Job ID = 11388813 sra ファイルのダウンロード中... Completed: 263451K bytes transferred in 8 seconds (248959K bits/sec), in 1 file. Completed: 260990K bytes transferred in 14 seconds (148360K 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 11920480 spots for /home/okishinya/chipatlas/results/rn6/SRX3657373/SRR6681064.sra Written 11920480 spots for /home/okishinya/chipatlas/results/rn6/SRX3657373/SRR6681064.sra Read 11995315 spots for /home/okishinya/chipatlas/results/rn6/SRX3657373/SRR6681063.sra Written 11995315 spots for /home/okishinya/chipatlas/results/rn6/SRX3657373/SRR6681063.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: 00:42:11 23915795 reads; of these: 23915795 (100.00%) were unpaired; of these: 4066591 (17.00%) aligned 0 times 14319928 (59.88%) aligned exactly 1 time 5529276 (23.12%) aligned >1 times 83.00% overall alignment rate Time searching: 00:42:16 Overall time: 00:42:16 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] 6263343 / 19849204 = 0.3155 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 23:47:02: # Command line: callpeak -t SRX3657373.bam -f BAM -g 2.15e9 -n SRX3657373.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX3657373.20 # format = BAM # ChIP-seq file = ['SRX3657373.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 23:47:02: #1 read tag files... INFO @ Wed, 12 Dec 2018 23:47:02: #1 read treatment tags... INFO @ Wed, 12 Dec 2018 23:47:02: # Command line: callpeak -t SRX3657373.bam -f BAM -g 2.15e9 -n SRX3657373.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX3657373.10 # format = BAM # ChIP-seq file = ['SRX3657373.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 23:47:02: #1 read tag files... INFO @ Wed, 12 Dec 2018 23:47:02: #1 read treatment tags... INFO @ Wed, 12 Dec 2018 23:47:02: # Command line: callpeak -t SRX3657373.bam -f BAM -g 2.15e9 -n SRX3657373.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX3657373.05 # format = BAM # ChIP-seq file = ['SRX3657373.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 23:47:02: #1 read tag files... INFO @ Wed, 12 Dec 2018 23:47:02: #1 read treatment tags... INFO @ Wed, 12 Dec 2018 23:47:12: 1000000 INFO @ Wed, 12 Dec 2018 23:47:12: 1000000 INFO @ Wed, 12 Dec 2018 23:47:13: 1000000 INFO @ Wed, 12 Dec 2018 23:47:22: 2000000 INFO @ Wed, 12 Dec 2018 23:47:24: 2000000 INFO @ Wed, 12 Dec 2018 23:47:24: 2000000 INFO @ Wed, 12 Dec 2018 23:47:35: 3000000 INFO @ Wed, 12 Dec 2018 23:47:35: 3000000 INFO @ Wed, 12 Dec 2018 23:47:37: 3000000 INFO @ Wed, 12 Dec 2018 23:47:44: 4000000 INFO @ Wed, 12 Dec 2018 23:47:48: 4000000 INFO @ Wed, 12 Dec 2018 23:47:48: 4000000 INFO @ Wed, 12 Dec 2018 23:47:54: 5000000 INFO @ Wed, 12 Dec 2018 23:48:00: 5000000 INFO @ Wed, 12 Dec 2018 23:48:02: 5000000 INFO @ Wed, 12 Dec 2018 23:48:04: 6000000 INFO @ Wed, 12 Dec 2018 23:48:14: 6000000 INFO @ Wed, 12 Dec 2018 23:48:14: 7000000 INFO @ Wed, 12 Dec 2018 23:48:18: 6000000 INFO @ Wed, 12 Dec 2018 23:48:24: 7000000 INFO @ Wed, 12 Dec 2018 23:48:27: 8000000 INFO @ Wed, 12 Dec 2018 23:48:32: 7000000 INFO @ Wed, 12 Dec 2018 23:48:36: 8000000 INFO @ Wed, 12 Dec 2018 23:48:39: 9000000 INFO @ Wed, 12 Dec 2018 23:48:43: 8000000 INFO @ Wed, 12 Dec 2018 23:48:52: 9000000 INFO @ Wed, 12 Dec 2018 23:48:53: 10000000 INFO @ Wed, 12 Dec 2018 23:48:54: 9000000 INFO @ Wed, 12 Dec 2018 23:49:08: 10000000 INFO @ Wed, 12 Dec 2018 23:49:09: 11000000 