Job ID = 10325496 sra ファイルのダウンロード中... Completed: 833542K bytes transferred in 41 seconds (163354K bits/sec), in 1 file. 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 30462059 spots for /home/okishinya/chipatlas/results/rn6/SRX3398846/SRR6297867.sra Written 30462059 spots total rm: cannot remove `[DSE]RX*': そのようなファイルやディレクトリはありません 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: 00:00:02 Time loading forward index: 00:00:02 Time loading mirror index: 00:00:02 Multiseed full-index search: 00:59:36 30462059 reads; of these: 30462059 (100.00%) were unpaired; of these: 1775788 (5.83%) aligned 0 times 22965698 (75.39%) aligned exactly 1 time 5720573 (18.78%) aligned >1 times 94.17% overall alignment rate Time searching: 00:59:42 Overall time: 00:59:42 マッピングが完了しました。 samtools でBAM に変換中... [samopen] SAM header is present: 953 sequences. [bam_sort_core] merging from 12 files... [bam_rmdupse_core] 3037946 / 28686271 = 0.1059 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 @ Fri, 12 Jan 2018 04:00:01: # Command line: callpeak -t SRX3398846.bam -f BAM -g 2.15e9 -n SRX3398846.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX3398846.20 # format = BAM # ChIP-seq file = ['SRX3398846.bam'] # control file = None # effective genome size = 2.15e+09 # 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 # Paired-End mode is off INFO @ Fri, 12 Jan 2018 04:00:01: #1 read tag files... INFO @ Fri, 12 Jan 2018 04:00:01: #1 read treatment tags... INFO @ Fri, 12 Jan 2018 04:00:01: # Command line: callpeak -t SRX3398846.bam -f BAM -g 2.15e9 -n SRX3398846.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX3398846.10 # format = BAM # ChIP-seq file = ['SRX3398846.bam'] # control file = None # effective genome size = 2.15e+09 # 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 # Paired-End mode is off INFO @ Fri, 12 Jan 2018 04:00:01: #1 read tag files... INFO @ Fri, 12 Jan 2018 04:00:01: #1 read treatment tags... INFO @ Fri, 12 Jan 2018 04:00:01: # Command line: callpeak -t SRX3398846.bam -f BAM -g 2.15e9 -n SRX3398846.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX3398846.05 # format = BAM # ChIP-seq file = ['SRX3398846.bam'] # control file = None # effective genome size = 2.15e+09 # 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 # Paired-End mode is off INFO @ Fri, 12 Jan 2018 04:00:01: #1 read tag files... INFO @ Fri, 12 Jan 2018 04:00:01: #1 read treatment tags... INFO @ Fri, 12 Jan 2018 04:00:19: 1000000 INFO @ Fri, 12 Jan 2018 04:00:19: 1000000 INFO @ Fri, 12 Jan 2018 04:00:20: 1000000 INFO @ Fri, 12 Jan 2018 04:00:37: 2000000 INFO @ Fri, 12 Jan 2018 04:00:37: 2000000 INFO @ Fri, 12 Jan 2018 04:00:38: 2000000 INFO @ Fri, 12 Jan 2018 04:00:55: 3000000 INFO @ Fri, 12 Jan 2018 04:00:55: 3000000 INFO @ Fri, 12 Jan 2018 04:00:56: 3000000 INFO @ Fri, 12 Jan 2018 04:01:13: 4000000 INFO @ Fri, 12 Jan 2018 04:01:13: 4000000 INFO @ Fri, 12 Jan 2018 04:01:14: 4000000 INFO @ Fri, 12 Jan 2018 04:01:31: 5000000 INFO @ Fri, 12 Jan 2018 04:01:31: 5000000 INFO @ Fri, 12 Jan 2018 04:01:32: 5000000 INFO @ Fri, 12 Jan 2018 04:01:49: 6000000 INFO @ Fri, 12 Jan 2018 04:01:50: 6000000 INFO @ Fri, 12 Jan 2018 04:01:50: 6000000 INFO @ Fri, 12 Jan 2018 04:02:07: 7000000 INFO @ Fri, 12 Jan 2018 04:02:08: 7000000 INFO @ Fri, 12 Jan 2018 04:02:09: 7000000 INFO @ Fri, 12 Jan 2018 04:02:25: 8000000 INFO @ Fri, 12 Jan 2018 04:02:26: 8000000 INFO @ Fri, 12 Jan 2018 04:02:27: 8000000 INFO @ Fri, 12 Jan 2018 04:02:43: 9000000 INFO @ Fri, 12 Jan 2018 04:02:44: 9000000 INFO @ Fri, 12 Jan 2018 04:02:45: 9000000 INFO @ Fri, 12 Jan 2018 04:03:01: 10000000 INFO @ Fri, 12 Jan 2018 04:03:02: 10000000 INFO @ Fri, 12 Jan 2018 04:03:03: 10000000 INFO @ Fri, 12 Jan 2018 04:03:19: 11000000 INFO @ Fri, 12 Jan 2018 04:03:20: 11000000 INFO @ Fri, 12 Jan 2018 04:03:22: 11000000 INFO @ Fri, 12 Jan 2018 04:03:38: 12000000 INFO @ Fri, 12 Jan 2018 04:03:39: 12000000 INFO @ Fri, 12 Jan 2018 04:03:40: 12000000 INFO @ Fri, 12 Jan 2018 04:03:56: 13000000 INFO @ Fri, 12 Jan 2018 04:03:57: 13000000 INFO @ Fri, 12 Jan 2018 04:03:59: 13000000 INFO @ Fri, 12 Jan 2018 04:04:14: 14000000 INFO @ Fri, 12 Jan 2018 04:04:16: 14000000 INFO @ Fri, 12 Jan 2018 04:04:17: 14000000 INFO @ Fri, 12 Jan 2018 04:04:32: 15000000 INFO @ Fri, 12 Jan 2018 04:04:33: 15000000 INFO @ Fri, 12 Jan 2018 04:04:36: 15000000 INFO @ Fri, 12 Jan 2018 04:04:50: 16000000 INFO @ Fri, 12 Jan 2018 04:04:51: 16000000 INFO @ Fri, 12 Jan 2018 04:04:55: 16000000 INFO @ Fri, 12 Jan 2018 04:05:09: 17000000 INFO @ Fri, 12 Jan 2018 04:05:10: 17000000 INFO @ Fri, 12 Jan 2018 04:05:12: 17000000 INFO @ Fri, 12 Jan 2018 04:05:27: 18000000 INFO @ Fri, 12 Jan 2018 04:05:28: 18000000 INFO @ Fri, 12 Jan 2018 04:05:31: 18000000 INFO @ Fri, 12 Jan 2018 04:05:46: 19000000 INFO @ Fri, 12 Jan 2018 04:05:47: 19000000 INFO @ Fri, 12 Jan 2018 04:05:50: 19000000 INFO @ Fri, 12 Jan 2018 04:06:05: 20000000 INFO @ Fri, 12 Jan 2018 04:06:05: 20000000 INFO @ Fri, 12 Jan 2018 04:06:08: 20000000 INFO @ Fri, 12 Jan 2018 04:06:23: 21000000 INFO @ Fri, 12 Jan 2018 04:06:23: 21000000 INFO @ Fri, 12 Jan 2018 04:06:25: 21000000 INFO @ Fri, 12 Jan 2018 04:06:41: 22000000 INFO @ Fri, 12 Jan 2018 04:06:42: 22000000 INFO @ Fri, 12 Jan 2018 04:06:44: 22000000 INFO @ Fri, 12 Jan 2018 04:06:59: 23000000 INFO @ Fri, 12 Jan 2018 04:07:00: 23000000 INFO @ Fri, 12 Jan 2018 04:07:03: 23000000 INFO @ Fri, 12 Jan 2018 04:07:17: 24000000 INFO @ Fri, 12 Jan 2018 04:07:19: 24000000 INFO @ Fri, 12 Jan 2018 04:07:22: 24000000 INFO @ Fri, 12 Jan 2018 04:07:37: 25000000 INFO @ Fri, 12 Jan 2018 04:07:39: 25000000 INFO @ Fri, 12 Jan 2018 04:07:41: 25000000 INFO @ Fri, 12 Jan 2018 04:07:50: #1 tag size is determined as 51 bps INFO @ Fri, 12 Jan 2018 04:07:50: #1 tag size = 51 INFO @ Fri, 12 Jan 2018 04:07:50: #1 total tags in treatment: 25648325 INFO @ Fri, 12 Jan 2018 04:07:50: #1 user defined the maximum tags... INFO @ Fri, 12 Jan 2018 04:07:50: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 12 Jan 2018 04:07:51: #1 tags after filtering in treatment: 25648170 