Job ID = 9039912 sra ファイルのダウンロード中... Completed: 1619176K bytes transferred in 20 seconds (661909K 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 --:--:-- 0 100 12695 0 12695 0 0 1551 0 --:--:-- 0:00:08 --:--:-- 8185 100 41829 0 41829 0 0 4558 0 --:--:-- 0:00:09 --:--:-- 16429 100 105k 0 105k 0 0 10666 0 --:--:-- 0:00:10 --:--:-- 30643 100 147k 0 147k 0 0 14196 0 --:--:-- 0:00:10 --:--:-- 37515 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 34101104 spots for /home/okishinya/chipatlas/results/dm3/SRX1085378/SRR2090177.sra Written 34101104 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: 00:07:17 34101104 reads; of these: 34101104 (100.00%) were unpaired; of these: 1934125 (5.67%) aligned 0 times 29791530 (87.36%) aligned exactly 1 time 2375449 (6.97%) aligned >1 times 94.33% overall alignment rate Time searching: 00:07:17 Overall time: 00:07:17 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 16 files... [bam_rmdupse_core] 14600698 / 32166979 = 0.4539 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 @ Sun, 04 Jun 2017 23:28:11: # Command line: callpeak -t SRX1085378.bam -f BAM -g dm -n SRX1085378.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX1085378.20 # format = BAM # ChIP-seq file = ['SRX1085378.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 @ Sun, 04 Jun 2017 23:28:11: # Command line: callpeak -t SRX1085378.bam -f BAM -g dm -n SRX1085378.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX1085378.10 # format = BAM # ChIP-seq file = ['SRX1085378.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 @ Sun, 04 Jun 2017 23:28:11: #1 read tag files... INFO @ Sun, 04 Jun 2017 23:28:11: #1 read tag files... INFO @ Sun, 04 Jun 2017 23:28:11: # Command line: callpeak -t SRX1085378.bam -f BAM -g dm -n SRX1085378.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX1085378.05 # format = BAM # ChIP-seq file = ['SRX1085378.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 @ Sun, 04 Jun 2017 23:28:11: #1 read treatment tags... INFO @ Sun, 04 Jun 2017 23:28:11: #1 read treatment tags... INFO @ Sun, 04 Jun 2017 23:28:11: #1 read tag files... INFO @ Sun, 04 Jun 2017 23:28:11: #1 read treatment tags... INFO @ Sun, 04 Jun 2017 23:28:19: 1000000 INFO @ Sun, 04 Jun 2017 23:28:20: 1000000 INFO @ Sun, 04 Jun 2017 23:28:20: 1000000 INFO @ Sun, 04 Jun 2017 23:28:27: 2000000 INFO @ Sun, 04 Jun 2017 23:28:28: 2000000 INFO @ Sun, 04 Jun 2017 23:28:28: 2000000 INFO @ Sun, 04 Jun 2017 23:28:35: 3000000 INFO @ Sun, 04 Jun 2017 23:28:36: 3000000 INFO @ Sun, 04 Jun 2017 23:28:36: 3000000 INFO @ Sun, 04 Jun 2017 23:28:42: 4000000 INFO @ Sun, 04 Jun 2017 23:28:45: 4000000 INFO @ Sun, 04 Jun 2017 23:28:45: 4000000 INFO @ Sun, 04 Jun 2017 23:28:50: 5000000 INFO @ Sun, 04 Jun 2017 23:28:53: 5000000 INFO @ Sun, 04 Jun 2017 23:28:53: 5000000 INFO @ Sun, 04 Jun 2017 23:28:58: 6000000 INFO @ Sun, 04 Jun 2017 23:29:02: 6000000 INFO @ Sun, 04 Jun 2017 23:29:02: 6000000 INFO @ Sun, 04 Jun 2017 23:29:06: 7000000 INFO @ Sun, 04 Jun 2017 23:29:10: 7000000 INFO @ Sun, 04 Jun 2017 23:29:10: 7000000 INFO @ Sun, 04 Jun 2017 23:29:13: 8000000 INFO @ Sun, 04 Jun 2017 23:29:18: 8000000 INFO @ Sun, 04 Jun 2017 23:29:18: 8000000 INFO @ Sun, 04 Jun 2017 23:29:21: 9000000 INFO @ Sun, 04 Jun 2017 23:29:27: 9000000 INFO @ Sun, 04 Jun 2017 23:29:27: 9000000 INFO @ Sun, 04 Jun 2017 23:29:29: 10000000 INFO @ Sun, 04 Jun 2017 23:29:35: 10000000 INFO @ Sun, 04 Jun 2017 23:29:35: 10000000 INFO @ Sun, 04 Jun 2017 23:29:36: 11000000 INFO @ Sun, 04 Jun 2017 23:29:43: 11000000 INFO @ Sun, 04 Jun 