Job ID = 9025597 sra ファイルのダウンロード中... Completed: 570755K bytes transferred in 117 seconds (39821K 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 0 0 0 0 0 0 0 0 --:--:-- 0:00:07 --:--:-- 0 0 0 0 0 0 0 0 0 --:--:-- 0:00:08 --:--:-- 0 100 12695 0 12695 0 0 1344 0 --:--:-- 0:00:09 --:--:-- 4460 100 34590 0 34590 0 0 3314 0 --:--:-- 0:00:10 --:--:-- 9003 100 59262 0 59262 0 0 5419 0 --:--:-- 0:00:10 --:--:-- 13654 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 20752801 spots for /home/okishinya/chipatlas/results/ce10/SRX1936242/SRR3879849.sra Written 20752801 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: 00:05:58 20752801 reads; of these: 20752801 (100.00%) were unpaired; of these: 2976063 (14.34%) aligned 0 times 14753070 (71.09%) aligned exactly 1 time 3023668 (14.57%) aligned >1 times 85.66% overall alignment rate Time searching: 00:05:58 Overall time: 00:05:58 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 8 files... [bam_rmdupse_core] 2462943 / 17776738 = 0.1385 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 04:40:08: # Command line: callpeak -t SRX1936242.bam -f BAM -g ce -n SRX1936242.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX1936242.10 # format = BAM # ChIP-seq file = ['SRX1936242.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 04:40:08: #1 read tag files... INFO @ Sat, 03 Jun 2017 04:40:08: #1 read treatment tags... INFO @ Sat, 03 Jun 2017 04:40:08: # Command line: callpeak -t SRX1936242.bam -f BAM -g ce -n SRX1936242.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX1936242.20 # format = BAM # ChIP-seq file = ['SRX1936242.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 04:40:08: #1 read tag files... INFO @ Sat, 03 Jun 2017 04:40:08: #1 read treatment tags... INFO @ Sat, 03 Jun 2017 04:40:08: # Command line: callpeak -t SRX1936242.bam -f BAM -g ce -n SRX1936242.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX1936242.05 # format = BAM # ChIP-seq file = ['SRX1936242.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 04:40:08: #1 read tag files... INFO @ Sat, 03 Jun 2017 04:40:08: #1 read treatment tags... INFO @ Sat, 03 Jun 2017 04:40:14: 1000000 INFO @ Sat, 03 Jun 2017 04:40:14: 1000000 INFO @ Sat, 03 Jun 2017 04:40:14: 1000000 INFO @ Sat, 03 Jun 2017 04:40:20: 2000000 INFO @ Sat, 03 Jun 2017 04:40:21: 2000000 INFO @ Sat, 03 Jun 2017 04:40:21: 2000000 INFO @ Sat, 03 Jun 2017 04:40:25: 3000000 INFO @ Sat, 03 Jun 2017 04:40:28: 3000000 INFO @ Sat, 03 Jun 2017 04:40:28: 3000000 INFO @ Sat, 03 Jun 2017 04:40:31: 4000000 INFO @ Sat, 03 Jun 2017 04:40:34: 4000000 INFO @ Sat, 03 Jun 2017 04:40:34: 4000000 INFO @ Sat, 03 Jun 2017 04:40:37: 5000000 INFO @ Sat, 03 Jun 2017 04:40:41: 5000000 INFO @ Sat, 03 Jun 2017 04:40:41: 5000000 INFO @ Sat, 03 Jun 2017 04:40:42: 6000000 INFO @ Sat, 03 Jun 2017 04:40:48: 6000000 INFO @ Sat, 03 Jun 2017 04:40:48: 7000000 INFO @ Sat, 03 Jun 2017 04:40:48: 6000000 INFO @ Sat, 03 Jun 2017 04:40:53: 8000000 INFO @ Sat, 03 Jun 2017 04:40:55: 7000000 INFO @ Sat, 03 Jun 2017 04:40:55: 7000000 INFO @ Sat, 03 Jun 2017 04:40:59: 9000000 INFO @ Sat, 03 Jun 2017 04:41:02: 8000000 INFO @ Sat, 03 Jun 2017 04:41:02: 8000000 INFO @ Sat, 03 Jun 2017 04:41:05: 10000000 INFO @ Sat, 03 Jun 2017 04:41:08: 9000000 INFO @ Sat, 03 Jun 2017 04:41:09: 9000000 INFO @ Sat, 03 Jun 2017 04:41:10: 11000000 INFO @ Sat, 03 Jun 2017 04:41:15: 10000000 INFO @ Sat, 03 Jun 2017 04:41:16: 12000000 INFO @ Sat, 03 Jun 2017 04:41:16: 10000000 INFO @ Sat, 03 Jun 2017 