Job ID = 11388816 sra ファイルのダウンロード中... Completed: 252697K bytes transferred in 9 seconds (221008K bits/sec), in 1 file. Completed: 250451K bytes transferred in 9 seconds (215282K 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 11457812 spots for /home/okishinya/chipatlas/results/rn6/SRX3657376/SRR6681070.sra Written 11457812 spots for /home/okishinya/chipatlas/results/rn6/SRX3657376/SRR6681070.sra Read 11523078 spots for /home/okishinya/chipatlas/results/rn6/SRX3657376/SRR6681069.sra Written 11523078 spots for /home/okishinya/chipatlas/results/rn6/SRX3657376/SRR6681069.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 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: 00:41:25 22980890 reads; of these: 22980890 (100.00%) were unpaired; of these: 1901457 (8.27%) aligned 0 times 15189620 (66.10%) aligned exactly 1 time 5889813 (25.63%) aligned >1 times 91.73% overall alignment rate Time searching: 00:41:30 Overall time: 00:41:30 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 12 files... [bam_rmdupse_core] 9773247 / 21079433 = 0.4636 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 @ Wed, 12 Dec 2018 23:49:13: # Command line: callpeak -t SRX3657376.bam -f BAM -g 2.15e9 -n SRX3657376.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX3657376.20 # format = BAM # ChIP-seq file = ['SRX3657376.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 @ Wed, 12 Dec 2018 23:49:13: #1 read tag files... INFO @ Wed, 12 Dec 2018 23:49:13: #1 read treatment tags... INFO @ Wed, 12 Dec 2018 23:49:13: # Command line: callpeak -t SRX3657376.bam -f BAM -g 2.15e9 -n SRX3657376.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX3657376.05 # format = BAM # ChIP-seq file = ['SRX3657376.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 @ Wed, 12 Dec 2018 23:49:13: #1 read tag files... INFO @ Wed, 12 Dec 2018 23:49:13: #1 read treatment tags... INFO @ Wed, 12 Dec 2018 23:49:13: # Command line: callpeak -t SRX3657376.bam -f BAM -g 2.15e9 -n SRX3657376.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX3657376.10 # format = BAM # ChIP-seq file = ['SRX3657376.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 @ Wed, 12 Dec 2018 23:49:13: #1 read tag files... INFO @ Wed, 12 Dec 2018 23:49:13: #1 read treatment tags... INFO @ Wed, 12 Dec 2018 23:49:24: 1000000 INFO @ Wed, 12 Dec 2018 23:49:29: 1000000 INFO @ Wed, 12 Dec 2018 23:49:33: 1000000 INFO @ Wed, 12 Dec 2018 23:49:38: 2000000 INFO @ Wed, 12 Dec 2018 23:49:42: 2000000 INFO @ Wed, 12 Dec 2018 23:49:50: 2000000 INFO @ Wed, 12 Dec 2018 23:49:50: 3000000 INFO @ Wed, 12 Dec 2018 23:49:56: 3000000 INFO @ Wed, 12 Dec 2018 23:50:02: 4000000 INFO @ Wed, 12 Dec 2018 23:50:06: 3000000 INFO @ Wed, 12 Dec 2018 23:50:08: 4000000 INFO @ Wed, 12 Dec 2018 23:50:14: 5000000 INFO @ Wed, 12 Dec 2018 23:50:19: 5000000 INFO @ Wed, 12 Dec 2018 23:50:23: 4000000 INFO @ Wed, 12 Dec 2018 23:50:24: 6000000 INFO @ Wed, 12 Dec 2018 23:50:31: 6000000 INFO @ Wed, 12 Dec 2018 23:50:37: 7000000 INFO @ Wed, 12 Dec 2018 23:50:40: 5000000 INFO @ Wed, 12 Dec 2018 23:50:44: 7000000 INFO @ Wed, 12 Dec 2018 23:50:51: 8000000 INFO @ Wed, 12 Dec 2018 23:50:58: 6000000 INFO @ Wed, 12 Dec 2018 23:51:00: 8000000 INFO @ Wed, 12 Dec 2018 23:51:07: 9000000 INFO @ Wed, 12 Dec 2018 23:51:11: 9000000 INFO @ Wed, 12 Dec 2018 23:51:17: 7000000 INFO @ Wed, 12 Dec 2018 23:51:22: 10000000 INFO @ Wed, 12 Dec 2018 23:51:25: 