Job ID = 9026625 sra ファイルのダウンロード中... Completed: 950549K bytes transferred in 11 seconds (693729K 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 12007 0 12007 0 0 1360 0 --:--:-- 0:00:08 --:--:-- 4984 100 50590 0 50590 0 0 5149 0 --:--:-- 0:00:09 --:--:-- 14853 100 61281 0 61281 0 0 6133 0 --:--:-- 0:00:09 --:--:-- 17151 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 27109067 spots for /home/okishinya/chipatlas/results/ce10/SRX373273/SRR1024191.sra Written 27109067 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: 00:08:14 27109067 reads; of these: 27109067 (100.00%) were unpaired; of these: 1071561 (3.95%) aligned 0 times 21113080 (77.88%) aligned exactly 1 time 4924426 (18.17%) aligned >1 times 96.05% overall alignment rate Time searching: 00:08:14 Overall time: 00:08:14 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 12 files... [bam_rmdupse_core] 4117675 / 26037506 = 0.1581 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 07:11:24: # Command line: callpeak -t SRX373273.bam -f BAM -g ce -n SRX373273.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX373273.05 # format = BAM # ChIP-seq file = ['SRX373273.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 07:11:24: #1 read tag files... INFO @ Sat, 03 Jun 2017 07:11:24: #1 read treatment tags... INFO @ Sat, 03 Jun 2017 07:11:24: # Command line: callpeak -t SRX373273.bam -f BAM -g ce -n SRX373273.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX373273.10 # format = BAM # ChIP-seq file = ['SRX373273.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 07:11:24: #1 read tag files... INFO @ Sat, 03 Jun 2017 07:11:24: #1 read treatment tags... INFO @ Sat, 03 Jun 2017 07:11:24: # Command line: callpeak -t SRX373273.bam -f BAM -g ce -n SRX373273.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX373273.20 # format = BAM # ChIP-seq file = ['SRX373273.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 07:11:24: #1 read tag files... INFO @ Sat, 03 Jun 2017 07:11:24: #1 read treatment tags... INFO @ Sat, 03 Jun 2017 07:11:32: 1000000 INFO @ Sat, 03 Jun 2017 07:11:32: 1000000 INFO @ Sat, 03 Jun 2017 07:11:33: 1000000 INFO @ Sat, 03 Jun 2017 07:11:39: 2000000 INFO @ Sat, 03 Jun 2017 07:11:39: 2000000 INFO @ Sat, 03 Jun 2017 07:11:41: 2000000 INFO @ Sat, 03 Jun 2017 07:11:47: 3000000 INFO @ Sat, 03 Jun 2017 07:11:47: 3000000 INFO @ Sat, 03 Jun 2017 07:11:49: 3000000 INFO @ Sat, 03 Jun 2017 07:11:54: 4000000 INFO @ Sat, 03 Jun 2017 07:11:54: 4000000 INFO @ Sat, 03 Jun 2017 07:11:57: 4000000 INFO @ Sat, 03 Jun 2017 07:12:01: 5000000 INFO @ Sat, 03 Jun 2017 07:12:02: 5000000 INFO @ Sat, 03 Jun 2017 07:12:04: 5000000 INFO @ Sat, 03 Jun 2017 07:12:09: 6000000 INFO @ Sat, 03 Jun 2017 07:12:09: 6000000 INFO @ Sat, 03 Jun 2017 07:12:12: 6000000 INFO @ Sat, 03 Jun 2017 07:12:16: 7000000 INFO @ Sat, 03 Jun 2017 07:12:17: 7000000 INFO @ Sat, 03 Jun 2017 07:12:20: 7000000 INFO @ Sat, 03 Jun 2017 07:12:23: 8000000 INFO @ Sat, 03 Jun 2017 07:12:24: 8000000 INFO @ Sat, 03 Jun 2017 07:12:28: 8000000 INFO @ Sat, 03 Jun 2017 07:12:30: 9000000 INFO @ Sat, 03 Jun 2017 07:12:31: 9000000 INFO @ Sat, 03 Jun 2017 07:12:35: 9000000 INFO @ Sat, 03 Jun 2017 07:12:38: 10000000 INFO @ Sat, 03 Jun 2017 07:12:39: 10000000 INFO @ Sat, 03 Jun 2017 07:12:43: 10000000 INFO @ Sat, 03 Jun 2017 07:12:45: 11000000 INFO @ Sat, 03 Jun 2017 07:12:46: 11000000 INFO @ Sat, 03 Jun 2017 07:12:50: 11000000 INFO @ Sat, 03 Jun 2017 07:12:52: 12000000 INFO @ Sat, 03 Jun 2017 07:12:53: 12000000 INFO @ Sat, 03 Jun 2017 07:12:58: 12000000 INFO @ Sat, 03 Jun 2017 07:12:59: 13000000 INFO @ Sat, 03 Jun 2017 07:13:01: 13000000 INFO @ Sat, 03 Jun 2017 07:13:05: 13000000 INFO @ Sat, 03 Jun 2017 07:13:06: 14000000 INFO @ Sat, 