INFO @ Wed, 12 Dec 2018 23:49:09: 10000000 INFO @ Wed, 12 Dec 2018 23:49:22: 11000000 INFO @ Wed, 12 Dec 2018 23:49:25: 11000000 INFO @ Wed, 12 Dec 2018 23:49:26: 12000000 INFO @ Wed, 12 Dec 2018 23:49:40: 12000000 INFO @ Wed, 12 Dec 2018 23:49:40: 12000000 INFO @ Wed, 12 Dec 2018 23:49:44: 13000000 INFO @ Wed, 12 Dec 2018 23:49:52: 13000000 INFO @ Wed, 12 Dec 2018 23:49:52: #1 tag size is determined as 50 bps INFO @ Wed, 12 Dec 2018 23:49:52: #1 tag size = 50 INFO @ Wed, 12 Dec 2018 23:49:52: #1 total tags in treatment: 13585861 INFO @ Wed, 12 Dec 2018 23:49:52: #1 user defined the maximum tags... INFO @ Wed, 12 Dec 2018 23:49:52: #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 23:49:53: #1 tags after filtering in treatment: 13585704 INFO @ Wed, 12 Dec 2018 23:49:53: #1 Redundant rate of treatment: 0.00 INFO @ Wed, 12 Dec 2018 23:49:53: #1 finished! INFO @ Wed, 12 Dec 2018 23:49:53: #2 Build Peak Model... INFO @ Wed, 12 Dec 2018 23:49:53: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 12 Dec 2018 23:49:55: 13000000 INFO @ Wed, 12 Dec 2018 23:49:55: #2 number of paired peaks: 7056 INFO @ Wed, 12 Dec 2018 23:49:55: start model_add_line... INFO @ Wed, 12 Dec 2018 23:49:56: start X-correlation... INFO @ Wed, 12 Dec 2018 23:49:56: end of X-cor INFO @ Wed, 12 Dec 2018 23:49:56: #2 finished! INFO @ Wed, 12 Dec 2018 23:49:56: #2 predicted fragment length is 49 bps INFO @ Wed, 12 Dec 2018 23:49:56: #2 alternative fragment length(s) may be 49,201,229,403 bps INFO @ Wed, 12 Dec 2018 23:49:56: #2.2 Generate R script for model : SRX3657373.10_model.r WARNING @ Wed, 12 Dec 2018 23:49:56: #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 23:49:56: #2 You may need to consider one of the other alternative d(s): 49,201,229,403 WARNING @ Wed, 12 Dec 2018 23:49:56: #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 23:49:56: #3 Call peaks... INFO @ Wed, 12 Dec 2018 23:49:56: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 12 Dec 2018 23:49:59: #1 tag size is determined as 50 bps INFO @ Wed, 12 Dec 2018 23:49:59: #1 tag size = 50 INFO @ Wed, 12 Dec 2018 23:49:59: #1 total tags in treatment: 13585861 INFO @ Wed, 12 Dec 2018 23:49:59: #1 user defined the maximum tags... INFO @ Wed, 12 Dec 2018 23:49:59: #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 23:49:59: #1 tags after filtering in treatment: 13585704 INFO @ Wed, 12 Dec 2018 23:49:59: #1 Redundant rate of treatment: 0.00 INFO @ Wed, 12 Dec 2018 23:49:59: #1 finished! INFO @ Wed, 12 Dec 2018 23:49:59: #2 Build Peak Model... INFO @ Wed, 12 Dec 2018 23:49:59: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 12 Dec 2018 23:50:01: #1 tag size is determined as 50 bps INFO @ Wed, 12 Dec 2018 23:50:01: #1 tag size = 50 INFO @ Wed, 12 Dec 2018 23:50:01: #1 total tags in treatment: 13585861 INFO @ Wed, 12 Dec 2018 23:50:01: #1 user defined the maximum tags... INFO @ Wed, 12 Dec 2018 23:50:01: #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 23:50:02: #2 number of paired peaks: 7056 INFO @ Wed, 12 Dec 2018 23:50:02: start model_add_line... INFO @ Wed, 12 Dec 2018 23:50:02: start X-correlation... INFO @ Wed, 12 Dec 2018 23:50:02: end of X-cor INFO @ Wed, 12 Dec 2018 23:50:02: #2 finished! INFO @ Wed, 12 Dec 2018 23:50:02: #2 predicted fragment length is 49 bps INFO @ Wed, 12 Dec 2018 23:50:02: #2 alternative fragment length(s) may be 