Job ID = 9031600 sra ファイルのダウンロード中... Completed: 1416810K bytes transferred in 25 seconds (460703K bits/sec), in 11 files, 12 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 22318 0 22318 0 0 2844 0 --:--:-- 0:00:07 --:--:-- 16843 100 41830 0 41830 0 0 4821 0 --:--:-- 0:00:08 --:--:-- 19410 100 50378 0 50378 0 0 5694 0 --:--:-- 0:00:08 --:--:-- 21658 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 2835006 spots for /home/okishinya/chipatlas/results/dm3/SRX475426/SRR1175666.sra Written 2835006 spots total Written 4000000 spots for /home/okishinya/chipatlas/results/dm3/SRX475426/SRR1175673.sra Written 4000000 spots total Written 4000000 spots for /home/okishinya/chipatlas/results/dm3/SRX475426/SRR1175665.sra Written 4000000 spots total Written 4000000 spots for /home/okishinya/chipatlas/results/dm3/SRX475426/SRR1175674.sra Written 4000000 spots total Written 4000000 spots for /home/okishinya/chipatlas/results/dm3/SRX475426/SRR1175667.sra Written 4000000 spots total Written 4000000 spots for /home/okishinya/chipatlas/results/dm3/SRX475426/SRR1175669.sra Written 4000000 spots total Written 4000000 spots for /home/okishinya/chipatlas/results/dm3/SRX475426/SRR1175671.sra Written 4000000 spots total Written 4000000 spots for /home/okishinya/chipatlas/results/dm3/SRX475426/SRR1175672.sra Written 4000000 spots total Written 4000000 spots for /home/okishinya/chipatlas/results/dm3/SRX475426/SRR1175664.sra Written 4000000 spots total Written 4000000 spots for /home/okishinya/chipatlas/results/dm3/SRX475426/SRR1175668.sra Written 4000000 spots total Written 4000000 spots for /home/okishinya/chipatlas/results/dm3/SRX475426/SRR1175670.sra Written 4000000 spots total 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: 00:15:33 42835006 reads; of these: 42835006 (100.00%) were unpaired; of these: 2202181 (5.14%) aligned 0 times 32313464 (75.44%) aligned exactly 1 time 8319361 (19.42%) aligned >1 times 94.86% overall alignment rate Time searching: 00:15:33 Overall time: 00:15:33 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_sort_core] merging from 20 files... [bam_rmdupse_core] 18536260 / 40632825 = 0.4562 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 20:46:58: # Command line: callpeak -t SRX475426.bam -f BAM -g dm -n SRX475426.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX475426.05 # format = BAM # ChIP-seq file = ['SRX475426.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 20:46:58: # Command line: callpeak -t SRX475426.bam -f BAM -g dm -n SRX475426.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX475426.10 # format = BAM # ChIP-seq file = ['SRX475426.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 20:46:58: #1 read tag files... INFO @ Sat, 03 Jun 2017 20:46:58: #1 read tag files... INFO @ Sat, 03 Jun 2017 20:46:58: #1 read treatment tags... INFO @ Sat, 03 Jun 2017 20:46:58: #1 read treatment tags... INFO @ Sat, 03 Jun 2017 20:46:58: # Command line: callpeak -t SRX475426.bam -f BAM -g dm -n SRX475426.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX475426.20 # format = BAM # ChIP-seq file = ['SRX475426.