Job ID = 10194938 sra ファイルのダウンロード中... Completed: 728671K bytes transferred in 11 seconds (518223K 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 33129818 spots for /home/okishinya/chipatlas/results/rn6/SRX2512948/SRR5197463.sra Written 33129818 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: 00:00:02 Time loading mirror index: 00:00:01 Multiseed full-index search: 00:29:50 33129818 reads; of these: 33129818 (100.00%) were unpaired; of these: 1710428 (5.16%) aligned 0 times 21466338 (64.79%) aligned exactly 1 time 9953052 (30.04%) aligned >1 times 94.84% overall alignment rate Time searching: 00:29:54 Overall time: 00:29:54 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 8 files... [bam_rmdupse_core] 1369077 / 31419390 = 0.0436 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 @ Sat, 11 Nov 2017 00:35:09: # Command line: callpeak -t SRX2512948.bam -f BAM -g 2.15e9 -n SRX2512948.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX2512948.20 # format = BAM # ChIP-seq file = ['SRX2512948.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 @ Sat, 11 Nov 2017 00:35:09: # Command line: callpeak -t SRX2512948.bam -f BAM -g 2.15e9 -n SRX2512948.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX2512948.05 # format = BAM # ChIP-seq file = ['SRX2512948.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 @ Sat, 11 Nov 2017 00:35:09: # Command line: callpeak -t SRX2512948.bam -f BAM -g 2.15e9 -n SRX2512948.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX2512948.10 # format = BAM # ChIP-seq file = ['SRX2512948.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 @ Sat, 11 Nov 2017 00:35:09: #1 read tag files... INFO @ Sat, 11 Nov 2017 00:35:09: #1 read tag files... INFO @ Sat, 11 Nov 2017 00:35:09: #1 read tag files... INFO @ Sat, 11 Nov 2017 00:35:09: #1 read treatment tags... INFO @ Sat, 11 Nov 2017 00:35:09: #1 read treatment tags... INFO @ Sat, 11 Nov 2017 00:35:09: #1 read treatment tags... INFO @ Sat, 11 Nov 2017 00:35:18: 1000000 INFO @ Sat, 11 Nov 2017 00:35:19: 1000000 INFO @ Sat, 11 Nov 2017 00:35:20: 1000000 INFO @ Sat, 11 Nov 2017 00:35:28: 2000000 INFO @ Sat, 11 Nov 2017 00:35:30: 2000000 INFO @ Sat, 11 Nov 2017 00:35:31: 2000000 INFO @ Sat, 11 Nov 2017 00:35:38: 3000000 INFO @ Sat, 11 Nov 2017 00:35:41: 3000000 INFO @ Sat, 11 Nov 2017 00:35:42: 3000000 INFO @ Sat, 11 Nov 2017 00:35:48: 4000000 INFO @ Sat, 11 Nov 2017 00:35:52: 4000000 INFO @ Sat, 11 Nov 2017 00:35:54: 4000000 INFO @ Sat, 11 Nov 2017 00:35:59: 5000000 INFO @ Sat, 11 Nov 2017 00:36:04: 5000000 INFO @ Sat, 11 Nov 2017 00:36:05: 5000000 INFO @ Sat, 11 Nov 2017 00:36:09: 6000000 INFO @ Sat, 11 Nov 2017 00:36:15: 6000000 INFO @ Sat, 11 Nov 2017 00:36:17: 6000000 INFO @ Sat, 11 Nov 2017 00:36:19: 7000000 INFO @ Sat, 11 Nov 2017 00:36:26: 7000000 INFO @ Sat, 11 Nov 2017 00:36:29: 7000000 INFO @ Sat, 11 Nov 2017 00:36:29: 8000000 INFO @ Sat, 11 Nov 2017 00:36:38: 8000000 INFO @ Sat, 11 Nov 2017 00:36:39: 9000000 INFO @ Sat, 11 Nov 2017 00:36:41: 8000000 INFO @ Sat, 11 Nov 2017 00:36:49: 9000000 INFO @ Sat, 11 