49,201,229,403 bps INFO @ Wed, 12 Dec 2018 23:50:02: #2.2 Generate R script for model : SRX3657373.05_model.r WARNING @ Wed, 12 Dec 2018 23:50:02: #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 23:50:02: #2 You may need to consider one of the other alternative d(s): 49,201,229,403 WARNING @ Wed, 12 Dec 2018 23:50:02: #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 23:50:02: #3 Call peaks... INFO @ Wed, 12 Dec 2018 23:50:02: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 12 Dec 2018 23:50:02: #1 tags after filtering in treatment: 13585704 INFO @ Wed, 12 Dec 2018 23:50:02: #1 Redundant rate of treatment: 0.00 INFO @ Wed, 12 Dec 2018 23:50:02: #1 finished! INFO @ Wed, 12 Dec 2018 23:50:02: #2 Build Peak Model... INFO @ Wed, 12 Dec 2018 23:50:02: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 12 Dec 2018 23:50:04: #2 number of paired peaks: 7056 INFO @ Wed, 12 Dec 2018 23:50:04: start model_add_line... INFO @ Wed, 12 Dec 2018 23:50:04: start X-correlation... INFO @ Wed, 12 Dec 2018 23:50:04: end of X-cor INFO @ Wed, 12 Dec 2018 23:50:04: #2 finished! INFO @ Wed, 12 Dec 2018 23:50:04: #2 predicted fragment length is 49 bps INFO @ Wed, 12 Dec 2018 23:50:04: #2 alternative fragment length(s) may be 49,201,229,403 bps INFO @ Wed, 12 Dec 2018 23:50:04: #2.2 Generate R script for model : SRX3657373.20_model.r WARNING @ Wed, 12 Dec 2018 23:50:04: #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 23:50:04: #2 You may need to consider one of the other alternative d(s): 49,201,229,403 WARNING @ Wed, 12 Dec 2018 23:50:04: #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 23:50:04: #3 Call peaks... INFO @ Wed, 12 Dec 2018 23:50:04: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 12 Dec 2018 23:50:40: #3 Call peaks for each chromosome... INFO @ Wed, 12 Dec 2018 23:50:48: #3 Call peaks for each chromosome... INFO @ Wed, 12 Dec 2018 23:50:50: #3 Call peaks for each chromosome... INFO @ Wed, 12 Dec 2018 23:51:05: #4 Write output xls file... SRX3657373.10_peaks.xls INFO @ Wed, 12 Dec 2018 23:51:05: #4 Write peak in narrowPeak format file... SRX3657373.10_peaks.narrowPeak INFO @ Wed, 12 Dec 2018 23:51:05: #4 Write summits bed file... SRX3657373.10_summits.bed INFO @ Wed, 12 Dec 2018 23:51:05: Done! pass1 - making usageList (58 chroms): 4 millis pass2 - checking and writing primary data (825 records, 4 fields): 12 millis CompletedMACS2peakCalling INFO @ Wed, 12 Dec 2018 23:51:15: #4 Write output xls file... SRX3657373.20_peaks.xls INFO @ Wed, 12 Dec 2018 23:51:15: #4 Write peak in narrowPeak format file... SRX3657373.20_peaks.narrowPeak INFO @ Wed, 12 Dec 2018 23:51:15: #4 Write summits bed file... SRX3657373.20_summits.bed INFO @ Wed, 12 Dec 2018 23:51:15: Done! pass1 - making usageList (50 chroms): 4 millis pass2 - checking and writing primary data (384 records, 4 fields): 11 millis CompletedMACS2peakCalling INFO @ Wed, 12 Dec 2018 23:51:16: #4 Write output xls file... SRX3657373.05_peaks.xls INFO @ Wed, 12 Dec 2018 23:51:16: #4 Write peak in narrowPeak format file... SRX3657373.05_peaks.narrowPeak INFO @ Wed, 12 Dec 2018 23:51:16: #4 Write summits bed file... SRX3657373.05_summits.bed INFO @ Wed, 12 Dec 2018 23:51:16: Done! pass1 - making usageList (65 chroms): 5 millis pass2 - checking and writing primary data (1317 records, 4 fields): 13 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。