Job ID = 10194727 sra ファイルのダウンロード中... Completed: 762756K bytes transferred in 11 seconds (536235K bits/sec), in 1 file. Completed: 758575K bytes transferred in 13 seconds (458405K 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 13939876 spots for /home/okishinya/chipatlas/results/rn6/SRX1056323/SRR2060188.sra Written 13939876 spots total Written 14186590 spots for /home/okishinya/chipatlas/results/rn6/SRX1056323/SRR2060187.sra Written 14186590 spots total rm: cannot remove `[DSE]RX*': No such file or directory 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: 01:50:13 28126466 reads; of these: 28126466 (100.00%) were unpaired; of these: 3814526 (13.56%) aligned 0 times 18188569 (64.67%) aligned exactly 1 time 6123371 (21.77%) aligned >1 times 86.44% overall alignment rate Time searching: 01:50:18 Overall time: 01:50:18 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] 1178158 / 24311940 = 0.0485 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 21:30:08: # Command line: callpeak -t SRX1056323.bam -f BAM -g 2.15e9 -n SRX1056323.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX1056323.20 # format = BAM # ChIP-seq file = ['SRX1056323.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 21:30:08: #1 read tag files... INFO @ Fri, 10 Nov 2017 21:30:08: #1 read treatment tags... INFO @ Fri, 10 Nov 2017 21:30:09: # Command line: callpeak -t SRX1056323.bam -f BAM -g 2.15e9 -n SRX1056323.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX1056323.05 # format = BAM # ChIP-seq file = ['SRX1056323.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 21:30:09: #1 read tag files... INFO @ Fri, 10 Nov 2017 21:30:09: #1 read treatment tags... INFO @ Fri, 10 Nov 2017 21:30:09: # Command line: callpeak -t SRX1056323.bam -f BAM -g 2.15e9 -n SRX1056323.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX1056323.10 # format = BAM # ChIP-seq file = ['SRX1056323.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 21:30:09: #1 read tag files... INFO @ Fri, 10 Nov 2017 21:30:09: #1 read treatment tags... INFO @ Fri, 10 Nov 2017 21:30:21: 1000000 INFO @ Fri, 10 Nov 2017 21:30:21: 1000000 INFO @ Fri, 10 Nov 2017 21:30:21: 1000000 INFO @ Fri, 10 Nov 2017 21:30:34: 2000000 INFO @ Fri, 10 Nov 2017 21:30:35: 2000000 INFO @ Fri, 10 Nov 2017 21:30:35: 2000000 INFO @ Fri, 10 Nov 2017 21:30:47: 3000000 INFO @ Fri, 10 Nov 2017 21:30:50: 3000000 INFO @ Fri, 10 Nov 2017 21:30:50: 3000000 INFO @ Fri, 10 Nov 2017 21:30:59: 4000000 INFO @ Fri, 10 Nov 2017 21:31:05: 4000000 INFO @ Fri, 10 Nov 2017 21:31:05: 4000000 INFO @ Fri, 10 Nov 2017 21:31:11: 5000000 INFO @ Fri, 10 Nov 2017 21:31:20: 5000000 INFO @ Fri, 10 Nov 2017 21:31:20: 5000000 INFO @ Fri, 10 Nov 2017 21:31:24: 6000000 INFO @ Fri, 10 Nov 2017 21:31:35: 6000000 INFO @ Fri, 10 Nov 2017 21:31:35: 6000000 INFO @ Fri, 10 Nov 2017 21:31:36: 7000000 INFO @ Fri, 10 Nov 2017 21:31:49: 8000000 INFO @ Fri, 10 Nov 2017 21:31:51: 7000000 INFO @ Fri, 10 Nov 2017 21:31:51: 7000000 INFO @ Fri, 10 Nov 2017 21:32:02: 9000000 INFO @ Fri, 10 Nov 2017 21:32:06: 8000000 INFO @ Fri, 10 Nov 2017 21:32:06: 8000000 INFO @ Fri, 10 Nov 2017 21:32:14: 10000000 INFO @ Fri, 10 Nov 2017 21:32:21: 9000000 INFO @ Fri, 10 Nov 2017 21:32:21: 9000000 INFO @ Fri, 10 Nov 2017 21:32:27: 11000000 INFO @ Fri, 10 Nov 2017 21:32:35: 10000000 INFO @ Fri, 10 Nov 2017 21:32:35: 10000000 INFO @ Fri, 10 Nov 2017 21:32:40: 12000000 INFO @ Fri, 10 Nov 2017 21:32:48: 11000000 INFO @ Fri, 10 Nov 2017 21:32:48: 11000000 INFO @ Fri, 10 Nov 2017 21:32:52: 13000000 INFO @ Fri, 10 Nov 2017 21:33:02: 12000000 INFO @ Fri, 10 Nov 2017 21:33:02: 12000000 INFO @ Fri, 10 Nov 2017 21:33:05: 14000000 INFO @ Fri, 10 Nov 2017 21:33:15: 13000000 INFO @ Fri, 10 Nov 2017 21:33:15: 13000000 INFO @ Fri, 10 Nov 2017 21:33:17: 15000000 INFO @ Fri, 10 Nov 2017 21:33:28: 14000000 INFO @ Fri, 10 Nov 2017 21:33:28: 14000000 INFO @ Fri, 10 Nov 2017 21:33:30: 16000000 INFO @ Fri, 10 Nov 2017 21:33:43: 15000000 INFO @ Fri, 10 Nov 2017 21:33:43: 15000000 INFO @ Fri, 10 Nov 2017 21:33:45: 17000000 INFO @ Fri, 10 Nov 2017 21:33:59: 16000000 INFO @ Fri, 10 Nov 2017 21:33:59: 16000000 INFO @ Fri, 10 Nov 2017 21:34:00: 18000000 INFO @ Fri, 10 Nov 2017 21:34:13: 17000000 INFO @ Fri, 10 Nov 2017 21:34:15: 17000000 INFO @ Fri, 10 Nov 2017 21:34:16: 19000000 INFO @ Fri, 10 Nov 2017 21:34:28: 18000000 INFO @ Fri, 10 Nov 2017 21:34:32: 20000000 INFO @ Fri, 10 Nov 2017 21:34:33: 18000000 INFO @ Fri, 10 Nov 2017 21:34:47: 21000000 INFO @ Fri, 10 Nov 2017 21:34:47: 19000000 INFO @ Fri, 10 Nov 2017 21:34:51: 19000000 INFO @ Fri, 10 Nov 2017 21:35:04: 22000000 INFO @ Fri, 10 Nov 2017 21:35:06: 20000000 INFO @ Fri, 10 Nov 2017 21:35:07: 20000000 INFO @ Fri, 10 Nov 2017 21:35:19: 23000000 INFO @ Fri, 10 Nov 2017 21:35:22: #1 tag size is determined as 100 bps INFO @ Fri, 10 Nov 2017 21:35:22: #1 tag size = 100 INFO @ Fri, 10 Nov 2017 21:35:22: #1 total tags in treatment: 23133782 INFO @ Fri, 10 Nov 2017 21:35:22: #1 user defined the maximum tags... INFO @ Fri, 10 Nov 2017 21:35:22: #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 21:35:23: #1 tags after filtering in treatment: 23133638 INFO @ Fri, 10 Nov 2017 21:35:23: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 10 Nov 2017 21:35:23: #1 finished! INFO @ Fri, 10 Nov 2017 21:35:23: #2 Build Peak Model... INFO @ Fri, 10 Nov 2017 21:35:23: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Nov 2017 21:35:24: 21000000 INFO @ Fri, 10 Nov 2017 21:35:24: 21000000 INFO @ Fri, 10 Nov 2017 21:35:26: #2 number of paired peaks: 6029 INFO @ Fri, 10 Nov 2017 21:35:26: start model_add_line... INFO @ Fri, 10 Nov 2017 21:35:26: start X-correlation... INFO @ Fri, 10 Nov 2017 21:35:26: end of X-cor INFO @ Fri, 10 Nov 2017 21:35:26: #2 finished! INFO @ Fri, 10 Nov 2017 21:35:26: #2 predicted fragment length is 99 bps INFO @ Fri, 10 Nov 2017 21:35:26: #2 alternative fragment length(s) may be 99 bps INFO @ Fri, 10 Nov 2017 21:35:26: #2.2 Generate R script for model : SRX1056323.05_model.r WARNING @ Fri, 10 Nov 2017 21:35:26: #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 21:35:26: #2 You may need to consider one of the other alternative d(s): 99 WARNING @ Fri, 10 Nov 2017 21:35:26: #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 21:35:26: #3 Call peaks... INFO @ Fri, 10 Nov 2017 21:35:26: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 10 Nov 2017 21:35:41: 22000000 INFO @ Fri, 10 Nov 2017 21:35:45: 22000000 INFO @ Fri, 10 Nov 2017 21:35:57: 23000000 INFO @ Fri, 10 Nov 2017 21:36:00: #1 tag size is determined as 100 bps INFO @ Fri, 10 Nov 2017 21:36:00: #1 tag size = 100 INFO @ Fri, 10 Nov 2017 21:36:00: #1 total tags in treatment: 23133782 INFO @ Fri, 10 Nov 2017 21:36:00: #1 user defined the maximum tags... INFO @ Fri, 10 Nov 2017 21:36:00: #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 21:36:01: #1 tags after filtering in treatment: 23133638 INFO @ Fri, 10 Nov 2017 21:36:01: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 10 Nov 2017 21:36:01: #1 finished! INFO @ Fri, 10 Nov 2017 21:36:01: #2 Build Peak Model... INFO @ Fri, 10 Nov 2017 21:36:01: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Nov 2017 21:36:03: 23000000 INFO @ Fri, 10 Nov 2017 21:36:04: #2 number of paired peaks: 6029 INFO @ Fri, 10 Nov 2017 21:36:04: start model_add_line... INFO @ Fri, 10 Nov 2017 21:36:04: start X-correlation... INFO @ Fri, 10 Nov 2017 21:36:04: end of X-cor INFO @ Fri, 10 Nov 2017 21:36:04: #2 finished! INFO @ Fri, 10 Nov 2017 21:36:04: #2 predicted fragment length is 99 bps INFO @ Fri, 10 Nov 2017 21:36:04: #2 alternative fragment length(s) may be 99 bps INFO @ Fri, 10 Nov 2017 21:36:04: #2.2 Generate R script for model : SRX1056323.20_model.r WARNING @ Fri, 10 Nov 2017 21:36:04: #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 21:36:04: #2 You may need to consider one of the other alternative d(s): 99 WARNING @ Fri, 10 Nov 2017 21:36:04: #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 21:36:04: #3 Call peaks... INFO @ Fri, 10 Nov 2017 21:36:04: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 10 Nov 2017 21:36:06: #1 tag size is determined as 100 bps INFO @ Fri, 10 Nov 2017 21:36:06: #1 tag size = 100 INFO @ Fri, 10 Nov 2017 21:36:06: #1 total tags in treatment: 23133782 INFO @ Fri, 10 Nov 2017 21:36:06: #1 user defined the maximum tags... INFO @ Fri, 10 Nov 2017 21:36:06: #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 21:36:07: #1 tags after filtering in treatment: 23133638 INFO @ Fri, 10 Nov 2017 21:36:07: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 10 Nov 2017 21:36:07: #1 finished! INFO @ Fri, 10 Nov 2017 21:36:07: #2 Build Peak Model... INFO @ Fri, 10 Nov 2017 21:36:07: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Nov 2017 21:36:10: #2 number of paired peaks: 6029 INFO @ Fri, 10 Nov 2017 21:36:10: start model_add_line... INFO @ Fri, 10 Nov 2017 21:36:10: start X-correlation... INFO @ Fri, 10 Nov 2017 21:36:10: end of X-cor INFO @ Fri, 10 Nov 2017 21:36:10: #2 finished! INFO @ Fri, 10 Nov 2017 21:36:10: #2 predicted fragment length is 99 bps INFO @ Fri, 10 Nov 2017 21:36:10: #2 alternative fragment length(s) may be 99 bps INFO @ Fri, 10 Nov 2017 21:36:10: #2.2 Generate R script for model : SRX1056323.10_model.r WARNING @ Fri, 10 Nov 2017 21:36:10: #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 21:36:10: #2 You may need to consider one of the other alternative d(s): 99 WARNING @ Fri, 10 Nov 2017 21:36:10: #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 21:36:10: #3 Call peaks... INFO @ Fri, 10 Nov 2017 21:36:10: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 10 Nov 2017 21:36:36: #3 Call peaks for each chromosome... INFO @ Fri, 10 Nov 2017 21:37:15: #3 Call peaks for each chromosome... INFO @ Fri, 10 Nov 2017 21:37:18: #4 Write output xls file... SRX1056323.05_peaks.xls INFO @ Fri, 10 Nov 2017 21:37:18: #4 Write peak in narrowPeak format file... SRX1056323.05_peaks.narrowPeak INFO @ Fri, 10 Nov 2017 21:37:18: #4 Write summits bed file... SRX1056323.05_summits.bed INFO @ Fri, 10 Nov 2017 21:37:18: Done! pass1 - making usageList (50 chroms): 4 millis pass2 - checking and writing primary data (1363 records, 4 fields): 20 millis CompletedMACS2peakCalling INFO @ Fri, 10 Nov 2017 21:37:57: #4 Write output xls file... SRX1056323.20_peaks.xls INFO @ Fri, 10 Nov 2017 21:37:57: #4 Write peak in narrowPeak format file... SRX1056323.20_peaks.narrowPeak INFO @ Fri, 10 Nov 2017 21:37:57: #4 Write summits bed file... SRX1056323.20_summits.bed INFO @ Fri, 10 Nov 2017 21:37:57: Done! pass1 - making usageList (28 chroms): 3 millis pass2 - checking and writing primary data (399 records, 4 fields): 8 millis CompletedMACS2peakCalling INFO @ Fri, 10 Nov 2017 21:38:01: #3 Call peaks for each chromosome... INFO @ Fri, 10 Nov 2017 21:38:58: #4 Write output xls file... SRX1056323.10_peaks.xls INFO @ Fri, 10 Nov 2017 21:38:58: #4 Write peak in narrowPeak format file... SRX1056323.10_peaks.narrowPeak INFO @ Fri, 10 Nov 2017 21:38:58: #4 Write summits bed file... SRX1056323.10_summits.bed INFO @ Fri, 10 Nov 2017 21:38:58: Done! pass1 - making usageList (41 chroms): 2 millis pass2 - checking and writing primary data (770 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。