Nov 2017 00:36:50: 10000000 INFO @ Sat, 11 Nov 2017 00:36:53: 9000000 INFO @ Sat, 11 Nov 2017 00:37:00: 11000000 INFO @ Sat, 11 Nov 2017 00:37:00: 10000000 INFO @ Sat, 11 Nov 2017 00:37:05: 10000000 INFO @ Sat, 11 Nov 2017 00:37:10: 12000000 INFO @ Sat, 11 Nov 2017 00:37:11: 11000000 INFO @ Sat, 11 Nov 2017 00:37:17: 11000000 INFO @ Sat, 11 Nov 2017 00:37:20: 13000000 INFO @ Sat, 11 Nov 2017 00:37:23: 12000000 INFO @ Sat, 11 Nov 2017 00:37:29: 12000000 INFO @ Sat, 11 Nov 2017 00:37:30: 14000000 INFO @ Sat, 11 Nov 2017 00:37:34: 13000000 INFO @ Sat, 11 Nov 2017 00:37:40: 15000000 INFO @ Sat, 11 Nov 2017 00:37:40: 13000000 INFO @ Sat, 11 Nov 2017 00:37:45: 14000000 INFO @ Sat, 11 Nov 2017 00:37:51: 16000000 INFO @ Sat, 11 Nov 2017 00:37:52: 14000000 INFO @ Sat, 11 Nov 2017 00:37:56: 15000000 INFO @ Sat, 11 Nov 2017 00:38:01: 17000000 INFO @ Sat, 11 Nov 2017 00:38:04: 15000000 INFO @ Sat, 11 Nov 2017 00:38:07: 16000000 INFO @ Sat, 11 Nov 2017 00:38:11: 18000000 INFO @ Sat, 11 Nov 2017 00:38:16: 16000000 INFO @ Sat, 11 Nov 2017 00:38:18: 17000000 INFO @ Sat, 11 Nov 2017 00:38:21: 19000000 INFO @ Sat, 11 Nov 2017 00:38:27: 17000000 INFO @ Sat, 11 Nov 2017 00:38:29: 18000000 INFO @ Sat, 11 Nov 2017 00:38:30: 20000000 INFO @ Sat, 11 Nov 2017 00:38:38: 18000000 INFO @ Sat, 11 Nov 2017 00:38:40: 19000000 INFO @ Sat, 11 Nov 2017 00:38:41: 21000000 INFO @ Sat, 11 Nov 2017 00:38:49: 19000000 INFO @ Sat, 11 Nov 2017 00:38:50: 22000000 INFO @ Sat, 11 Nov 2017 00:38:51: 20000000 INFO @ Sat, 11 Nov 2017 00:39:01: 20000000 INFO @ Sat, 11 Nov 2017 00:39:01: 23000000 INFO @ Sat, 11 Nov 2017 00:39:02: 21000000 INFO @ Sat, 11 Nov 2017 00:39:11: 24000000 INFO @ Sat, 11 Nov 2017 00:39:11: 21000000 INFO @ Sat, 11 Nov 2017 00:39:14: 22000000 INFO @ Sat, 11 Nov 2017 00:39:21: 25000000 INFO @ Sat, 11 Nov 2017 00:39:23: 22000000 INFO @ Sat, 11 Nov 2017 00:39:25: 23000000 INFO @ Sat, 11 Nov 2017 00:39:31: 26000000 INFO @ Sat, 11 Nov 2017 00:39:34: 23000000 INFO @ Sat, 11 Nov 2017 00:39:37: 24000000 INFO @ Sat, 11 Nov 2017 00:39:42: 27000000 INFO @ Sat, 11 Nov 2017 00:39:46: 24000000 INFO @ Sat, 11 Nov 2017 00:39:47: 25000000 INFO @ Sat, 11 Nov 2017 00:39:52: 28000000 INFO @ Sat, 11 Nov 2017 00:39:58: 25000000 INFO @ Sat, 11 Nov 2017 00:39:59: 26000000 INFO @ Sat, 11 Nov 2017 00:40:02: 29000000 INFO @ Sat, 11 Nov 2017 00:40:10: 26000000 INFO @ Sat, 11 Nov 2017 00:40:10: 27000000 INFO @ Sat, 11 Nov 2017 00:40:13: 30000000 INFO @ Sat, 11 Nov 2017 00:40:14: #1 tag size is determined as 36 bps INFO @ Sat, 11 Nov 2017 00:40:14: #1 tag size = 36 INFO @ Sat, 11 Nov 2017 00:40:14: #1 total tags in treatment: 30050313 INFO @ Sat, 11 Nov 2017 00:40:14: #1 user defined the maximum tags... INFO @ Sat, 11 Nov 2017 00:40:14: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 11 Nov 2017 00:40:15: #1 tags after filtering in treatment: 30050241 INFO @ Sat, 11 Nov 2017 00:40:15: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 11 Nov 2017 00:40:15: #1 finished! INFO @ Sat, 11 Nov 2017 00:40:15: #2 Build Peak Model... INFO @ Sat, 11 Nov 2017 