Job ID = 10608878 sra ファイルのダウンロード中... Completed: 1015204K bytes transferred in 83 seconds (99968K 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 31720602 spots for /home/okishinya/chipatlas/results/rn6/SRX3145016/SRR5989263.sra Written 31720602 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: 00:00:00 Time loading forward index: 00:00:02 Time loading mirror index: 00:00:01 Multiseed full-index search: 00:23:27 31720602 reads; of these: 31720602 (100.00%) were unpaired; of these: 904835 (2.85%) aligned 0 times 21299744 (67.15%) aligned exactly 1 time 9516023 (30.00%) aligned >1 times 97.15% overall alignment rate Time searching: 00:23:30 Overall time: 00:23:30 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] 1199661 / 30815767 = 0.0389 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, 03 May 2018 22:54:27: # Command line: callpeak -t SRX3145016.bam -f BAM -g 2.15e9 -n SRX3145016.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX3145016.20 # format = BAM # ChIP-seq file = ['SRX3145016.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, 03 May 2018 22:54:27: # Command line: callpeak -t SRX3145016.bam -f BAM -g 2.15e9 -n SRX3145016.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX3145016.05 # format = BAM # ChIP-seq file = ['SRX3145016.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, 03 May 2018 22:54:27: # Command line: callpeak -t SRX3145016.bam -f BAM -g 2.15e9 -n SRX3145016.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX3145016.10 # format = BAM # ChIP-seq file = ['SRX3145016.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, 03 May 2018 22:54:27: #1 read tag files... INFO @ Thu, 03 May 2018 22:54:27: #1 read tag files... INFO @ Thu, 03 May 2018 22:54:27: #1 read tag files... INFO @ Thu, 03 May 2018 22:54:27: #1 read treatment tags... INFO @ Thu, 03 May 2018 22:54:27: #1 read treatment tags... INFO @ Thu, 03 May 2018 22:54:27: #1 read treatment tags... INFO @ Thu, 03 May 2018 22:54:33: 1000000 INFO @ Thu, 03 May 2018 22:54:34: 1000000 INFO @ Thu, 03 May 2018 22:54:34: 1000000 INFO @ Thu, 03 May 2018 22:54:40: 2000000 INFO @ Thu, 03 May 2018 22:54:40: 2000000 INFO @ Thu, 03 May 2018 22:54:41: 2000000 INFO @ Thu, 03 May 2018 22:54:46: 3000000 INFO @ Thu, 03 May 2018 22:54:47: 3000000 INFO @ Thu, 03 May 2018 22:54:48: 3000000 INFO @ Thu, 03 May 2018 22:54:52: 4000000 INFO @ Thu, 03 May 2018 22:54:53: 4000000 INFO @ Thu, 03 May 2018 22:54:55: 4000000 INFO @ Thu, 03 May 2018 22:54:58: 5000000 INFO @ Thu, 03 May 2018 22:55:00: 5000000 INFO @ Thu, 03 May 2018 22:55:02: 5000000 INFO @ Thu, 03 May 2018 22:55:05: 6000000 INFO @ Thu, 03 May 2018 22:55:07: 6000000 INFO @ Thu, 03 May 2018 22:55:09: 6000000 INFO @ Thu, 03 May 2018 22:55:11: 7000000 INFO @ Thu, 03 May 2018 22:55:13: 7000000 INFO @ Thu, 03 May 2018 22:55:16: 7000000 INFO @ Thu, 03 May 2018 22:55:17: 8000000 INFO @ Thu, 03 May 2018 22:55:20: 8000000 INFO @ Thu, 03 May 2018 22:55:22: 8000000 INFO @ Thu, 03 May 2018 22:55:23: 9000000 INFO @ Thu, 03 May 2018 22:55:26: 9000000 INFO @ Thu, 03 