Job ID = 11388793 sra ファイルのダウンロード中... Completed: 911619K bytes transferred in 24 seconds (309322K 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... Read 36280065 spots for /home/okishinya/chipatlas/results/rn6/SRX2867571/SRR5627024.sra Written 36280065 spots for /home/okishinya/chipatlas/results/rn6/SRX2867571/SRR5627024.sra 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: 01:27:13 36280065 reads; of these: 36280065 (100.00%) were unpaired; of these: 1418878 (3.91%) aligned 0 times 25299953 (69.74%) aligned exactly 1 time 9561234 (26.35%) aligned >1 times 96.09% overall alignment rate Time searching: 01:27:19 Overall time: 01:27:19 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] 4962964 / 34861187 = 0.1424 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 @ Thu, 13 Dec 2018 00:28:22: # Command line: callpeak -t SRX2867571.bam -f BAM -g 2.15e9 -n SRX2867571.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX2867571.10 # format = BAM # ChIP-seq file = ['SRX2867571.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 @ Thu, 13 Dec 2018 00:28:22: #1 read tag files... INFO @ Thu, 13 Dec 2018 00:28:22: #1 read treatment tags... INFO @ Thu, 13 Dec 2018 00:28:22: # Command line: callpeak -t SRX2867571.bam -f BAM -g 2.15e9 -n SRX2867571.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX2867571.20 # format = BAM # ChIP-seq file = ['SRX2867571.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 @ Thu, 13 Dec 2018 00:28:22: #1 read tag files... INFO @ Thu, 13 Dec 2018 00:28:22: #1 read treatment tags... INFO @ Thu, 13 Dec 2018 00:28:22: # Command line: callpeak -t SRX2867571.bam -f BAM -g 2.15e9 -n SRX2867571.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX2867571.05 # format = BAM # ChIP-seq file = ['SRX2867571.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 @ Thu, 13 Dec 2018 00:28:22: #1 read tag files... INFO @ Thu, 13 Dec 2018 00:28:22: #1 read treatment tags... INFO @ Thu, 13 Dec 2018 00:28:35: 1000000 INFO @ Thu, 13 Dec 2018 00:28:35: 1000000 INFO @ Thu, 13 Dec 2018 00:28:36: 1000000 INFO @ Thu, 13 Dec 2018 00:28:48: 2000000 INFO @ Thu, 13 Dec 2018 00:28:48: 2000000 INFO @ Thu, 13 Dec 2018 00:28:50: 2000000 INFO @ Thu, 13 Dec 2018 00:28:59: 3000000 INFO @ Thu, 13 Dec 2018 00:29:00: 3000000 INFO @ Thu, 13 Dec 2018 00:29:05: 3000000 INFO @ Thu, 13 Dec 2018 00:29:10: 4000000 INFO @ Thu, 13 Dec 2018 00:29:11: 4000000 INFO @ Thu, 13 Dec 2018 00:29:17: 4000000 INFO @ Thu, 13 Dec 2018 00:29:22: 5000000 INFO @ Thu, 13 Dec 2018 00:29:22: 5000000 INFO @ Thu, 13 Dec 2018 00:29:29: 5000000 INFO @ Thu, 13 Dec 2018 00:29:31: 6000000 INFO @ Thu, 13 Dec 2018 00:29:33: 6000000 INFO @ Thu, 13 Dec 2018 00:29:41: 7000000 INFO @ Thu, 13 Dec 2018 00:29:42: 6000000 INFO @ Thu, 13 Dec 2018 00:29:45: 7000000 INFO @ Thu, 13 Dec 2018 00:29:50: 8000000 INFO @ Thu, 13 Dec 2018 00:29:54: 7000000 INFO @ Thu, 13 Dec 2018 00:29:56: 8000000 INFO @ Thu, 13 Dec 2018 00:29:59: 9000000 INFO @ Thu, 13 Dec 2018 00:30:06: 8000000 INFO @ Thu, 13 Dec 2018 00:30:08: 