Job ID = 9025595 sra ファイルのダウンロード中... Completed: 649993K bytes transferred in 225 seconds (23589K 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 22318 0 22318 0 0 2388 0 --:--:-- 0:00:09 --:--:-- 7690 100 46318 0 46318 0 0 4553 0 --:--:-- 0:00:10 --:--:-- 12411 100 53655 0 53655 0 0 5274 0 --:--:-- 0:00:10 --:--:-- 14373 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 23692485 spots for /home/okishinya/chipatlas/results/ce10/SRX1936240/SRR3879847.sra Written 23692485 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: 00:06:43 23692485 reads; of these: 23692485 (100.00%) were unpaired; of these: 1184591 (5.00%) aligned 0 times 19156914 (80.86%) aligned exactly 1 time 3350980 (14.14%) aligned >1 times 95.00% overall alignment rate Time searching: 00:06:43 Overall time: 00:06:43 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] 3228110 / 22507894 = 0.1434 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 04:43:30: # Command line: callpeak -t SRX1936240.bam -f BAM -g ce -n SRX1936240.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX1936240.10 # format = BAM # ChIP-seq file = ['SRX1936240.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 04:43:30: #1 read tag files... INFO @ Sat, 03 Jun 2017 04:43:30: #1 read treatment tags... INFO @ Sat, 03 Jun 2017 04:43:30: # Command line: callpeak -t SRX1936240.bam -f BAM -g ce -n SRX1936240.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX1936240.20 # format = BAM # ChIP-seq file = ['SRX1936240.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 04:43:30: #1 read tag files... INFO @ Sat, 03 Jun 2017 04:43:30: #1 read treatment tags... INFO @ Sat, 03 Jun 2017 04:43:30: # Command line: callpeak -t SRX1936240.bam -f BAM -g ce -n SRX1936240.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX1936240.05 # format = BAM # ChIP-seq file = ['SRX1936240.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 04:43:30: #1 read tag files... INFO @ Sat, 03 Jun 2017 04:43:30: #1 read treatment tags... INFO @ Sat, 03 Jun 2017 04:43:38: 1000000 INFO @ Sat, 03 Jun 2017 04:43:38: 1000000 INFO @ Sat, 03 Jun 2017 04:43:40: 1000000 INFO @ Sat, 03 Jun 2017 04:43:46: 2000000 INFO @ Sat, 03 Jun 2017 04:43:46: 2000000 INFO @ Sat, 03 Jun 2017 04:43:51: 2000000 INFO @ Sat, 03 Jun 2017 04:43:54: 3000000 INFO @ Sat, 03 Jun 2017 04:43:55: 3000000 INFO @ Sat, 03 Jun 2017 04:44:01: 3000000 INFO @ Sat, 03 Jun 2017 04:44:03: 4000000 INFO @ Sat, 03 Jun 2017 04:44:03: 4000000 INFO @ Sat, 03 Jun 2017 04:44:11: 5000000 INFO @ Sat, 03 Jun 2017 04:44:11: 5000000 INFO @ Sat, 03 Jun 2017 04:44:12: 4000000 INFO @ Sat, 03 Jun 2017 04:44:19: 6000000 INFO @ Sat, 03 Jun 2017 04:44:20: 6000000 INFO @ Sat, 03 Jun 2017 04:44:22: 5000000 INFO @ Sat, 03 Jun 2017 04:44:28: 7000000 INFO @ Sat, 03 Jun 2017 04:44:28: 7000000 INFO @ Sat, 03 Jun 2017 04:44:32: 6000000 INFO @ Sat, 03 Jun 2017 04:44:36: 8000000 INFO @ Sat, 03 Jun 2017 04:44:37: 8000000 INFO @ Sat, 03 Jun 2017 04:44:43: 7000000 INFO @ Sat, 03 Jun 2017 04:44:44: 9000000 INFO @ Sat, 03 Jun 2017 04:44:45: 9000000 INFO @ Sat, 03 Jun 2017 04:44:53: 10000000 INFO @ Sat, 03 Jun 2017 04:44:53: 8000000 INFO @ Sat, 03 Jun 2017 04:44:53: 10000000 INFO @ Sat, 03 Jun 2017 04:45:01: 11000000 INFO @ Sat, 03 Jun 2017 04:45:01: 11000000 INFO @ Sat, 03 Jun 2017 04:45:03: 9000000 INFO @ Sat, 03 Jun 2017 04:45:09: 12000000 INFO @ Sat, 03 Jun 2017 04:45:10: 12000000 INFO @ Sat, 03 Jun 2017 04:45:14: 10000000 INFO @ Sat, 03 Jun 2017 04:45:17: 13000000 INFO @ Sat, 03 Jun 2017 04:45:18: 13000000 INFO @ Sat, 03 Jun 2017 04:45:24: 11000000 INFO @ Sat, 03 Jun 2017 04:45:26: 14000000 INFO @ Sat, 03 Jun 2017 