May 2018 22:55:29: 9000000 INFO @ Thu, 03 May 2018 22:55:30: 10000000 INFO @ Thu, 03 May 2018 22:55:33: 10000000 INFO @ Thu, 03 May 2018 22:55:37: 10000000 INFO @ Thu, 03 May 2018 22:55:37: 11000000 INFO @ Thu, 03 May 2018 22:55:40: 11000000 INFO @ Thu, 03 May 2018 22:55:44: 11000000 INFO @ Thu, 03 May 2018 22:55:45: 12000000 INFO @ Thu, 03 May 2018 22:55:48: 12000000 INFO @ Thu, 03 May 2018 22:55:52: 12000000 INFO @ Thu, 03 May 2018 22:55:53: 13000000 INFO @ Thu, 03 May 2018 22:55:55: 13000000 INFO @ Thu, 03 May 2018 22:56:00: 13000000 INFO @ Thu, 03 May 2018 22:56:01: 14000000 INFO @ Thu, 03 May 2018 22:56:02: 14000000 INFO @ Thu, 03 May 2018 22:56:08: 14000000 INFO @ Thu, 03 May 2018 22:56:09: 15000000 INFO @ Thu, 03 May 2018 22:56:10: 15000000 INFO @ Thu, 03 May 2018 22:56:15: 15000000 INFO @ Thu, 03 May 2018 22:56:16: 16000000 INFO @ Thu, 03 May 2018 22:56:17: 16000000 INFO @ Thu, 03 May 2018 22:56:23: 16000000 INFO @ Thu, 03 May 2018 22:56:24: 17000000 INFO @ Thu, 03 May 2018 22:56:24: 17000000 INFO @ Thu, 03 May 2018 22:56:30: 17000000 INFO @ Thu, 03 May 2018 22:56:31: 18000000 INFO @ Thu, 03 May 2018 22:56:31: 18000000 INFO @ Thu, 03 May 2018 22:56:38: 18000000 INFO @ Thu, 03 May 2018 22:56:38: 19000000 INFO @ Thu, 03 May 2018 22:56:39: 19000000 INFO @ Thu, 03 May 2018 22:56:45: 20000000 INFO @ Thu, 03 May 2018 22:56:45: 19000000 INFO @ Thu, 03 May 2018 22:56:46: 20000000 INFO @ Thu, 03 May 2018 22:56:52: 21000000 INFO @ Thu, 03 May 2018 22:56:53: 20000000 INFO @ Thu, 03 May 2018 22:56:54: 21000000 INFO @ Thu, 03 May 2018 22:56:59: 22000000 INFO @ Thu, 03 May 2018 22:57:00: 21000000 INFO @ Thu, 03 May 2018 22:57:00: 22000000 INFO @ Thu, 03 May 2018 22:57:06: 23000000 INFO @ Thu, 03 May 2018 22:57:06: 23000000 INFO @ Thu, 03 May 2018 22:57:07: 22000000 INFO @ Thu, 03 May 2018 22:57:12: 24000000 INFO @ Thu, 03 May 2018 22:57:13: 24000000 INFO @ Thu, 03 May 2018 22:57:14: 23000000 INFO @ Thu, 03 May 2018 22:57:19: 25000000 INFO @ Thu, 03 May 2018 22:57:19: 25000000 INFO @ Thu, 03 May 2018 22:57:21: 24000000 INFO @ Thu, 03 May 2018 22:57:25: 26000000 INFO @ Thu, 03 May 2018 22:57:26: 26000000 INFO @ Thu, 03 May 2018 22:57:28: 25000000 INFO @ Thu, 03 May 2018 22:57:32: 27000000 INFO @ Thu, 03 May 2018 22:57:32: 27000000 INFO @ Thu, 03 May 2018 22:57:35: 26000000 INFO @ Thu, 03 May 2018 22:57:38: 28000000 INFO @ Thu, 03 May 2018 22:57:39: 28000000 INFO @ Thu, 03 May 2018 22:57:42: 27000000 INFO @ Thu, 03 May 2018 22:57:45: 29000000 INFO @ Thu, 03 May 2018 22:57:46: 29000000 INFO @ Thu, 03 May 2018 22:57:49: #1 tag size is determined as 51 bps INFO @ Thu, 03 May 2018 22:57:49: #1 tag size = 51 INFO @ Thu, 03 May 2018 22:57:49: #1 total tags in treatment: 29616106 INFO @ Thu, 03 May 2018 22:57:49: #1 user defined the maximum tags... INFO @ Thu, 03 May 2018 22:57:49: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Thu, 03 May 2018 22:57:49: 28000000 INFO @ Thu, 03 May 2018 22:57:50: #1 tags after filtering in treatment: 29616013 INFO @ Thu, 03 May 2018 22:57:50: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 