Job ID = 9041707 sra ファイルのダウンロード中... Completed: 1884375K bytes transferred in 16 seconds (958533K 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 7663 0 7663 0 0 1085 0 --:--:-- 0:00:07 --:--:-- 11319 100 28797 0 28797 0 0 3575 0 --:--:-- 0:00:08 --:--:-- 17223 100 59205 0 59205 0 0 6663 0 --:--:-- 0:00:08 --:--:-- 23653 100 107k 0 107k 0 0 11515 0 --:--:-- 0:00:09 --:--:-- 34731 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 56635007 spots for /home/okishinya/chipatlas/results/dm3/SRX1361355/SRR2749793.sra Written 56635007 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: 00:10:40 56635007 reads; of these: 56635007 (100.00%) were unpaired; of these: 2381040 (4.20%) aligned 0 times 39504162 (69.75%) aligned exactly 1 time 14749805 (26.04%) aligned >1 times 95.80% overall alignment rate Time searching: 00:10:40 Overall time: 00:10:40 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 24 files... [bam_rmdupse_core] 24736148 / 54253967 = 0.4559 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 @ Mon, 05 Jun 2017 01:56:29: # Command line: callpeak -t SRX1361355.bam -f BAM -g dm -n SRX1361355.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX1361355.20 # format = BAM # ChIP-seq file = ['SRX1361355.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 @ Mon, 05 Jun 2017 01:56:29: #1 read tag files... INFO @ Mon, 05 Jun 2017 01:56:29: #1 read treatment tags... INFO @ Mon, 05 Jun 2017 01:56:29: # Command line: callpeak -t SRX1361355.bam -f BAM -g dm -n SRX1361355.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX1361355.05 # format = BAM # ChIP-seq file = ['SRX1361355.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 @ Mon, 05 Jun 2017 01:56:29: #1 read tag files... INFO @ Mon, 05 Jun 2017 01:56:29: #1 read treatment tags... INFO @ Mon, 05 Jun 2017 01:56:29: # Command line: callpeak -t SRX1361355.bam -f BAM -g dm -n SRX1361355.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX1361355.10 # format = BAM # ChIP-seq file = ['SRX1361355.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 @ Mon, 05 Jun 2017 01:56:29: #1 read tag files... INFO @ Mon, 05 Jun 2017 01:56:29: #1 read treatment tags... INFO @ Mon, 05 Jun 2017 01:56:35: 1000000 INFO @ Mon, 05 Jun 2017 01:56:35: 1000000 INFO @ Mon, 05 Jun 2017 01:56:35: 1000000 INFO @ Mon, 05 Jun 2017 01:56:41: 2000000 INFO @ Mon, 05 Jun 2017 01:56:41: 2000000 INFO @ Mon, 05 Jun 2017 01:56:41: 2000000 INFO @ Mon, 05 Jun 2017 01:56:46: 3000000 INFO @ Mon, 05 Jun 2017 01:56:46: 3000000 INFO @ Mon, 05 Jun 2017 01:56:47: 3000000 INFO @ Mon, 05 Jun 2017 01:56:52: 4000000 INFO @ Mon, 05 Jun 2017 01:56:52: 4000000 INFO @ Mon, 05 Jun 2017 01:56:53: 4000000 INFO @ Mon, 05 Jun 2017 01:56:58: 5000000 INFO @ Mon, 05 Jun 2017 01:56:58: 5000000 INFO @ Mon, 05 Jun 2017 01:56:59: 5000000 INFO @ Mon, 05 Jun 2017 01:57:04: 6000000 INFO @ Mon, 05 Jun 2017 01:57:05: 6000000 INFO @ Mon, 05 Jun 2017 01:57:05: 6000000 