04:45:27: 14000000 INFO @ Sat, 03 Jun 2017 04:45:34: 15000000 INFO @ Sat, 03 Jun 2017 04:45:35: 12000000 INFO @ Sat, 03 Jun 2017 04:45:35: 15000000 INFO @ Sat, 03 Jun 2017 04:45:42: 16000000 INFO @ Sat, 03 Jun 2017 04:45:43: 16000000 INFO @ Sat, 03 Jun 2017 04:45:45: 13000000 INFO @ Sat, 03 Jun 2017 04:45:51: 17000000 INFO @ Sat, 03 Jun 2017 04:45:52: 17000000 INFO @ Sat, 03 Jun 2017 04:45:56: 14000000 INFO @ Sat, 03 Jun 2017 04:45:59: 18000000 INFO @ Sat, 03 Jun 2017 04:46:00: 18000000 INFO @ Sat, 03 Jun 2017 04:46:06: 15000000 INFO @ Sat, 03 Jun 2017 04:46:07: 19000000 INFO @ Sat, 03 Jun 2017 04:46:08: 19000000 INFO @ Sat, 03 Jun 2017 04:46:10: #1 tag size is determined as 52 bps INFO @ Sat, 03 Jun 2017 04:46:10: #1 tag size = 52 INFO @ Sat, 03 Jun 2017 04:46:10: #1 total tags in treatment: 19279784 INFO @ Sat, 03 Jun 2017 04:46:10: #1 user defined the maximum tags... INFO @ Sat, 03 Jun 2017 04:46:10: #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 04:46:11: #1 tag size is determined as 52 bps INFO @ Sat, 03 Jun 2017 04:46:11: #1 tag size = 52 INFO @ Sat, 03 Jun 2017 04:46:11: #1 total tags in treatment: 19279784 INFO @ Sat, 03 Jun 2017 04:46:11: #1 user defined the maximum tags... INFO @ Sat, 03 Jun 2017 04:46:11: #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 04:46:13: #1 tags after filtering in treatment: 19276082 INFO @ Sat, 03 Jun 2017 04:46:13: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 03 Jun 2017 04:46:13: #1 finished! INFO @ Sat, 03 Jun 2017 04:46:13: #2 Build Peak Model... INFO @ Sat, 03 Jun 2017 04:46:14: #1 tags after filtering in treatment: 19276082 INFO @ Sat, 03 Jun 2017 04:46:14: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 03 Jun 2017 04:46:14: #1 finished! INFO @ Sat, 03 Jun 2017 04:46:14: #2 Build Peak Model... INFO @ Sat, 03 Jun 2017 04:46:15: 16000000 INFO @ Sat, 03 Jun 2017 04:46:17: #2 number of paired peaks: 139 WARNING @ Sat, 03 Jun 2017 04:46:17: Fewer paired peaks (139) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 139 pairs to build model! INFO @ Sat, 03 Jun 2017 04:46:17: start model_add_line... INFO @ Sat, 03 Jun 2017 04:46:18: #2 number of paired peaks: 139 WARNING @ Sat, 03 Jun 2017 04:46:18: Fewer paired peaks (139) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 139 pairs to build model! INFO @ Sat, 03 Jun 2017 04:46:18: start model_add_line... INFO @ Sat, 03 Jun 2017 04:46:21: start X-correlation... INFO @ Sat, 03 Jun 2017 04:46:21: end of X-cor INFO @ Sat, 03 Jun 2017 04:46:21: #2 finished! INFO @ Sat, 03 Jun 2017 04:46:21: #2 predicted fragment length is 43 bps INFO @ Sat, 03 Jun 2017 04:46:21: #2 alternative fragment length(s) may be 2,43,480,522 bps INFO @ Sat, 03 Jun 2017 04:46:21: #2.2 Generate R script for model : SRX1936240.10_model.r WARNING @ Sat, 03 Jun 2017 04:46:21: #2 Since the d (43) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 03 Jun 2017 04:46:21: #2 You may need to consider one of the other alternative d(s): 2,43,480,522 WARNING @ Sat, 03 Jun 2017 04:46:21: #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 04:46:21: #3 Call peaks... INFO @ Sat, 03 Jun 2017 04:46:21: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Jun 2017 04:46:22: start X-correlation... INFO @ Sat, 03 Jun 2017 04:46:22: end of X-cor INFO @ Sat, 03 Jun 2017 04:46:22: #2 finished! INFO @ Sat, 03 Jun 2017 04:46:22: #2 predicted fragment length is 43 bps INFO @ Sat, 03 Jun 2017 04:46:22: #2 alternative fragment length(s) may be 2,43,480,522 bps INFO @ Sat, 03 Jun 2017 04:46:22: #2.2 Generate R script for model : SRX1936240.05_model.r WARNING @ Sat, 03 Jun 2017 04:46:22: #2 Since