Job ID = 9029787 sra ファイルのダウンロード中... Completed: 1291638K bytes transferred in 16 seconds (642523K 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 12695 0 12695 0 0 1719 0 --:--:-- 0:00:07 --:--:-- 15221 100 31059 0 31059 0 0 3859 0 --:--:-- 0:00:08 --:--:-- 20761 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 26225419 spots for /home/okishinya/chipatlas/results/dm3/SRX2055967/SRR4069199.sra Written 26225419 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: 00:11:36 26225419 reads; of these: 26225419 (100.00%) were unpaired; of these: 2819325 (10.75%) aligned 0 times 16030170 (61.12%) aligned exactly 1 time 7375924 (28.13%) aligned >1 times 89.25% overall alignment rate Time searching: 00:11:36 Overall time: 00:11:36 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 12 files... [bam_rmdupse_core] 2368741 / 23406094 = 0.1012 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 15:31:01: # Command line: callpeak -t SRX2055967.bam -f BAM -g dm -n SRX2055967.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX2055967.05 # format = BAM # ChIP-seq file = ['SRX2055967.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 15:31:01: #1 read tag files... INFO @ Sat, 03 Jun 2017 15:31:01: # Command line: callpeak -t SRX2055967.bam -f BAM -g dm -n SRX2055967.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX2055967.10 # format = BAM # ChIP-seq file = ['SRX2055967.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 15:31:01: #1 read treatment tags... INFO @ Sat, 03 Jun 2017 15:31:01: #1 read tag files... INFO @ Sat, 03 Jun 2017 15:31:01: #1 read treatment tags... INFO @ Sat, 03 Jun 2017 15:31:01: # Command line: callpeak -t SRX2055967.bam -f BAM -g dm -n SRX2055967.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX2055967.20 # format = BAM # ChIP-seq file = ['SRX2055967.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 15:31:01: #1 read tag files... INFO @ Sat, 03 Jun 2017 15:31:01: #1 read treatment tags... INFO @ Sat, 03 Jun 2017 15:31:08: 1000000 INFO @ Sat, 03 Jun 2017 15:31:08: 1000000 INFO @ Sat, 03 Jun 2017 15:31:08: 1000000 INFO @ Sat, 03 Jun 2017 15:31:16: 2000000 INFO @ Sat, 03 Jun 2017 15:31:16: 2000000 INFO @ Sat, 03 Jun 2017 15:31:16: 2000000 INFO @ Sat, 03 Jun 2017 15:31:23: 3000000 INFO @ Sat, 03 Jun 2017 15:31:23: 3000000 INFO @ Sat, 03 Jun 2017 15:31:23: 3000000 INFO @ Sat, 03 Jun 2017 15:31:30: 4000000 INFO @ Sat, 03 Jun 2017 15:31:30: 4000000 INFO @ Sat, 03 Jun 2017 15:31:30: 4000000 INFO @ Sat, 03 Jun 2017 15:31:38: 5000000 INFO @ Sat, 03 Jun 2017 15:31:38: 5000000 INFO @ Sat, 03 Jun 2017 15:31:38: 5000000 INFO @ Sat, 03 Jun 2017 15:31:45: 6000000 INFO @ Sat, 03 Jun 2017 15:31:45: 6000000 INFO @ Sat, 03 Jun 2017 15:31:45: 6000000 INFO @ Sat, 03 Jun 2017 15:31:53: 7000000 INFO @ Sat, 03 Jun 2017 15:31:53: 7000000 INFO @ Sat, 03 Jun 2017 15:31:53: 7000000 INFO @ Sat, 03 Jun 2017 15:32:01: 8000000 INFO @ Sat, 03 Jun 2017 15:32:01: 8000000 INFO @ Sat, 03 Jun 2017 15:32:01: 8000000 INFO @ Sat, 03 Jun 2017 15:32:08: 9000000 INFO @ Sat, 03 Jun 2017 15:32:08: 9000000 INFO @ Sat, 03 Jun 2017 15:32:09: 9000000 INFO @ Sat, 03 Jun 2017 15:32:16: 10000000 INFO @ Sat, 03 Jun 2017 15:32:16: 10000000 INFO @ Sat, 03 Jun 2017 15:32:16: 10000000 INFO @ Sat, 03 Jun 2017 15:32:23: 11000000 INFO @ Sat, 03 Jun 2017 15:32:23: 11000000 INFO @ Sat, 03 Jun 2017 15:32:23: 11000000 INFO @ Sat, 03 Jun 2017 15:32:30: 12000000 INFO @ Sat, 03 Jun 2017 15:32:30: 12000000 INFO @ Sat, 03 Jun 2017 15:32:30: 12000000 INFO @ Sat, 03 Jun 2017 15:32:38: 13000000 INFO @ Sat, 03 Jun 2017 15:32:38: 13000000 INFO @ Sat, 03 Jun 2017 15:32:38: 13000000 INFO @ Sat, 03 Jun 2017 15:32:45: 14000000 INFO @ Sat, 03 Jun 2017 15:32:45: 14000000 INFO @ Sat, 03 Jun 2017 15:32:45: 14000000 INFO @ Sat, 03 Jun 2017 15:32:52: 15000000 INFO @ Sat, 03 Jun 2017 15:32:52: 15000000 INFO @ Sat, 03 Jun 2017 15:32:52: 15000000 INFO @ Sat, 03 Jun 2017 15:32:59: 16000000 INFO @ Sat, 03 Jun 2017 15:32:59: 16000000 INFO @ Sat, 03 Jun 2017 15:33:00: 16000000 INFO @ Sat, 03 Jun 2017 15:33:07: 17000000 INFO @ Sat, 03 Jun 2017 15:33:07: 17000000 INFO @ Sat, 03 Jun 2017 15:33:07: 17000000 INFO @ Sat, 03 Jun 2017 15:33:14: 18000000 INFO @ Sat, 03 Jun 2017 15:33:14: 18000000 INFO @ Sat, 03 Jun 2017 15:33:14: 18000000 INFO @ Sat, 03 Jun 2017 15:33:21: 19000000 INFO @ Sat, 03 Jun 2017 15:33:22: 19000000 INFO @ Sat, 03 Jun 2017 15:33:22: 19000000 INFO @ Sat, 03 Jun 2017 15:33:28: 20000000 INFO @ Sat, 03 Jun 2017 15:33:29: 20000000 INFO @ Sat, 03 Jun 2017 15:33:29: 20000000 INFO @ Sat, 03 Jun 2017 15:33:36: 21000000 INFO @ Sat, 03 Jun 2017 15:33:36: 21000000 INFO @ Sat, 03 Jun 2017 15:33:36: 21000000 INFO @ Sat, 03 Jun 2017 15:33:36: #1 tag size is determined as 50 bps INFO @ Sat, 03 Jun 2017 15:33:36: #1 tag size = 50 INFO @ Sat, 03 Jun 2017 15:33:36: #1 total tags in treatment: 21037353 INFO @ Sat, 03 Jun 2017 15:33:36: #1 user defined the maximum tags... INFO @ Sat, 03 Jun 2017 15:33:36: #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 15:33:37: #1 tag size is determined as 50 bps INFO @ Sat, 03 Jun 2017 15:33:37: #1 tag size = 50 INFO @ Sat, 03 Jun 2017 15:33:37: #1 total tags in treatment: 21037353 INFO @ Sat, 03 Jun 2017 15:33:37: #1 user defined the maximum tags... INFO @ Sat, 03 Jun 2017 15:33:37: #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 15:33:37: #1 tag size is determined as 50 bps INFO @ Sat, 03 Jun 2017 15:33:37: #1 tag size = 50 INFO @ Sat, 03 Jun 2017 15:33:37: #1 total tags in treatment: 21037353 INFO @ Sat, 03 Jun 2017 15:33:37: #1 user defined the maximum tags... INFO @ Sat, 03 Jun 2017 15:33:37: #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 15:33:40: #1 tags after filtering in treatment: 21033511 INFO @ Sat, 03 Jun 2017 15:33:40: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 03 Jun 2017 15:33:40: #1 finished! INFO @ Sat, 03 Jun 2017 15:33:40: #2 Build Peak Model... INFO @ Sat, 03 Jun 2017 15:33:40: #1 tags after filtering in treatment: 21033511 INFO @ Sat, 03 Jun 2017 15:33:40: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 03 Jun 2017 15:33:40: #1 finished! INFO @ Sat, 03 Jun 2017 15:33:40: #2 Build Peak Model... INFO @ Sat, 03 Jun 2017 15:33:41: #1 tags after filtering in treatment: 21033511 INFO @ Sat, 03 Jun 2017 15:33:41: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 03 Jun 2017 15:33:41: #1 finished! INFO @ Sat, 03 Jun 2017 15:33:41: #2 Build Peak Model... INFO @ Sat, 03 Jun 2017 15:33:44: #2 number of paired peaks: 461 WARNING @ Sat, 03 Jun 2017 15:33:44: Fewer paired peaks (461) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 461 pairs to build model! INFO @ Sat, 03 Jun 2017 15:33:44: start model_add_line... INFO @ Sat, 03 Jun 2017 15:33:44: #2 number of paired peaks: 461 WARNING @ Sat, 03 Jun 2017 15:33:44: Fewer paired peaks (461) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 461 pairs to build model! INFO @ Sat, 03 Jun 2017 15:33:44: start model_add_line... INFO @ Sat, 03 Jun 2017 15:33:44: #2 number of paired peaks: 461 WARNING @ Sat, 03 Jun 2017 15:33:44: Fewer paired peaks (461) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 461 pairs to build model! INFO @ Sat, 03 Jun 2017 15:33:44: start model_add_line... INFO @ Sat, 03 Jun 2017 15:33:51: start X-correlation... INFO @ Sat, 03 Jun 2017 15:33:51: end of X-cor INFO @ Sat, 03 Jun 2017 15:33:51: #2 finished! INFO @ Sat, 03 Jun 2017 15:33:51: #2 predicted fragment length