Job ID = 11388805 sra ファイルのダウンロード中... Completed: 257671K bytes transferred in 11 seconds (176507K bits/sec), in 1 file. Completed: 255243K bytes transferred in 9 seconds (221260K 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 11599148 spots for /home/okishinya/chipatlas/results/rn6/SRX3657372/SRR6681062.sra Written 11599148 spots for /home/okishinya/chipatlas/results/rn6/SRX3657372/SRR6681062.sra Read 11681264 spots for /home/okishinya/chipatlas/results/rn6/SRX3657372/SRR6681061.sra Written 11681264 spots for /home/okishinya/chipatlas/results/rn6/SRX3657372/SRR6681061.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: 00:43:00 23280412 reads; of these: 23280412 (100.00%) were unpaired; of these: 2033070 (8.73%) aligned 0 times 15297028 (65.71%) aligned exactly 1 time 5950314 (25.56%) aligned >1 times 91.27% overall alignment rate Time searching: 00:43:04 Overall time: 00:43:04 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] 2883520 / 21247342 = 0.1357 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 23:48:19: # Command line: callpeak -t SRX3657372.bam -f BAM -g 2.15e9 -n SRX3657372.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX3657372.20 # format = BAM # ChIP-seq file = ['SRX3657372.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 23:48:19: #1 read tag files... INFO @ Wed, 12 Dec 2018 23:48:19: #1 read treatment tags... INFO @ Wed, 12 Dec 2018 23:48:19: # Command line: callpeak -t SRX3657372.bam -f BAM -g 2.15e9 -n SRX3657372.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX3657372.10 # format = BAM # ChIP-seq file = ['SRX3657372.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 23:48:19: #1 read tag files... INFO @ Wed, 12 Dec 2018 23:48:19: #1 read treatment tags... INFO @ Wed, 12 Dec 2018 23:48:19: # Command line: callpeak -t SRX3657372.bam -f BAM -g 2.15e9 -n SRX3657372.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX3657372.05 # format = BAM # ChIP-seq file = ['SRX3657372.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 23:48:19: #1 read tag files... INFO @ Wed, 12 Dec 2018 23:48:19: #1 read treatment tags... INFO @ Wed, 12 Dec 2018 23:48:31: 1000000 INFO @ Wed, 12 Dec 2018 23:48:31: 1000000 INFO @ Wed, 12 Dec 2018 23:48:31: 1000000 INFO @ Wed, 12 Dec 2018 23:48:41: 2000000 INFO @ Wed, 12 Dec 2018 23:48:44: 2000000 INFO @ Wed, 12 Dec 2018 23:48:47: 2000000 INFO @ Wed, 12 Dec 2018 23:48:53: 3000000 INFO @ Wed, 12 Dec 2018 23:49:01: 3000000 INFO @ Wed, 12 Dec 2018 23:49:04: 4000000 INFO @ Wed, 12 Dec 2018 23:49:05: 3000000 INFO @ Wed, 12 Dec 2018 23:49:15: 4000000 INFO @ Wed, 12 Dec 2018 23:49:16: 5000000 INFO @ Wed, 12 Dec 2018 23:49:22: 4000000 INFO @ Wed, 12 Dec 2018 23:49:25: 5000000 INFO @ Wed, 12 Dec 2018 23:49:28: 6000000 INFO @ Wed, 12 Dec 2018 23:49:36: 6000000 INFO @ Wed, 12 Dec 2018 23:49:39: 5000000 INFO @ Wed, 12 Dec 2018 23:49:40: 7000000 INFO @ Wed, 12 Dec 2018 23:49:48: 7000000 INFO @ Wed, 12 Dec 2018 23:49:51: 8000000 INFO @ Wed, 12 Dec 2018 23:49:54: 6000000 INFO @ Wed, 12 Dec 2018 23:50:00: 8000000 INFO @ Wed, 12 Dec 2018 23:50:02: 9000000 INFO @ Wed, 12 Dec 2018 23:50:10: 7000000 INFO @ Wed, 12 Dec 2018 23:50:13: 9000000 INFO @ Wed, 12 Dec 2018 23:50:15: 10000000 INFO @ Wed, 12 Dec 2018 23:50:23: 8000000 INFO @ Wed, 12 Dec 2018 23:50:25: 11000000 INFO @ Wed, 12 Dec 2018 23:50:26: 10000000 INFO @ Wed, 12 Dec 2018 23:50:34: 9000000 INFO @ Wed, 12 Dec 2018 23:50:36: 12000000 INFO @ Wed, 12 Dec 2018 23:50:38: 11000000 