INFO @ Fri, 12 Jan 2018 04:07:51: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 12 Jan 2018 04:07:51: #1 finished! INFO @ Fri, 12 Jan 2018 04:07:51: #2 Build Peak Model... INFO @ Fri, 12 Jan 2018 04:07:51: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 12 Jan 2018 04:07:51: #1 tag size is determined as 51 bps INFO @ Fri, 12 Jan 2018 04:07:51: #1 tag size = 51 INFO @ Fri, 12 Jan 2018 04:07:51: #1 total tags in treatment: 25648325 INFO @ Fri, 12 Jan 2018 04:07:51: #1 user defined the maximum tags... INFO @ Fri, 12 Jan 2018 04:07:51: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 12 Jan 2018 04:07:53: #1 tags after filtering in treatment: 25648170 INFO @ Fri, 12 Jan 2018 04:07:53: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 12 Jan 2018 04:07:53: #1 finished! INFO @ Fri, 12 Jan 2018 04:07:53: #2 Build Peak Model... INFO @ Fri, 12 Jan 2018 04:07:53: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 12 Jan 2018 04:07:54: #1 tag size is determined as 51 bps INFO @ Fri, 12 Jan 2018 04:07:54: #1 tag size = 51 INFO @ Fri, 12 Jan 2018 04:07:54: #1 total tags in treatment: 25648325 INFO @ Fri, 12 Jan 2018 04:07:54: #1 user defined the maximum tags... INFO @ Fri, 12 Jan 2018 04:07:54: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 12 Jan 2018 04:07:55: #1 tags after filtering in treatment: 25648170 INFO @ Fri, 12 Jan 2018 04:07:55: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 12 Jan 2018 04:07:55: #1 finished! INFO @ Fri, 12 Jan 2018 04:07:55: #2 Build Peak Model... INFO @ Fri, 12 Jan 2018 04:07:55: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 12 Jan 2018 04:07:59: #2 number of paired peaks: 44437 INFO @ Fri, 12 Jan 2018 04:07:59: start model_add_line... INFO @ Fri, 12 Jan 2018 04:08:00: start X-correlation... INFO @ Fri, 12 Jan 2018 04:08:00: end of X-cor INFO @ Fri, 12 Jan 2018 04:08:00: #2 finished! INFO @ Fri, 12 Jan 2018 04:08:00: #2 predicted fragment length is 101 bps INFO @ Fri, 12 Jan 2018 04:08:00: #2 alternative fragment length(s) may be 101,296 bps INFO @ Fri, 12 Jan 2018 04:08:00: #2.2 Generate R script for model : SRX3398846.05_model.r WARNING @ Fri, 12 Jan 2018 04:08:00: #2 Since the d (101) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 12 Jan 2018 04:08:00: #2 You may need to consider one of the other alternative d(s): 101,296 WARNING @ Fri, 12 Jan 2018 04:08:00: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Fri, 12 Jan 2018 04:08:00: #3 Call peaks... INFO @ Fri, 12 Jan 2018 04:08:00: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 12 Jan 2018 04:08:01: #2 number of paired peaks: 44437 INFO @ Fri, 12 Jan 2018 04:08:01: start model_add_line... INFO @ Fri, 12 Jan 2018 04:08:02: start X-correlation... INFO @ Fri, 12 Jan 2018 04:08:02: end of X-cor INFO @ Fri, 12 Jan 2018 04:08:02: #2 finished! INFO @ Fri, 12 Jan 2018 04:08:02: #2 predicted fragment length is 101 bps INFO @ Fri, 12 Jan 2018 04:08:02: #2 alternative fragment length(s) may be 101,296 bps INFO @ Fri, 12 Jan 2018 04:08:02: #2.2 