9000000 INFO @ Thu, 13 Dec 2018 00:30:08: 10000000 INFO @ Thu, 13 Dec 2018 00:30:18: 11000000 INFO @ Thu, 13 Dec 2018 00:30:19: 10000000 INFO @ Thu, 13 Dec 2018 00:30:20: 9000000 INFO @ Thu, 13 Dec 2018 00:30:27: 12000000 INFO @ Thu, 13 Dec 2018 00:30:30: 11000000 INFO @ Thu, 13 Dec 2018 00:30:35: 10000000 INFO @ Thu, 13 Dec 2018 00:30:37: 13000000 INFO @ Thu, 13 Dec 2018 00:30:42: 12000000 INFO @ Thu, 13 Dec 2018 00:30:46: 11000000 INFO @ Thu, 13 Dec 2018 00:30:46: 14000000 INFO @ Thu, 13 Dec 2018 00:30:53: 13000000 INFO @ Thu, 13 Dec 2018 00:30:56: 15000000 INFO @ Thu, 13 Dec 2018 00:30:57: 12000000 INFO @ Thu, 13 Dec 2018 00:31:06: 14000000 INFO @ Thu, 13 Dec 2018 00:31:09: 16000000 INFO @ Thu, 13 Dec 2018 00:31:10: 13000000 INFO @ Thu, 13 Dec 2018 00:31:18: 15000000 INFO @ Thu, 13 Dec 2018 00:31:23: 17000000 INFO @ Thu, 13 Dec 2018 00:31:24: 14000000 INFO @ Thu, 13 Dec 2018 00:31:31: 16000000 INFO @ Thu, 13 Dec 2018 00:31:37: 18000000 INFO @ Thu, 13 Dec 2018 00:31:37: 15000000 INFO @ Thu, 13 Dec 2018 00:31:43: 17000000 INFO @ Thu, 13 Dec 2018 00:31:49: 19000000 INFO @ Thu, 13 Dec 2018 00:31:50: 16000000 INFO @ Thu, 13 Dec 2018 00:31:56: 18000000 INFO @ Thu, 13 Dec 2018 00:32:01: 20000000 INFO @ Thu, 13 Dec 2018 00:32:03: 17000000 INFO @ Thu, 13 Dec 2018 00:32:08: 19000000 INFO @ Thu, 13 Dec 2018 00:32:14: 21000000 INFO @ Thu, 13 Dec 2018 00:32:16: 18000000 INFO @ Thu, 13 Dec 2018 00:32:21: 20000000 INFO @ Thu, 13 Dec 2018 00:32:25: 22000000 INFO @ Thu, 13 Dec 2018 00:32:28: 19000000 INFO @ Thu, 13 Dec 2018 00:32:33: 21000000 INFO @ Thu, 13 Dec 2018 00:32:35: 23000000 INFO @ Thu, 13 Dec 2018 00:32:39: 20000000 INFO @ Thu, 13 Dec 2018 00:32:44: 24000000 INFO @ Thu, 13 Dec 2018 00:32:44: 22000000 INFO @ Thu, 13 Dec 2018 00:32:49: 21000000 INFO @ Thu, 13 Dec 2018 00:32:54: 25000000 INFO @ Thu, 13 Dec 2018 00:32:54: 23000000 INFO @ Thu, 13 Dec 2018 00:33:00: 22000000 INFO @ Thu, 13 Dec 2018 00:33:04: 24000000 INFO @ Thu, 13 Dec 2018 00:33:04: 26000000 INFO @ Thu, 13 Dec 2018 00:33:11: 23000000 INFO @ Thu, 13 Dec 2018 00:33:14: 25000000 INFO @ Thu, 13 Dec 2018 00:33:15: 27000000 INFO @ Thu, 13 Dec 2018 00:33:24: 26000000 INFO @ Thu, 13 Dec 2018 00:33:25: 28000000 INFO @ Thu, 13 Dec 2018 00:33:25: 24000000 INFO @ Thu, 13 Dec 2018 00:33:34: 29000000 INFO @ Thu, 13 Dec 2018 00:33:34: 27000000 INFO @ Thu, 13 Dec 2018 00:33:37: 25000000 INFO @ Thu, 13 Dec 2018 00:33:43: #1 tag size is determined as 76 bps INFO @ Thu, 13 Dec 2018 00:33:43: #1 tag size = 76 INFO @ Thu, 13 Dec 2018 00:33:43: #1 total tags in treatment: 29898223 INFO @ Thu, 13 Dec 2018 00:33:43: #1 user defined the maximum tags... INFO @ Thu, 13 Dec 2018 00:33:43: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Thu, 13 Dec 2018 00:33:44: #1 tags after filtering in treatment: 29898131 INFO @ Thu, 13 Dec 2018 00:33:44: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 13 Dec 2018 00:33:44: #1 finished! INFO @ Thu, 13 Dec 2018 00:33:44: #2 Build Peak Model... INFO @ Thu, 13 Dec 2018 