is 55 bps INFO @ Sat, 03 Jun 2017 15:33:51: #2 alternative fragment length(s) may be 3,55 bps INFO @ Sat, 03 Jun 2017 15:33:51: #2.2 Generate R script for model : SRX2055967.10_model.r WARNING @ Sat, 03 Jun 2017 15:33:51: #2 Since the d (55) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 03 Jun 2017 15:33:51: #2 You may need to consider one of the other alternative d(s): 3,55 WARNING @ Sat, 03 Jun 2017 15:33:51: #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 15:33:51: #3 Call peaks... INFO @ Sat, 03 Jun 2017 15:33:51: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Jun 2017 15:33:51: start X-correlation... INFO @ Sat, 03 Jun 2017 15:33:51: end of X-cor INFO @ Sat, 03 Jun 2017 15:33:51: #2 finished! INFO @ Sat, 03 Jun 2017 15:33:51: #2 predicted fragment length is 55 bps INFO @ Sat, 03 Jun 2017 15:33:51: #2 alternative fragment length(s) may be 3,55 bps INFO @ Sat, 03 Jun 2017 15:33:51: #2.2 Generate R script for model : SRX2055967.05_model.r WARNING @ Sat, 03 Jun 2017 15:33:51: #2 Since the d (55) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 03 Jun 2017 15:33:51: #2 You may need to consider one of the other alternative d(s): 3,55 WARNING @ Sat, 03 Jun 2017 15:33:51: #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 15:33:51: #3 Call peaks... INFO @ Sat, 03 Jun 2017 15:33:51: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Jun 2017 15:33:52: start X-correlation... INFO @ Sat, 03 Jun 2017 15:33:52: end of X-cor INFO @ Sat, 03 Jun 2017 15:33:52: #2 finished! INFO @ Sat, 03 Jun 2017 15:33:52: #2 predicted fragment length is 55 bps INFO @ Sat, 03 Jun 2017 15:33:52: #2 alternative fragment length(s) may be 3,55 bps INFO @ Sat, 03 Jun 2017 15:33:52: #2.2 Generate R script for model : SRX2055967.20_model.r WARNING @ Sat, 03 Jun 2017 15:33:52: #2 Since the d (55) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 03 Jun 2017 15:33:52: #2 You may need to consider one of the other alternative d(s): 3,55 WARNING @ Sat, 03 Jun 2017 15:33:52: #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 15:33:52: #3 Call peaks... INFO @ Sat, 03 Jun 2017 15:33:52: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Jun 2017 15:35:32: #3 Call peaks for each chromosome... INFO @ Sat, 03 Jun 2017 15:35:34: #3 Call peaks for each chromosome... INFO @ Sat, 03 Jun 2017 15:35:39: #3 Call peaks for each chromosome... INFO @ Sat, 03 Jun 2017 15:36:46: #4 Write output xls file... SRX2055967.10_peaks.xls INFO @ Sat, 03 Jun 2017 15:36:46: #4 Write peak in narrowPeak format file... SRX2055967.10_peaks.narrowPeak INFO @ Sat, 03 Jun 2017 15:36:46: #4 Write summits bed file... SRX2055967.10_summits.bed INFO @ Sat, 03 Jun 2017 15:36:46: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (2410 records, 4 fields): 5 millis CompletedMACS2peakCalling INFO @ Sat, 03 Jun 2017 15:36:53: #4 Write output xls file... SRX2055967.05_peaks.xls INFO @ Sat, 03 Jun 2017 15:36:53: #4 Write peak in narrowPeak format file... SRX2055967.05_peaks.narrowPeak INFO @ Sat, 03 Jun 2017 15:36:53: #4 Write summits bed file... SRX2055967.05_summits.bed INFO @ Sat, 03 Jun 2017 15:36:54: Done! pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (3595 records, 4 fields): 6 millis CompletedMACS2peakCalling INFO @ Sat, 03 Jun 2017 15:37:02: #4 Write output xls file... SRX2055967.20_peaks.xls INFO @ Sat, 03 Jun 2017 15:37:02: #4 Write peak in narrowPeak format file... SRX2055967.20_peaks.narrowPeak INFO @ Sat, 03 Jun 2017 15:37:02: #4 Write summits bed file... SRX2055967.20_summits.bed INFO @ Sat, 03 Jun 2017 15:37:02: Done! pass1 - making usageList (12 chroms): 1 millis pass2 - checking and writing primary data (1278 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。