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 20:46:58: #1 read tag files... INFO @ Sat, 03 Jun 2017 20:46:58: #1 read treatment tags... INFO @ Sat, 03 Jun 2017 20:47:05: 1000000 INFO @ Sat, 03 Jun 2017 20:47:05: 1000000 INFO @ Sat, 03 Jun 2017 20:47:05: 1000000 INFO @ Sat, 03 Jun 2017 20:47:12: 2000000 INFO @ Sat, 03 Jun 2017 20:47:12: 2000000 INFO @ Sat, 03 Jun 2017 20:47:12: 2000000 INFO @ Sat, 03 Jun 2017 20:47:18: 3000000 INFO @ Sat, 03 Jun 2017 20:47:18: 3000000 INFO @ Sat, 03 Jun 2017 20:47:18: 3000000 INFO @ Sat, 03 Jun 2017 20:47:25: 4000000 INFO @ Sat, 03 Jun 2017 20:47:25: 4000000 INFO @ Sat, 03 Jun 2017 20:47:25: 4000000 INFO @ Sat, 03 Jun 2017 20:47:32: 5000000 INFO @ Sat, 03 Jun 2017 20:47:32: 5000000 INFO @ Sat, 03 Jun 2017 20:47:32: 5000000 INFO @ Sat, 03 Jun 2017 20:47:38: 6000000 INFO @ Sat, 03 Jun 2017 20:47:38: 6000000 INFO @ Sat, 03 Jun 2017 20:47:38: 6000000 INFO @ Sat, 03 Jun 2017 20:47:45: 7000000 INFO @ Sat, 03 Jun 2017 20:47:45: 7000000 INFO @ Sat, 03 Jun 2017 20:47:45: 7000000 INFO @ Sat, 03 Jun 2017 20:47:52: 8000000 INFO @ Sat, 03 Jun 2017 20:47:52: 8000000 INFO @ Sat, 03 Jun 2017 20:47:52: 8000000 INFO @ Sat, 03 Jun 2017 20:47:59: 9000000 INFO @ Sat, 03 Jun 2017 20:47:59: 9000000 INFO @ Sat, 03 Jun 2017 20:47:59: 9000000 INFO @ Sat, 03 Jun 2017 20:48:05: 10000000 INFO @ Sat, 03 Jun 2017 20:48:05: 10000000 INFO @ Sat, 03 Jun 2017 20:48:05: 10000000 INFO @ Sat, 03 Jun 2017 20:48:12: 11000000 INFO @ Sat, 03 Jun 2017 20:48:12: 11000000 INFO @ Sat, 03 Jun 2017 20:48:12: 11000000 INFO @ Sat, 03 Jun 2017 20:48:19: 12000000 INFO @ Sat, 03 Jun 2017 20:48:19: 12000000 INFO @ Sat, 03 Jun 2017 20:48:19: 12000000 INFO @ Sat, 03 Jun 2017 20:48:26: 13000000 INFO @ Sat, 03 Jun 2017 20:48:26: 13000000 INFO @ Sat, 03 Jun 2017 20:48:26: 13000000 INFO @ Sat, 03 Jun 2017 20:48:33: 14000000 INFO @ Sat, 03 Jun 2017 20:48:33: 14000000 INFO @ Sat, 03 Jun 2017 20:48:33: 14000000 INFO @ Sat, 03 Jun 2017 20:48:39: 15000000 INFO @ Sat, 03 Jun 2017 20:48:39: 15000000 INFO @ Sat, 03 Jun 2017 20:48:39: 15000000 INFO @ Sat, 03 Jun 2017 20:48:46: 16000000 INFO @ Sat, 03 Jun 2017 20:48:46: 16000000 INFO @ Sat, 03 Jun 2017 20:48:46: 16000000 INFO @ Sat, 03 Jun 2017 20:48:53: 17000000 INFO @ Sat, 03 Jun 2017 20:48:53: 17000000 INFO @ Sat, 03 Jun 2017 20:48:53: 17000000 INFO @ Sat, 03 Jun 2017 20:49:00: 18000000 INFO @ Sat, 03 Jun 2017 20:49:00: 18000000 INFO @ Sat, 03 Jun 2017 20:49:00: 18000000 INFO @ Sat, 03 Jun 2017 20:49:07: 19000000 INFO @ Sat, 03 Jun 2017 20:49:07: 19000000 INFO @ Sat, 03 Jun 2017 20:49:07: 19000000 INFO @ Sat, 03 Jun 2017 20:49:14: 20000000 INFO @ Sat, 03 Jun 2017 20:49:14: 20000000 INFO @ Sat, 03 Jun 2017 20:49:14: 20000000 INFO @ Sat, 03 Jun 2017 20:49:21: 21000000 INFO @ Sat, 03 Jun 2017 20:49:21: 21000000 INFO @ Sat, 03 Jun 2017 20:49:21: 21000000 INFO @ Sat, 03 Jun 2017 20:49:27: 22000000 INFO @ Sat, 03 Jun 2017 20:49:27: 22000000 INFO @ Sat, 03 Jun 2017 20:49:27: 22000000 INFO @ Sat, 03 Jun 2017 20:49:28: #1 tag size is determined as 50 bps INFO @ Sat, 03 Jun 2017 20:49:28: #1 tag size = 50 INFO @ Sat, 03 Jun 2017 20:49:28: #1 total tags in treatment: 22096565 INFO @ Sat, 03 Jun 2017 20:49:28: #1 