Job ID = 9025669 sra ファイルのダウンロード中... Completed: 2431478K bytes transferred in 39 seconds (506642K bits/sec), in 1 file, 2 directories. % Total % Received % Xferd Average Speed Time Time Time Current Dload Upload Total Spent Left Speed 0 0 0 0 0 0 0 0 --:--:-- 0:00:06 --:--:-- 0 101 5455 0 5455 0 0 725 0 --:--:-- 0:00:07 --:--:-- 5041 100 24454 0 24454 0 0 2872 0 --:--:-- 0:00:08 --:--:-- 11756 100 31168 0 31168 0 0 3590 0 --:--:-- 0:00:08 --:--:-- 13870 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 41298351 spots for /home/okishinya/chipatlas/results/ce10/SRX2163949/SRR4242864.sra Written 41298351 spots total 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: 00:00:00 Time loading mirror index: 00:00:00 Multiseed full-index search: 00:16:12 41298351 reads; of these: 41298351 (100.00%) were unpaired; of these: 9783373 (23.69%) aligned 0 times 27298432 (66.10%) aligned exactly 1 time 4216546 (10.21%) aligned >1 times 76.31% overall alignment rate Time searching: 00:16:12 Overall time: 00:16:12 マッピングが完了しました。 samtools でBAM に変換中... [samopen] SAM header is present: 7 sequences. [bam_sort_core] merging from 16 files... [bam_rmdupse_core] 14723508 / 31514978 = 0.4672 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 @ Sat, 03 Jun 2017 05:19:46: # Command line: callpeak -t SRX2163949.bam -f BAM -g ce -n SRX2163949.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX2163949.05 # format = BAM # ChIP-seq file = ['SRX2163949.bam'] # control file = None # effective genome size = 9.00e+07 # 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 INFO @ Sat, 03 Jun 2017 05:19:46: #1 read tag files... INFO @ Sat, 03 Jun 2017 05:19:46: #1 read treatment tags... INFO @ Sat, 03 Jun 2017 05:19:46: # Command line: callpeak -t SRX2163949.bam -f BAM -g ce -n SRX2163949.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX2163949.20 # format = BAM # ChIP-seq file = ['SRX2163949.bam'] # control file = None # effective genome size = 9.00e+07 # 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 INFO @ Sat, 03 Jun 2017 05:19:46: #1 read tag files... INFO @ Sat, 03 Jun 2017 05:19:46: #1 read treatment tags... INFO @ Sat, 03 Jun 2017 05:19:46: # Command line: callpeak -t SRX2163949.bam -f BAM -g ce -n SRX2163949.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX2163949.10 # format = BAM # ChIP-seq file = ['SRX2163949.bam'] # control file = None # effective genome size = 9.00e+07 # 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 INFO @ Sat, 03 Jun 2017 05:19:46: #1 read tag files... INFO @ Sat, 03 Jun 2017 05:19:46: #1 read treatment tags... INFO @ Sat, 03 Jun 2017 05:19:56: 1000000 INFO @ Sat, 03 Jun 2017 05:19:56: 1000000 INFO @ Sat, 03 Jun 2017 05:19:56: 1000000 INFO @ Sat, 03 Jun 2017 05:20:05: 2000000 INFO @ Sat, 03 Jun 2017 05:20:05: 2000000 INFO @ Sat, 03 Jun 2017 05:20:05: 2000000 INFO @ Sat, 03 Jun 2017 05:20:14: 3000000 INFO @ Sat, 03 Jun 2017 05:20:14: 3000000 INFO @ Sat, 03 Jun 2017 05:20:14: 3000000 INFO @ Sat, 03 Jun 2017 05:20:22: 4000000 INFO @ Sat, 03 Jun 2017 05:20:22: 4000000 INFO @ Sat, 03 Jun 2017 05:20:22: 4000000 INFO @ Sat, 03 Jun 2017 05:20:31: 5000000 INFO @ Sat, 03 Jun 2017 05:20:31: 5000000 INFO @ Sat, 03 Jun 2017 05:20:31: 5000000 INFO @ Sat, 03 Jun 2017 05:20:40: 6000000 INFO @ Sat, 03 Jun 2017 05:20:40: 6000000 INFO @ Sat, 03 Jun 2017 05:20:40: 6000000 INFO @ Sat, 03 Jun 2017 05:20:49: 7000000 INFO @ Sat, 03 Jun 2017 05:20:49: 7000000 INFO @ Sat, 03 Jun 2017 05:20:49: 7000000 INFO @ Sat, 03 Jun 2017 05:20:59: 8000000 INFO @ Sat, 03 Jun 2017 05:20:59: 8000000 INFO @ Sat, 03 Jun 