10000000 INFO @ Wed, 12 Dec 2018 23:51:35: 8000000 INFO @ Wed, 12 Dec 2018 23:51:39: 11000000 INFO @ Wed, 12 Dec 2018 23:51:41: 11000000 INFO @ Wed, 12 Dec 2018 23:51:44: #1 tag size is determined as 50 bps INFO @ Wed, 12 Dec 2018 23:51:44: #1 tag size = 50 INFO @ Wed, 12 Dec 2018 23:51:44: #1 total tags in treatment: 11306186 INFO @ Wed, 12 Dec 2018 23:51:44: #1 user defined the maximum tags... INFO @ Wed, 12 Dec 2018 23:51:44: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Wed, 12 Dec 2018 23:51:45: #1 tags after filtering in treatment: 11306017 INFO @ Wed, 12 Dec 2018 23:51:45: #1 Redundant rate of treatment: 0.00 INFO @ Wed, 12 Dec 2018 23:51:45: #1 finished! INFO @ Wed, 12 Dec 2018 23:51:45: #2 Build Peak Model... INFO @ Wed, 12 Dec 2018 23:51:45: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 12 Dec 2018 23:51:46: #1 tag size is determined as 50 bps INFO @ Wed, 12 Dec 2018 23:51:46: #1 tag size = 50 INFO @ Wed, 12 Dec 2018 23:51:46: #1 total tags in treatment: 11306186 INFO @ Wed, 12 Dec 2018 23:51:46: #1 user defined the maximum tags... INFO @ Wed, 12 Dec 2018 23:51:46: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Wed, 12 Dec 2018 23:51:47: #2 number of paired peaks: 9519 INFO @ Wed, 12 Dec 2018 23:51:47: start model_add_line... INFO @ Wed, 12 Dec 2018 23:51:47: start X-correlation... INFO @ Wed, 12 Dec 2018 23:51:47: end of X-cor INFO @ Wed, 12 Dec 2018 23:51:47: #2 finished! INFO @ Wed, 12 Dec 2018 23:51:47: #2 predicted fragment length is 49 bps INFO @ Wed, 12 Dec 2018 23:51:47: #2 alternative fragment length(s) may be 49,221,590 bps INFO @ Wed, 12 Dec 2018 23:51:47: #2.2 Generate R script for model : SRX3657376.10_model.r WARNING @ Wed, 12 Dec 2018 23:51:47: #2 Since the d (49) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Wed, 12 Dec 2018 23:51:47: #2 You may need to consider one of the other alternative d(s): 49,221,590 WARNING @ Wed, 12 Dec 2018 23:51:47: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Wed, 12 Dec 2018 23:51:47: #3 Call peaks... INFO @ Wed, 12 Dec 2018 23:51:47: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 12 Dec 2018 23:51:47: #1 tags after filtering in treatment: 11306017 INFO @ Wed, 12 Dec 2018 23:51:47: #1 Redundant rate of treatment: 0.00 INFO @ Wed, 12 Dec 2018 23:51:47: #1 finished! INFO @ Wed, 12 Dec 2018 23:51:47: #2 Build Peak Model... INFO @ Wed, 12 Dec 2018 23:51:47: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 12 Dec 2018 23:51:49: #2 number of paired peaks: 9519 INFO @ Wed, 12 Dec 2018 23:51:49: start model_add_line... INFO @ Wed, 12 Dec 2018 23:51:49: start X-correlation... INFO @ Wed, 12 Dec 2018 23:51:49: end of X-cor INFO @ Wed, 12 Dec 2018 23:51:49: #2 finished! INFO @ Wed, 12 Dec 2018 23:51:49: #2 predicted fragment length is 49 bps INFO @ Wed, 12 Dec 2018 23:51:49: #2 alternative fragment length(s) may be 49,221,590 bps INFO @ Wed, 12 Dec 2018 23:51:49: #2.2 Generate R script for model : SRX3657376.05_model.r WARNING @ Wed, 12 Dec 2018 23:51:49: #2 Since the d (49) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Wed, 12 Dec 2018 23:51:49: #2 You may need to consider one of the other alternative d(s): 49,221,590 WARNING @ Wed, 12 Dec 2018 23:51:49: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Wed, 12 Dec 2018 23:51:49: #3 Call peaks... INFO @ Wed, 12 Dec 2018 23:51:49: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 