Job ID = 10194730 sra ファイルのダウンロード中... Completed: 1258015K bytes transferred in 20 seconds (494219K bits/sec), in 1 file. Completed: 1227566K bytes transferred in 14 seconds (677779K 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 20724751 spots for /home/okishinya/chipatlas/results/rn6/SRX1056326/SRR2060194.sra Written 20724751 spots total Written 21551859 spots for /home/okishinya/chipatlas/results/rn6/SRX1056326/SRR2060193.sra Written 21551859 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 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: 02:30:33 42276610 reads; of these: 42276610 (100.00%) were unpaired; of these: 5539680 (13.10%) aligned 0 times 27439310 (64.90%) aligned exactly 1 time 9297620 (21.99%) aligned >1 times 86.90% overall alignment rate Time searching: 02:30:38 Overall time: 02:30:38 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 16 files... [bam_rmdupse_core] 6548963 / 36736930 = 0.1783 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, 10 Nov 2017 22:35:19: # Command line: callpeak -t SRX1056326.bam -f BAM -g 2.15e9 -n SRX1056326.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX1056326.05 # format = BAM # ChIP-seq file = ['SRX1056326.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, 10 Nov 2017 22:35:19: # Command line: callpeak -t SRX1056326.bam -f BAM -g 2.15e9 -n SRX1056326.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX1056326.20 # format = BAM # ChIP-seq file = ['SRX1056326.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, 10 Nov 2017 22:35:19: #1 read tag files... INFO @ Fri, 10 Nov 2017 22:35:19: #1 read tag files... INFO @ Fri, 10 Nov 2017 22:35:19: #1 read treatment tags... INFO @ Fri, 10 Nov 2017 22:35:19: #1 read treatment tags... INFO @ Fri, 10 Nov 2017 22:35:19: # Command line: callpeak -t SRX1056326.bam -f BAM -g 2.15e9 -n SRX1056326.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX1056326.10 # format = BAM # ChIP-seq file = ['SRX1056326.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, 10 Nov 2017 22:35:19: #1 read tag files... INFO @ Fri, 10 Nov 2017 22:35:19: #1 read treatment tags... INFO @ Fri, 10 Nov 2017 22:35:31: 1000000 INFO @ Fri, 10 Nov 2017 22:35:33: 1000000 INFO @ Fri, 10 Nov 2017 22:35:33: 1000000 INFO @ Fri, 10 Nov 2017 22:35:42: 2000000 INFO @ Fri, 10 Nov 2017 22:35:47: 2000000 INFO @ Fri, 10 Nov 2017 22:35:47: 2000000 INFO @ Fri, 10 Nov 2017 22:35:55: 3000000 INFO @ Fri, 10 Nov 2017 22:36:01: 3000000 INFO @ Fri, 10 Nov 2017 22:36:01: 3000000 INFO @ Fri, 10 Nov 2017 22:36:08: 4000000 INFO @ Fri, 10 Nov 2017 22:36:15: 4000000 INFO @ Fri, 10 Nov 2017 22:36:15: 4000000 INFO @ Fri, 10 Nov 2017 22:36:22: 5000000 INFO @ Fri, 10 Nov 2017 22:36:28: 5000000 INFO @ Fri, 10 Nov 2017 22:36:30: 5000000 INFO @ Fri, 10 Nov 2017 22:36:37: 6000000 INFO @ Fri, 10 Nov 2017 22:36:41: 6000000 INFO @ Fri, 10 Nov 2017 22:36:44: 6000000 INFO @ Fri, 10 Nov 2017 22:36:52: 7000000 INFO @ Fri, 10 Nov 2017 22:36:54: 7000000 INFO @ Fri, 10 Nov 2017 22:36:59: 7000000 INFO @ Fri, 10 Nov 2017 22:37:07: 8000000 INFO @ Fri, 10 Nov 2017 22:37:07: 8000000 INFO @ Fri, 10 Nov 