2017 05:20:59: 8000000 INFO @ Sat, 03 Jun 2017 05:21:08: 9000000 INFO @ Sat, 03 Jun 2017 05:21:08: 9000000 INFO @ Sat, 03 Jun 2017 05:21:08: 9000000 INFO @ Sat, 03 Jun 2017 05:21:17: 10000000 INFO @ Sat, 03 Jun 2017 05:21:17: 10000000 INFO @ Sat, 03 Jun 2017 05:21:17: 10000000 INFO @ Sat, 03 Jun 2017 05:21:26: 11000000 INFO @ Sat, 03 Jun 2017 05:21:26: 11000000 INFO @ Sat, 03 Jun 2017 05:21:26: 11000000 INFO @ Sat, 03 Jun 2017 05:21:35: 12000000 INFO @ Sat, 03 Jun 2017 05:21:35: 12000000 INFO @ Sat, 03 Jun 2017 05:21:35: 12000000 INFO @ Sat, 03 Jun 2017 05:21:44: 13000000 INFO @ Sat, 03 Jun 2017 05:21:44: 13000000 INFO @ Sat, 03 Jun 2017 05:21:44: 13000000 INFO @ Sat, 03 Jun 2017 05:21:53: 14000000 INFO @ Sat, 03 Jun 2017 05:21:53: 14000000 INFO @ Sat, 03 Jun 2017 05:21:53: 14000000 INFO @ Sat, 03 Jun 2017 05:22:03: 15000000 INFO @ Sat, 03 Jun 2017 05:22:03: 15000000 INFO @ Sat, 03 Jun 2017 05:22:03: 15000000 INFO @ Sat, 03 Jun 2017 05:22:11: 16000000 INFO @ Sat, 03 Jun 2017 05:22:11: 16000000 INFO @ Sat, 03 Jun 2017 05:22:11: 16000000 INFO @ Sat, 03 Jun 2017 05:22:17: #1 tag size is determined as 92 bps INFO @ Sat, 03 Jun 2017 05:22:17: #1 tag size = 92 INFO @ Sat, 03 Jun 2017 05:22:17: #1 total tags in treatment: 16791470 INFO @ Sat, 03 Jun 2017 05:22:17: #1 user defined the maximum tags... INFO @ Sat, 03 Jun 2017 05:22:17: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 03 Jun 2017 05:22:18: #1 tag size is determined as 92 bps INFO @ Sat, 03 Jun 2017 05:22:18: #1 tag size = 92 INFO @ Sat, 03 Jun 2017 05:22:18: #1 total tags in treatment: 16791470 INFO @ Sat, 03 Jun 2017 05:22:18: #1 user defined the maximum tags... INFO @ Sat, 03 Jun 2017 05:22:18: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 03 Jun 2017 05:22:18: #1 tag size is determined as 92 bps INFO @ Sat, 03 Jun 2017 05:22:18: #1 tag size = 92 INFO @ Sat, 03 Jun 2017 05:22:18: #1 total tags in treatment: 16791470 INFO @ Sat, 03 Jun 2017 05:22:18: #1 user defined the maximum tags... INFO @ Sat, 03 Jun 2017 05:22:18: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 03 Jun 2017 05:22:21: #1 tags after filtering in treatment: 16766963 INFO @ Sat, 03 Jun 2017 05:22:21: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 03 Jun 2017 05:22:21: #1 finished! INFO @ Sat, 03 Jun 2017 05:22:21: #2 Build Peak Model... INFO @ Sat, 03 Jun 2017 05:22:21: #1 tags after filtering in treatment: 16766963 INFO @ Sat, 03 Jun 2017 05:22:21: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 03 Jun 2017 05:22:21: #1 finished! INFO @ Sat, 03 Jun 2017 05:22:21: #2 Build Peak Model... INFO @ Sat, 03 Jun 2017 05:22:21: #1 tags after filtering in treatment: 16766963 INFO @ Sat, 03 Jun 2017 05:22:21: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 03 Jun 2017 05:22:21: #1 finished! INFO @ Sat, 03 Jun 2017 05:22:21: #2 Build Peak Model... INFO @ Sat, 03 Jun 2017 05:22:24: #2 number of paired peaks: 1378 INFO @ Sat, 03 Jun 2017 05:22:24: start model_add_line... INFO @ Sat, 03 Jun 2017 05:22:24: #2 number of paired peaks: 1378 INFO @ Sat, 03 Jun 2017 05:22:24: start model_add_line... INFO @ Sat, 03 Jun 2017 05:22:24: #2 number of paired peaks: 1378 INFO @ Sat, 03 Jun 2017 05:22:24: start model_add_line... INFO @ Sat, 03 Jun 2017 05:22:43: start X-correlation... INFO @ Sat, 03 Jun 2017 05:22:43: end of X-cor INFO @ Sat, 03 Jun 2017 05:22:43: #2 finished! INFO @ Sat, 03 Jun 2017 05:22:43: #2 predicted fragment length is 181 bps INFO @ Sat, 03 Jun 2017 05:22:43: #2 alternative fragment length(s) may be 181 bps INFO @ Sat, 03 Jun 2017 05:22:43: #2.2 Generate R