Job ID = 10325495 sra ファイルのダウンロード中... Completed: 783070K bytes transferred in 35 seconds (178497K 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 28792879 spots for /home/okishinya/chipatlas/results/rn6/SRX3398845/SRR6297866.sra Written 28792879 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: 00:00:01 Multiseed full-index search: 00:54:49 28792879 reads; of these: 28792879 (100.00%) were unpaired; of these: 1130156 (3.93%) aligned 0 times 21985044 (76.36%) aligned exactly 1 time 5677679 (19.72%) aligned >1 times 96.07% overall alignment rate Time searching: 00:54:54 Overall time: 00:54:54 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] 2486860 / 27662723 = 0.0899 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 03:54:01: # Command line: callpeak -t SRX3398845.bam -f BAM -g 2.15e9 -n SRX3398845.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX3398845.05 # format = BAM # ChIP-seq file = ['SRX3398845.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 03:54:01: #1 read tag files... INFO @ Fri, 12 Jan 2018 03:54:01: #1 read treatment tags... INFO @ Fri, 12 Jan 2018 03:54:01: # Command line: callpeak -t SRX3398845.bam -f BAM -g 2.15e9 -n SRX3398845.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX3398845.20 # format = BAM # ChIP-seq file = ['SRX3398845.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 03:54:01: #1 read tag files... INFO @ Fri, 12 Jan 2018 03:54:01: #1 read treatment tags... INFO @ Fri, 12 Jan 2018 03:54:01: # Command line: callpeak -t SRX3398845.bam -f BAM -g 2.15e9 -n SRX3398845.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX3398845.10 # format = BAM # ChIP-seq file = ['SRX3398845.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 03:54:01: #1 read tag files... INFO @ Fri, 12 Jan 2018 03:54:01: #1 read treatment tags... INFO @ Fri, 12 Jan 2018 03:54:16: 1000000 INFO @ Fri, 12 Jan 2018 03:54:16: 1000000 INFO @ Fri, 12 Jan 2018 03:54:17: 1000000 INFO @ Fri, 12 Jan 2018 03:54:31: 2000000 INFO @ Fri, 12 Jan 2018 03:54:32: 2000000 INFO @ Fri, 12 Jan 2018 03:54:34: 2000000 INFO @ Fri, 12 Jan 2018 03:54:46: 3000000 INFO @ Fri, 12 Jan 2018 03:54:48: 3000000 INFO @ Fri, 12 Jan 2018 03:54:50: 3000000 INFO @ Fri, 12 Jan 2018 03:55:02: 4000000 INFO @ Fri, 12 Jan 2018 03:55:03: 4000000 INFO @ Fri, 12 Jan 2018 03:55:07: 4000000 INFO @ Fri, 12 Jan 2018 03:55:17: 5000000 INFO @ Fri, 12 Jan 2018 03:55:20: 5000000 INFO @ Fri, 12 Jan 2018 03:55:24: 5000000 INFO @ Fri, 12 Jan 2018 03:55:32: 6000000 INFO @ Fri, 12 Jan 2018 03:55:36: 6000000 INFO @ Fri, 12 Jan 2018 03:55:40: 6000000 INFO @ Fri, 12 Jan 2018 03:55:48: 7000000 INFO @ Fri, 12 Jan 2018 03:55:51: 7000000 INFO @ Fri, 12 Jan 2018 03:55:57: 7000000 INFO @ Fri, 12 Jan 2018 03:56:03: 8000000 INFO @ Fri, 12 Jan 2018 03:56:06: 8000000 INFO @ Fri, 12 Jan 2018 03:56:14: 8000000 INFO @ Fri, 12 Jan 2018 03:56:19: 9000000 INFO @ Fri, 12 Jan 2018 03:56:22: 9000000 INFO @ Fri, 12 Jan 2018 03:56:30: 9000000 INFO @ Fri, 12 Jan 2018 03:56:34: 10000000 INFO @ Fri, 12 Jan 2018 03:56:38: 10000000 INFO @ Fri, 12 Jan 2018 03:56:46: 10000000 INFO @ Fri, 12 Jan 2018 03:56:50: 11000000 INFO @ Fri, 12 Jan 2018 03:56:54: 11000000 INFO @ Fri, 12 Jan 2018 03:57:03: 11000000 INFO @ Fri, 12 Jan 2018 03:57:05: 12000000 INFO @ Fri, 12 Jan 2018 03:57:09: 12000000 INFO @ Fri, 12 Jan 2018 03:57:20: 12000000 INFO @ Fri, 12 Jan 2018 03:57:20: 13000000 INFO @ Fri, 12 Jan 2018 03:57:25: 13000000 INFO @ Fri, 12 Jan 2018 03:57:36: 14000000 INFO @ Fri, 12 Jan 2018 03:57:36: 13000000 INFO @ Fri, 12 Jan 2018 03:57:41: 14000000 INFO @ Fri, 12 Jan 2018 03:57:51: 15000000 INFO @ Fri, 12 Jan 2018 03:57:52: 14000000 INFO @ Fri, 12 Jan 2018 03:57:57: 15000000 INFO @ Fri, 12 Jan 2018 03:58:06: 16000000 INFO @ Fri, 12 Jan 2018 03:58:09: 15000000 INFO @ Fri, 12 Jan 2018 03:58:12: 16000000 