Job ID = 9025549 sra ファイルのダウンロード中... Completed: 1360231K bytes transferred in 16 seconds (680721K 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 --:--:-- 0:00:06 --:--:-- 0 100 14324 0 14324 0 0 1891 0 --:--:-- 0:00:07 --:--:-- 12274 100 54317 0 54317 0 0 6433 0 --:--:-- 0:00:08 --:--:-- 26652 100 114k 0 114k 0 0 12596 0 --:--:-- 0:00:09 --:--:-- 40714 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 57969022 spots for /home/okishinya/chipatlas/results/ce10/SRX1674096/SRR3320142.sra Written 57969022 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: 00:12:16 57969022 reads; of these: 57969022 (100.00%) were unpaired; of these: 22457783 (38.74%) aligned 0 times 30035766 (51.81%) aligned exactly 1 time 5475473 (9.45%) aligned >1 times 61.26% overall alignment rate Time searching: 00:12:16 Overall time: 00:12:16 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] 14986347 / 35511239 = 0.4220 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 04:40:51: # Command line: callpeak -t SRX1674096.bam -f BAM -g ce -n SRX1674096.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX1674096.05 # format = BAM # ChIP-seq file = ['SRX1674096.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 04:40:51: #1 read tag files... INFO @ Sat, 03 Jun 2017 04:40:51: #1 read treatment tags... INFO @ Sat, 03 Jun 2017 04:40:51: # Command line: callpeak -t SRX1674096.bam -f BAM -g ce -n SRX1674096.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX1674096.20 # format = BAM # ChIP-seq file = ['SRX1674096.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 04:40:51: #1 read tag files... INFO @ Sat, 03 Jun 2017 04:40:51: #1 read treatment tags... INFO @ Sat, 03 Jun 2017 04:40:51: # Command line: callpeak -t SRX1674096.bam -f BAM -g ce -n SRX1674096.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX1674096.10 # format = BAM # ChIP-seq file = ['SRX1674096.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 04:40:51: #1 read tag files... INFO @ Sat, 03 Jun 2017 04:40:51: #1 read treatment tags... INFO @ Sat, 03 Jun 2017 04:40:56: 1000000 INFO @ Sat, 03 Jun 2017 04:40:57: 1000000 INFO @ Sat, 03 Jun 2017 04:40:57: 1000000 INFO @ Sat, 03 Jun 2017 04:41:02: 2000000 INFO @ Sat, 03 Jun 2017 04:41:02: 2000000 INFO @ Sat, 03 Jun 2017 04:41:04: 2000000 INFO @ Sat, 03 Jun 2017 04:41:08: 3000000 INFO @ Sat, 03 Jun 2017 04:41:08: 3000000 INFO @ Sat, 03 Jun 2017 04:41:10: 3000000 INFO @ Sat, 03 Jun 2017 04:41:13: 4000000 INFO @ Sat, 03 Jun 2017 04:41:14: 4000000 INFO @ Sat, 03 Jun 2017 04:41:17: 4000000 INFO @ Sat, 03 Jun 2017 04:41:19: 5000000 INFO @ Sat, 03 Jun 2017 04:41:20: 5000000 INFO @ Sat, 03 Jun 2017 04:41:23: 5000000 INFO @ Sat, 03 Jun 2017 04:41:24: 6000000 INFO @ Sat, 03 Jun 2017 04:41:27: 6000000 INFO @ Sat, 03 Jun 2017 04:41:29: 6000000 INFO @ Sat, 03 Jun 2017 04:41:29: 7000000 INFO @ Sat, 03 Jun 2017 04:41:33: 7000000 INFO @ Sat, 03 Jun 2017 04:41:35: 8000000 INFO @ Sat, 03 Jun 2017 04:41:36: 7000000 INFO @ Sat, 03 Jun 2017 04:41:39: 8000000 INFO @ Sat, 03 Jun 2017 04:41:40: 9000000 INFO @ Sat, 03 Jun 2017 04:41:42: 8000000 INFO @ Sat, 03 Jun 2017 04:41:45: 9000000 INFO @ Sat, 03 Jun 2017 04:41:46: 10000000 INFO @ Sat, 03 Jun 2017 04:41:48: 9000000 INFO @ Sat, 03 Jun 2017 04:41:51: 11000000 INFO @ Sat, 03 Jun 2017 04:41:52: 10000000 INFO @ Sat, 03 Jun 2017 04:41:54: 10000000 INFO @ Sat, 03 Jun 2017 04:41:57: 12000000 INFO @ Sat, 03 Jun 2017 04:41:58: 11000000 INFO @ Sat, 03 Jun 2017 