00:40:15: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Nov 2017 00:40:18: #2 number of paired peaks: 6683 INFO @ Sat, 11 Nov 2017 00:40:18: start model_add_line... INFO @ Sat, 11 Nov 2017 00:40:19: start X-correlation... INFO @ Sat, 11 Nov 2017 00:40:19: end of X-cor INFO @ Sat, 11 Nov 2017 00:40:19: #2 finished! INFO @ Sat, 11 Nov 2017 00:40:19: #2 predicted fragment length is 36 bps INFO @ Sat, 11 Nov 2017 00:40:19: #2 alternative fragment length(s) may be 36,571 bps INFO @ Sat, 11 Nov 2017 00:40:19: #2.2 Generate R script for model : SRX2512948.20_model.r WARNING @ Sat, 11 Nov 2017 00:40:19: #2 Since the d (36) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 11 Nov 2017 00:40:19: #2 You may need to consider one of the other alternative d(s): 36,571 WARNING @ Sat, 11 Nov 2017 00:40:19: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sat, 11 Nov 2017 00:40:19: #3 Call peaks... INFO @ Sat, 11 Nov 2017 00:40:19: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Nov 2017 00:40:21: 28000000 INFO @ Sat, 11 Nov 2017 00:40:22: 27000000 INFO @ Sat, 11 Nov 2017 00:40:33: 29000000 INFO @ Sat, 11 Nov 2017 00:40:33: 28000000 INFO @ Sat, 11 Nov 2017 00:40:44: 30000000 INFO @ Sat, 11 Nov 2017 00:40:44: 29000000 INFO @ Sat, 11 Nov 2017 00:40:45: #1 tag size is determined as 36 bps INFO @ Sat, 11 Nov 2017 00:40:45: #1 tag size = 36 INFO @ Sat, 11 Nov 2017 00:40:45: #1 total tags in treatment: 30050313 INFO @ Sat, 11 Nov 2017 00:40:45: #1 user defined the maximum tags... INFO @ Sat, 11 Nov 2017 00:40:45: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 11 Nov 2017 00:40:46: #1 tags after filtering in treatment: 30050241 INFO @ Sat, 11 Nov 2017 00:40:46: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 11 Nov 2017 00:40:46: #1 finished! INFO @ Sat, 11 Nov 2017 00:40:46: #2 Build Peak Model... INFO @ Sat, 11 Nov 2017 00:40:46: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Nov 2017 00:40:49: #2 number of paired peaks: 6683 INFO @ Sat, 11 Nov 2017 00:40:49: start model_add_line... INFO @ Sat, 11 Nov 2017 00:40:50: start X-correlation... INFO @ Sat, 11 Nov 2017 00:40:50: end of X-cor INFO @ Sat, 11 Nov 2017 00:40:50: #2 finished! INFO @ Sat, 11 Nov 2017 00:40:50: #2 predicted fragment length is 36 bps INFO @ Sat, 11 Nov 2017 00:40:50: #2 alternative fragment length(s) may be 36,571 bps INFO @ Sat, 11 Nov 2017 00:40:50: #2.2 Generate R script for model : SRX2512948.05_model.r WARNING @ Sat, 11 Nov 2017 00:40:50: #2 Since the d (36) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 11 Nov 2017 00:40:50: #2 You may need to consider one of the other alternative d(s): 36,571 WARNING @ Sat, 11 Nov 2017 00:40:50: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sat, 11 Nov 2017 00:40:50: #3 Call peaks... INFO @ Sat, 11 Nov 2017 00:40:50: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Nov 2017 00:40:55: 30000000 INFO @ Sat, 11 Nov 2017 00:40:56: #1 tag size is determined as 36 bps INFO @ Sat, 11 Nov 2017 00:40:56: #1 tag size = 36 INFO @ Sat, 11 Nov 2017 00:40:56: #1 total tags in treatment: 30050313 