03 Jun 2017 07:13:08: 14000000 INFO @ Sat, 03 Jun 2017 07:13:13: 14000000 INFO @ Sat, 03 Jun 2017 07:13:14: 15000000 INFO @ Sat, 03 Jun 2017 07:13:16: 15000000 INFO @ Sat, 03 Jun 2017 07:13:20: 15000000 INFO @ Sat, 03 Jun 2017 07:13:21: 16000000 INFO @ Sat, 03 Jun 2017 07:13:23: 16000000 INFO @ Sat, 03 Jun 2017 07:13:28: 17000000 INFO @ Sat, 03 Jun 2017 07:13:28: 16000000 INFO @ Sat, 03 Jun 2017 07:13:30: 17000000 INFO @ Sat, 03 Jun 2017 07:13:35: 18000000 INFO @ Sat, 03 Jun 2017 07:13:35: 17000000 INFO @ Sat, 03 Jun 2017 07:13:37: 18000000 INFO @ Sat, 03 Jun 2017 07:13:42: 19000000 INFO @ Sat, 03 Jun 2017 07:13:43: 18000000 INFO @ Sat, 03 Jun 2017 07:13:45: 19000000 INFO @ Sat, 03 Jun 2017 07:13:49: 20000000 INFO @ Sat, 03 Jun 2017 07:13:51: 19000000 INFO @ Sat, 03 Jun 2017 07:13:52: 20000000 INFO @ Sat, 03 Jun 2017 07:13:57: 21000000 INFO @ Sat, 03 Jun 2017 07:13:58: 20000000 INFO @ Sat, 03 Jun 2017 07:13:59: 21000000 INFO @ Sat, 03 Jun 2017 07:14:04: #1 tag size is determined as 51 bps INFO @ Sat, 03 Jun 2017 07:14:04: #1 tag size = 51 INFO @ Sat, 03 Jun 2017 07:14:04: #1 total tags in treatment: 21919831 INFO @ Sat, 03 Jun 2017 07:14:04: #1 user defined the maximum tags... INFO @ Sat, 03 Jun 2017 07:14:04: #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 07:14:06: 21000000 INFO @ Sat, 03 Jun 2017 07:14:06: #1 tag size is determined as 51 bps INFO @ Sat, 03 Jun 2017 07:14:06: #1 tag size = 51 INFO @ Sat, 03 Jun 2017 07:14:06: #1 total tags in treatment: 21919831 INFO @ Sat, 03 Jun 2017 07:14:06: #1 user defined the maximum tags... INFO @ Sat, 03 Jun 2017 07:14:06: #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 07:14:08: #1 tags after filtering in treatment: 21914800 INFO @ Sat, 03 Jun 2017 07:14:08: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 03 Jun 2017 07:14:08: #1 finished! INFO @ Sat, 03 Jun 2017 07:14:08: #2 Build Peak Model... INFO @ Sat, 03 Jun 2017 07:14:11: #1 tags after filtering in treatment: 21914800 INFO @ Sat, 03 Jun 2017 07:14:11: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 03 Jun 2017 07:14:11: #1 finished! INFO @ Sat, 03 Jun 2017 07:14:11: #2 Build Peak Model... INFO @ Sat, 03 Jun 2017 07:14:12: #2 number of paired peaks: 206 WARNING @ Sat, 03 Jun 2017 07:14:12: Fewer paired peaks (206) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 206 pairs to build model! INFO @ Sat, 03 Jun 2017 07:14:12: start model_add_line... INFO @ Sat, 03 Jun 2017 07:14:12: #1 tag size is determined as 51 bps INFO @ Sat, 03 Jun 2017 07:14:12: #1 tag size = 51 INFO @ Sat, 03 Jun 2017 07:14:12: #1 total tags in treatment: 21919831 INFO @ Sat, 03 Jun 2017 07:14:12: #1 user defined the maximum tags... INFO @ Sat, 03 Jun 2017 07:14:12: #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 07:14:14: #2 number of paired peaks: 206 WARNING @ Sat, 03 Jun 2017 07:14:14: Fewer paired peaks (206) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 206 pairs to build model! INFO @ Sat, 03 Jun 2017 07:14:14: start model_add_line... INFO @ Sat, 03 Jun 2017 07:14:16: #1 tags after filtering in treatment: 21914800 INFO @ Sat, 03 Jun 2017 07:14:16: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 03 Jun 2017 07:14:16: #1 finished! INFO @ Sat, 03 Jun 2017 07:14:16: #2 Build Peak Model... INFO @ Sat, 03 Jun 2017 07:14:17: start X-correlation... INFO @ Sat, 03 Jun 2017 07:14:17: end of X-cor INFO @ Sat, 03 Jun 2017 07:14:17: #2 finished! INFO @ Sat, 03 Jun 2017 07:14:17: #2 predicted fragment length is 46 bps INFO @ Sat, 03 Jun 2017 07:14:17: #2 alternative fragment length(s) may be 1,46,585 bps INFO @ Sat, 03 Jun 2017 07:14:17: #2.2 Generate R script for model : SRX373273.05_model.r WARNING @ Sat, 03 Jun 2017 07:14:17: #2 Since