00:33:44: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 13 Dec 2018 00:33:45: 28000000 INFO @ Thu, 13 Dec 2018 00:33:47: #2 number of paired peaks: 6734 INFO @ Thu, 13 Dec 2018 00:33:47: start model_add_line... INFO @ Thu, 13 Dec 2018 00:33:48: start X-correlation... INFO @ Thu, 13 Dec 2018 00:33:48: end of X-cor INFO @ Thu, 13 Dec 2018 00:33:48: #2 finished! INFO @ Thu, 13 Dec 2018 00:33:48: #2 predicted fragment length is 78 bps INFO @ Thu, 13 Dec 2018 00:33:48: #2 alternative fragment length(s) may be 78 bps INFO @ Thu, 13 Dec 2018 00:33:48: #2.2 Generate R script for model : SRX2867571.10_model.r WARNING @ Thu, 13 Dec 2018 00:33:48: #2 Since the d (78) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 13 Dec 2018 00:33:48: #2 You may need to consider one of the other alternative d(s): 78 WARNING @ Thu, 13 Dec 2018 00:33:48: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Thu, 13 Dec 2018 00:33:48: #3 Call peaks... INFO @ Thu, 13 Dec 2018 00:33:48: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 13 Dec 2018 00:33:48: 26000000 INFO @ Thu, 13 Dec 2018 00:33:56: 29000000 INFO @ Thu, 13 Dec 2018 00:33:59: 27000000 INFO @ Thu, 13 Dec 2018 00:34:06: #1 tag size is determined as 76 bps INFO @ Thu, 13 Dec 2018 00:34:06: #1 tag size = 76 INFO @ Thu, 13 Dec 2018 00:34:06: #1 total tags in treatment: 29898223 INFO @ Thu, 13 Dec 2018 00:34:06: #1 user defined the maximum tags... INFO @ Thu, 13 Dec 2018 00:34:06: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Thu, 13 Dec 2018 00:34:07: #1 tags after filtering in treatment: 29898131 INFO @ Thu, 13 Dec 2018 00:34:07: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 13 Dec 2018 00:34:07: #1 finished! INFO @ Thu, 13 Dec 2018 00:34:07: #2 Build Peak Model... INFO @ Thu, 13 Dec 2018 00:34:07: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 13 Dec 2018 00:34:09: 28000000 INFO @ Thu, 13 Dec 2018 00:34:11: #2 number of paired peaks: 6734 INFO @ Thu, 13 Dec 2018 00:34:11: start model_add_line... INFO @ Thu, 13 Dec 2018 00:34:12: start X-correlation... INFO @ Thu, 13 Dec 2018 00:34:12: end of X-cor INFO @ Thu, 13 Dec 2018 00:34:12: #2 finished! INFO @ Thu, 13 Dec 2018 00:34:12: #2 predicted fragment length is 78 bps INFO @ Thu, 13 Dec 2018 00:34:12: #2 alternative fragment length(s) may be 78 bps INFO @ Thu, 13 Dec 2018 00:34:12: #2.2 Generate R script for model : SRX2867571.05_model.r WARNING @ Thu, 13 Dec 2018 00:34:12: #2 Since the d (78) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 13 Dec 2018 00:34:12: #2 You may need to consider one of the other alternative d(s): 78 WARNING @ Thu, 13 Dec 2018 00:34:12: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Thu, 13 Dec 2018 00:34:12: #3 Call peaks... INFO @ Thu, 13 Dec 2018 00:34:12: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 13 Dec 2018 00:34:18: 29000000 INFO @ Thu, 13 Dec 2018 00:34:26: #1 tag size is determined as 76 bps INFO @ Thu, 13 Dec 2018 00:34:26: #1 tag size = 76 INFO @ Thu, 13 Dec 2018 00:34:26: #1 total tags in treatment: 29898223 INFO @ Thu, 13 Dec 