Job ID = 10453665 sra ファイルのダウンロード中... Completed: 468410K bytes transferred in 11 seconds (345772K 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 27557444 spots for /home/okishinya/chipatlas/results/rn6/SRX3478270/SRR6384649.sra Written 27557444 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: 00:00:01 Time loading forward index: 00:00:02 Time loading mirror index: 00:00:02 Multiseed full-index search: 00:22:49 27557444 reads; of these: 27557444 (100.00%) were unpaired; of these: 706210 (2.56%) aligned 0 times 18599221 (67.49%) aligned exactly 1 time 8252013 (29.94%) aligned >1 times 97.44% overall alignment rate Time searching: 00:22:54 Overall time: 00:22:54 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] 739974 / 26851234 = 0.0276 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, 08 Feb 2018 17:35:41: # Command line: callpeak -t SRX3478270.bam -f BAM -g 2.15e9 -n SRX3478270.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX3478270.05 # format = BAM # ChIP-seq file = ['SRX3478270.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, 08 Feb 2018 17:35:41: # Command line: callpeak -t SRX3478270.bam -f BAM -g 2.15e9 -n SRX3478270.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX3478270.20 # format = BAM # ChIP-seq file = ['SRX3478270.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, 08 Feb 2018 17:35:41: # Command line: callpeak -t SRX3478270.bam -f BAM -g 2.15e9 -n SRX3478270.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX3478270.10 # format = BAM # ChIP-seq file = ['SRX3478270.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, 08 Feb 2018 17:35:41: #1 read tag files... INFO @ Thu, 08 Feb 2018 17:35:41: #1 read tag files... INFO @ Thu, 08 Feb 2018 17:35:41: #1 read tag files... INFO @ Thu, 08 Feb 2018 17:35:41: #1 read treatment tags... INFO @ Thu, 08 Feb 2018 17:35:41: #1 read treatment tags... INFO @ Thu, 08 Feb 2018 17:35:41: #1 read treatment tags... INFO @ Thu, 08 Feb 2018 17:35:50: 1000000 INFO @ Thu, 08 Feb 2018 17:35:50: 1000000 INFO @ Thu, 08 Feb 2018 17:35:50: 1000000 INFO @ Thu, 08 Feb 2018 17:35:57: 2000000 INFO @ Thu, 08 Feb 2018 17:35:57: 2000000 INFO @ Thu, 08 Feb 2018 17:35:57: 2000000 INFO @ Thu, 08 Feb 2018 17:36:04: 3000000 INFO @ Thu, 08 Feb 2018 17:36:05: 3000000 INFO @ Thu, 08 Feb 2018 17:36:05: 3000000 INFO @ Thu, 08 Feb 2018 17:36:11: 4000000 INFO @ Thu, 08 Feb 2018 17:36:12: 4000000 INFO @ Thu, 08 Feb 2018 17:36:12: 4000000 INFO @ Thu, 08 Feb 2018 17:36:18: 5000000 INFO @ Thu, 08 Feb 2018 17:36:20: 5000000 INFO @ Thu, 08 Feb 2018 17:36:20: 5000000 INFO @ Thu, 08 Feb 2018 17:36:26: 6000000 INFO @ Thu, 08 Feb 2018 17:36:27: 6000000 INFO @ Thu, 08 Feb 2018 17:36:27: 6000000 INFO @ Thu, 08 Feb 2018 17:36:33: 7000000 INFO @ Thu, 08 Feb 2018 17:36:35: 7000000 INFO @ Thu, 08 Feb 2018 17:36:35: 7000000 INFO @ Thu, 08 Feb 2018 17:36:40: 8000000 INFO @ Thu, 08 Feb 2018 17:36:42: 8000000 INFO @ Thu, 08 Feb 2018 17:36:42: 8000000 