Job ID = 9025593 sra ファイルのダウンロード中... Completed: 549696K bytes transferred in 207 seconds (21752K 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 --:--:-- 0 100 9111 0 9111 0 0 1228 0 --:--:-- 0:00:07 --:--:-- 11016 100 30318 0 30318 0 0 3675 0 --:--:-- 0:00:08 --:--:-- 18285 100 48252 0 48252 0 0 5622 0 --:--:-- 0:00:08 --:--:-- 24247 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 20074105 spots for /home/okishinya/chipatlas/results/ce10/SRX1936238/SRR3879845.sra Written 20074105 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: 00:05:14 20074105 reads; of these: 20074105 (100.00%) were unpaired; of these: 1309882 (6.53%) aligned 0 times 15601711 (77.72%) aligned exactly 1 time 3162512 (15.75%) aligned >1 times 93.47% overall alignment rate Time searching: 00:05:14 Overall time: 00:05:14 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 8 files... [bam_rmdupse_core] 2569927 / 18764223 = 0.1370 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 04:40:20: # Command line: callpeak -t SRX1936238.bam -f BAM -g ce -n SRX1936238.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX1936238.05 # format = BAM # ChIP-seq file = ['SRX1936238.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 04:40:20: #1 read tag files... INFO @ Sat, 03 Jun 2017 04:40:20: #1 read treatment tags... INFO @ Sat, 03 Jun 2017 04:40:20: # Command line: callpeak -t SRX1936238.bam -f BAM -g ce -n SRX1936238.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX1936238.20 # format = BAM # ChIP-seq file = ['SRX1936238.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 04:40:20: #1 read tag files... INFO @ Sat, 03 Jun 2017 04:40:20: #1 read treatment tags... INFO @ Sat, 03 Jun 2017 04:40:20: # Command line: callpeak -t SRX1936238.bam -f BAM -g ce -n SRX1936238.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX1936238.10 # format = BAM # ChIP-seq file = ['SRX1936238.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 04:40:20: #1 read tag files... INFO @ Sat, 03 Jun 2017 04:40:20: #1 read treatment tags... INFO @ Sat, 03 Jun 2017 04:40:28: 1000000 INFO @ Sat, 03 Jun 2017 04:40:28: 1000000 INFO @ Sat, 03 Jun 2017 04:40:29: 1000000 INFO @ Sat, 03 Jun 2017 04:40:36: 2000000 INFO @ Sat, 03 Jun 2017 04:40:36: 2000000 INFO @ Sat, 03 Jun 2017 04:40:38: 2000000 INFO @ Sat, 03 Jun 2017 04:40:44: 3000000 INFO @ Sat, 03 Jun 2017 04:40:44: 3000000 INFO @ Sat, 03 Jun 2017 04:40:47: 3000000 INFO @ Sat, 03 Jun 2017 04:40:52: 4000000 INFO @ Sat, 03 Jun 2017 04:40:52: 4000000 INFO @ Sat, 03 Jun 2017 04:40:56: 4000000 INFO @ Sat, 03 Jun 2017 04:40:59: 5000000 INFO @ Sat, 03 Jun 2017 04:40:59: 5000000 INFO @ Sat, 03 Jun 2017 04:41:05: 5000000 INFO @ Sat, 03 Jun 2017 04:41:08: 6000000 INFO @ Sat, 03 Jun 2017 04:41:08: 6000000 INFO @ Sat, 03 Jun 2017 04:41:14: 6000000 INFO @ Sat, 03 Jun 2017 04:41:16: 7000000 INFO @ Sat, 03 Jun 2017 04:41:16: 7000000 INFO @ Sat, 03 Jun 2017 04:41:22: 7000000 INFO @ Sat, 03 Jun 2017 04:41:25: 8000000 INFO @ Sat, 03 Jun 2017 04:41:25: 8000000 INFO @ Sat, 03 Jun 2017 04:41:31: 8000000 INFO @ Sat, 03 Jun 2017 04:41:34: 9000000 INFO @ Sat, 03 Jun 2017 04:41:34: 9000000 INFO @ Sat, 03 Jun 2017 04:41:39: 9000000 INFO @ Sat, 03 Jun 2017 04:41:43: 10000000 INFO @ Sat, 03 Jun 2017 04:41:43: 10000000 INFO @ Sat, 03 Jun 2017 04:41:47: 10000000 INFO @ Sat, 03 Jun 2017 04:41:52: 11000000 INFO @ Sat, 03 Jun 2017 04:41:52: 11000000 INFO @ Sat, 03 Jun 2017 04:41:56: 11000000 INFO @ Sat, 03 Jun 2017 04:42:01: 12000000 INFO @ Sat, 03 Jun 2017 04:42:01: 12000000 INFO @ Sat, 03 Jun 2017 04:42:04: 12000000 INFO @ Sat, 03 Jun 2017 04:42:11: 13000000 INFO @ Sat, 03 Jun 2017 04:42:11: 13000000 INFO @ Sat, 03 Jun 2017 04:42:13: 13000000 INFO @ Sat, 03 Jun 2017 04:42:20: 14000000 INFO @ Sat, 03 Jun 2017 04:42:20: 14000000 INFO @ Sat, 03 Jun 2017 04:42:21: 14000000 INFO @ Sat, 03 Jun 2017 04:42:29: 15000000 INFO @ Sat, 03 Jun 2017 04:42:29: 15000000 INFO @ Sat, 03 Jun 2017 04:42:29: 15000000 INFO @ Sat, 03 Jun 2017 04:42:38: 16000000 INFO @ Sat, 03 Jun 2017 04:42:38: 16000000 INFO @ Sat, 03 Jun 2017 04:42:38: 16000000 INFO @ Sat, 03 Jun 2017 04:42:40: #1 tag size is determined as 52 bps INFO @ Sat, 03 Jun 2017 04:42:40: #1 tag size is determined as 52 bps INFO @ Sat, 03 Jun 2017 04:42:40: #1 tag size = 52 INFO @ Sat, 03 Jun 2017 04:42:40: #1 tag size = 52 INFO @ Sat, 03 Jun 2017 04:42:40: #1 total tags in treatment: 16194296 INFO @ Sat, 03 Jun 2017 04:42:40: #1 total tags in treatment: 16194296 INFO @ Sat, 03 Jun 2017 04:42:40: #1 user defined the maximum tags... INFO @ Sat, 03 Jun 2017 04:42:40: #1 user defined the maximum tags... INFO @ Sat, 03 Jun 2017 04:42:40: #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 04:42:40: #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 04:42:40: #1 tag size is determined as 52 bps INFO @ Sat, 03 Jun 2017 04:42:40: #1 tag size = 52 INFO @ Sat, 03 Jun 2017 04:42:40: #1 total tags in treatment: 16194296 INFO @ Sat, 03 Jun 2017 04:42:40: #1 user defined the maximum tags... INFO @ Sat, 03 Jun 2017 04:42:40: #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 04:42:43: #1 tags after filtering in treatment: 16191262 INFO @ Sat, 03 Jun 2017 04:42:43: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 03 Jun 2017 04:42:43: #1 finished! INFO @ Sat, 03 Jun 2017 04:42:43: #2 Build Peak Model... INFO @ Sat, 03 Jun 2017 04:42:43: #1 tags after filtering in treatment: 16191262 INFO @ Sat, 03 Jun 2017 04:42:43: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 03 Jun 2017 04:42:43: #1 finished! INFO @ Sat, 03 Jun 2017 04:42:43: #2 Build Peak Model... INFO @ Sat, 03 Jun 2017 04:42:43: #1 tags after filtering in treatment: 16191262 INFO @ Sat, 03 Jun 2017 04:42:43: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 03 Jun 2017 04:42:43: #1 finished! INFO @ Sat, 03 Jun 2017 04:42:43: #2 Build Peak Model... INFO @ Sat, 03 Jun 2017 04:42:46: #2 number of paired peaks: 243 WARNING @ Sat, 03 Jun 2017 04:42:46: Fewer paired peaks (243) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 243 pairs to build model! INFO @ Sat, 03 Jun 2017 04:42:46: start model_add_line... INFO @ Sat, 03 Jun 2017 04:42:46: #2 number of paired peaks: 243 WARNING @ Sat, 03 Jun 2017 04:42:46: Fewer paired peaks (243) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 243 pairs to build model! INFO @ Sat, 03 Jun 2017 04:42:46: start model_add_line... INFO @ Sat, 03 Jun 2017 04:42:46: #2 number of paired peaks: 243 WARNING @ Sat, 03 Jun 2017 04:42:46: Fewer paired peaks (243) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 243 pairs to build model! INFO @ Sat, 03 Jun 2017 04:42:46: start model_add_line... INFO @ Sat, 03 Jun 2017 04:42:51: start X-correlation... INFO @ Sat, 03 Jun 2017 04:42:51: end of X-cor INFO @ Sat, 03 Jun 2017 04:42:51: #2 finished! INFO @ Sat, 03 Jun 2017 04:42:51: #2 predicted fragment length is 47 bps INFO @ Sat, 03 Jun 2017 04:42:51: #2 alternative fragment length(s) may be 1,47,568,573 bps INFO @ Sat, 03 Jun 2017 04:42:51: #2.2 Generate R script for model : SRX1936238.05_model.r WARNING @ Sat, 03 Jun 2017 04:42:51: #2 Since the d (47) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 03 Jun 2017 04:42:51: #2 You may need to consider one of the other alternative d(s): 1,47,568,573 WARNING @ Sat, 03 Jun 2017 04:42:51: #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 04:42:51: #3 Call peaks... INFO @ Sat, 03 Jun 2017 04:42:51: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Jun 2017 04:42:51: start X-correlation... INFO @ Sat, 03 Jun 2017 04:42:51: end of X-cor INFO @ Sat, 03 Jun 2017 04:42:51: #2 finished! INFO @ Sat, 03 Jun 2017 04:42:51: #2 predicted fragment length is 47 bps INFO @ Sat, 03 Jun 2017 04:42:51: #2 alternative fragment length(s) may be 1,47,568,573 bps INFO @ Sat, 03 Jun 2017 04:42:51: #2.2 Generate R script for model : SRX1936238.20_model.r WARNING @ Sat, 03 Jun 2017 04:42:51: #2 Since the d (47) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 03 Jun 2017 04:42:51: #2 You may need to consider one of the other alternative d(s): 1,47,568,573 WARNING @ Sat, 03 Jun 2017 04:42:51: #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 04:42:51: #3 Call peaks... INFO @ Sat, 03 Jun 2017 04:42:51: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Jun 2017 04:42:52: start X-correlation... INFO @ Sat, 03 Jun 2017 04:42:52: end of X-cor INFO @ Sat, 03 Jun 2017 04:42:52: #2 finished! INFO @ Sat, 03 Jun 2017 04:42:52: #2 predicted fragment length is 47 bps INFO @ Sat, 03 Jun 2017 04:42:52: #2 alternative fragment length(s) may be 1,47,568,573 bps INFO @ Sat, 03 Jun 2017 04:42:52: #2.2 Generate R script for model : SRX1936238.10_model.r WARNING @ Sat, 03 Jun 2017 04:42:52: #2 Since the d (47) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 03 Jun 2017 04:42:52: #2 You may need to consider one of the other alternative d(s): 1,47,568,573 WARNING @ Sat, 03 Jun 2017 04:42:52: #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 04:42:52: #3 Call peaks... INFO @ Sat, 03 Jun 2017 04:42:52: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Jun 2017 04:44:06: #3 Call peaks for each chromosome... INFO @ Sat, 03 Jun 2017 04:44:08: #3 Call peaks for each chromosome... INFO @ Sat, 03 Jun 2017 04:44:20: #3 Call peaks for each chromosome... INFO @ Sat, 03 Jun 2017 04:45:00: #4 Write output xls file... SRX1936238.20_peaks.xls INFO @ Sat, 03 Jun 2017 04:45:00: #4 Write peak in narrowPeak format file... SRX1936238.20_peaks.narrowPeak INFO @ Sat, 03 Jun 2017 04:45:00: #4 Write summits bed file... SRX1936238.20_summits.bed INFO @ Sat, 03 Jun 2017 04:45:00: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (153 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Sat, 03 Jun 2017 04:45:04: #4 Write output xls file... SRX1936238.05_peaks.xls INFO @ Sat, 03 Jun 2017 04:45:04: #4 Write peak in narrowPeak format file... SRX1936238.05_peaks.narrowPeak INFO @ Sat, 03 Jun 2017 04:45:04: #4 Write summits bed file... SRX1936238.05_summits.bed INFO @ Sat, 03 Jun 2017 04:45:04: Done! pass1 - making usageList (7 chroms): 0 millis pass2 - checking and writing primary data (711 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Sat, 03 Jun 2017 04:45:18: #4 Write output xls file... SRX1936238.10_peaks.xls INFO @ Sat, 03 Jun 2017 04:45:18: #4 Write peak in narrowPeak format file... SRX1936238.10_peaks.narrowPeak INFO @ Sat, 03 Jun 2017 04:45:18: #4 Write summits bed file... SRX1936238.10_summits.bed INFO @ Sat, 03 Jun 2017 04:45:18: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (447 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。