2017 23:29:43: 11000000 INFO @ Sun, 04 Jun 2017 23:29:44: 12000000 INFO @ Sun, 04 Jun 2017 23:29:51: 12000000 INFO @ Sun, 04 Jun 2017 23:29:51: 12000000 INFO @ Sun, 04 Jun 2017 23:29:52: 13000000 INFO @ Sun, 04 Jun 2017 23:29:59: 13000000 INFO @ Sun, 04 Jun 2017 23:29:59: 13000000 INFO @ Sun, 04 Jun 2017 23:30:01: 14000000 INFO @ Sun, 04 Jun 2017 23:30:07: 14000000 INFO @ Sun, 04 Jun 2017 23:30:07: 14000000 INFO @ Sun, 04 Jun 2017 23:30:09: 15000000 INFO @ Sun, 04 Jun 2017 23:30:15: 15000000 INFO @ Sun, 04 Jun 2017 23:30:15: 15000000 INFO @ Sun, 04 Jun 2017 23:30:18: 16000000 INFO @ Sun, 04 Jun 2017 23:30:23: 16000000 INFO @ Sun, 04 Jun 2017 23:30:23: 16000000 INFO @ Sun, 04 Jun 2017 23:30:26: 17000000 INFO @ Sun, 04 Jun 2017 23:30:31: 17000000 INFO @ Sun, 04 Jun 2017 23:30:31: 17000000 INFO @ Sun, 04 Jun 2017 23:30:31: #1 tag size is determined as 80 bps INFO @ Sun, 04 Jun 2017 23:30:31: #1 tag size = 80 INFO @ Sun, 04 Jun 2017 23:30:31: #1 total tags in treatment: 17566281 INFO @ Sun, 04 Jun 2017 23:30:31: #1 user defined the maximum tags... INFO @ Sun, 04 Jun 2017 23:30:31: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sun, 04 Jun 2017 23:30:35: #1 tags after filtering in treatment: 17543035 INFO @ Sun, 04 Jun 2017 23:30:35: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 04 Jun 2017 23:30:35: #1 finished! INFO @ Sun, 04 Jun 2017 23:30:35: #2 Build Peak Model... INFO @ Sun, 04 Jun 2017 23:30:35: #1 tag size is determined as 80 bps INFO @ Sun, 04 Jun 2017 23:30:35: #1 tag size = 80 INFO @ Sun, 04 Jun 2017 23:30:35: #1 total tags in treatment: 17566281 INFO @ Sun, 04 Jun 2017 23:30:35: #1 user defined the maximum tags... INFO @ Sun, 04 Jun 2017 23:30:35: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sun, 04 Jun 2017 23:30:35: #1 tag size is determined as 80 bps INFO @ Sun, 04 Jun 2017 23:30:35: #1 tag size = 80 INFO @ Sun, 04 Jun 2017 23:30:35: #1 total tags in treatment: 17566281 INFO @ Sun, 04 Jun 2017 23:30:35: #1 user defined the maximum tags... INFO @ Sun, 04 Jun 2017 23:30:35: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sun, 04 Jun 2017 23:30:38: #1 tags after filtering in treatment: 17543035 INFO @ Sun, 04 Jun 2017 23:30:38: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 04 Jun 2017 23:30:38: #1 finished! INFO @ Sun, 04 Jun 2017 23:30:38: #2 Build Peak Model... INFO @ Sun, 04 Jun 2017 23:30:38: #1 tags after filtering in treatment: 17543035 INFO @ Sun, 04 Jun 2017 23:30:38: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 04 Jun 2017 23:30:38: #1 finished! INFO @ Sun, 04 Jun 2017 23:30:38: #2 Build Peak Model... INFO @ Sun, 04 Jun 2017 23:30:40: #2 number of paired peaks: 5862 INFO @ Sun, 04 Jun 2017 23:30:40: start model_add_line... INFO @ Sun, 04 Jun 2017 23:30:42: #2 number of paired peaks: 5862 INFO @ Sun, 04 Jun 2017 23:30:42: start model_add_line... INFO @ Sun, 04 Jun 2017 23:30:42: #2 number of paired peaks: 5862 INFO @ Sun, 04 Jun 2017 23:30:42: start model_add_line... INFO @ Sun, 04 Jun 2017 23:31:49: start X-correlation... INFO @ Sun, 04 Jun 2017 23:31:49: end of X-cor INFO @ Sun, 04 Jun 2017 23:31:49: #2 finished! INFO @ Sun, 04 Jun 2017 23:31:49: #2 predicted fragment length is 114 bps INFO @ Sun, 04 Jun 2017 23:31:49: #2 alternative fragment length(s) may be 114 bps INFO @ Sun, 04 Jun 2017 23:31:49: #2.2 Generate R script for model : SRX1085378.20_model.r WARNING @ Sun, 04 Jun 2017 23:31:49: #2 Since the d (114) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 04 Jun 2017 23:31:49: #2 You may need to consider one of the