INFO @ Wed, 12 Dec 2018 23:50:45: 10000000 INFO @ Wed, 12 Dec 2018 23:50:47: 13000000 INFO @ Wed, 12 Dec 2018 23:50:50: 12000000 INFO @ Wed, 12 Dec 2018 23:50:58: 11000000 INFO @ Wed, 12 Dec 2018 23:51:02: 14000000 INFO @ Wed, 12 Dec 2018 23:51:02: 13000000 INFO @ Wed, 12 Dec 2018 23:51:12: 12000000 INFO @ Wed, 12 Dec 2018 23:51:15: 15000000 INFO @ Wed, 12 Dec 2018 23:51:19: 14000000 INFO @ Wed, 12 Dec 2018 23:51:25: 13000000 INFO @ Wed, 12 Dec 2018 23:51:28: 16000000 INFO @ Wed, 12 Dec 2018 23:51:31: 15000000 INFO @ Wed, 12 Dec 2018 23:51:36: 14000000 INFO @ Wed, 12 Dec 2018 23:51:41: 16000000 INFO @ Wed, 12 Dec 2018 23:51:41: 17000000 INFO @ Wed, 12 Dec 2018 23:51:47: 15000000 INFO @ Wed, 12 Dec 2018 23:51:52: 17000000 INFO @ Wed, 12 Dec 2018 23:51:54: 18000000 INFO @ Wed, 12 Dec 2018 23:51:58: 16000000 INFO @ Wed, 12 Dec 2018 23:51:59: #1 tag size is determined as 50 bps INFO @ Wed, 12 Dec 2018 23:51:59: #1 tag size = 50 INFO @ Wed, 12 Dec 2018 23:51:59: #1 total tags in treatment: 18363822 INFO @ Wed, 12 Dec 2018 23:51:59: #1 user defined the maximum tags... INFO @ Wed, 12 Dec 2018 23:51:59: #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 23:52:00: #1 tags after filtering in treatment: 18363698 INFO @ Wed, 12 Dec 2018 23:52:00: #1 Redundant rate of treatment: 0.00 INFO @ Wed, 12 Dec 2018 23:52:00: #1 finished! INFO @ Wed, 12 Dec 2018 23:52:00: #2 Build Peak Model... INFO @ Wed, 12 Dec 2018 23:52:00: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 12 Dec 2018 23:52:02: #2 number of paired peaks: 5336 INFO @ Wed, 12 Dec 2018 23:52:02: start model_add_line... INFO @ Wed, 12 Dec 2018 23:52:03: start X-correlation... INFO @ Wed, 12 Dec 2018 23:52:03: end of X-cor INFO @ Wed, 12 Dec 2018 23:52:03: #2 finished! INFO @ Wed, 12 Dec 2018 23:52:03: #2 predicted fragment length is 50 bps INFO @ Wed, 12 Dec 2018 23:52:03: #2 alternative fragment length(s) may be 50,221,383,408 bps INFO @ Wed, 12 Dec 2018 23:52:03: #2.2 Generate R script for model : SRX3657372.05_model.r WARNING @ Wed, 12 Dec 2018 23:52:03: #2 Since the d (50) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Wed, 12 Dec 2018 23:52:03: #2 You may need to consider one of the other alternative d(s): 50,221,383,408 WARNING @ Wed, 12 Dec 2018 23:52:03: #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 23:52:03: #3 Call peaks... INFO @ Wed, 12 Dec 2018 23:52:03: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 12 Dec 2018 23:52:03: 18000000 INFO @ Wed, 12 Dec 2018 23:52:07: #1 tag size is determined as 50 bps INFO @ Wed, 12 Dec 2018 23:52:07: #1 tag size = 50 INFO @ Wed, 12 Dec 2018 23:52:07: #1 total tags in treatment: 18363822 INFO @ Wed, 12 Dec 2018 23:52:07: #1 user defined the maximum tags... INFO @ Wed, 12 Dec 2018 23:52:07: #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 23:52:08: #1 tags after filtering in treatment: 18363698 INFO @ Wed, 12 Dec 2018 23:52:08: #1 Redundant rate of treatment: 0.00 INFO @ Wed, 12 Dec 2018 23:52:08: #1 finished! INFO @ Wed, 12 Dec 2018 23:52:08: #2 Build Peak Model... INFO @ Wed, 12 Dec 2018 23:52:08: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 12 Dec 2018 23:52:08: 17000000 INFO @ Wed, 12 Dec 2018 23:52:10: #2 number of paired peaks: 5336 INFO @ Wed, 12 Dec 2018 23:52:10: start model_add_line... INFO @ Wed, 12 Dec 2018 23:52:11: start X-correlation... INFO @ Wed, 12 Dec 2018 23:52:11: end of X-cor INFO @ Wed, 12 Dec 2018 23:52:11: #2 finished! INFO @ Wed, 