INFO @ Mon, 05 Jun 2017 01:57:10: 7000000 INFO @ Mon, 05 Jun 2017 01:57:11: 7000000 INFO @ Mon, 05 Jun 2017 01:57:12: 7000000 INFO @ Mon, 05 Jun 2017 01:57:16: 8000000 INFO @ Mon, 05 Jun 2017 01:57:17: 8000000 INFO @ Mon, 05 Jun 2017 01:57:19: 8000000 INFO @ Mon, 05 Jun 2017 01:57:22: 9000000 INFO @ Mon, 05 Jun 2017 01:57:24: 9000000 INFO @ Mon, 05 Jun 2017 01:57:25: 9000000 INFO @ Mon, 05 Jun 2017 01:57:27: 10000000 INFO @ Mon, 05 Jun 2017 01:57:30: 10000000 INFO @ Mon, 05 Jun 2017 01:57:32: 10000000 INFO @ Mon, 05 Jun 2017 01:57:33: 11000000 INFO @ Mon, 05 Jun 2017 01:57:36: 11000000 INFO @ Mon, 05 Jun 2017 01:57:38: 11000000 INFO @ Mon, 05 Jun 2017 01:57:39: 12000000 INFO @ Mon, 05 Jun 2017 01:57:43: 12000000 INFO @ Mon, 05 Jun 2017 01:57:45: 12000000 INFO @ Mon, 05 Jun 2017 01:57:45: 13000000 INFO @ Mon, 05 Jun 2017 01:57:49: 13000000 INFO @ Mon, 05 Jun 2017 01:57:51: 14000000 INFO @ Mon, 05 Jun 2017 01:57:51: 13000000 INFO @ Mon, 05 Jun 2017 01:57:56: 14000000 INFO @ Mon, 05 Jun 2017 01:57:56: 15000000 INFO @ Mon, 05 Jun 2017 01:57:58: 14000000 INFO @ Mon, 05 Jun 2017 01:58:02: 15000000 INFO @ Mon, 05 Jun 2017 01:58:02: 16000000 INFO @ Mon, 05 Jun 2017 01:58:04: 15000000 INFO @ Mon, 05 Jun 2017 01:58:08: 16000000 INFO @ Mon, 05 Jun 2017 01:58:08: 17000000 INFO @ Mon, 05 Jun 2017 01:58:11: 16000000 INFO @ Mon, 05 Jun 2017 01:58:14: 18000000 INFO @ Mon, 05 Jun 2017 01:58:14: 17000000 INFO @ Mon, 05 Jun 2017 01:58:17: 17000000 INFO @ Mon, 05 Jun 2017 01:58:20: 19000000 INFO @ Mon, 05 Jun 2017 01:58:21: 18000000 INFO @ Mon, 05 Jun 2017 01:58:24: 18000000 INFO @ Mon, 05 Jun 2017 01:58:26: 20000000 INFO @ Mon, 05 Jun 2017 01:58:27: 19000000 INFO @ Mon, 05 Jun 2017 01:58:30: 19000000 INFO @ Mon, 05 Jun 2017 01:58:31: 21000000 INFO @ Mon, 05 Jun 2017 01:58:33: 20000000 INFO @ Mon, 05 Jun 2017 01:58:37: 20000000 INFO @ Mon, 05 Jun 2017 01:58:37: 22000000 INFO @ Mon, 05 Jun 2017 01:58:40: 21000000 INFO @ Mon, 05 Jun 2017 01:58:43: 23000000 INFO @ Mon, 05 Jun 2017 01:58:43: 21000000 INFO @ Mon, 05 Jun 2017 01:58:46: 22000000 INFO @ Mon, 05 Jun 2017 01:58:49: 24000000 INFO @ Mon, 05 Jun 2017 01:58:50: 22000000 INFO @ Mon, 05 Jun 2017 01:58:52: 23000000 INFO @ Mon, 05 Jun 2017 01:58:55: 25000000 INFO @ Mon, 05 Jun 2017 01:58:56: 23000000 INFO @ Mon, 05 Jun 2017 01:58:59: 24000000 INFO @ Mon, 05 Jun 2017 01:59:01: 26000000 INFO @ Mon, 05 Jun 2017 01:59:03: 24000000 INFO @ Mon, 05 Jun 2017 01:59:05: 25000000 INFO @ Mon, 05 Jun 2017 01:59:06: 27000000 INFO @ Mon, 05 Jun 2017 01:59:10: 25000000 INFO @ Mon, 05 Jun 2017 01:59:12: 26000000 INFO @ Mon, 05 Jun 2017 01:59:12: 28000000 INFO @ Mon, 05 Jun 2017 01:59:17: 26000000 INFO @ Mon, 05 Jun 2017 01:59:18: 29000000 INFO @ Mon, 05 Jun 2017 01:59:18: 27000000 INFO @ Mon, 05 Jun 2017 01:59:21: #1 tag size is determined as 50 bps INFO @ Mon, 05 Jun 2017 01:59:21: #1 tag size = 50 INFO @ Mon, 05 Jun 2017 01:59:21: #1 total tags in treatment: 