Job ID = 9029240 sra ファイルのダウンロード中... Completed: 717782K bytes transferred in 13 seconds (445122K 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 1938 0 --:--:-- 0:00:07 --:--:-- 13399 100 38317 0 38317 0 0 4569 0 --:--:-- 0:00:08 --:--:-- 18546 100 86029 0 86029 0 0 9170 0 --:--:-- 0:00:09 --:--:-- 28104 100 110k 0 110k 0 0 11622 0 --:--:-- 0:00:09 --:--:-- 33273 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 32381362 spots for /home/okishinya/chipatlas/results/dm3/SRX1433380/SRR2919845.sra Written 32381362 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: 00:13:09 32381362 reads; of these: 32381362 (100.00%) were unpaired; of these: 2075461 (6.41%) aligned 0 times 23215948 (71.70%) aligned exactly 1 time 7089953 (21.90%) aligned >1 times 93.59% overall alignment rate Time searching: 00:13:09 Overall time: 00:13:09 マッピングが完了しました。 samtools でBAM に変換中... [samopen] SAM header is present: 15 sequences. [bam_sort_core] merging from 16 files... [bam_rmdupse_core] 11112149 / 30305901 = 0.3667 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 13:14:01: # Command line: callpeak -t SRX1433380.bam -f BAM -g dm -n SRX1433380.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX1433380.05 # format = BAM # ChIP-seq file = ['SRX1433380.bam'] # control file = None # effective genome size = 1.20e+08 # 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 13:14:01: #1 read tag files... INFO @ Sat, 03 Jun 2017 13:14:01: #1 read treatment tags... INFO @ Sat, 03 Jun 2017 13:14:01: # Command line: callpeak -t SRX1433380.bam -f BAM -g dm -n SRX1433380.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX1433380.20 # format = BAM # ChIP-seq file = ['SRX1433380.bam'] # control file = None # effective genome size = 1.20e+08 # 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 13:14:01: #1 read tag files... INFO @ Sat, 03 Jun 2017 13:14:01: #1 read treatment tags... INFO @ Sat, 03 Jun 2017 13:14:01: # Command line: callpeak -t SRX1433380.bam -f BAM -g dm -n SRX1433380.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX1433380.10 # format = BAM # ChIP-seq file = ['SRX1433380.bam'] # control file = None # effective genome size = 1.20e+08 # 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 13:14:01: #1 read tag files... INFO @ Sat, 03 Jun 2017 13:14:01: #1 read treatment tags... INFO @ Sat, 03 Jun 2017 13:14:06: 1000000 INFO @ Sat, 03 Jun 2017 13:14:06: 1000000 INFO @ Sat, 03 Jun 2017 13:14:07: 1000000 INFO @ Sat, 03 Jun 2017 13:14:12: 2000000 INFO @ Sat, 03 Jun 2017 13:14:12: 2000000 INFO @ Sat, 03 Jun 2017 13:14:13: 2000000 INFO @ Sat, 03 Jun 2017 13:14:17: 3000000 INFO @ Sat, 03 Jun 2017 13:14:18: 3000000 INFO @ Sat, 03 Jun 2017 13:14:20: 3000000 INFO @ Sat, 03 Jun 2017 13:14:23: 4000000 INFO @ Sat, 03 Jun 2017 13:14:24: 4000000 INFO @ Sat, 03 Jun 2017 13:14:27: 4000000 INFO @ Sat, 03 Jun 2017 13:14:28: 5000000 INFO @ Sat, 03 Jun 2017 13:14:30: 5000000 INFO @ Sat, 03 Jun 2017 13:14:33: 6000000 INFO @ Sat, 03 Jun 2017 13:14:33: 5000000 INFO @ Sat, 03 Jun 2017 13:14:36: 6000000 INFO @ Sat, 03 Jun 2017 13:14:39: 7000000 INFO @ Sat, 03 Jun 2017 13:14:40: 6000000 INFO @ Sat, 03 Jun 2017 13:14:42: 7000000 INFO @ Sat, 03 Jun 2017 13:14:44: 8000000 INFO @ Sat, 03 Jun 2017 13:14:47: 7000000 INFO @ Sat, 03 Jun 2017 13:14:48: 8000000 INFO @ Sat, 03 Jun 2017 13:14:49: 9000000 INFO @ Sat, 03 Jun 2017 13:14:54: 9000000 INFO @ Sat, 03 Jun 2017 13:14:54: 8000000 INFO @ Sat, 03 Jun 2017 13:14:55: 10000000 INFO @ Sat, 