2017 22:37:14: 8000000 INFO @ Fri, 10 Nov 2017 22:37:20: 9000000 INFO @ Fri, 10 Nov 2017 22:37:21: 9000000 INFO @ Fri, 10 Nov 2017 22:37:28: 9000000 INFO @ Fri, 10 Nov 2017 22:37:33: 10000000 INFO @ Fri, 10 Nov 2017 22:37:35: 10000000 INFO @ Fri, 10 Nov 2017 22:37:42: 10000000 INFO @ Fri, 10 Nov 2017 22:37:45: 11000000 INFO @ Fri, 10 Nov 2017 22:37:49: 11000000 INFO @ Fri, 10 Nov 2017 22:37:56: 11000000 INFO @ Fri, 10 Nov 2017 22:37:58: 12000000 INFO @ Fri, 10 Nov 2017 22:38:03: 12000000 INFO @ Fri, 10 Nov 2017 22:38:10: 12000000 INFO @ Fri, 10 Nov 2017 22:38:11: 13000000 INFO @ Fri, 10 Nov 2017 22:38:17: 13000000 INFO @ Fri, 10 Nov 2017 22:38:24: 14000000 INFO @ Fri, 10 Nov 2017 22:38:25: 13000000 INFO @ Fri, 10 Nov 2017 22:38:31: 14000000 INFO @ Fri, 10 Nov 2017 22:38:38: 15000000 INFO @ Fri, 10 Nov 2017 22:38:40: 14000000 INFO @ Fri, 10 Nov 2017 22:38:42: 15000000 INFO @ Fri, 10 Nov 2017 22:38:49: 16000000 INFO @ Fri, 10 Nov 2017 22:38:51: 15000000 INFO @ Fri, 10 Nov 2017 22:38:52: 16000000 INFO @ Fri, 10 Nov 2017 22:39:00: 17000000 INFO @ Fri, 10 Nov 2017 22:39:02: 16000000 INFO @ Fri, 10 Nov 2017 22:39:03: 17000000 INFO @ Fri, 10 Nov 2017 22:39:11: 18000000 INFO @ Fri, 10 Nov 2017 22:39:13: 17000000 INFO @ Fri, 10 Nov 2017 22:39:14: 18000000 INFO @ Fri, 10 Nov 2017 22:39:22: 19000000 INFO @ Fri, 10 Nov 2017 22:39:24: 18000000 INFO @ Fri, 10 Nov 2017 22:39:25: 19000000 INFO @ Fri, 10 Nov 2017 22:39:33: 20000000 INFO @ Fri, 10 Nov 2017 22:39:35: 19000000 INFO @ Fri, 10 Nov 2017 22:39:36: 20000000 INFO @ Fri, 10 Nov 2017 22:39:44: 21000000 INFO @ Fri, 10 Nov 2017 22:39:46: 20000000 INFO @ Fri, 10 Nov 2017 22:39:47: 21000000 INFO @ Fri, 10 Nov 2017 22:39:55: 22000000 INFO @ Fri, 10 Nov 2017 22:39:57: 21000000 INFO @ Fri, 10 Nov 2017 22:39:58: 22000000 INFO @ Fri, 10 Nov 2017 22:40:05: 23000000 INFO @ Fri, 10 Nov 2017 22:40:08: 22000000 INFO @ Fri, 10 Nov 2017 22:40:08: 23000000 INFO @ Fri, 10 Nov 2017 22:40:16: 24000000 INFO @ Fri, 10 Nov 2017 22:40:19: 23000000 INFO @ Fri, 10 Nov 2017 22:40:19: 24000000 INFO @ Fri, 10 Nov 2017 22:40:27: 25000000 INFO @ Fri, 10 Nov 2017 22:40:30: 24000000 INFO @ Fri, 10 Nov 2017 22:40:30: 25000000 INFO @ Fri, 10 Nov 2017 22:40:38: 26000000 INFO @ Fri, 10 Nov 2017 22:40:41: 25000000 INFO @ Fri, 10 Nov 2017 22:40:41: 26000000 INFO @ Fri, 10 Nov 2017 22:40:49: 27000000 INFO @ Fri, 10 Nov 2017 22:40:52: 27000000 INFO @ Fri, 10 Nov 2017 22:40:52: 26000000 INFO @ Fri, 10 Nov 2017 22:41:00: 28000000 INFO @ Fri, 10 Nov 2017 22:41:02: 28000000 INFO @ Fri, 10 Nov 2017 22:41:03: 27000000 INFO @ Fri, 10 Nov 2017 22:41:11: 29000000 INFO @ Fri, 10 Nov 2017 22:41:13: 29000000 INFO @ Fri, 10 Nov 2017 22:41:14: 28000000 INFO @ Fri, 10 Nov 2017 22:41:22: 30000000 INFO @ Fri, 10 Nov 2017 22:41:24: 30000000 INFO @ Fri, 10 Nov 2017 22:41:25: #1 tag size is determined as 100 bps INFO @ Fri, 10 Nov 2017 22:41:25: #1 tag size = 100 INFO @ Fri, 10 Nov 2017 22:41:25: #1 total tags in treatment: 30187967 INFO @ Fri, 10 Nov 2017 22:41:25: #1 user defined the maximum tags... INFO @ Fri, 10 Nov 2017 22:41:25: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 