INFO @ Thu, 08 Feb 2018 17:36:47: 9000000 INFO @ Thu, 08 Feb 2018 17:36:50: 9000000 INFO @ Thu, 08 Feb 2018 17:36:50: 9000000 INFO @ Thu, 08 Feb 2018 17:36:57: 10000000 INFO @ Thu, 08 Feb 2018 17:36:59: 10000000 INFO @ Thu, 08 Feb 2018 17:36:59: 10000000 INFO @ Thu, 08 Feb 2018 17:37:06: 11000000 INFO @ Thu, 08 Feb 2018 17:37:09: 11000000 INFO @ Thu, 08 Feb 2018 17:37:09: 11000000 INFO @ Thu, 08 Feb 2018 17:37:17: 12000000 INFO @ Thu, 08 Feb 2018 17:37:18: 12000000 INFO @ Thu, 08 Feb 2018 17:37:18: 12000000 INFO @ Thu, 08 Feb 2018 17:37:27: 13000000 INFO @ Thu, 08 Feb 2018 17:37:28: 13000000 INFO @ Thu, 08 Feb 2018 17:37:28: 13000000 INFO @ Thu, 08 Feb 2018 17:37:37: 14000000 INFO @ Thu, 08 Feb 2018 17:37:37: 14000000 INFO @ Thu, 08 Feb 2018 17:37:37: 14000000 INFO @ Thu, 08 Feb 2018 17:37:46: 15000000 INFO @ Thu, 08 Feb 2018 17:37:46: 15000000 INFO @ Thu, 08 Feb 2018 17:37:46: 15000000 INFO @ Thu, 08 Feb 2018 17:37:55: 16000000 INFO @ Thu, 08 Feb 2018 17:37:56: 16000000 INFO @ Thu, 08 Feb 2018 17:37:56: 16000000 INFO @ Thu, 08 Feb 2018 17:38:05: 17000000 INFO @ Thu, 08 Feb 2018 17:38:05: 17000000 INFO @ Thu, 08 Feb 2018 17:38:05: 17000000 INFO @ Thu, 08 Feb 2018 17:38:14: 18000000 INFO @ Thu, 08 Feb 2018 17:38:14: 18000000 INFO @ Thu, 08 Feb 2018 17:38:15: 18000000 INFO @ Thu, 08 Feb 2018 17:38:23: 19000000 INFO @ Thu, 08 Feb 2018 17:38:23: 19000000 INFO @ Thu, 08 Feb 2018 17:38:25: 19000000 INFO @ Thu, 08 Feb 2018 17:38:32: 20000000 INFO @ Thu, 08 Feb 2018 17:38:32: 20000000 INFO @ Thu, 08 Feb 2018 17:38:34: 20000000 INFO @ Thu, 08 Feb 2018 17:38:42: 21000000 INFO @ Thu, 08 Feb 2018 17:38:42: 21000000 INFO @ Thu, 08 Feb 2018 17:38:44: 21000000 INFO @ Thu, 08 Feb 2018 17:38:51: 22000000 INFO @ Thu, 08 Feb 2018 17:38:51: 22000000 INFO @ Thu, 08 Feb 2018 17:38:53: 22000000 INFO @ Thu, 08 Feb 2018 17:39:00: 23000000 INFO @ Thu, 08 Feb 2018 17:39:00: 23000000 INFO @ Thu, 08 Feb 2018 17:39:03: 23000000 INFO @ Thu, 08 Feb 2018 17:39:09: 24000000 INFO @ Thu, 08 Feb 2018 17:39:09: 24000000 INFO @ Thu, 08 Feb 2018 17:39:13: 24000000 INFO @ Thu, 08 Feb 2018 17:39:19: 25000000 INFO @ Thu, 08 Feb 2018 17:39:19: 25000000 INFO @ Thu, 08 Feb 2018 17:39:22: 25000000 INFO @ Thu, 08 Feb 2018 17:39:28: 26000000 INFO @ Thu, 08 Feb 2018 17:39:28: 26000000 INFO @ Thu, 08 Feb 2018 17:39:29: #1 tag size is determined as 51 bps INFO @ Thu, 08 Feb 2018 17:39:29: #1 tag size = 51 INFO @ Thu, 08 Feb 2018 17:39:29: #1 total tags in treatment: 26111260 INFO @ Thu, 08 Feb 2018 17:39:29: #1 user defined the maximum tags... INFO @ Thu, 08 Feb 2018 17:39:29: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Thu, 08 Feb 2018 17:39:29: #1 tag size is determined as 51 bps INFO @ Thu, 08 Feb 2018 17:39:29: #1 tag size = 51 INFO @ Thu, 08 Feb 2018 17:39:29: #1 total tags in treatment: 26111260 INFO @ Thu, 08 Feb 2018 17:39:29: #1 user defined the maximum tags... INFO @ Thu, 08 Feb 2018 17:39:29: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Thu, 