04:41:21: 13000000 INFO @ Sat, 03 Jun 2017 04:41:22: 11000000 INFO @ Sat, 03 Jun 2017 04:41:23: 11000000 INFO @ Sat, 03 Jun 2017 04:41:27: 14000000 INFO @ Sat, 03 Jun 2017 04:41:29: 12000000 INFO @ Sat, 03 Jun 2017 04:41:30: 12000000 INFO @ Sat, 03 Jun 2017 04:41:33: 15000000 INFO @ Sat, 03 Jun 2017 04:41:35: #1 tag size is determined as 52 bps INFO @ Sat, 03 Jun 2017 04:41:35: #1 tag size = 52 INFO @ Sat, 03 Jun 2017 04:41:35: #1 total tags in treatment: 15313795 INFO @ Sat, 03 Jun 2017 04:41:35: #1 user defined the maximum tags... INFO @ Sat, 03 Jun 2017 04:41:35: #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 04:41:37: 13000000 INFO @ Sat, 03 Jun 2017 04:41:37: #1 tags after filtering in treatment: 15310674 INFO @ Sat, 03 Jun 2017 04:41:37: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 03 Jun 2017 04:41:37: #1 finished! INFO @ Sat, 03 Jun 2017 04:41:37: #2 Build Peak Model... INFO @ Sat, 03 Jun 2017 04:41:38: 13000000 INFO @ Sat, 03 Jun 2017 04:41:40: #2 number of paired peaks: 284 WARNING @ Sat, 03 Jun 2017 04:41:40: Fewer paired peaks (284) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 284 pairs to build model! INFO @ Sat, 03 Jun 2017 04:41:40: start model_add_line... INFO @ Sat, 03 Jun 2017 04:41:44: 14000000 INFO @ Sat, 03 Jun 2017 04:41:45: 14000000 INFO @ Sat, 03 Jun 2017 04:41:45: start X-correlation... INFO @ Sat, 03 Jun 2017 04:41:45: end of X-cor INFO @ Sat, 03 Jun 2017 04:41:45: #2 finished! INFO @ Sat, 03 Jun 2017 04:41:45: #2 predicted fragment length is 40 bps INFO @ Sat, 03 Jun 2017 04:41:45: #2 alternative fragment length(s) may be 2,40,485 bps INFO @ Sat, 03 Jun 2017 04:41:45: #2.2 Generate R script for model : SRX1936242.05_model.r WARNING @ Sat, 03 Jun 2017 04:41:45: #2 Since the d (40) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 03 Jun 2017 04:41:45: #2 You may need to consider one of the other alternative d(s): 2,40,485 WARNING @ Sat, 03 Jun 2017 04:41:45: #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 04:41:45: #3 Call peaks... INFO @ Sat, 03 Jun 2017 04:41:45: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Jun 2017 04:41:50: 15000000 INFO @ Sat, 03 Jun 2017 04:41:52: 15000000 INFO @ Sat, 03 Jun 2017 04:41:53: #1 tag size is determined as 52 bps INFO @ Sat, 03 Jun 2017 04:41:53: #1 tag size = 52 INFO @ Sat, 03 Jun 2017 04:41:53: #1 total tags in treatment: 15313795 INFO @ Sat, 03 Jun 2017 04:41:53: #1 user defined the maximum tags... INFO @ Sat, 03 Jun 2017 04:41:53: #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 04:41:54: #1 tag size is determined as 52 bps INFO @ Sat, 03 Jun 2017 04:41:54: #1 tag size = 52 INFO @ Sat, 03 Jun 2017 04:41:54: #1 total tags in treatment: 15313795 INFO @ Sat, 03 Jun 2017 04:41:54: #1 user defined the maximum tags... INFO @ Sat, 03 Jun 2017 04:41:54: #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 04:41:56: #1 tags after filtering in treatment: 15310674 INFO @ Sat, 03 Jun 2017 04:41:56: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 03 Jun 2017 04:41:56: #1 finished! INFO @ Sat, 03 Jun 2017 04:41:56: #2 Build Peak Model... INFO @ Sat, 03 Jun 2017 04:41:57: #1 tags after filtering in treatment: 15310674 INFO @ Sat, 03 Jun 2017 04:41:57: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 03 Jun 2017 04:41:57: #1 finished! INFO @ Sat, 03 Jun 2017 04:41:57: #2 Build Peak Model... INFO @ Sat, 03 Jun 2017 04:41:58: #2 number of paired peaks: 284 WARNING @ Sat, 03 Jun 2017 04:41:58: Fewer paired peaks (284) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 284 pairs to build model! INFO @ Sat, 03 Jun 2017 04:41:58: start model_add_line... INFO @ Sat, 03 Jun 2017 04:41:59: #2 number of paired peaks: 284 WARNING @ Sat, 03 Jun 2017 04:41:59: Fewer paired peaks (284) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 284 pairs to build model! INFO @ Sat, 03 Jun 2017 04:41:59: start model_add_line... INFO @ Sat, 03 Jun 2017 04:42:04: start X-correlation... INFO @ Sat, 03 Jun 2017 04:42:04: end of X-cor INFO @ Sat, 03 Jun 2017 04:42:04: #2 finished! INFO @ Sat, 03 Jun 2017 04:42:04: #2 predicted fragment length is 40 bps INFO @ Sat, 03 Jun 2017 04:42:04: #2 alternative fragment length(s) may be 2,40,485 bps INFO @ Sat, 03 Jun 2017 04:42:04: #2.2 Generate R script for model : SRX1936242.10_model.r WARNING @ Sat, 03 Jun 2017 04:42:04: #2 Since the d (40) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 03 Jun 2017 04:42:04: #2 You may need to consider one of the other alternative d(s): 2,40,485 WARNING @ Sat, 03 Jun 2017 04:42:04: #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 04:42:04: #3 Call peaks... INFO @ Sat, 03 Jun 2017 04:42:04: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Jun 2017 04:42:05: start X-correlation... INFO @ Sat, 03 Jun 2017 04:42:05: end of X-cor INFO @ Sat, 03 Jun 2017 04:42:05: #2 finished! INFO @ Sat, 03 Jun 2017 04:42:05: #2 predicted fragment length is 40 bps INFO @ Sat, 03 Jun 2017 04:42:05: #2 alternative fragment length(s) may be 2,40,485 bps INFO @ Sat, 03 Jun 2017 04:42:05: #2.2 Generate R script for model : SRX1936242.20_model.r WARNING @ Sat, 03 Jun 2017 04:42:05: #2 Since the d (40) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 03 Jun 2017 04:42:05: #2 You may need to consider one of the other alternative d(s): 2,40,485 WARNING @ Sat, 03 Jun 2017 04:42:05: #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 04:42:05: #3 Call peaks... INFO @ Sat, 03 Jun 2017 04:42:05: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Jun 2017 04:43:05: #3 Call peaks for each chromosome... INFO @ Sat, 03 Jun 2017 04:43:15: #3 Call peaks for each chromosome... INFO @ Sat, 03 Jun 2017 04:43:18: #3 Call peaks for each chromosome... INFO @ Sat, 03 Jun 2017 04:44:00: #4 Write output xls file... SRX1936242.05_peaks.xls INFO @ Sat, 03 Jun 2017 04:44:00: #4 Write peak in narrowPeak format file... SRX1936242.05_peaks.narrowPeak INFO @ Sat, 03 Jun 2017 04:44:00: #4 Write summits bed file... SRX1936242.05_summits.bed INFO @ Sat, 03 Jun 2017 04:44:00: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (693 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Sat, 03 Jun 2017 04:44:07: #4 Write output xls file... SRX1936242.10_peaks.xls INFO @ Sat, 03 Jun 2017 04:44:07: #4 Write peak in narrowPeak format file... SRX1936242.10_peaks.narrowPeak INFO @ Sat, 03 Jun 2017 04:44:07: #4 Write summits bed file... SRX1936242.10_summits.bed INFO @ Sat, 03 Jun 2017 04:44:07: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (402 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Sat, 03 Jun 2017 04:44:18: #4 Write output xls file... SRX1936242.20_peaks.xls INFO @ Sat, 03 Jun 2017 04:44:18: #4 Write peak in narrowPeak format file... SRX1936242.20_peaks.narrowPeak INFO @ Sat, 03 Jun 2017 04:44:18: #4 Write summits bed file... SRX1936242.20_summits.bed INFO @ Sat, 03 Jun 2017 04:44:18: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (119 records, 4 fields): 2 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。