2018 00:34:26: #1 user defined the maximum tags... INFO @ Thu, 13 Dec 2018 00:34:26: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Thu, 13 Dec 2018 00:34:28: #1 tags after filtering in treatment: 29898131 INFO @ Thu, 13 Dec 2018 00:34:28: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 13 Dec 2018 00:34:28: #1 finished! INFO @ Thu, 13 Dec 2018 00:34:28: #2 Build Peak Model... INFO @ Thu, 13 Dec 2018 00:34:28: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 13 Dec 2018 00:34:31: #2 number of paired peaks: 6734 INFO @ Thu, 13 Dec 2018 00:34:31: start model_add_line... INFO @ Thu, 13 Dec 2018 00:34:32: start X-correlation... INFO @ Thu, 13 Dec 2018 00:34:32: end of X-cor INFO @ Thu, 13 Dec 2018 00:34:32: #2 finished! INFO @ Thu, 13 Dec 2018 00:34:32: #2 predicted fragment length is 78 bps INFO @ Thu, 13 Dec 2018 00:34:32: #2 alternative fragment length(s) may be 78 bps INFO @ Thu, 13 Dec 2018 00:34:32: #2.2 Generate R script for model : SRX2867571.20_model.r WARNING @ Thu, 13 Dec 2018 00:34:32: #2 Since the d (78) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 13 Dec 2018 00:34:32: #2 You may need to consider one of the other alternative d(s): 78 WARNING @ Thu, 13 Dec 2018 00:34:32: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Thu, 13 Dec 2018 00:34:32: #3 Call peaks... INFO @ Thu, 13 Dec 2018 00:34:32: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 13 Dec 2018 00:35:17: #3 Call peaks for each chromosome... INFO @ Thu, 13 Dec 2018 00:35:37: #3 Call peaks for each chromosome... INFO @ Thu, 13 Dec 2018 00:35:56: #3 Call peaks for each chromosome... INFO @ Thu, 13 Dec 2018 00:36:10: #4 Write output xls file... SRX2867571.10_peaks.xls INFO @ Thu, 13 Dec 2018 00:36:10: #4 Write peak in narrowPeak format file... SRX2867571.10_peaks.narrowPeak INFO @ Thu, 13 Dec 2018 00:36:10: #4 Write summits bed file... SRX2867571.10_summits.bed INFO @ Thu, 13 Dec 2018 00:36:10: Done! pass1 - making usageList (50 chroms): 2 millis pass2 - checking and writing primary data (1111 records, 4 fields): 9 millis CompletedMACS2peakCalling INFO @ Thu, 13 Dec 2018 00:36:25: #4 Write output xls file... SRX2867571.05_peaks.xls INFO @ Thu, 13 Dec 2018 00:36:25: #4 Write peak in narrowPeak format file... SRX2867571.05_peaks.narrowPeak INFO @ Thu, 13 Dec 2018 00:36:26: #4 Write summits bed file... SRX2867571.05_summits.bed INFO @ Thu, 13 Dec 2018 00:36:26: Done! pass1 - making usageList (64 chroms): 3 millis pass2 - checking and writing primary data (2212 records, 4 fields): 12 millis CompletedMACS2peakCalling INFO @ Thu, 13 Dec 2018 00:36:45: #4 Write output xls file... SRX2867571.20_peaks.xls INFO @ Thu, 13 Dec 2018 00:36:45: #4 Write peak in narrowPeak format file... SRX2867571.20_peaks.narrowPeak INFO @ Thu, 13 Dec 2018 00:36:45: #4 Write summits bed file... SRX2867571.20_summits.bed INFO @ Thu, 13 Dec 2018 00:36:45: Done! pass1 - making usageList (39 chroms): 2 millis pass2 - checking and writing primary data (530 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。