INFO @ Sat, 11 Nov 2017 00:40:56: #1 user defined the maximum tags... INFO @ Sat, 11 Nov 2017 00:40:56: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 11 Nov 2017 00:40:57: #1 tags after filtering in treatment: 30050241 INFO @ Sat, 11 Nov 2017 00:40:57: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 11 Nov 2017 00:40:57: #1 finished! INFO @ Sat, 11 Nov 2017 00:40:57: #2 Build Peak Model... INFO @ Sat, 11 Nov 2017 00:40:57: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Nov 2017 00:41:01: #2 number of paired peaks: 6683 INFO @ Sat, 11 Nov 2017 00:41:01: start model_add_line... INFO @ Sat, 11 Nov 2017 00:41:01: start X-correlation... INFO @ Sat, 11 Nov 2017 00:41:01: end of X-cor INFO @ Sat, 11 Nov 2017 00:41:01: #2 finished! INFO @ Sat, 11 Nov 2017 00:41:01: #2 predicted fragment length is 36 bps INFO @ Sat, 11 Nov 2017 00:41:01: #2 alternative fragment length(s) may be 36,571 bps INFO @ Sat, 11 Nov 2017 00:41:01: #2.2 Generate R script for model : SRX2512948.10_model.r WARNING @ Sat, 11 Nov 2017 00:41:01: #2 Since the d (36) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 11 Nov 2017 00:41:01: #2 You may need to consider one of the other alternative d(s): 36,571 WARNING @ Sat, 11 Nov 2017 00:41:01: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sat, 11 Nov 2017 00:41:01: #3 Call peaks... INFO @ Sat, 11 Nov 2017 00:41:01: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Nov 2017 00:41:43: #3 Call peaks for each chromosome... INFO @ Sat, 11 Nov 2017 00:42:12: #3 Call peaks for each chromosome... INFO @ Sat, 11 Nov 2017 00:42:24: #3 Call peaks for each chromosome... INFO @ Sat, 11 Nov 2017 00:42:36: #4 Write output xls file... SRX2512948.20_peaks.xls INFO @ Sat, 11 Nov 2017 00:42:36: #4 Write peak in narrowPeak format file... SRX2512948.20_peaks.narrowPeak INFO @ Sat, 11 Nov 2017 00:42:36: #4 Write summits bed file... SRX2512948.20_summits.bed INFO @ Sat, 11 Nov 2017 00:42:36: Done! pass1 - making usageList (35 chroms): 1 millis pass2 - checking and writing primary data (613 records, 4 fields): 6 millis CompletedMACS2peakCalling INFO @ Sat, 11 Nov 2017 00:43:03: #4 Write output xls file... SRX2512948.05_peaks.xls INFO @ Sat, 11 Nov 2017 00:43:03: #4 Write peak in narrowPeak format file... SRX2512948.05_peaks.narrowPeak INFO @ Sat, 11 Nov 2017 00:43:03: #4 Write summits bed file... SRX2512948.05_summits.bed INFO @ Sat, 11 Nov 2017 00:43:03: Done! pass1 - making usageList (54 chroms): 2 millis pass2 - checking and writing primary data (2563 records, 4 fields): 11 millis CompletedMACS2peakCalling INFO @ Sat, 11 Nov 2017 00:43:15: #4 Write output xls file... SRX2512948.10_peaks.xls INFO @ Sat, 11 Nov 2017 00:43:15: #4 Write peak in narrowPeak format file... SRX2512948.10_peaks.narrowPeak INFO @ Sat, 11 Nov 2017 00:43:15: #4 Write summits bed file... SRX2512948.10_summits.bed INFO @ Sat, 11 Nov 2017 00:43:15: Done! pass1 - making usageList (43 chroms): 2 millis pass2 - checking and writing primary data (1367 records, 4 fields): 8 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。