000 INFO @ Sat, 03 Jun 2017 15:46:45: 1000000 INFO @ Sat, 03 Jun 2017 15:46:52: 2000000 INFO @ Sat, 03 Jun 2017 15:46:52: 2000000 INFO @ Sat, 03 Jun 2017 15:46:52: 2000000 INFO @ Sat, 03 Jun 2017 15:46:58: 3000000 INFO @ Sat, 03 Jun 2017 15:46:59: 3000000 INFO @ Sat, 03 Jun 2017 15:46:59: 3000000 INFO @ Sat, 03 Jun 2017 15:47:05: 4000000 INFO @ Sat, 03 Jun 2017 15:47:06: 4000000 INFO @ Sat, 03 Jun 2017 15:47:06: 4000000 INFO @ Sat, 03 Jun 2017 15:47:11: 5000000 INFO @ Sat, 03 Jun 2017 15:47:13: 5000000 INFO @ Sat, 03 Jun 2017 15:47:13: 5000000 INFO @ Sat, 03 Jun 2017 15:47:18: 6000000 INFO @ Sat, 03 Jun 2017 15:47:20: 6000000 INFO @ Sat, 03 Jun 2017 15:47:20: 6000000 INFO @ Sat, 03 Jun 2017 15:47:25: 7000000 INFO @ Sat, 03 Jun 2017 15:47:26: 7000000 INFO @ Sat, 03 Jun 2017 15:47:26: 7000000 INFO @ Sat, 03 Jun 2017 15:47:29: #1 tag size is determined as 51 bps INFO @ Sat, 03 Jun 2017 15:47:29: #1 tag size = 51 INFO @ Sat, 03 Jun 2017 15:47:29: #1 total tags in treatment: 7682316 INFO @ Sat, 03 Jun 2017 15:47:29: #1 user defined the maximum tags... INFO @ Sat, 03 Jun 2017 15:47:29: #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 15:47:31: #1 tags after filtering in treatment: 7680502 INFO @ Sat, 03 Jun 2017 15:47:31: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 03 Jun 2017 15:47:31: #1 finished! INFO @ Sat, 03 Jun 2017 15:47:31: #2 Build Peak Model... INFO @ Sat, 03 Jun 2017 15:47:32: #1 tag size is determined as 51 bps INFO @ Sat, 03 Jun 2017 15:47:32: #1 tag size = 51 INFO @ Sat, 03 Jun 2017 15:47:32: #1 total tags in treatment: 7682316 INFO @ Sat, 03 Jun 2017 15:47:32: #1 user defined the maximum tags... INFO @ Sat, 03 Jun 2017 15:47:32: #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 15:47:32: #1 tag size is determined as 51 bps INFO @ Sat, 03 Jun 2017 15:47:32: #1 tag size = 51 INFO @ Sat, 03 Jun 2017 15:47:32: #1 total tags in treatment: 7682316 INFO @ Sat, 03 Jun 2017 15:47:32: #1 user defined the maximum tags... INFO @ Sat, 03 Jun 2017 15:47:32: #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 15:47:32: #2 number of paired peaks: 385 WARNING @ Sat, 03 Jun 2017 15:47:32: Fewer paired peaks (385) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 385 pairs to build model! INFO @ Sat, 03 Jun 2017 15:47:32: start model_add_line... INFO @ Sat, 03 Jun 2017 15:47:33: #1 tags after filtering in treatment: 7680502 INFO @ Sat, 03 Jun 2017 15:47:33: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 03 Jun 2017 15:47:33: #1 finished! INFO @ Sat, 03 Jun 2017 15:47:33: #2 Build Peak Model... INFO @ Sat, 03 Jun 2017 15:47:33: #1 tags after filtering in treatment: 7680502 INFO @ Sat, 03 Jun 2017 15:47:33: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 03 Jun 2017 15:47:33: #1 finished! INFO @ Sat, 03 Jun 2017 15:47:33: #2 Build Peak Model... INFO @ Sat, 03 Jun 2017 15:47:34: #2 number of paired peaks: 385 WARNING @ Sat, 03 Jun 2017 15:47:34: Fewer paired peaks (385) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 385 pairs to build model! INFO @ Sat, 03 Jun 2017 15:47:34: start model_add_line... INFO @ Sat, 03 Jun 2017 15:47:34: #2 number of paired peaks: 385 WARNING @ Sat, 03 Jun 2017 15:47:34: Fewer paired peaks (385) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 385 pairs to build model! INFO @ Sat, 03 Jun 2017 15:47:34: start model_add_line... INFO @ Sat, 03 Jun 2017 15:47:35: start X-correlation... INFO @ Sat, 03 Jun 2017 15:47:35: end of X-cor INFO @ Sat, 03 Jun 2017 15:47:35: #2 finished! INFO @ Sat, 03 Jun 2017 15:47:35: #2 predicted fragment length is 59 bps INFO @ Sat, 03 Jun 2017 15:47:35: #2 alternative fragment length(s) may be 59 bps INFO @ Sat, 03 Jun 