29517819 INFO @ Mon, 05 Jun 2017 01:59:21: #1 user defined the maximum tags... INFO @ Mon, 05 Jun 2017 01:59:21: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Mon, 05 Jun 2017 01:59:23: 27000000 INFO @ Mon, 05 Jun 2017 01:59:25: 28000000 INFO @ Mon, 05 Jun 2017 01:59:27: #1 tags after filtering in treatment: 29502936 INFO @ Mon, 05 Jun 2017 01:59:27: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 05 Jun 2017 01:59:27: #1 finished! INFO @ Mon, 05 Jun 2017 01:59:27: #2 Build Peak Model... INFO @ Mon, 05 Jun 2017 01:59:30: 28000000 INFO @ Mon, 05 Jun 2017 01:59:31: 29000000 INFO @ Mon, 05 Jun 2017 01:59:31: #2 number of paired peaks: 545 WARNING @ Mon, 05 Jun 2017 01:59:31: Fewer paired peaks (545) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 545 pairs to build model! INFO @ Mon, 05 Jun 2017 01:59:31: start model_add_line... INFO @ Mon, 05 Jun 2017 01:59:35: #1 tag size is determined as 50 bps INFO @ Mon, 05 Jun 2017 01:59:35: #1 tag size = 50 INFO @ Mon, 05 Jun 2017 01:59:35: #1 total tags in treatment: 29517819 INFO @ Mon, 05 Jun 2017 01:59:35: #1 user defined the maximum tags... INFO @ Mon, 05 Jun 2017 01:59:35: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Mon, 05 Jun 2017 01:59:36: 29000000 INFO @ Mon, 05 Jun 2017 01:59:39: #1 tag size is determined as 50 bps INFO @ Mon, 05 Jun 2017 01:59:39: #1 tag size = 50 INFO @ Mon, 05 Jun 2017 01:59:39: #1 total tags in treatment: 29517819 INFO @ Mon, 05 Jun 2017 01:59:39: #1 user defined the maximum tags... INFO @ Mon, 05 Jun 2017 01:59:39: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Mon, 05 Jun 2017 01:59:40: #1 tags after filtering in treatment: 29502936 INFO @ Mon, 05 Jun 2017 01:59:40: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 05 Jun 2017 01:59:40: #1 finished! INFO @ Mon, 05 Jun 2017 01:59:40: #2 Build Peak Model... INFO @ Mon, 05 Jun 2017 01:59:42: start X-correlation... INFO @ Mon, 05 Jun 2017 01:59:42: end of X-cor INFO @ Mon, 05 Jun 2017 01:59:42: #2 finished! INFO @ Mon, 05 Jun 2017 01:59:42: #2 predicted fragment length is 195 bps INFO @ Mon, 05 Jun 2017 01:59:42: #2 alternative fragment length(s) may be 195 bps INFO @ Mon, 05 Jun 2017 01:59:42: #2.2 Generate R script for model : SRX1361355.10_model.r INFO @ Mon, 05 Jun 2017 01:59:42: #3 Call peaks... INFO @ Mon, 05 Jun 2017 01:59:42: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 05 Jun 2017 01:59:45: #1 tags after filtering in treatment: 29502936 INFO @ Mon, 05 Jun 2017 01:59:45: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 05 Jun 2017 01:59:45: #1 finished! INFO @ Mon, 05 Jun 2017 01:59:45: #2 Build Peak Model... INFO @ Mon, 05 Jun 2017 01:59:45: #2 number of paired peaks: 545 WARNING @ Mon, 05 Jun 2017 01:59:45: Fewer paired peaks (545) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 545 pairs to build model! INFO @ Mon, 05 Jun 2017 01:59:45: start model_add_line... INFO @ Mon, 05 Jun 2017 