03 Jun 2017 13:14:59: 10000000 INFO @ Sat, 03 Jun 2017 13:15:00: 11000000 INFO @ Sat, 03 Jun 2017 13:15:00: 9000000 INFO @ Sat, 03 Jun 2017 13:15:05: 12000000 INFO @ Sat, 03 Jun 2017 13:15:05: 11000000 INFO @ Sat, 03 Jun 2017 13:15:07: 10000000 INFO @ Sat, 03 Jun 2017 13:15:10: 13000000 INFO @ Sat, 03 Jun 2017 13:15:11: 12000000 INFO @ Sat, 03 Jun 2017 13:15:14: 11000000 INFO @ Sat, 03 Jun 2017 13:15:16: 14000000 INFO @ Sat, 03 Jun 2017 13:15:18: 13000000 INFO @ Sat, 03 Jun 2017 13:15:21: 12000000 INFO @ Sat, 03 Jun 2017 13:15:21: 15000000 INFO @ Sat, 03 Jun 2017 13:15:23: 14000000 INFO @ Sat, 03 Jun 2017 13:15:26: 16000000 INFO @ Sat, 03 Jun 2017 13:15:27: 13000000 INFO @ Sat, 03 Jun 2017 13:15:30: 15000000 INFO @ Sat, 03 Jun 2017 13:15:31: 17000000 INFO @ Sat, 03 Jun 2017 13:15:34: 14000000 INFO @ Sat, 03 Jun 2017 13:15:36: 16000000 INFO @ Sat, 03 Jun 2017 13:15:36: 18000000 INFO @ Sat, 03 Jun 2017 13:15:41: 15000000 INFO @ Sat, 03 Jun 2017 13:15:42: 17000000 INFO @ Sat, 03 Jun 2017 13:15:42: 19000000 INFO @ Sat, 03 Jun 2017 13:15:43: #1 tag size is determined as 50 bps INFO @ Sat, 03 Jun 2017 13:15:43: #1 tag size = 50 INFO @ Sat, 03 Jun 2017 13:15:43: #1 total tags in treatment: 19193752 INFO @ Sat, 03 Jun 2017 13:15:43: #1 user defined the maximum tags... INFO @ Sat, 03 Jun 2017 13:15:43: #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 13:15:46: #1 tags after filtering in treatment: 19188198 INFO @ Sat, 03 Jun 2017 13:15:46: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 03 Jun 2017 13:15:46: #1 finished! INFO @ Sat, 03 Jun 2017 13:15:46: #2 Build Peak Model... INFO @ Sat, 03 Jun 2017 13:15:47: 18000000 INFO @ Sat, 03 Jun 2017 13:15:48: 16000000 INFO @ Sat, 03 Jun 2017 13:15:49: #2 number of paired peaks: 463 WARNING @ Sat, 03 Jun 2017 13:15:49: Fewer paired peaks (463) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 463 pairs to build model! INFO @ Sat, 03 Jun 2017 13:15:49: start model_add_line... INFO @ Sat, 03 Jun 2017 13:15:53: 19000000 INFO @ Sat, 03 Jun 2017 13:15:54: 17000000 INFO @ Sat, 03 Jun 2017 13:15:55: #1 tag size is determined as 50 bps INFO @ Sat, 03 Jun 2017 13:15:55: #1 tag size = 50 INFO @ Sat, 03 Jun 2017 13:15:55: #1 total tags in treatment: 19193752 INFO @ Sat, 03 Jun 2017 13:15:55: #1 user defined the maximum tags... INFO @ Sat, 03 Jun 2017 13:15:55: #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 13:15:56: start X-correlation... INFO @ Sat, 03 Jun 2017 13:15:56: end of X-cor INFO @ Sat, 03 Jun 2017 13:15:56: #2 finished! INFO @ Sat, 03 Jun 2017 13:15:56: #2 predicted fragment length is 171 bps INFO @ Sat, 03 Jun 2017 13:15:56: #2 alternative fragment length(s) may be 171 bps INFO @ Sat, 03 Jun 2017 13:15:56: #2.2 Generate R script for model : SRX1433380.20_model.r INFO @ Sat, 03 Jun 2017 13:15:56: #3 Call peaks... INFO @ Sat, 03 Jun 2017 13:15:56: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Jun 2017 13:15:58: #1 tags after filtering in treatment: 19188198 INFO @ Sat, 03 Jun 2017 13:15:58: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 03 Jun 2017 13:15:58: #1 finished! INFO @ Sat, 03 Jun 2017 13:15:58: #2 Build Peak Model... INFO @ Sat, 03 Jun 2017 13:16:00: 18000000 INFO @ Sat, 03 Jun 2017 13:16:02: #2 number of paired peaks: 463 WARNING @ Sat, 03 Jun 2017 13:16:02: Fewer paired peaks (463) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 463 pairs to build model! INFO @ Sat, 03 Jun 2017 13:16:02: start model_add_line... INFO @ Sat, 03 Jun 2017 13:16:05: 19000000 INFO @ Sat, 03 Jun 2017 13:16:07: #1 tag size is determined as 50 bps INFO @ Sat, 03 Jun 2017 13:16:07: #1 tag size = 50 INFO @ Sat, 03 Jun 2017 13:16:07: #1 total tags in treatment: 19193752 INFO @ Sat, 03 Jun 2017 13:16:07: #1 user defined the maximum tags... INFO @ Sat, 03 Jun 2017 13:16:07: #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 13:16:08: start X-correlation... INFO @ Sat, 03 Jun 2017 13:16:08: end of X-cor INFO @ Sat, 03 Jun 2017 13:16:08: #2 finished! INFO @ Sat, 03 Jun 2017 13:16:08: #2 predicted fragment length is 171 bps INFO @ Sat, 03 Jun 2017 13:16:08: #2 alternative fragment length(s) may be 171 bps INFO @ Sat, 03 Jun 2017 13:16:08: #2.2 Generate R script for model : SRX1433380.05_model.r INFO @ Sat, 03 Jun 2017 13:16:08: #3 Call peaks... INFO @ Sat, 03 Jun 2017 13:16:08: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Jun 2017 13:16:10: #1 tags after filtering in treatment: 19188198 INFO @ Sat, 03 Jun 2017 13:16:10: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 03 Jun 2017 13:16:10: #1 finished! INFO @ Sat, 03 Jun 2017 13:16:10: #2 Build Peak Model... INFO @ Sat, 03 Jun 2017 13:16:14: #2 number of paired peaks: 463 WARNING @ Sat, 03 Jun 2017 13:16:14: Fewer paired peaks (463) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 463 pairs to build model! INFO @ Sat, 03 Jun 2017 13:16:14: start model_add_line... INFO @ Sat, 03 Jun 2017 13:16:20: start X-correlation... INFO @ Sat, 03 Jun 2017 13:16:20: end of X-cor INFO @ Sat, 03 Jun 2017 13:16:20: #2 finished! INFO @ Sat, 03 Jun 2017 13:16:20: #2 predicted fragment length is 171 bps INFO @ Sat, 03 Jun 2017 13:16:20: #2 alternative fragment length(s) may be 171 bps INFO @ Sat, 03 Jun 2017 13:16:20: #2.2 Generate R script for model : SRX1433380.10_model.r INFO @ Sat, 03 Jun 2017 13:16:20: #3 Call peaks... INFO @ Sat, 03 Jun 2017 13:16:20: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Jun 2017 13:17:44: #3 Call peaks for each chromosome... INFO @ Sat, 03 Jun 2017 13:17:47: #3 Call peaks for each chromosome... INFO @ Sat, 03 Jun 2017 13:18:11: #3 Call peaks for each chromosome... INFO @ Sat, 03 Jun 2017 13:19:03: #4 Write output xls file... SRX1433380.20_peaks.xls INFO @ Sat, 03 Jun 2017 13:19:04: #4 Write peak in narrowPeak format file... SRX1433380.20_peaks.narrowPeak INFO @ Sat, 03 Jun 2017 13:19:04: #4 Write summits bed file... SRX1433380.20_summits.bed INFO @ Sat, 03 Jun 2017 13:19:04: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (2946 records, 4 fields): 5 millis CompletedMACS2peakCalling INFO @ Sat, 03 Jun 2017 13:19:11: #4 Write output xls file... SRX1433380.05_peaks.xls INFO @ Sat, 03 Jun 2017 13:19:11: #4 Write peak in narrowPeak format file... SRX1433380.05_peaks.narrowPeak INFO @ Sat, 03 Jun 2017 13:19:11: #4 Write summits bed file... SRX1433380.05_summits.bed INFO @ Sat, 03 Jun 2017 13:19:11: Done! pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (7379 records, 4 fields): 10 millis CompletedMACS2peakCalling INFO @ Sat, 03 Jun 2017 13:19:36: #4 Write output xls file... SRX1433380.10_peaks.xls INFO @ Sat, 03 Jun 2017 13:19:36: #4 Write peak in narrowPeak format file... SRX1433380.10_peaks.narrowPeak INFO @ Sat, 03 Jun 2017 13:19:36: #4 Write summits bed file... SRX1433380.10_summits.bed INFO @ Sat, 03 Jun 2017 13:19:36: Done! pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (5023 records, 4 fields): 8 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。