Job ID = 10325499 sra ファイルのダウンロード中... Completed: 486202K bytes transferred in 24 seconds (160419K 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 30080399 spots for /home/okishinya/chipatlas/results/rn6/SRX3398848/SRR6297869.sra Written 30080399 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: 00:00:01 Time loading forward index: 00:00:03 Time loading mirror index: 00:00:02 Multiseed full-index search: 00:58:23 30080399 reads; of these: 30080399 (100.00%) were unpaired; of these: 2495677 (8.30%) aligned 0 times 19712074 (65.53%) aligned exactly 1 time 7872648 (26.17%) aligned >1 times 91.70% overall alignment rate Time searching: 00:58:29 Overall time: 00:58:29 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] 2551739 / 27584722 = 0.0925 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 03:59:03: # Command line: callpeak -t SRX3398848.bam -f BAM -g 2.15e9 -n SRX3398848.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX3398848.20 # format = BAM # ChIP-seq file = ['SRX3398848.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 03:59:03: #1 read tag files... INFO @ Fri, 12 Jan 2018 03:59:03: #1 read treatment tags... INFO @ Fri, 12 Jan 2018 03:59:03: # Command line: callpeak -t SRX3398848.bam -f BAM -g 2.15e9 -n SRX3398848.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX3398848.10 # format = BAM # ChIP-seq file = ['SRX3398848.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 03:59:03: #1 read tag files... INFO @ Fri, 12 Jan 2018 03:59:03: #1 read treatment tags... INFO @ Fri, 12 Jan 2018 03:59:03: # Command line: callpeak -t SRX3398848.bam -f BAM -g 2.15e9 -n SRX3398848.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX3398848.05 # format = BAM # ChIP-seq file = ['SRX3398848.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 03:59:03: #1 read tag files... INFO @ Fri, 12 Jan 2018 03:59:03: #1 read treatment tags... INFO @ Fri, 12 Jan 2018 03:59:19: 1000000 INFO @ Fri, 12 Jan 2018 03:59:20: 1000000 INFO @ Fri, 12 Jan 2018 03:59:20: 1000000 INFO @ Fri, 12 Jan 2018 03:59:36: 2000000 INFO @ Fri, 12 Jan 2018 03:59:37: 2000000 INFO @ Fri, 12 Jan 2018 03:59:39: 2000000 INFO @ Fri, 12 Jan 2018 03:59:51: 3000000 INFO @ Fri, 12 Jan 2018 03:59:52: 3000000 INFO @ Fri, 12 Jan 2018 03:59:55: 3000000 INFO @ Fri, 12 Jan 2018 04:00:06: 4000000 INFO @ Fri, 12 Jan 2018 04:00:07: 4000000 INFO @ Fri, 12 Jan 2018 04:00:10: 4000000 INFO @ Fri, 12 Jan 2018 04:00:21: 5000000 INFO @ Fri, 12 Jan 2018 04:00:21: 5000000 INFO @ Fri, 12 Jan 2018 04:00:24: 5000000 INFO @ Fri, 12 Jan 2018 04:00:36: 6000000 INFO @ Fri, 12 Jan 2018 04:00:36: 6000000 INFO @ Fri, 12 Jan 2018 04:00:38: 6000000 INFO @ Fri, 12 Jan 2018 04:00:50: 7000000 INFO @ Fri, 12 Jan 2018 04:00:50: 7000000 INFO @ Fri, 12 Jan 2018 04:00:53: 7000000 INFO @ Fri, 12 Jan 2018 04:01:04: 8000000 INFO @ Fri, 12 Jan 2018 04:01:05: 8000000 INFO @ Fri, 12 Jan 2018 04:01:08: 8000000 INFO @ Fri, 12 Jan 2018 04:01:19: 9000000 INFO @ Fri, 12 Jan 2018 04:01:20: 9000000 INFO @ Fri, 12 Jan 2018 04:01:22: 9000000 INFO @ Fri, 12 Jan 2018 04:01:34: 10000000 INFO @ Fri, 12 Jan 2018 04:01:35: 10000000 INFO @ Fri, 12 Jan 2018 04:01:36: 10000000 INFO @ Fri, 12 Jan 2018 04:01:49: 11000000 INFO @ Fri, 12 Jan 2018 04:01:50: 11000000 INFO @ Fri, 12 Jan 2018 04:01:51: 11000000 INFO @ Fri, 12 Jan 2018 04:02:06: 12000000 INFO @ Fri, 12 Jan 2018 04:02:08: 12000000 INFO @ Fri, 12 Jan 2018 04:02:08: 12000000 INFO @ Fri, 12 Jan 2018 04:02:23: 13000000 INFO @ Fri, 12 Jan 2018 04:02:24: 13000000 INFO @ Fri, 12 Jan 2018 04:02:25: 13000000 INFO @ Fri, 12 Jan 2018 04:02:38: 14000000 INFO @ Fri, 12 Jan 2018 04:02:38: 14000000 INFO @ Fri, 12 Jan 2018 04:02:39: 14000000 INFO @ Fri, 12 Jan 2018 04:02:52: 15000000 INFO @ Fri, 12 Jan 2018 04:02:52: 15000000 INFO @ Fri, 12 Jan 2018 04:02:53: 15000000 INFO @ Fri, 12 Jan 2018 04:03:06: 16000000 INFO @ Fri, 12 Jan 2018 04:03:06: 16000000 INFO @ Fri, 12 Jan 2018 04:03:08: 16000000 INFO @ Fri, 12 Jan 2018 04:03:20: 17000000 INFO @ Fri, 12 Jan 2018 04:03:20: 17000000 INFO @ Fri, 12 Jan 2018 04:03:22: 17000000 INFO @ Fri, 12 Jan 2018 04:03:35: 18000000 INFO @ Fri, 12 Jan 2018 04:03:35: 18000000 INFO @ Fri, 12 Jan 2018 04:03:36: 18000000 INFO @ Fri, 12 Jan 2018 04:03:49: 19000000 INFO @ Fri, 12 Jan 2018 04:03:49: 19000000 INFO @ Fri, 12 Jan 2018 04:03:50: 19000000 INFO @ Fri, 12 Jan 2018 04:04:03: 20000000 INFO @ Fri, 12 Jan 2018 04:04:04: 20000000 INFO @ Fri, 12 Jan 2018 04:04:05: 20000000 INFO @ Fri, 12 Jan 2018 04:04:17: 21000000 INFO @ Fri, 12 Jan 2018 04:04:18: 21000000 INFO @ Fri, 12 Jan 2018 04:04:18: 21000000 INFO @ Fri, 12 Jan 2018 04:04:33: 22000000 INFO @ Fri, 12 Jan 2018 04:04:34: 22000000 INFO @ Fri, 12 Jan 2018 04:04:35: 22000000 INFO @ Fri, 12 Jan 2018 04:04:50: 23000000 INFO @ Fri, 12 Jan 2018 04:04:50: 23000000 INFO @ Fri, 12 Jan 2018 04:04:53: 23000000 INFO @ Fri, 12 Jan 2018 04:05:07: 24000000 INFO @ Fri, 12 Jan 2018 04:05:08: 24000000 INFO @ Fri, 12 Jan 2018 04:05:11: 24000000 INFO @ Fri, 12 Jan 2018 04:05:24: 25000000 INFO @ Fri, 12 Jan 2018 04:05:24: #1 tag size is determined as 51 bps INFO @ Fri, 12 Jan 2018 04:05:24: #1 tag size = 51 INFO @ Fri, 12 Jan 2018 04:05:24: #1 total tags in treatment: 25032983 INFO @ Fri, 12 Jan 2018 04:05:24: #1 user defined the maximum tags... INFO @ Fri, 12 Jan 2018 04:05:24: #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 04:05:25: 25000000 INFO @ Fri, 12 Jan 2018 04:05:26: #1 tags after filtering in treatment: 25032876 INFO @ Fri, 12 Jan 2018 04:05:26: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 12 Jan 2018 04:05:26: #1 finished! INFO @ Fri, 12 Jan 2018 04:05:26: #2 Build Peak Model... INFO @ Fri, 12 Jan 2018 04:05:26: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 12 Jan 2018 04:05:26: #1 tag size is determined as 51 bps INFO @ Fri, 12 Jan 2018 04:05:26: #1 tag size = 51 INFO @ Fri, 12 Jan 2018 04:05:26: #1 total tags in treatment: 25032983 INFO @ Fri, 12 Jan 2018 04:05:26: #1 user defined the maximum tags... INFO @ Fri, 12 Jan 2018 04:05:26: #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 04:05:28: 25000000 INFO @ Fri, 12 Jan 2018 04:05:28: #1 tags after filtering in treatment: 25032876 INFO @ Fri, 12 Jan 2018 04:05:28: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 12 Jan 2018 04:05:28: #1 finished! INFO @ Fri, 12 Jan 2018 04:05:28: #2 Build Peak Model... INFO @ Fri, 12 Jan 2018 04:05:28: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 12 Jan 2018 04:05:29: #1 tag size is determined as 51 bps INFO @ Fri, 12 Jan 2018 04:05:29: #1 tag size = 51 INFO @ Fri, 12 Jan 2018 04:05:29: #1 total tags in treatment: 25032983 INFO @ Fri, 12 Jan 2018 04:05:29: #1 user defined the maximum tags... INFO @ Fri, 12 Jan 2018 04:05:29: #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 04:05:30: #1 tags after filtering in treatment: 25032876 INFO @ Fri, 12 Jan 2018 04:05:30: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 12 Jan 2018 04:05:30: #1 finished! INFO @ Fri, 12 Jan 2018 04:05:30: #2 Build Peak Model... INFO @ Fri, 12 Jan 2018 04:05:30: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 12 Jan 2018 04:05:31: #2 number of paired peaks: 4682 INFO @ Fri, 12 Jan 2018 04:05:31: start model_add_line... INFO @ Fri, 12 Jan 2018 04:05:32: start X-correlation... INFO @ Fri, 12 Jan 2018 04:05:32: end of X-cor INFO @ Fri, 12 Jan 2018 04:05:32: #2 finished! INFO @ Fri, 12 Jan 2018 04:05:32: #2 predicted fragment length is 61 bps INFO @ Fri, 12 Jan 2018 04:05:32: #2 alternative fragment length(s) may be 61,419,519,574 bps INFO @ Fri, 12 Jan 2018 04:05:32: #2.2 Generate R script for model : SRX3398848.20_model.r WARNING @ Fri, 12 Jan 2018 04:05:32: #2 Since the d (61) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 12 Jan 2018 04:05:32: #2 You may need to consider one of the other alternative d(s): 61,419,519,574 WARNING @ Fri, 12 Jan 2018 04:05:32: #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 04:05:32: #3 Call peaks... INFO @ Fri, 12 Jan 2018 04:05:32: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 12 Jan 2018 04:05:33: #2 number of paired peaks: 4682 INFO @ Fri, 12 Jan 2018 04:05:33: start model_add_line... INFO @ Fri, 12 Jan 2018 04:05:34: start X-correlation... INFO @ Fri, 12 Jan 2018 04:05:34: end of X-cor INFO @ Fri, 12 Jan 2018 04:05:34: #2 finished! INFO @ Fri, 12 Jan 2018 04:05:34: #2 predicted fragment length is 61 bps INFO @ Fri, 12 Jan 2018 04:05:34: #2 alternative fragment length(s) may be 61,419,519,574 bps INFO @ Fri, 12 Jan 2018 04:05:34: #2.2 Generate R script for model : SRX3398848.05_model.r WARNING @ Fri, 12 Jan 2018 04:05:34: #2 Since the d (61) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 12 Jan 2018 04:05:34: #2 You may need to consider one of the other alternative d(s): 61,419,519,574 WARNING @ Fri, 12 Jan 2018 04:05:34: #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 04:05:34: #3 Call peaks... INFO @ Fri, 12 Jan 2018 04:05:34: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 12 Jan 2018 04:05:35: #2 number of paired peaks: 4682 INFO @ Fri, 12 Jan 2018 04:05:35: start model_add_line... INFO @ Fri, 12 Jan 2018 04:05:35: start X-correlation... INFO @ Fri, 12 Jan 2018 04:05:35: end of X-cor INFO @ Fri, 12 Jan 2018 04:05:35: #2 finished! INFO @ Fri, 12 Jan 2018 04:05:35: #2 predicted fragment length is 61 bps INFO @ Fri, 12 Jan 2018 04:05:35: #2 alternative fragment length(s) may be 61,419,519,574 bps INFO @ Fri, 12 Jan 2018 04:05:35: #2.2 Generate R script for model : SRX3398848.10_model.r WARNING @ Fri, 12 Jan 2018 04:05:35: #2 Since the d (61) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 12 Jan 2018 04:05:35: #2 You may need to consider one of the other alternative d(s): 61,419,519,574 WARNING @ Fri, 12 Jan 2018 04:05:35: #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 04:05:35: #3 Call peaks... INFO @ Fri, 12 Jan 2018 04:05:35: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 12 Jan 2018 04:07:36: #3 Call peaks for each chromosome... INFO @ Fri, 12 Jan 2018 04:07:46: #3 Call peaks for each chromosome... INFO @ Fri, 12 Jan 2018 04:07:48: #3 Call peaks for each chromosome... INFO @ Fri, 12 Jan 2018 04:08:49: #4 Write output xls file... SRX3398848.20_peaks.xls INFO @ Fri, 12 Jan 2018 04:08:49: #4 Write peak in narrowPeak format file... SRX3398848.20_peaks.narrowPeak INFO @ Fri, 12 Jan 2018 04:08:49: #4 Write summits bed file... SRX3398848.20_summits.bed INFO @ Fri, 12 Jan 2018 04:08:49: Done! pass1 - making usageList (24 chroms): 3 millis pass2 - checking and writing primary data (179 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Fri, 12 Jan 2018 04:08:55: #4 Write output xls file... SRX3398848.10_peaks.xls INFO @ Fri, 12 Jan 2018 04:08:55: #4 Write peak in narrowPeak format file... SRX3398848.10_peaks.narrowPeak INFO @ Fri, 12 Jan 2018 04:08:55: #4 Write summits bed file... SRX3398848.10_summits.bed INFO @ Fri, 12 Jan 2018 04:08:55: Done! pass1 - making usageList (36 chroms): 1 millis pass2 - checking and writing primary data (539 records, 4 fields): 5 millis CompletedMACS2peakCalling INFO @ Fri, 12 Jan 2018 04:08:57: #4 Write output xls file... SRX3398848.05_peaks.xls INFO @ Fri, 12 Jan 2018 04:08:57: #4 Write peak in narrowPeak format file... SRX3398848.05_peaks.narrowPeak INFO @ Fri, 12 Jan 2018 04:08:57: #4 Write summits bed file... SRX3398848.05_summits.bed INFO @ Fri, 12 Jan 2018 04:08:58: Done! pass1 - making usageList (48 chroms): 6 millis pass2 - checking and writing primary data (1143 records, 4 fields): 6 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。