other alternative d(s): 114 WARNING @ Sun, 04 Jun 2017 23:31:49: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sun, 04 Jun 2017 23:31:49: #3 Call peaks... INFO @ Sun, 04 Jun 2017 23:31:49: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 04 Jun 2017 23:31:49: start X-correlation... INFO @ Sun, 04 Jun 2017 23:31:49: end of X-cor INFO @ Sun, 04 Jun 2017 23:31:49: #2 finished! INFO @ Sun, 04 Jun 2017 23:31:49: #2 predicted fragment length is 114 bps INFO @ Sun, 04 Jun 2017 23:31:49: #2 alternative fragment length(s) may be 114 bps INFO @ Sun, 04 Jun 2017 23:31:49: #2.2 Generate R script for model : SRX1085378.10_model.r WARNING @ Sun, 04 Jun 2017 23:31:49: #2 Since the d (114) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 04 Jun 2017 23:31:49: #2 You may need to consider one of the other alternative d(s): 114 WARNING @ Sun, 04 Jun 2017 23:31:49: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sun, 04 Jun 2017 23:31:49: #3 Call peaks... INFO @ Sun, 04 Jun 2017 23:31:49: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 04 Jun 2017 23:31:51: start X-correlation... INFO @ Sun, 04 Jun 2017 23:31:51: end of X-cor INFO @ Sun, 04 Jun 2017 23:31:51: #2 finished! INFO @ Sun, 04 Jun 2017 23:31:51: #2 predicted fragment length is 114 bps INFO @ Sun, 04 Jun 2017 23:31:51: #2 alternative fragment length(s) may be 114 bps INFO @ Sun, 04 Jun 2017 23:31:51: #2.2 Generate R script for model : SRX1085378.05_model.r WARNING @ Sun, 04 Jun 2017 23:31:51: #2 Since the d (114) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 04 Jun 2017 23:31:51: #2 You may need to consider one of the other alternative d(s): 114 WARNING @ Sun, 04 Jun 2017 23:31:51: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sun, 04 Jun 2017 23:31:51: #3 Call peaks... INFO @ Sun, 04 Jun 2017 23:31:51: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 04 Jun 2017 23:33:25: #3 Call peaks for each chromosome... INFO @ Sun, 04 Jun 2017 23:33:26: #3 Call peaks for each chromosome... INFO @ Sun, 04 Jun 2017 23:33:26: #3 Call peaks for each chromosome... BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 04 Jun 2017 23:34:40: #4 Write output xls file... SRX1085378.20_peaks.xls INFO @ Sun, 04 Jun 2017 23:34:40: #4 Write peak in narrowPeak format file... SRX1085378.20_peaks.narrowPeak INFO @ Sun, 04 Jun 2017 23:34:40: #4 Write summits bed file... SRX1085378.20_summits.bed INFO @ Sun, 04 Jun 2017 23:34:40: Done! pass1 - making usageList (13 chroms): 2 millis pass2 - checking and writing primary data (9123 records, 4 fields): 14 millis CompletedMACS2peakCalling INFO @ Sun, 04 Jun 2017 23:34:44: #4 Write output xls file... SRX1085378.10_peaks.xls INFO @ Sun, 04 Jun 2017 23:34:44: #4 Write peak in narrowPeak format file... SRX1085378.10_peaks.narrowPeak INFO @ Sun, 04 Jun 2017 23:34:44: #4 Write summits bed file... SRX1085378.10_summits.bed INFO @ Sun, 04 Jun 2017 23:34:44: Done! pass1 - making usageList (14 chroms): 2 millis pass2 - checking and writing primary data (12639 records, 4 fields): 17 millis CompletedMACS2peakCalling INFO @ Sun, 04 Jun 2017 23:34:55: #4 Write output xls file... SRX1085378.05_peaks.xls BigWig に変換しました。 INFO @ Sun, 04 Jun 2017 23:34:55: #4 Write peak in narrowPeak format file... SRX1085378.05_peaks.narrowPeak INFO @ Sun, 04 Jun 2017 23:34:55: #4 Write summits bed file... SRX1085378.05_summits.bed INFO @ Sun, 04 Jun 2017 23:34:55: Done! pass1 - making usageList (14 chroms): 4 millis pass2 - checking and writing primary data (16305 records, 4 fields): 20 millis CompletedMACS2peakCalling