12 Dec 2018 23:52:11: #2 predicted fragment length is 50 bps INFO @ Wed, 12 Dec 2018 23:52:11: #2 alternative fragment length(s) may be 50,221,383,408 bps INFO @ Wed, 12 Dec 2018 23:52:11: #2.2 Generate R script for model : SRX3657372.20_model.r WARNING @ Wed, 12 Dec 2018 23:52:11: #2 Since the d (50) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Wed, 12 Dec 2018 23:52:11: #2 You may need to consider one of the other alternative d(s): 50,221,383,408 WARNING @ Wed, 12 Dec 2018 23:52:11: #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 23:52:11: #3 Call peaks... INFO @ Wed, 12 Dec 2018 23:52:11: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 12 Dec 2018 23:52:17: 18000000 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: 18363822 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: 18363698 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 23:52:25: #2 number of paired peaks: 5336 INFO @ Wed, 12 Dec 2018 23:52:25: start model_add_line... INFO @ Wed, 12 Dec 2018 23:52:26: start X-correlation... INFO @ Wed, 12 Dec 2018 23:52:26: end of X-cor INFO @ Wed, 12 Dec 2018 23:52:26: #2 finished! INFO @ Wed, 12 Dec 2018 23:52:26: #2 predicted fragment length is 50 bps INFO @ Wed, 12 Dec 2018 23:52:26: #2 alternative fragment length(s) may be 50,221,383,408 bps INFO @ Wed, 12 Dec 2018 23:52:26: #2.2 Generate R script for model : SRX3657372.10_model.r WARNING @ Wed, 12 Dec 2018 23:52:26: #2 Since the d (50) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Wed, 12 Dec 2018 23:52:26: #2 You may need to consider one of the other alternative d(s): 50,221,383,408 WARNING @ Wed, 12 Dec 2018 23:52:26: #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 23:52:26: #3 Call peaks... INFO @ Wed, 12 Dec 2018 23:52:26: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 12 Dec 2018 23:53:03: #3 Call peaks for each chromosome... INFO @ Wed, 12 Dec 2018 23:53:08: #3 Call peaks for each chromosome... INFO @ Wed, 12 Dec 2018 23:53:26: #3 Call peaks for each chromosome... INFO @ Wed, 12 Dec 2018 23:53:39: #4 Write output xls file... SRX3657372.05_peaks.xls INFO @ Wed, 12 Dec 2018 23:53:39: #4 Write peak in narrowPeak format file... SRX3657372.05_peaks.narrowPeak INFO @ Wed, 12 Dec 2018 23:53:39: #4 Write summits bed file... SRX3657372.05_summits.bed INFO @ Wed, 12 Dec 2018 23:53:39: Done! pass1 - making usageList (63 chroms): 6 millis pass2 - checking and writing primary data (1457 records, 4 fields): 13 millis CompletedMACS2peakCalling INFO @ Wed, 12 Dec 2018 23:53:41: #4 Write output xls file... SRX3657372.20_peaks.xls INFO @ Wed, 12 Dec 2018 23:53:41: #4 Write peak in narrowPeak format file... SRX3657372.20_peaks.narrowPeak INFO @ Wed, 12 Dec 2018 23:53:41: #4 Write summits bed file... SRX3657372.20_summits.bed INFO @ Wed, 12 Dec 2018 23:53:41: Done! pass1 - making usageList (46 chroms): 5 millis pass2 - checking and writing primary data (431 records, 4 fields): 11 millis CompletedMACS2peakCalling INFO @ Wed, 12 Dec 2018 23:54:01: #4 Write output xls file... SRX3657372.10_peaks.xls INFO @ Wed, 12 Dec 2018 23:54:01: #4 Write peak in narrowPeak format file... SRX3657372.10_peaks.narrowPeak INFO @ Wed, 12 Dec 2018 23:54:01: #4 Write summits bed file... SRX3657372.10_summits.bed INFO @ Wed, 12 Dec 2018 23:54:01: Done! pass1 - making usageList (56 chroms): 4 millis pass2 - checking and writing primary data (897 records, 4 fields): 12 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。