the d (43) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 03 Jun 2017 04:46:22: #2 You may need to consider one of the other alternative d(s): 2,43,480,522 WARNING @ Sat, 03 Jun 2017 04:46:22: #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 04:46:22: #3 Call peaks... INFO @ Sat, 03 Jun 2017 04:46:22: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Jun 2017 04:46:23: 17000000 INFO @ Sat, 03 Jun 2017 04:46:30: 18000000 INFO @ Sat, 03 Jun 2017 04:46:38: 19000000 INFO @ Sat, 03 Jun 2017 04:46:40: #1 tag size is determined as 52 bps INFO @ Sat, 03 Jun 2017 04:46:40: #1 tag size = 52 INFO @ Sat, 03 Jun 2017 04:46:40: #1 total tags in treatment: 19279784 INFO @ Sat, 03 Jun 2017 04:46:40: #1 user defined the maximum tags... INFO @ Sat, 03 Jun 2017 04:46:40: #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 04:46:43: #1 tags after filtering in treatment: 19276082 INFO @ Sat, 03 Jun 2017 04:46:43: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 03 Jun 2017 04:46:43: #1 finished! INFO @ Sat, 03 Jun 2017 04:46:43: #2 Build Peak Model... INFO @ Sat, 03 Jun 2017 04:46:47: #2 number of paired peaks: 139 WARNING @ Sat, 03 Jun 2017 04:46:47: Fewer paired peaks (139) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 139 pairs to build model! INFO @ Sat, 03 Jun 2017 04:46:47: start model_add_line... INFO @ Sat, 03 Jun 2017 04:46:51: start X-correlation... INFO @ Sat, 03 Jun 2017 04:46:51: end of X-cor INFO @ Sat, 03 Jun 2017 04:46:51: #2 finished! INFO @ Sat, 03 Jun 2017 04:46:51: #2 predicted fragment length is 43 bps INFO @ Sat, 03 Jun 2017 04:46:51: #2 alternative fragment length(s) may be 2,43,480,522 bps INFO @ Sat, 03 Jun 2017 04:46:51: #2.2 Generate R script for model : SRX1936240.20_model.r WARNING @ Sat, 03 Jun 2017 04:46:51: #2 Since the d (43) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 03 Jun 2017 04:46:51: #2 You may need to consider one of the other alternative d(s): 2,43,480,522 WARNING @ Sat, 03 Jun 2017 04:46:51: #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 04:46:51: #3 Call peaks... INFO @ Sat, 03 Jun 2017 04:46:51: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Jun 2017 04:47:47: #3 Call peaks for each chromosome... INFO @ Sat, 03 Jun 2017 04:47:47: #3 Call peaks for each chromosome... INFO @ Sat, 03 Jun 2017 04:48:24: #3 Call peaks for each chromosome... INFO @ Sat, 03 Jun 2017 04:48:50: #4 Write output xls file... SRX1936240.05_peaks.xls INFO @ Sat, 03 Jun 2017 04:48:50: #4 Write peak in narrowPeak format file... SRX1936240.05_peaks.narrowPeak INFO @ Sat, 03 Jun 2017 04:48:50: #4 Write summits bed file... SRX1936240.05_summits.bed INFO @ Sat, 03 Jun 2017 04:48:50: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (633 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Sat, 03 Jun 2017 04:48:53: #4 Write output xls file... SRX1936240.10_peaks.xls INFO @ Sat, 03 Jun 2017 04:48:53: #4 Write peak in narrowPeak format file... SRX1936240.10_peaks.narrowPeak INFO @ Sat, 03 Jun 2017 04:48:53: #4 Write summits bed file... SRX1936240.10_summits.bed INFO @ Sat, 03 Jun 2017 04:48:53: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (352 records, 4 fields): 4 millis CompletedMACS2peakCalling INFO @ Sat, 03 Jun 2017 04:49:31: #4 Write output xls file... SRX1936240.20_peaks.xls INFO @ Sat, 03 Jun 2017 04:49:31: #4 Write peak in narrowPeak format file... SRX1936240.20_peaks.narrowPeak INFO @ Sat, 03 Jun 2017 04:49:31: #4 Write summits bed file... SRX1936240.20_summits.bed INFO @ Sat, 03 Jun 2017 04:49:31: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (114 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。