script for model : SRX2163949.10_model.r WARNING @ Sat, 03 Jun 2017 05:22:43: #2 Since the d (181) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 03 Jun 2017 05:22:43: #2 You may need to consider one of the other alternative d(s): 181 WARNING @ Sat, 03 Jun 2017 05:22:43: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sat, 03 Jun 2017 05:22:43: #3 Call peaks... INFO @ Sat, 03 Jun 2017 05:22:43: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Jun 2017 05:22:43: start X-correlation... INFO @ Sat, 03 Jun 2017 05:22:43: end of X-cor INFO @ Sat, 03 Jun 2017 05:22:43: #2 finished! INFO @ Sat, 03 Jun 2017 05:22:43: #2 predicted fragment length is 181 bps INFO @ Sat, 03 Jun 2017 05:22:43: #2 alternative fragment length(s) may be 181 bps INFO @ Sat, 03 Jun 2017 05:22:43: #2.2 Generate R script for model : SRX2163949.05_model.r WARNING @ Sat, 03 Jun 2017 05:22:43: #2 Since the d (181) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 03 Jun 2017 05:22:43: #2 You may need to consider one of the other alternative d(s): 181 WARNING @ Sat, 03 Jun 2017 05:22:43: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sat, 03 Jun 2017 05:22:43: #3 Call peaks... INFO @ Sat, 03 Jun 2017 05:22:43: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Jun 2017 05:22:44: start X-correlation... INFO @ Sat, 03 Jun 2017 05:22:44: end of X-cor INFO @ Sat, 03 Jun 2017 05:22:44: #2 finished! INFO @ Sat, 03 Jun 2017 05:22:44: #2 predicted fragment length is 181 bps INFO @ Sat, 03 Jun 2017 05:22:44: #2 alternative fragment length(s) may be 181 bps INFO @ Sat, 03 Jun 2017 05:22:44: #2.2 Generate R script for model : SRX2163949.20_model.r WARNING @ Sat, 03 Jun 2017 05:22:44: #2 Since the d (181) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 03 Jun 2017 05:22:44: #2 You may need to consider one of the other alternative d(s): 181 WARNING @ Sat, 03 Jun 2017 05:22:44: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sat, 03 Jun 2017 05:22:44: #3 Call peaks... INFO @ Sat, 03 Jun 2017 05:22:44: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Jun 2017 05:24:15: #3 Call peaks for each chromosome... INFO @ Sat, 03 Jun 2017 05:24:17: #3 Call peaks for each chromosome... INFO @ Sat, 03 Jun 2017 05:24:17: #3 Call peaks for each chromosome... INFO @ Sat, 03 Jun 2017 05:25:20: #4 Write output xls file... SRX2163949.20_peaks.xls INFO @ Sat, 03 Jun 2017 05:25:20: #4 Write peak in narrowPeak format file... SRX2163949.20_peaks.narrowPeak INFO @ Sat, 03 Jun 2017 05:25:20: #4 Write summits bed file... SRX2163949.20_summits.bed INFO @ Sat, 03 Jun 2017 05:25:20: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (2834 records, 4 fields): 5 millis CompletedMACS2peakCalling INFO @ Sat, 03 Jun 2017 05:25:27: #4 Write output xls file... SRX2163949.10_peaks.xls INFO @ Sat, 03 Jun 2017 05:25:27: #4 Write peak in narrowPeak format file... SRX2163949.10_peaks.narrowPeak INFO @ Sat, 03 Jun 2017 05:25:27: #4 Write summits bed file... SRX2163949.10_summits.bed INFO @ Sat, 03 Jun 2017 05:25:27: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (3895 records, 4 fields): 6 millis CompletedMACS2peakCalling INFO @ Sat, 03 Jun 2017 05:25:29: #4 Write output xls file... SRX2163949.05_peaks.xls INFO @ Sat, 03 Jun 2017 05:25:29: #4 Write peak in narrowPeak format file... SRX2163949.05_peaks.narrowPeak INFO @ Sat, 03 Jun 2017 05:25:29: #4 Write summits bed file... SRX2163949.05_summits.bed INFO @ Sat, 03 Jun 2017 05:25:29: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (5067 records, 4 fields): 7 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。