INFO @ Fri, 12 Jan 2018 03:58:21: 17000000 INFO @ Fri, 12 Jan 2018 03:58:26: 16000000 INFO @ Fri, 12 Jan 2018 03:58:28: 17000000 INFO @ Fri, 12 Jan 2018 03:58:37: 18000000 INFO @ Fri, 12 Jan 2018 03:58:42: 17000000 INFO @ Fri, 12 Jan 2018 03:58:44: 18000000 INFO @ Fri, 12 Jan 2018 03:58:52: 19000000 INFO @ Fri, 12 Jan 2018 03:58:59: 18000000 INFO @ Fri, 12 Jan 2018 03:59:00: 19000000 INFO @ Fri, 12 Jan 2018 03:59:07: 20000000 INFO @ Fri, 12 Jan 2018 03:59:15: 20000000 INFO @ Fri, 12 Jan 2018 03:59:16: 19000000 INFO @ Fri, 12 Jan 2018 03:59:23: 21000000 INFO @ Fri, 12 Jan 2018 03:59:32: 21000000 INFO @ Fri, 12 Jan 2018 03:59:33: 20000000 INFO @ Fri, 12 Jan 2018 03:59:38: 22000000 INFO @ Fri, 12 Jan 2018 03:59:47: 22000000 INFO @ Fri, 12 Jan 2018 03:59:50: 21000000 INFO @ Fri, 12 Jan 2018 03:59:53: 23000000 INFO @ Fri, 12 Jan 2018 04:00:03: 23000000 INFO @ Fri, 12 Jan 2018 04:00:06: 22000000 INFO @ Fri, 12 Jan 2018 04:00:08: 24000000 INFO @ Fri, 12 Jan 2018 04:00:19: 24000000 INFO @ Fri, 12 Jan 2018 04:00:22: 23000000 INFO @ Fri, 12 Jan 2018 04:00:23: 25000000 INFO @ Fri, 12 Jan 2018 04:00:26: #1 tag size is determined as 51 bps INFO @ Fri, 12 Jan 2018 04:00:26: #1 tag size = 51 INFO @ Fri, 12 Jan 2018 04:00:26: #1 total tags in treatment: 25175863 INFO @ Fri, 12 Jan 2018 04:00:26: #1 user defined the maximum tags... INFO @ Fri, 12 Jan 2018 04:00:26: #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 04:00:28: #1 tags after filtering in treatment: 25175707 INFO @ Fri, 12 Jan 2018 04:00:28: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 12 Jan 2018 04:00:28: #1 finished! INFO @ Fri, 12 Jan 2018 04:00:28: #2 Build Peak Model... INFO @ Fri, 12 Jan 2018 04:00:28: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 12 Jan 2018 04:00:34: 25000000 INFO @ Fri, 12 Jan 2018 04:00:35: #2 number of paired peaks: 38369 INFO @ Fri, 12 Jan 2018 04:00:35: start model_add_line... INFO @ Fri, 12 Jan 2018 04:00:36: start X-correlation... INFO @ Fri, 12 Jan 2018 04:00:36: end of X-cor INFO @ Fri, 12 Jan 2018 04:00:36: #2 finished! INFO @ Fri, 12 Jan 2018 04:00:36: #2 predicted fragment length is 92 bps INFO @ Fri, 12 Jan 2018 04:00:36: #2 alternative fragment length(s) may be 92,293 bps INFO @ Fri, 12 Jan 2018 04:00:36: #2.2 Generate R script for model : SRX3398845.20_model.r WARNING @ Fri, 12 Jan 2018 04:00:36: #2 Since the d (92) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 12 Jan 2018 04:00:36: #2 You may need to consider one of the other alternative d(s): 92,293 WARNING @ Fri, 12 Jan 2018 04:00:36: #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 04:00:36: #3 Call peaks... INFO @ Fri, 12 Jan 2018 04:00:36: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 12 Jan 2018 04:00:37: #1 tag size is determined as 51 bps INFO @ Fri, 12 Jan 2018 04:00:37: #1 tag size = 51 INFO @ Fri, 12 Jan 2018 04:00:37: #1 total tags in treatment: 25175863 INFO @ Fri, 12 Jan 2018 04:00:37: #1 user defined the maximum tags... INFO @ Fri, 12 Jan 2018 04:00:37: #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 04:00:38: 24000000 INFO @ Fri, 12 Jan 2018 04:00:39: #1 tags after filtering in treatment: 25175707 INFO @ Fri, 12 Jan 2018 04:00:39: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 12 Jan 2018 04:00:39: #1 finished! INFO @ Fri, 12 Jan 2018 04:00:39: #2 Build Peak Model... INFO @ Fri, 12 Jan 2018 04:00:39: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 12 Jan 2018 04:00:46: #2 number of paired peaks: 38369 INFO @ Fri, 12 Jan 2018 04:00:46: start model_add_line... INFO @ Fri, 12 Jan 2018 04:00:47: start X-correlation... INFO @ Fri, 12 Jan 2018 04:00:47: end of X-cor INFO @ Fri, 12 Jan 2018 04:00:47: #2 finished! INFO @ Fri, 12 Jan 2018 04:00:47: #2 predicted fragment length is 92 bps INFO @ Fri, 12 Jan 2018 04:00:47: #2 alternative