08 Feb 2018 17:39:30: #1 tags after filtering in treatment: 26111163 INFO @ Thu, 08 Feb 2018 17:39:30: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 08 Feb 2018 17:39:30: #1 finished! INFO @ Thu, 08 Feb 2018 17:39:30: #2 Build Peak Model... INFO @ Thu, 08 Feb 2018 17:39:30: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 08 Feb 2018 17:39:30: #1 tags after filtering in treatment: 26111163 INFO @ Thu, 08 Feb 2018 17:39:30: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 08 Feb 2018 17:39:30: #1 finished! INFO @ Thu, 08 Feb 2018 17:39:30: #2 Build Peak Model... INFO @ Thu, 08 Feb 2018 17:39:30: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 08 Feb 2018 17:39:32: 26000000 INFO @ Thu, 08 Feb 2018 17:39:32: #2 number of paired peaks: 6224 INFO @ Thu, 08 Feb 2018 17:39:32: start model_add_line... INFO @ Thu, 08 Feb 2018 17:39:32: #2 number of paired peaks: 6224 INFO @ Thu, 08 Feb 2018 17:39:32: start model_add_line... INFO @ Thu, 08 Feb 2018 17:39:33: start X-correlation... INFO @ Thu, 08 Feb 2018 17:39:33: end of X-cor INFO @ Thu, 08 Feb 2018 17:39:33: #2 finished! INFO @ Thu, 08 Feb 2018 17:39:33: #2 predicted fragment length is 50 bps INFO @ Thu, 08 Feb 2018 17:39:33: #2 alternative fragment length(s) may be 50,221,404,595 bps INFO @ Thu, 08 Feb 2018 17:39:33: #2.2 Generate R script for model : SRX3478270.20_model.r WARNING @ Thu, 08 Feb 2018 17:39:33: #2 Since the d (50) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 08 Feb 2018 17:39:33: #2 You may need to consider one of the other alternative d(s): 50,221,404,595 WARNING @ Thu, 08 Feb 2018 17:39:33: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Thu, 08 Feb 2018 17:39:33: #3 Call peaks... INFO @ Thu, 08 Feb 2018 17:39:33: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 08 Feb 2018 17:39:33: start X-correlation... INFO @ Thu, 08 Feb 2018 17:39:33: end of X-cor INFO @ Thu, 08 Feb 2018 17:39:33: #2 finished! INFO @ Thu, 08 Feb 2018 17:39:33: #2 predicted fragment length is 50 bps INFO @ Thu, 08 Feb 2018 17:39:33: #2 alternative fragment length(s) may be 50,221,404,595 bps INFO @ Thu, 08 Feb 2018 17:39:33: #2.2 Generate R script for model : SRX3478270.10_model.r WARNING @ Thu, 08 Feb 2018 17:39:33: #2 Since the d (50) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 08 Feb 2018 17:39:33: #2 You may need to consider one of the other alternative d(s): 50,221,404,595 WARNING @ Thu, 08 Feb 2018 17:39:33: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Thu, 08 Feb 2018 17:39:33: #3 Call peaks... INFO @ Thu, 08 Feb 2018 17:39:33: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 08 Feb 2018 17:39:33: #1 tag size is determined as 51 bps INFO @ Thu, 08 Feb 2018 17:39:33: #1 tag size = 51 INFO @ Thu, 08 Feb 2018 17:39:33: #1 total tags in treatment: 26111260 INFO @ Thu, 08 Feb 2018 17:39:33: #1 user defined the maximum tags... INFO @ Thu, 08 Feb 2018 17:39:33: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Thu, 