03 May 2018 22:57:50: #1 finished! INFO @ Thu, 03 May 2018 22:57:50: #2 Build Peak Model... INFO @ Thu, 03 May 2018 22:57:50: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 03 May 2018 22:57:50: #1 tag size is determined as 51 bps INFO @ Thu, 03 May 2018 22:57:50: #1 tag size = 51 INFO @ Thu, 03 May 2018 22:57:50: #1 total tags in treatment: 29616106 INFO @ Thu, 03 May 2018 22:57:50: #1 user defined the maximum tags... INFO @ Thu, 03 May 2018 22:57:50: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Thu, 03 May 2018 22:57:51: #1 tags after filtering in treatment: 29616013 INFO @ Thu, 03 May 2018 22:57:51: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 03 May 2018 22:57:51: #1 finished! INFO @ Thu, 03 May 2018 22:57:51: #2 Build Peak Model... INFO @ Thu, 03 May 2018 22:57:51: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 03 May 2018 22:57:52: #2 number of paired peaks: 5838 INFO @ Thu, 03 May 2018 22:57:52: start model_add_line... INFO @ Thu, 03 May 2018 22:57:53: start X-correlation... INFO @ Thu, 03 May 2018 22:57:53: end of X-cor INFO @ Thu, 03 May 2018 22:57:53: #2 finished! INFO @ Thu, 03 May 2018 22:57:53: #2 predicted fragment length is 51 bps INFO @ Thu, 03 May 2018 22:57:53: #2 alternative fragment length(s) may be 51,225,410,504 bps INFO @ Thu, 03 May 2018 22:57:53: #2.2 Generate R script for model : SRX3145016.20_model.r WARNING @ Thu, 03 May 2018 22:57:53: #2 Since the d (51) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 03 May 2018 22:57:53: #2 You may need to consider one of the other alternative d(s): 51,225,410,504 WARNING @ Thu, 03 May 2018 22:57:53: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Thu, 03 May 2018 22:57:53: #3 Call peaks... INFO @ Thu, 03 May 2018 22:57:53: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 03 May 2018 22:57:54: #2 number of paired peaks: 5838 INFO @ Thu, 03 May 2018 22:57:54: start model_add_line... INFO @ Thu, 03 May 2018 22:57:54: start X-correlation... INFO @ Thu, 03 May 2018 22:57:54: end of X-cor INFO @ Thu, 03 May 2018 22:57:54: #2 finished! INFO @ Thu, 03 May 2018 22:57:54: #2 predicted fragment length is 51 bps INFO @ Thu, 03 May 2018 22:57:54: #2 alternative fragment length(s) may be 51,225,410,504 bps INFO @ Thu, 03 May 2018 22:57:54: #2.2 Generate R script for model : SRX3145016.05_model.r WARNING @ Thu, 03 May 2018 22:57:54: #2 Since the d (51) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 03 May 2018 22:57:54: #2 You may need to consider one of the other alternative d(s): 51,225,410,504 WARNING @ Thu, 03 May 2018 22:57:54: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Thu, 03 May 2018 22:57:54: #3 Call peaks... INFO @ Thu, 03 May 2018 22:57:54: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 03 May 2018 22:57:56: 29000000 INFO @ Thu, 03 May 2018 22:58:00: #1 tag size is determined as 51 bps INFO @ Thu, 03 May 2018 22:58:00: #1 tag size = 51 INFO @ Thu, 03 May 2018 22:58:00: #1 total tags in treatment: 29616106 INFO @ Thu, 03 May 2018 22:58:00: #1 user defined the maximum tags... INFO @ Thu, 03 May 2018 22:58:00: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Thu, 03 May 2018 22:58:01: #1 tags after filtering in treatment: 29616013 INFO @ Thu, 03 May 2018 22:58:01: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 03 May 2018 22:58:01: #1 finished! INFO @ Thu, 03 May 2018 22:58:01: #2 Build Peak Model... INFO @ Thu, 03 May 2018 22:58:01: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 03 May 2018 22:58:04: #2 number of paired peaks: 5838 INFO @ Thu, 03 May 2018 22:58:04: start model_add_line... INFO @ Thu, 03 May 2018 22:58:04: start X-correlation... INFO @ Thu, 03 May 2018 22:58:04: end of X-cor INFO @ Thu, 03 May 2018 22:58:04: #2 finished! INFO @ Thu, 03 May 2018 22:58:04: #2 predicted fragment length is 51 bps INFO @ Thu, 03 May 2018 22:58:04: #2 alternative fragment length(s) may be 51,225,410,504 bps INFO @ Thu, 03 May 2018 22:58:04: #2.2 Generate R script for model : SRX3145016.10_model.r WARNING @ Thu, 03 May 2018 22:58:04: #2 Since the d (51) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 03 May 2018 22:58:04: #2 You may need to consider one of the other alternative d(s): 51,225,410,504 WARNING @ Thu, 03 May 2018 22:58:04: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Thu, 03 May 2018 22:58:04: #3 Call peaks... INFO @ Thu, 03 May 2018 22:58:04: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 03 May 2018 22:59:08: #3 Call peaks for each chromosome... INFO @ Thu, 03 May 2018 22:59:09: #3 Call peaks for each chromosome... INFO @ Thu, 03 May 2018 22:59:15: #3 Call peaks for each chromosome... INFO @ Thu, 03 May 2018 22:59:55: #4 Write output xls file... SRX3145016.20_peaks.xls INFO @ Thu, 03 May 2018 22:59:55: #4 Write peak in narrowPeak format file... SRX3145016.20_peaks.narrowPeak INFO @ Thu, 03 May 2018 22:59:55: #4 Write summits bed file... SRX3145016.20_summits.bed INFO @ Thu, 03 May 2018 22:59:55: Done! pass1 - making usageList (33 chroms): 1 millis pass2 - checking and writing primary data (546 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Thu, 03 May 2018 22:59:55: #4 Write output xls file... SRX3145016.05_peaks.xls INFO @ Thu, 03 May 2018 22:59:55: #4 Write peak in narrowPeak format file... SRX3145016.05_peaks.narrowPeak INFO @ Thu, 03 May 2018 22:59:55: #4 Write summits bed file... SRX3145016.05_summits.bed INFO @ Thu, 03 May 2018 22:59:55: Done! pass1 - making usageList (47 chroms): 1 millis pass2 - checking and writing primary data (1853 records, 4 fields): 6 millis CompletedMACS2peakCalling INFO @ Thu, 03 May 2018 22:59:58: #4 Write output xls file... SRX3145016.10_peaks.xls INFO @ Thu, 03 May 2018 22:59:58: #4 Write peak in narrowPeak format file... SRX3145016.10_peaks.narrowPeak INFO @ Thu, 03 May 2018 22:59:58: #4 Write summits bed file... SRX3145016.10_summits.bed INFO @ Thu, 03 May 2018 22:59:58: Done! pass1 - making usageList (41 chroms): 1 millis pass2 - checking and writing primary data (1105 records, 4 fields): 5 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。