04:42:01: 11000000 INFO @ Sat, 03 Jun 2017 04:42:02: 13000000 INFO @ Sat, 03 Jun 2017 04:42:04: 12000000 INFO @ Sat, 03 Jun 2017 04:42:07: 12000000 INFO @ Sat, 03 Jun 2017 04:42:08: 14000000 INFO @ Sat, 03 Jun 2017 04:42:10: 13000000 INFO @ Sat, 03 Jun 2017 04:42:13: 13000000 INFO @ Sat, 03 Jun 2017 04:42:14: 15000000 INFO @ Sat, 03 Jun 2017 04:42:16: 14000000 INFO @ Sat, 03 Jun 2017 04:42:19: 14000000 INFO @ Sat, 03 Jun 2017 04:42:19: 16000000 INFO @ Sat, 03 Jun 2017 04:42:22: 15000000 INFO @ Sat, 03 Jun 2017 04:42:25: 17000000 INFO @ Sat, 03 Jun 2017 04:42:25: 15000000 INFO @ Sat, 03 Jun 2017 04:42:28: 16000000 INFO @ Sat, 03 Jun 2017 04:42:31: 18000000 INFO @ Sat, 03 Jun 2017 04:42:31: 16000000 INFO @ Sat, 03 Jun 2017 04:42:34: 17000000 INFO @ Sat, 03 Jun 2017 04:42:36: 19000000 INFO @ Sat, 03 Jun 2017 04:42:37: 17000000 INFO @ Sat, 03 Jun 2017 04:42:40: 18000000 INFO @ Sat, 03 Jun 2017 04:42:42: 20000000 INFO @ Sat, 03 Jun 2017 04:42:43: 18000000 INFO @ Sat, 03 Jun 2017 04:42:45: #1 tag size is determined as 51 bps INFO @ Sat, 03 Jun 2017 04:42:45: #1 tag size = 51 INFO @ Sat, 03 Jun 2017 04:42:45: #1 total tags in treatment: 20524892 INFO @ Sat, 03 Jun 2017 04:42:45: #1 user defined the maximum tags... INFO @ Sat, 03 Jun 2017 04:42:45: #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 04:42:46: 19000000 INFO @ Sat, 03 Jun 2017 04:42:49: 19000000 INFO @ Sat, 03 Jun 2017 04:42:49: #1 tags after filtering in treatment: 20501038 INFO @ Sat, 03 Jun 2017 04:42:49: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 03 Jun 2017 04:42:49: #1 finished! INFO @ Sat, 03 Jun 2017 04:42:49: #2 Build Peak Model... INFO @ Sat, 03 Jun 2017 04:42:52: 20000000 INFO @ Sat, 03 Jun 2017 04:42:53: #2 number of paired peaks: 769 WARNING @ Sat, 03 Jun 2017 04:42:53: Fewer paired peaks (769) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 769 pairs to build model! INFO @ Sat, 03 Jun 2017 04:42:53: start model_add_line... INFO @ Sat, 03 Jun 2017 04:42:55: 20000000 INFO @ Sat, 03 Jun 2017 04:42:55: #1 tag size is determined as 51 bps INFO @ Sat, 03 Jun 2017 04:42:55: #1 tag size = 51 INFO @ Sat, 03 Jun 2017 04:42:55: #1 total tags in treatment: 20524892 INFO @ Sat, 03 Jun 2017 04:42:55: #1 user defined the maximum tags... INFO @ Sat, 03 Jun 2017 04:42:55: #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 04:42:58: #1 tag size is determined as 51 bps INFO @ Sat, 03 Jun 2017 04:42:58: #1 tag size = 51 INFO @ Sat, 03 Jun 2017 04:42:58: #1 total tags in treatment: 20524892 INFO @ Sat, 03 Jun 2017 04:42:58: #1 user defined the maximum tags... INFO @ Sat, 03 Jun 2017 04:42:58: #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 04:42:59: #1 tags after filtering in treatment: 20501038 INFO @ Sat, 03 Jun 2017 04:42:59: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 03 Jun 2017 04:42:59: #1 finished! INFO @ Sat, 03 Jun 2017 04:42:59: #2 Build Peak Model... INFO @ Sat, 03 Jun 2017 04:43:02: #1 tags after filtering in treatment: 20501038 INFO @ Sat, 03 Jun 2017 04:43:02: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 03 Jun 2017 04:43:02: #1 finished! INFO @ Sat, 03 Jun 2017 04:43:02: #2 Build Peak Model... INFO @ Sat, 03 Jun 2017 04:43:03: #2 number of paired peaks: 769 WARNING @ Sat, 03 Jun 2017 04:43:03: Fewer paired peaks (769) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 769 pairs to build model! INFO @ Sat, 03 Jun 2017 04:43:03: start model_add_line... INFO @ Sat, 03 Jun 2017 04:43:06: #2 number of paired peaks: 769 WARNING @ Sat, 03 Jun 2017 04:43:06: Fewer paired peaks (769) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 769 pairs to build model! INFO @ Sat, 03 Jun 2017 04:43:06: start model_add_line... INFO @ Sat, 03 Jun 2017 04:43:06: start X-correlation... INFO @ Sat, 03 Jun 2017 04:43:06: end of X-cor INFO @ Sat, 03 Jun 2017 04:43:06: #2 finished! INFO @ Sat, 03 Jun 2017 04:43:06: #2 predicted fragment length is 229 bps INFO @ Sat, 03 Jun 2017 04:43:06: #2 alternative fragment length(s) may be 229 bps INFO @ Sat, 03 Jun 2017 04:43:06: #2.2 Generate R script for model : SRX1674096.10_model.r INFO @ Sat, 03 Jun 2017 04:43:06: #3 Call peaks... INFO @ Sat, 03 Jun 2017 04:43:07: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Jun 2017 04:43:17: start X-correlation... INFO @ Sat, 03 Jun 2017 04:43:17: end of X-cor INFO @ Sat, 03 Jun 2017 04:43:17: #2 finished! INFO @ Sat, 03 Jun 2017 04:43:17: #2 predicted fragment length is 229 bps INFO @ Sat, 03 Jun 2017 04:43:17: #2 alternative fragment length(s) may be 229 bps INFO @ Sat, 03 Jun 2017 04:43:17: #2.2 Generate R script for model : SRX1674096.05_model.r INFO @ Sat, 03 Jun 2017 04:43:17: #3 Call peaks... INFO @ Sat, 03 Jun 2017 04:43:17: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Jun 2017 04:43:19: start X-correlation... INFO @ Sat, 03 Jun 2017 04:43:19: end of X-cor INFO @ Sat, 03 Jun 2017 04:43:19: #2 finished! INFO @ Sat, 03 Jun 2017 04:43:19: #2 predicted fragment length is 229 bps INFO @ Sat, 03 Jun 2017 04:43:19: #2 alternative fragment length(s) may be 229 bps INFO @ Sat, 03 Jun 2017 04:43:19: #2.2 Generate R script for model : SRX1674096.20_model.r INFO @ Sat, 03 Jun 2017 04:43:19: #3 Call peaks... INFO @ Sat, 03 Jun 2017 04:43:19: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Jun 2017 04:44:57: #3 Call peaks for each chromosome... INFO @ Sat, 03 Jun 2017 04:45:07: #3 Call peaks for each chromosome... INFO @ Sat, 03 Jun 2017 04:45:17: #3 Call peaks for each chromosome... INFO @ Sat, 03 Jun 2017 04:46:33: #4 Write output xls file... SRX1674096.10_peaks.xls INFO @ Sat, 03 Jun 2017 04:46:33: #4 Write peak in narrowPeak format file... SRX1674096.10_peaks.narrowPeak INFO @ Sat, 03 Jun 2017 04:46:33: #4 Write summits bed file... SRX1674096.10_summits.bed INFO @ Sat, 03 Jun 2017 04:46:33: Done! pass1 - making usageList (7 chroms): 3 millis pass2 - checking and writing primary data (10027 records, 4 fields): 13 millis CompletedMACS2peakCalling INFO @ Sat, 03 Jun 2017 04:46:42: #4 Write output xls file... SRX1674096.20_peaks.xls INFO @ Sat, 03 Jun 2017 04:46:42: #4 Write peak in narrowPeak format file... SRX1674096.20_peaks.narrowPeak INFO @ Sat, 03 Jun 2017 04:46:42: #4 Write summits bed file... SRX1674096.20_summits.bed INFO @ Sat, 03 Jun 2017 04:46:42: Done! pass1 - making usageList (6 chroms): 2 millis pass2 - checking and writing primary data (5292 records, 4 fields): 7 millis CompletedMACS2peakCalling INFO @ Sat, 03 Jun 2017 04:46:54: #4 Write output xls file... SRX1674096.05_peaks.xls INFO @ Sat, 03 Jun 2017 04:46:55: #4 Write peak in narrowPeak format file... SRX1674096.05_peaks.narrowPeak INFO @ Sat, 03 Jun 2017 04:46:55: #4 Write summits bed file... SRX1674096.05_summits.bed INFO @ Sat, 03 Jun 2017 04:46:55: Done! pass1 - making usageList (7 chroms): 3 millis pass2 - checking and writing primary data (16628 records, 4 fields): 20 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。