10 Nov 2017 22:41:25: 29000000 INFO @ Fri, 10 Nov 2017 22:41:26: #1 tags after filtering in treatment: 30187860 INFO @ Fri, 10 Nov 2017 22:41:26: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 10 Nov 2017 22:41:26: #1 finished! INFO @ Fri, 10 Nov 2017 22:41:26: #2 Build Peak Model... INFO @ Fri, 10 Nov 2017 22:41:26: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Nov 2017 22:41:27: #1 tag size is determined as 100 bps INFO @ Fri, 10 Nov 2017 22:41:27: #1 tag size = 100 INFO @ Fri, 10 Nov 2017 22:41:27: #1 total tags in treatment: 30187967 INFO @ Fri, 10 Nov 2017 22:41:27: #1 user defined the maximum tags... INFO @ Fri, 10 Nov 2017 22:41:27: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 10 Nov 2017 22:41:28: #1 tags after filtering in treatment: 30187860 INFO @ Fri, 10 Nov 2017 22:41:28: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 10 Nov 2017 22:41:28: #1 finished! INFO @ Fri, 10 Nov 2017 22:41:28: #2 Build Peak Model... INFO @ Fri, 10 Nov 2017 22:41:28: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Nov 2017 22:41:29: #2 number of paired peaks: 6249 INFO @ Fri, 10 Nov 2017 22:41:29: start model_add_line... INFO @ Fri, 10 Nov 2017 22:41:30: start X-correlation... INFO @ Fri, 10 Nov 2017 22:41:30: end of X-cor INFO @ Fri, 10 Nov 2017 22:41:30: #2 finished! INFO @ Fri, 10 Nov 2017 22:41:30: #2 predicted fragment length is 99 bps INFO @ Fri, 10 Nov 2017 22:41:30: #2 alternative fragment length(s) may be 99 bps INFO @ Fri, 10 Nov 2017 22:41:30: #2.2 Generate R script for model : SRX1056326.20_model.r WARNING @ Fri, 10 Nov 2017 22:41:30: #2 Since the d (99) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 10 Nov 2017 22:41:30: #2 You may need to consider one of the other alternative d(s): 99 WARNING @ Fri, 10 Nov 2017 22:41:30: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Fri, 10 Nov 2017 22:41:30: #3 Call peaks... INFO @ Fri, 10 Nov 2017 22:41:30: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 10 Nov 2017 22:41:31: #2 number of paired peaks: 6249 INFO @ Fri, 10 Nov 2017 22:41:31: start model_add_line... INFO @ Fri, 10 Nov 2017 22:41:32: start X-correlation... INFO @ Fri, 10 Nov 2017 22:41:32: end of X-cor INFO @ Fri, 10 Nov 2017 22:41:32: #2 finished! INFO @ Fri, 10 Nov 2017 22:41:32: #2 predicted fragment length is 99 bps INFO @ Fri, 10 Nov 2017 22:41:32: #2 alternative fragment length(s) may be 99 bps INFO @ Fri, 10 Nov 2017 22:41:32: #2.2 Generate R script for model : SRX1056326.05_model.r WARNING @ Fri, 10 Nov 2017 22:41:32: #2 Since the d (99) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 10 Nov 2017 22:41:32: #2 You may need to consider one of the other alternative d(s): 99 WARNING @ Fri, 10 Nov 2017 22:41:32: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Fri, 10 Nov 2017 22:41:32: #3 Call peaks... INFO @ Fri, 10 Nov 2017 22:41:32: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 10 Nov 2017 22:41:35: 30000000 INFO @ Fri, 10 Nov 2017 22:41:37: #1 tag size is determined as 100 bps INFO @ Fri, 10 Nov 2017 22:41:37: #1 tag size = 100 INFO @ Fri, 10 Nov 2017 