2017 15:47:35: #2.2 Generate R script for model : SRX2541751.05_model.r WARNING @ Sat, 03 Jun 2017 15:47:35: #2 Since the d (59) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 03 Jun 2017 15:47:35: #2 You may need to consider one of the other alternative d(s): 59 WARNING @ Sat, 03 Jun 2017 15:47:35: #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 15:47:35: #3 Call peaks... INFO @ Sat, 03 Jun 2017 15:47:35: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Jun 2017 15:47:37: start X-correlation... INFO @ Sat, 03 Jun 2017 15:47:37: end of X-cor INFO @ Sat, 03 Jun 2017 15:47:37: #2 finished! INFO @ Sat, 03 Jun 2017 15:47:37: #2 predicted fragment length is 59 bps INFO @ Sat, 03 Jun 2017 15:47:37: #2 alternative fragment length(s) may be 59 bps INFO @ Sat, 03 Jun 2017 15:47:37: #2.2 Generate R script for model : SRX2541751.10_model.r WARNING @ Sat, 03 Jun 2017 15:47:37: #2 Since the d (59) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 03 Jun 2017 15:47:37: #2 You may need to consider one of the other alternative d(s): 59 WARNING @ Sat, 03 Jun 2017 15:47:37: #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 15:47:37: #3 Call peaks... INFO @ Sat, 03 Jun 2017 15:47:37: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Jun 2017 15:47:38: start X-correlation... INFO @ Sat, 03 Jun 2017 15:47:38: end of X-cor INFO @ Sat, 03 Jun 2017 15:47:38: #2 finished! INFO @ Sat, 03 Jun 2017 15:47:38: #2 predicted fragment length is 59 bps INFO @ Sat, 03 Jun 2017 15:47:38: #2 alternative fragment length(s) may be 59 bps INFO @ Sat, 03 Jun 2017 15:47:38: #2.2 Generate R script for model : SRX2541751.20_model.r WARNING @ Sat, 03 Jun 2017 15:47:38: #2 Since the d (59) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 03 Jun 2017 15:47:38: #2 You may need to consider one of the other alternative d(s): 59 WARNING @ Sat, 03 Jun 2017 15:47:38: #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 15:47:38: #3 Call peaks... INFO @ Sat, 03 Jun 2017 15:47:38: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Jun 2017 15:48:21: #3 Call peaks for each chromosome... INFO @ Sat, 03 Jun 2017 15:48:22: #3 Call peaks for each chromosome... INFO @ Sat, 03 Jun 2017 15:48:27: #3 Call peaks for each chromosome... INFO @ Sat, 03 Jun 2017 15:48:54: #4 Write output xls file... SRX2541751.05_peaks.xls INFO @ Sat, 03 Jun 2017 15:48:54: #4 Write peak in narrowPeak format file... SRX2541751.05_peaks.narrowPeak INFO @ Sat, 03 Jun 2017 15:48:54: #4 Write summits bed file... SRX2541751.05_summits.bed INFO @ Sat, 03 Jun 2017 15:48:54: Done! pass1 - making usageList (12 chroms): 10 millis pass2 - checking and writing primary data (1931 records, 4 fields): 4 millis CompletedMACS2peakCalling INFO @ Sat, 03 Jun 2017 15:48:57: #4 Write output xls file... SRX2541751.10_peaks.xls INFO @ Sat, 03 Jun 2017 15:48:57: #4 Write peak in narrowPeak format file... SRX2541751.10_peaks.narrowPeak INFO @ Sat, 03 Jun 2017 15:48:57: #4 Write summits bed file... SRX2541751.10_summits.bed INFO @ Sat, 03 Jun 2017 15:48:57: Done! pass1 - making usageList (10 chroms): 1 millis pass2 - checking and writing primary data (1373 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Sat, 03 Jun 2017 15:49:00: #4 Write output xls file... SRX2541751.20_peaks.xls INFO @ Sat, 03 Jun 2017 15:49:00: #4 Write peak in narrowPeak format file... SRX2541751.20_peaks.narrowPeak INFO @ Sat, 03 Jun 2017 15:49:00: #4 Write summits bed file... SRX2541751.20_summits.bed INFO @ Sat, 03 Jun 2017 15:49:00: Done! pass1 - making usageList (10 chroms): 1 millis pass2 - checking and writing primary data (872 records, 4 fields): 3 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。