the d (46) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 03 Jun 2017 07:14:17: #2 You may need to consider one of the other alternative d(s): 1,46,585 WARNING @ Sat, 03 Jun 2017 07:14:17: #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 07:14:17: #3 Call peaks... INFO @ Sat, 03 Jun 2017 07:14:17: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Jun 2017 07:14:20: start X-correlation... INFO @ Sat, 03 Jun 2017 07:14:20: end of X-cor INFO @ Sat, 03 Jun 2017 07:14:20: #2 finished! INFO @ Sat, 03 Jun 2017 07:14:20: #2 predicted fragment length is 46 bps INFO @ Sat, 03 Jun 2017 07:14:20: #2 alternative fragment length(s) may be 1,46,585 bps INFO @ Sat, 03 Jun 2017 07:14:20: #2.2 Generate R script for model : SRX373273.10_model.r WARNING @ Sat, 03 Jun 2017 07:14:20: #2 Since the d (46) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 03 Jun 2017 07:14:20: #2 You may need to consider one of the other alternative d(s): 1,46,585 WARNING @ Sat, 03 Jun 2017 07:14:20: #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 07:14:20: #3 Call peaks... INFO @ Sat, 03 Jun 2017 07:14:20: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Jun 2017 07:14:20: #2 number of paired peaks: 206 WARNING @ Sat, 03 Jun 2017 07:14:20: Fewer paired peaks (206) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 206 pairs to build model! INFO @ Sat, 03 Jun 2017 07:14:20: start model_add_line... INFO @ Sat, 03 Jun 2017 07:14:25: start X-correlation... INFO @ Sat, 03 Jun 2017 07:14:25: end of X-cor INFO @ Sat, 03 Jun 2017 07:14:25: #2 finished! INFO @ Sat, 03 Jun 2017 07:14:25: #2 predicted fragment length is 46 bps INFO @ Sat, 03 Jun 2017 07:14:25: #2 alternative fragment length(s) may be 1,46,585 bps INFO @ Sat, 03 Jun 2017 07:14:25: #2.2 Generate R script for model : SRX373273.20_model.r WARNING @ Sat, 03 Jun 2017 07:14:25: #2 Since the d (46) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 03 Jun 2017 07:14:25: #2 You may need to consider one of the other alternative d(s): 1,46,585 WARNING @ Sat, 03 Jun 2017 07:14:25: #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 07:14:25: #3 Call peaks... INFO @ Sat, 03 Jun 2017 07:14:25: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Jun 2017 07:15:57: #3 Call peaks for each chromosome... INFO @ Sat, 03 Jun 2017 07:15:58: #3 Call peaks for each chromosome... INFO @ Sat, 03 Jun 2017 07:16:11: #3 Call peaks for each chromosome... INFO @ Sat, 03 Jun 2017 07:17:09: #4 Write output xls file... SRX373273.05_peaks.xls INFO @ Sat, 03 Jun 2017 07:17:09: #4 Write peak in narrowPeak format file... SRX373273.05_peaks.narrowPeak INFO @ Sat, 03 Jun 2017 07:17:09: #4 Write summits bed file... SRX373273.05_summits.bed INFO @ Sat, 03 Jun 2017 07:17:09: Done! pass1 - making usageList (7 chroms): 0 millis pass2 - checking and writing primary data (734 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Sat, 03 Jun 2017 07:17:16: #4 Write output xls file... SRX373273.10_peaks.xls INFO @ Sat, 03 Jun 2017 07:17:16: #4 Write peak in narrowPeak format file... SRX373273.10_peaks.narrowPeak INFO @ Sat, 03 Jun 2017 07:17:16: #4 Write summits bed file... SRX373273.10_summits.bed INFO @ Sat, 03 Jun 2017 07:17:16: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (400 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Sat, 03 Jun 2017 07:17:22: #4 Write output xls file... SRX373273.20_peaks.xls INFO @ Sat, 03 Jun 2017 07:17:22: #4 Write peak in narrowPeak format file... SRX373273.20_peaks.narrowPeak INFO @ Sat, 03 Jun 2017 07:17:22: #4 Write summits bed file... SRX373273.20_summits.bed INFO @ Sat, 03 Jun 2017 07:17:22: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (145 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。