22:41:37: #1 total tags in treatment: 30187967 INFO @ Fri, 10 Nov 2017 22:41:37: #1 user defined the maximum tags... INFO @ Fri, 10 Nov 2017 22:41:37: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 10 Nov 2017 22:41:38: #1 tags after filtering in treatment: 30187860 INFO @ Fri, 10 Nov 2017 22:41:38: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 10 Nov 2017 22:41:38: #1 finished! INFO @ Fri, 10 Nov 2017 22:41:38: #2 Build Peak Model... INFO @ Fri, 10 Nov 2017 22:41:38: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Nov 2017 22:41:42: #2 number of paired peaks: 6249 INFO @ Fri, 10 Nov 2017 22:41:42: start model_add_line... INFO @ Fri, 10 Nov 2017 22:41:42: start X-correlation... INFO @ Fri, 10 Nov 2017 22:41:42: end of X-cor INFO @ Fri, 10 Nov 2017 22:41:42: #2 finished! INFO @ Fri, 10 Nov 2017 22:41:42: #2 predicted fragment length is 99 bps INFO @ Fri, 10 Nov 2017 22:41:42: #2 alternative fragment length(s) may be 99 bps INFO @ Fri, 10 Nov 2017 22:41:42: #2.2 Generate R script for model : SRX1056326.10_model.r WARNING @ Fri, 10 Nov 2017 22:41:42: #2 Since the d (99) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 10 Nov 2017 22:41:42: #2 You may need to consider one of the other alternative d(s): 99 WARNING @ Fri, 10 Nov 2017 22:41:42: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Fri, 10 Nov 2017 22:41:42: #3 Call peaks... INFO @ Fri, 10 Nov 2017 22:41:42: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 10 Nov 2017 22:42:54: #3 Call peaks for each chromosome... INFO @ Fri, 10 Nov 2017 22:42:56: #3 Call peaks for each chromosome... INFO @ Fri, 10 Nov 2017 22:43:06: #3 Call peaks for each chromosome... INFO @ Fri, 10 Nov 2017 22:43:43: #4 Write output xls file... SRX1056326.20_peaks.xls INFO @ Fri, 10 Nov 2017 22:43:43: #4 Write peak in narrowPeak format file... SRX1056326.20_peaks.narrowPeak INFO @ Fri, 10 Nov 2017 22:43:43: #4 Write summits bed file... SRX1056326.20_summits.bed INFO @ Fri, 10 Nov 2017 22:43:43: Done! pass1 - making usageList (39 chroms): 2 millis pass2 - checking and writing primary data (556 records, 4 fields): 5 millis CompletedMACS2peakCalling INFO @ Fri, 10 Nov 2017 22:43:45: #4 Write output xls file... SRX1056326.05_peaks.xls INFO @ Fri, 10 Nov 2017 22:43:45: #4 Write peak in narrowPeak format file... SRX1056326.05_peaks.narrowPeak INFO @ Fri, 10 Nov 2017 22:43:45: #4 Write summits bed file... SRX1056326.05_summits.bed INFO @ Fri, 10 Nov 2017 22:43:45: Done! pass1 - making usageList (60 chroms): 2 millis pass2 - checking and writing primary data (1875 records, 4 fields): 10 millis CompletedMACS2peakCalling INFO @ Fri, 10 Nov 2017 22:43:53: #4 Write output xls file... SRX1056326.10_peaks.xls INFO @ Fri, 10 Nov 2017 22:43:53: #4 Write peak in narrowPeak format file... SRX1056326.10_peaks.narrowPeak INFO @ Fri, 10 Nov 2017 22:43:53: #4 Write summits bed file... SRX1056326.10_summits.bed INFO @ Fri, 10 Nov 2017 22:43:53: Done! pass1 - making usageList (47 chroms): 1 millis pass2 - checking and writing primary data (1027 records, 4 fields): 7 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。