08 Feb 2018 17:39:34: #1 tags after filtering in treatment: 26111163 INFO @ Thu, 08 Feb 2018 17:39:34: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 08 Feb 2018 17:39:34: #1 finished! INFO @ Thu, 08 Feb 2018 17:39:34: #2 Build Peak Model... INFO @ Thu, 08 Feb 2018 17:39:34: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 08 Feb 2018 17:39:36: #2 number of paired peaks: 6224 INFO @ Thu, 08 Feb 2018 17:39:36: start model_add_line... INFO @ Thu, 08 Feb 2018 17:39:36: start X-correlation... INFO @ Thu, 08 Feb 2018 17:39:36: end of X-cor INFO @ Thu, 08 Feb 2018 17:39:36: #2 finished! INFO @ Thu, 08 Feb 2018 17:39:36: #2 predicted fragment length is 50 bps INFO @ Thu, 08 Feb 2018 17:39:36: #2 alternative fragment length(s) may be 50,221,404,595 bps INFO @ Thu, 08 Feb 2018 17:39:36: #2.2 Generate R script for model : SRX3478270.05_model.r WARNING @ Thu, 08 Feb 2018 17:39:37: #2 Since the d (50) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 08 Feb 2018 17:39:37: #2 You may need to consider one of the other alternative d(s): 50,221,404,595 WARNING @ Thu, 08 Feb 2018 17:39:37: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Thu, 08 Feb 2018 17:39:37: #3 Call peaks... INFO @ Thu, 08 Feb 2018 17:39:37: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 08 Feb 2018 17:40:33: #3 Call peaks for each chromosome... INFO @ Thu, 08 Feb 2018 17:40:35: #3 Call peaks for each chromosome... INFO @ Thu, 08 Feb 2018 17:40:43: #3 Call peaks for each chromosome... INFO @ Thu, 08 Feb 2018 17:41:10: #4 Write output xls file... SRX3478270.10_peaks.xls INFO @ Thu, 08 Feb 2018 17:41:10: #4 Write peak in narrowPeak format file... SRX3478270.10_peaks.narrowPeak INFO @ Thu, 08 Feb 2018 17:41:10: #4 Write summits bed file... SRX3478270.10_summits.bed INFO @ Thu, 08 Feb 2018 17:41:10: Done! pass1 - making usageList (39 chroms): 1 millis pass2 - checking and writing primary data (993 records, 4 fields): 5 millis CompletedMACS2peakCalling INFO @ Thu, 08 Feb 2018 17:41:11: #4 Write output xls file... SRX3478270.20_peaks.xls INFO @ Thu, 08 Feb 2018 17:41:11: #4 Write peak in narrowPeak format file... SRX3478270.20_peaks.narrowPeak INFO @ Thu, 08 Feb 2018 17:41:11: #4 Write summits bed file... SRX3478270.20_summits.bed INFO @ Thu, 08 Feb 2018 17:41:11: Done! pass1 - making usageList (32 chroms): 1 millis pass2 - checking and writing primary data (477 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Thu, 08 Feb 2018 17:41:18: #4 Write output xls file... SRX3478270.05_peaks.xls INFO @ Thu, 08 Feb 2018 17:41:18: #4 Write peak in narrowPeak format file... SRX3478270.05_peaks.narrowPeak INFO @ Thu, 08 Feb 2018 17:41:18: #4 Write summits bed file... SRX3478270.05_summits.bed INFO @ Thu, 08 Feb 2018 17:41:18: Done! pass1 - making usageList (47 chroms): 1 millis pass2 - checking and writing primary data (1714 records, 4 fields): 6 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。