user defined the maximum tags... INFO @ Sat, 03 Jun 2017 20:49:28: #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 20:49:28: #1 tag size is determined as 50 bps INFO @ Sat, 03 Jun 2017 20:49:28: #1 tag size = 50 INFO @ Sat, 03 Jun 2017 20:49:28: #1 total tags in treatment: 22096565 INFO @ Sat, 03 Jun 2017 20:49:28: #1 user defined the maximum tags... INFO @ Sat, 03 Jun 2017 20:49:28: #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 20:49:28: #1 tag size is determined as 50 bps INFO @ Sat, 03 Jun 2017 20:49:28: #1 tag size = 50 INFO @ Sat, 03 Jun 2017 20:49:28: #1 total tags in treatment: 22096565 INFO @ Sat, 03 Jun 2017 20:49:28: #1 user defined the maximum tags... INFO @ Sat, 03 Jun 2017 20:49:28: #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 20:49:33: #1 tags after filtering in treatment: 22089901 INFO @ Sat, 03 Jun 2017 20:49:33: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 03 Jun 2017 20:49:33: #1 finished! INFO @ Sat, 03 Jun 2017 20:49:33: #2 Build Peak Model... INFO @ Sat, 03 Jun 2017 20:49:33: #1 tags after filtering in treatment: 22089901 INFO @ Sat, 03 Jun 2017 20:49:33: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 03 Jun 2017 20:49:33: #1 finished! INFO @ Sat, 03 Jun 2017 20:49:33: #2 Build Peak Model... INFO @ Sat, 03 Jun 2017 20:49:33: #1 tags after filtering in treatment: 22089901 INFO @ Sat, 03 Jun 2017 20:49:33: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 03 Jun 2017 20:49:33: #1 finished! INFO @ Sat, 03 Jun 2017 20:49:33: #2 Build Peak Model... INFO @ Sat, 03 Jun 2017 20:49:36: #2 number of paired peaks: 642 WARNING @ Sat, 03 Jun 2017 20:49:36: Fewer paired peaks (642) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 642 pairs to build model! INFO @ Sat, 03 Jun 2017 20:49:36: start model_add_line... INFO @ Sat, 03 Jun 2017 20:49:37: #2 number of paired peaks: 642 WARNING @ Sat, 03 Jun 2017 20:49:37: Fewer paired peaks (642) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 642 pairs to build model! INFO @ Sat, 03 Jun 2017 20:49:37: start model_add_line... INFO @ Sat, 03 Jun 2017 20:49:37: #2 number of paired peaks: 642 WARNING @ Sat, 03 Jun 2017 20:49:37: Fewer paired peaks (642) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 642 pairs to build model! INFO @ Sat, 03 Jun 2017 20:49:37: start model_add_line... INFO @ Sat, 03 Jun 2017 20:49:47: start X-correlation... INFO @ Sat, 03 Jun 2017 20:49:47: end of X-cor INFO @ Sat, 03 Jun 2017 20:49:47: #2 finished! INFO @ Sat, 03 Jun 2017 20:49:47: #2 predicted fragment length is 85 bps INFO @ Sat, 03 Jun 2017 20:49:47: #2 alternative fragment length(s) may be 85 bps INFO @ Sat, 03 Jun 2017 20:49:47: #2.2 Generate R script for model : SRX475426.10_model.r WARNING @ Sat, 03 Jun 2017 20:49:47: #2 Since the d (85) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 03 Jun 2017 20:49:47: #2 You may need to consider one of the other alternative d(s): 85 WARNING @ Sat, 03 Jun 2017 20:49:47: #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 20:49:47: #3 Call peaks... INFO @ Sat, 03 Jun 2017 20:49:47: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Jun 2017 20:49:47: start X-correlation... INFO @ Sat, 03 Jun 2017 20:49:47: end of X-cor INFO @ Sat, 03 Jun 2017 20:49:47: #2 finished! INFO @ Sat, 03 Jun 2017 20:49:47: #2 predicted fragment length is 85 bps INFO @ Sat, 03 Jun 2017 20:49:47: #2 alternative fragment length(s) may be 85 bps INFO @ Sat, 03 Jun 2017 20:49:47: #2.2 Generate R script for model : SRX475426.05_model.r WARNING @ Sat, 03 Jun 2017 20:49:47: #2 Since the d (85) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 03 Jun 2017 20:49:47: #2 You may need to consider one of the other alternative d(s): 85 WARNING @ Sat, 03 Jun 2017 20:49:47: #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 20:49:47: #3 Call peaks... INFO @ Sat, 03 Jun 2017 20:49:47: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Jun 2017 20:49:48: start X-correlation... INFO @ Sat, 03 Jun 2017 20:49:48: end of X-cor INFO @ Sat, 03 Jun 2017 20:49:48: #2 finished! INFO @ Sat, 03 Jun 2017 20:49:48: #2 predicted fragment length is 85 bps INFO @ Sat, 03 Jun 2017 20:49:48: #2 alternative fragment length(s) may be 85 bps INFO @ Sat, 03 Jun 2017 20:49:48: #2.2 Generate R script for model : SRX475426.20_model.r WARNING @ Sat, 03 Jun 2017 20:49:48: #2 Since the d (85) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 03 Jun 2017 20:49:48: #2 You may need to consider one of the other alternative d(s): 85 WARNING @ Sat, 03 Jun 2017 20:49:48: #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 20:49:48: #3 Call peaks... INFO @ Sat, 03 Jun 2017 20:49:48: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Jun 2017 20:51:35: #3 Call peaks for each chromosome... INFO @ Sat, 03 Jun 2017 20:51:35: #3 Call peaks for each chromosome... INFO @ Sat, 03 Jun 2017 20:51:40: #3 Call peaks for each chromosome... INFO @ Sat, 03 Jun 2017 20:52:56: #4 Write output xls file... SRX475426.20_peaks.xls INFO @ Sat, 03 Jun 2017 20:52:56: #4 Write peak in narrowPeak format file... SRX475426.20_peaks.narrowPeak INFO @ Sat, 03 Jun 2017 20:52:56: #4 Write summits bed file... SRX475426.20_summits.bed INFO @ Sat, 03 Jun 2017 20:52:56: Done! pass1 - making usageList (14 chroms): 0 millis pass2 - checking and writing primary data (2215 records, 4 fields): 5 millis CompletedMACS2peakCalling INFO @ Sat, 03 Jun 2017 20:53:04: #4 Write output xls file... SRX475426.10_peaks.xls INFO @ Sat, 03 Jun 2017 20:53:04: #4 Write peak in narrowPeak format file... SRX475426.10_peaks.narrowPeak INFO @ Sat, 03 Jun 2017 20:53:04: #4 Write summits bed file... SRX475426.10_summits.bed INFO @ Sat, 03 Jun 2017 20:53:04: Done! pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (3966 records, 4 fields): 6 millis CompletedMACS2peakCalling INFO @ Sat, 03 Jun 2017 20:53:08: #4 Write output xls file... SRX475426.05_peaks.xls INFO @ Sat, 03 Jun 2017 20:53:08: #4 Write peak in narrowPeak format file... SRX475426.05_peaks.narrowPeak INFO @ Sat, 03 Jun 2017 20:53:08: #4 Write summits bed file... SRX475426.05_summits.bed INFO @ Sat, 03 Jun 2017 20:53:08: Done! pass1 - making usageList (15 chroms): 2 millis pass2 - checking and writing primary data (8682 records, 4 fields): 11 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。