fragment length(s) may be 92,293 bps INFO @ Fri, 12 Jan 2018 04:00:47: #2.2 Generate R script for model : SRX3398845.05_model.r WARNING @ Fri, 12 Jan 2018 04:00:47: #2 Since the d (92) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 12 Jan 2018 04:00:47: #2 You may need to consider one of the other alternative d(s): 92,293 WARNING @ Fri, 12 Jan 2018 04:00:47: #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 04:00:47: #3 Call peaks... INFO @ Fri, 12 Jan 2018 04:00:47: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 12 Jan 2018 04:00:54: 25000000 INFO @ Fri, 12 Jan 2018 04:00:57: #1 tag size is determined as 51 bps INFO @ Fri, 12 Jan 2018 04:00:57: #1 tag size = 51 INFO @ Fri, 12 Jan 2018 04:00:57: #1 total tags in treatment: 25175863 INFO @ Fri, 12 Jan 2018 04:00:57: #1 user defined the maximum tags... INFO @ Fri, 12 Jan 2018 04:00:57: #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 04:00:59: #1 tags after filtering in treatment: 25175707 INFO @ Fri, 12 Jan 2018 04:00:59: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 12 Jan 2018 04:00:59: #1 finished! INFO @ Fri, 12 Jan 2018 04:00:59: #2 Build Peak Model... INFO @ Fri, 12 Jan 2018 04:00:59: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 12 Jan 2018 04:01:07: #2 number of paired peaks: 38369 INFO @ Fri, 12 Jan 2018 04:01:07: start model_add_line... INFO @ Fri, 12 Jan 2018 04:01:08: start X-correlation... INFO @ Fri, 12 Jan 2018 04:01:08: end of X-cor INFO @ Fri, 12 Jan 2018 04:01:08: #2 finished! INFO @ Fri, 12 Jan 2018 04:01:08: #2 predicted fragment length is 92 bps INFO @ Fri, 12 Jan 2018 04:01:08: #2 alternative fragment length(s) may be 92,293 bps INFO @ Fri, 12 Jan 2018 04:01:08: #2.2 Generate R script for model : SRX3398845.10_model.r WARNING @ Fri, 12 Jan 2018 04:01:08: #2 Since the d (92) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 12 Jan 2018 04:01:08: #2 You may need to consider one of the other alternative d(s): 92,293 WARNING @ Fri, 12 Jan 2018 04:01:08: #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 04:01:08: #3 Call peaks... INFO @ Fri, 12 Jan 2018 04:01:08: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 12 Jan 2018 04:02:41: #3 Call peaks for each chromosome... INFO @ Fri, 12 Jan 2018 04:02:58: #3 Call peaks for each chromosome... INFO @ Fri, 12 Jan 2018 04:03:07: #3 Call peaks for each chromosome... INFO @ Fri, 12 Jan 2018 04:03:46: #4 Write output xls file... SRX3398845.20_peaks.xls INFO @ Fri, 12 Jan 2018 04:03:46: #4 Write peak in narrowPeak format file... SRX3398845.20_peaks.narrowPeak INFO @ Fri, 12 Jan 2018 04:03:46: #4 Write summits bed file... SRX3398845.20_summits.bed INFO @ Fri, 12 Jan 2018 04:03:46: Done! pass1 - making usageList (17 chroms): 1 millis pass2 - checking and writing primary data (47 records, 4 fields): 15 millis CompletedMACS2peakCalling INFO @ Fri, 12 Jan 2018 04:04:07: #4 Write output xls file... SRX3398845.05_peaks.xls INFO @ Fri, 12 Jan 2018 04:04:07: #4 Write peak in narrowPeak format file... SRX3398845.05_peaks.narrowPeak INFO @ Fri, 12 Jan 2018 04:04:07: #4 Write summits bed file... SRX3398845.05_summits.bed INFO @ Fri, 12 Jan 2018 04:04:07: Done! pass1 - making usageList (43 chroms): 1 millis pass2 - checking and writing primary data (613 records, 4 fields): 4 millis CompletedMACS2peakCalling INFO @ Fri, 12 Jan 2018 04:04:22: #4 Write output xls file... SRX3398845.10_peaks.xls INFO @ Fri, 12 Jan 2018 04:04:22: #4 Write peak in narrowPeak format file... SRX3398845.10_peaks.narrowPeak INFO @ Fri, 12 Jan 2018 04:04:22: #4 Write summits bed file... SRX3398845.10_summits.bed INFO @ Fri, 12 Jan 2018 04:04:22: Done! pass1 - making usageList (26 chroms): 1 millis pass2 - checking and writing primary data (202 records, 4 fields): 4 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。