01:59:50: #2 number of paired peaks: 545 WARNING @ Mon, 05 Jun 2017 01:59:50: Fewer paired peaks (545) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 545 pairs to build model! INFO @ Mon, 05 Jun 2017 01:59:50: start model_add_line... INFO @ Mon, 05 Jun 2017 01:59:56: start X-correlation... INFO @ Mon, 05 Jun 2017 01:59:56: end of X-cor INFO @ Mon, 05 Jun 2017 01:59:56: #2 finished! INFO @ Mon, 05 Jun 2017 01:59:56: #2 predicted fragment length is 195 bps INFO @ Mon, 05 Jun 2017 01:59:56: #2 alternative fragment length(s) may be 195 bps INFO @ Mon, 05 Jun 2017 01:59:56: #2.2 Generate R script for model : SRX1361355.05_model.r INFO @ Mon, 05 Jun 2017 01:59:56: #3 Call peaks... INFO @ Mon, 05 Jun 2017 01:59:56: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 05 Jun 2017 02:00:01: start X-correlation... INFO @ Mon, 05 Jun 2017 02:00:01: end of X-cor INFO @ Mon, 05 Jun 2017 02:00:01: #2 finished! INFO @ Mon, 05 Jun 2017 02:00:01: #2 predicted fragment length is 195 bps INFO @ Mon, 05 Jun 2017 02:00:01: #2 alternative fragment length(s) may be 195 bps INFO @ Mon, 05 Jun 2017 02:00:01: #2.2 Generate R script for model : SRX1361355.20_model.r INFO @ Mon, 05 Jun 2017 02:00:01: #3 Call peaks... INFO @ Mon, 05 Jun 2017 02:00:01: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 05 Jun 2017 02:02:24: #3 Call peaks for each chromosome... INFO @ Mon, 05 Jun 2017 02:02:28: #3 Call peaks for each chromosome... INFO @ Mon, 05 Jun 2017 02:02:36: #3 Call peaks for each chromosome... INFO @ Mon, 05 Jun 2017 02:04:26: #4 Write output xls file... SRX1361355.10_peaks.xls INFO @ Mon, 05 Jun 2017 02:04:26: #4 Write peak in narrowPeak format file... SRX1361355.10_peaks.narrowPeak INFO @ Mon, 05 Jun 2017 02:04:26: #4 Write summits bed file... SRX1361355.10_summits.bed INFO @ Mon, 05 Jun 2017 02:04:26: Done! pass1 - making usageList (15 chroms): 2 millis pass2 - checking and writing primary data (7460 records, 4 fields): 10 millis CompletedMACS2peakCalling INFO @ Mon, 05 Jun 2017 02:04:29: #4 Write output xls file... SRX1361355.05_peaks.xls INFO @ Mon, 05 Jun 2017 02:04:29: #4 Write peak in narrowPeak format file... SRX1361355.05_peaks.narrowPeak INFO @ Mon, 05 Jun 2017 02:04:29: #4 Write summits bed file... SRX1361355.05_summits.bed INFO @ Mon, 05 Jun 2017 02:04:29: Done! pass1 - making usageList (15 chroms): 2 millis pass2 - checking and writing primary data (9334 records, 4 fields): 14 millis CompletedMACS2peakCalling INFO @ Mon, 05 Jun 2017 02:04:30: #4 Write output xls file... SRX1361355.20_peaks.xls INFO @ Mon, 05 Jun 2017 02:04:30: #4 Write peak in narrowPeak format file... SRX1361355.20_peaks.narrowPeak INFO @ Mon, 05 Jun 2017 02:04:30: #4 Write summits bed file... SRX1361355.20_summits.bed INFO @ Mon, 05 Jun 2017 02:04:30: Done! pass1 - making usageList (14 chroms): 2 millis pass2 - checking and writing primary data (5630 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。