Generate R script for model : SRX3398846.20_model.r WARNING @ Fri, 12 Jan 2018 04:08:02: #2 Since the d (101) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 12 Jan 2018 04:08:02: #2 You may need to consider one of the other alternative d(s): 101,296 WARNING @ Fri, 12 Jan 2018 04:08:02: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Fri, 12 Jan 2018 04:08:02: #3 Call peaks... INFO @ Fri, 12 Jan 2018 04:08:02: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 12 Jan 2018 04:08:03: #2 number of paired peaks: 44437 INFO @ Fri, 12 Jan 2018 04:08:03: start model_add_line... INFO @ Fri, 12 Jan 2018 04:08:04: start X-correlation... INFO @ Fri, 12 Jan 2018 04:08:04: end of X-cor INFO @ Fri, 12 Jan 2018 04:08:04: #2 finished! INFO @ Fri, 12 Jan 2018 04:08:04: #2 predicted fragment length is 101 bps INFO @ Fri, 12 Jan 2018 04:08:04: #2 alternative fragment length(s) may be 101,296 bps INFO @ Fri, 12 Jan 2018 04:08:04: #2.2 Generate R script for model : SRX3398846.10_model.r WARNING @ Fri, 12 Jan 2018 04:08:04: #2 Since the d (101) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 12 Jan 2018 04:08:04: #2 You may need to consider one of the other alternative d(s): 101,296 WARNING @ Fri, 12 Jan 2018 04:08:04: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Fri, 12 Jan 2018 04:08:04: #3 Call peaks... INFO @ Fri, 12 Jan 2018 04:08:04: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 12 Jan 2018 04:10:12: #3 Call peaks for each chromosome... INFO @ Fri, 12 Jan 2018 04:10:12: #3 Call peaks for each chromosome... INFO @ Fri, 12 Jan 2018 04:10:20: #3 Call peaks for each chromosome... INFO @ Fri, 12 Jan 2018 04:11:24: #4 Write output xls file... SRX3398846.05_peaks.xls INFO @ Fri, 12 Jan 2018 04:11:24: #4 Write peak in narrowPeak format file... SRX3398846.05_peaks.narrowPeak INFO @ Fri, 12 Jan 2018 04:11:24: #4 Write summits bed file... SRX3398846.05_summits.bed INFO @ Fri, 12 Jan 2018 04:11:24: Done! pass1 - making usageList (49 chroms): 0 millis pass2 - checking and writing primary data (694 records, 4 fields): 5 millis CompletedMACS2peakCalling INFO @ Fri, 12 Jan 2018 04:11:29: #4 Write output xls file... SRX3398846.20_peaks.xls INFO @ Fri, 12 Jan 2018 04:11:29: #4 Write peak in narrowPeak format file... SRX3398846.20_peaks.narrowPeak INFO @ Fri, 12 Jan 2018 04:11:29: #4 Write summits bed file... SRX3398846.20_summits.bed INFO @ Fri, 12 Jan 2018 04:11:29: Done! pass1 - making usageList (18 chroms): 1 millis pass2 - checking and writing primary data (50 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Fri, 12 Jan 2018 04:11:34: #4 Write output xls file... SRX3398846.10_peaks.xls INFO @ Fri, 12 Jan 2018 04:11:34: #4 Write peak in narrowPeak format file... SRX3398846.10_peaks.narrowPeak INFO @ Fri, 12 Jan 2018 04:11:34: #4 Write summits bed file... SRX3398846.10_summits.bed INFO @ Fri, 12 Jan 2018 04:11:34: Done! pass1 - making usageList (32 chroms): 1 millis pass2 - checking and writing primary data (213 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。