12 Dec 2018 23:51:51: 9000000 INFO @ Wed, 12 Dec 2018 23:52:05: 10000000 INFO @ Wed, 12 Dec 2018 23:52:18: 11000000 INFO @ Wed, 12 Dec 2018 23:52:21: #3 Call peaks for each chromosome... INFO @ Wed, 12 Dec 2018 23:52:22: #1 tag size is determined as 50 bps INFO @ Wed, 12 Dec 2018 23:52:22: #1 tag size = 50 INFO @ Wed, 12 Dec 2018 23:52:22: #1 total tags in treatment: 11306186 INFO @ Wed, 12 Dec 2018 23:52:22: #1 user defined the maximum tags... INFO @ Wed, 12 Dec 2018 23:52:22: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Wed, 12 Dec 2018 23:52:23: #1 tags after filtering in treatment: 11306017 INFO @ Wed, 12 Dec 2018 23:52:23: #1 Redundant rate of treatment: 0.00 INFO @ Wed, 12 Dec 2018 23:52:23: #1 finished! INFO @ Wed, 12 Dec 2018 23:52:23: #2 Build Peak Model... INFO @ Wed, 12 Dec 2018 23:52:23: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 12 Dec 2018 23:52:24: #3 Call peaks for each chromosome... INFO @ Wed, 12 Dec 2018 23:52:25: #2 number of paired peaks: 9519 INFO @ Wed, 12 Dec 2018 23:52:25: start model_add_line... INFO @ Wed, 12 Dec 2018 23:52:25: start X-correlation... INFO @ Wed, 12 Dec 2018 23:52:25: end of X-cor INFO @ Wed, 12 Dec 2018 23:52:25: #2 finished! INFO @ Wed, 12 Dec 2018 23:52:25: #2 predicted fragment length is 49 bps INFO @ Wed, 12 Dec 2018 23:52:25: #2 alternative fragment length(s) may be 49,221,590 bps INFO @ Wed, 12 Dec 2018 23:52:25: #2.2 Generate R script for model : SRX3657376.20_model.r WARNING @ Wed, 12 Dec 2018 23:52:25: #2 Since the d (49) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Wed, 12 Dec 2018 23:52:25: #2 You may need to consider one of the other alternative d(s): 49,221,590 WARNING @ Wed, 12 Dec 2018 23:52:25: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Wed, 12 Dec 2018 23:52:25: #3 Call peaks... INFO @ Wed, 12 Dec 2018 23:52:25: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 12 Dec 2018 23:52:42: #4 Write output xls file... SRX3657376.10_peaks.xls INFO @ Wed, 12 Dec 2018 23:52:43: #4 Write peak in narrowPeak format file... SRX3657376.10_peaks.narrowPeak INFO @ Wed, 12 Dec 2018 23:52:43: #4 Write summits bed file... SRX3657376.10_summits.bed INFO @ Wed, 12 Dec 2018 23:52:43: Done! pass1 - making usageList (51 chroms): 5 millis pass2 - checking and writing primary data (744 records, 4 fields): 12 millis CompletedMACS2peakCalling INFO @ Wed, 12 Dec 2018 23:52:44: #4 Write output xls file... SRX3657376.05_peaks.xls INFO @ Wed, 12 Dec 2018 23:52:44: #4 Write peak in narrowPeak format file... SRX3657376.05_peaks.narrowPeak INFO @ Wed, 12 Dec 2018 23:52:44: #4 Write summits bed file... SRX3657376.05_summits.bed INFO @ Wed, 12 Dec 2018 23:52:44: Done! pass1 - making usageList (62 chroms): 4 millis pass2 - checking and writing primary data (1259 records, 4 fields): 13 millis CompletedMACS2peakCalling INFO @ Wed, 12 Dec 2018 23:53:00: #3 Call peaks for each chromosome... INFO @ Wed, 12 Dec 2018 23:53:21: #4 Write output xls file... SRX3657376.20_peaks.xls INFO @ Wed, 12 Dec 2018 23:53:21: #4 Write peak in narrowPeak format file... SRX3657376.20_peaks.narrowPeak INFO @ Wed, 12 Dec 2018 23:53:21: #4 Write summits bed file... SRX3657376.20_summits.bed INFO @ Wed, 12 Dec 2018 23:53:21: Done! pass1 - making usageList (39 chroms): 5 millis pass2 - checking and writing primary data (347 records, 4 fields): 9 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。