Job ID = 9041709 sra ファイルのダウンロード中... Completed: 1745880K bytes transferred in 16 seconds (865664K 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 1032 0 --:--:-- 0:00:07 --:--:-- 9111 100 38317 0 38317 0 0 4550 0 --:--:-- 0:00:08 --:--:-- 20858 100 103k 0 103k 0 0 11278 0 --:--:-- 0:00:09 --:--:-- 37487 100 105k 0 105k 0 0 11476 0 --:--:-- 0:00:09 --:--:-- 38147 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 52141678 spots for /home/okishinya/chipatlas/results/dm3/SRX1361357/SRR2749795.sra Written 52141678 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: 00:11:46 52141678 reads; of these: 52141678 (100.00%) were unpaired; of these: 4322755 (8.29%) aligned 0 times 36310432 (69.64%) aligned exactly 1 time 11508491 (22.07%) aligned >1 times 91.71% overall alignment rate Time searching: 00:11:46 Overall time: 00:11:46 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] 23954450 / 47818923 = 0.5009 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 01:56:57: # Command line: callpeak -t SRX1361357.bam -f BAM -g dm -n SRX1361357.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX1361357.05 # format = BAM # ChIP-seq file = ['SRX1361357.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 01:56:57: #1 read tag files... INFO @ Mon, 05 Jun 2017 01:56:57: #1 read treatment tags... INFO @ Mon, 05 Jun 2017 01:56:57: # Command line: callpeak -t SRX1361357.bam -f BAM -g dm -n SRX1361357.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX1361357.10 # format = BAM # ChIP-seq file = ['SRX1361357.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 01:56:57: #1 read tag files... INFO @ Mon, 05 Jun 2017 01:56:57: #1 read treatment tags... INFO @ Mon, 05 Jun 2017 01:56:57: # Command line: callpeak -t SRX1361357.bam -f BAM -g dm -n SRX1361357.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX1361357.20 # format = BAM # ChIP-seq file = ['SRX1361357.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 01:56:57: #1 read tag files... INFO @ Mon, 05 Jun 2017 01:56:57: #1 read treatment tags... INFO @ Mon, 05 Jun 2017 01:57:03: 1000000 INFO @ Mon, 05 Jun 2017 01:57:05: 1000000 INFO @ Mon, 05 Jun 2017 01:57:05: 1000000 INFO @ Mon, 05 Jun 2017 01:57:10: 2000000 INFO @ Mon, 05 Jun 2017 01:57:14: 2000000 INFO @ Mon, 05 Jun 2017 01:57:14: 2000000 INFO @ Mon, 05 Jun 2017 01:57:16: 3000000 INFO @ Mon, 05 Jun 2017 01:57:22: 3000000 INFO @ Mon, 05 Jun 2017 01:57:22: 3000000 INFO @ Mon, 05 Jun 2017 01:57:23: 4000000 INFO @ Mon, 05 Jun 2017 01:57:29: 5000000 INFO @ Mon, 05 Jun 2017 01:57:30: 4000000 INFO @ Mon, 05 Jun 2017 01:57:30: 4000000 INFO @ Mon, 05 Jun 2017 01:57:35: 6000000 INFO @ Mon, 05 Jun 2017 01:57:38: 5000000 INFO @ Mon, 05 Jun 2017 01:57:38: 5000000 INFO @ Mon, 05 Jun 2017 01:57:42: 7000000 INFO @ Mon, 05 Jun 2017 01:57:47: 6000000 INFO @ Mon, 05 Jun 2017 01:57:47: 6000000 INFO @ Mon, 05 Jun 2017 01:57:48: 8000000 INFO @ Mon, 05 Jun 2017 01:57:54: 9000000 INFO @ Mon, 05 Jun 2017 01:57:55: 7000000 INFO @ Mon, 05 Jun 2017 01:57:55: 7000000 INFO @ Mon, 05 Jun 2017 01:58:01: 10000000 INFO @ Mon, 05 Jun 2017 01:58:03: 8000000 INFO @ Mon, 05 Jun 2017 01:58:03: 8000000 INFO @ Mon, 05 Jun 2017 01:58:07: 11000000 INFO @ Mon, 05 Jun 2017 01:58:11: 9000000 INFO @ Mon, 05 Jun 2017 01:58:11: 9000000 INFO @ Mon, 05 Jun 2017 01:58:14: 12000000 INFO @ Mon, 05 Jun 2017 01:58:20: 10000000 INFO @ Mon, 05 Jun 2017 01:58:20: 10000000 INFO @ Mon, 05 Jun 2017 01:58:20: 13000000 INFO @ Mon, 05 Jun 2017 01:58:26: 14000000 INFO @ Mon, 05 Jun 2017 01:58:28: 11000000 INFO @ Mon, 05 Jun 2017 01:58:28: 11000000 INFO @ Mon, 05 Jun 2017 01:58:33: 15000000 INFO @ Mon, 05 Jun 2017 01:58:36: 12000000 INFO @ Mon, 05 Jun 2017 01:58:36: 12000000 INFO @ Mon, 05 Jun 2017 01:58:39: 16000000 INFO @ Mon, 05 Jun 2017 01:58:44: 13000000 INFO @ Mon, 05 Jun 2017 01:58:44: 13000000 INFO @ Mon, 05 Jun 2017 01:58:46: 17000000 INFO @ Mon, 05 Jun 2017 01:58:52: 18000000 INFO @ Mon, 05 Jun 2017 01:58:53: 14000000 INFO @ Mon, 05 Jun 2017 01:58:53: 14000000 INFO @ Mon, 05 Jun 2017 01:58:58: 19000000 INFO @ Mon, 05 Jun 2017 01:59:01: 15000000 INFO @ Mon, 05 Jun 2017 01:59:01: 15000000 INFO @ Mon, 05 Jun 2017 01:59:04: 20000000 INFO @ Mon, 05 Jun 2017 01:59:09: 16000000 INFO @ Mon, 05 Jun 2017 01:59:09: 16000000 INFO @ Mon, 05 Jun 2017 01:59:10: 21000000 INFO @ Mon, 05 Jun 2017 01:59:16: 22000000 INFO @ Mon, 05 Jun 2017 01:59:16: 17000000 INFO @ Mon, 05 Jun 2017 01:59:16: 17000000 INFO @ Mon, 05 Jun 2017 01:59:21: 23000000 INFO @ Mon, 05 Jun 2017 01:59:23: 18000000 INFO @ Mon, 05 Jun 2017 01:59:23: 18000000 INFO @ Mon, 05 Jun 2017 01:59:27: #1 tag size is determined as 50 bps INFO @ Mon, 05 Jun 2017 01:59:27: #1 tag size = 50 INFO @ Mon, 05 Jun 2017 01:59:27: #1 total tags in treatment: 23864473 INFO @ Mon, 05 Jun 2017 01:59:27: #1 user defined the maximum tags... INFO @ Mon, 05 Jun 2017 01:59:27: #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 01:59:30: 19000000 INFO @ Mon, 05 Jun 2017 01:59:30: 19000000 INFO @ Mon, 05 Jun 2017 01:59:31: #1 tags after filtering in treatment: 23854602 INFO @ Mon, 05 Jun 2017 01:59:31: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 05 Jun 2017 01:59:31: #1 finished! INFO @ Mon, 05 Jun 2017 01:59:31: #2 Build Peak Model... INFO @ Mon, 05 Jun 2017 01:59:35: #2 number of paired peaks: 767 WARNING @ Mon, 05 Jun 2017 01:59:35: Fewer paired peaks (767) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 767 pairs to build model! INFO @ Mon, 05 Jun 2017 01:59:35: start model_add_line... INFO @ Mon, 05 Jun 2017 01:59:36: 20000000 INFO @ Mon, 05 Jun 2017 01:59:36: 20000000 INFO @ Mon, 05 Jun 2017 01:59:41: 21000000 INFO @ Mon, 05 Jun 2017 01:59:42: 21000000 INFO @ Mon, 05 Jun 2017 01:59:46: start X-correlation... INFO @ Mon, 05 Jun 2017 01:59:46: end of X-cor INFO @ Mon, 05 Jun 2017 01:59:46: #2 finished! INFO @ Mon, 05 Jun 2017 01:59:46: #2 predicted fragment length is 228 bps INFO @ Mon, 05 Jun 2017 01:59:46: #2 alternative fragment length(s) may be 228 bps INFO @ Mon, 05 Jun 2017 01:59:46: #2.2 Generate R script for model : SRX1361357.05_model.r INFO @ Mon, 05 Jun 2017 01:59:46: #3 Call peaks... INFO @ Mon, 05 Jun 2017 01:59:46: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 05 Jun 2017 01:59:47: 22000000 INFO @ Mon, 05 Jun 2017 01:59:48: 22000000 INFO @ Mon, 05 Jun 2017 01:59:53: 23000000 INFO @ Mon, 05 Jun 2017 01:59:54: 23000000 INFO @ Mon, 05 Jun 2017 01:59:59: #1 tag size is determined as 50 bps INFO @ Mon, 05 Jun 2017 01:59:59: #1 tag size = 50 INFO @ Mon, 05 Jun 2017 01:59:59: #1 total tags in treatment: 23864473 INFO @ Mon, 05 Jun 2017 01:59:59: #1 user defined the maximum tags... INFO @ Mon, 05 Jun 2017 01:59:59: #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 01:59:59: #1 tag size is determined as 50 bps INFO @ Mon, 05 Jun 2017 01:59:59: #1 tag size = 50 INFO @ Mon, 05 Jun 2017 01:59:59: #1 total tags in treatment: 23864473 INFO @ Mon, 05 Jun 2017 01:59:59: #1 user defined the maximum tags... INFO @ Mon, 05 Jun 2017 01:59:59: #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 02:00:03: #1 tags after filtering in treatment: 23854602 INFO @ Mon, 05 Jun 2017 02:00:03: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 05 Jun 2017 02:00:03: #1 finished! INFO @ Mon, 05 Jun 2017 02:00:03: #2 Build Peak Model... INFO @ Mon, 05 Jun 2017 02:00:04: #1 tags after filtering in treatment: 23854602 INFO @ Mon, 05 Jun 2017 02:00:04: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 05 Jun 2017 02:00:04: #1 finished! INFO @ Mon, 05 Jun 2017 02:00:04: #2 Build Peak Model... INFO @ Mon, 05 Jun 2017 02:00:08: #2 number of paired peaks: 767 WARNING @ Mon, 05 Jun 2017 02:00:08: Fewer paired peaks (767) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 767 pairs to build model! INFO @ Mon, 05 Jun 2017 02:00:08: start model_add_line... INFO @ Mon, 05 Jun 2017 02:00:08: #2 number of paired peaks: 767 WARNING @ Mon, 05 Jun 2017 02:00:08: Fewer paired peaks (767) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 767 pairs to build model! INFO @ Mon, 05 Jun 2017 02:00:08: start model_add_line... INFO @ Mon, 05 Jun 2017 02:00:19: start X-correlation... INFO @ Mon, 05 Jun 2017 02:00:19: end of X-cor INFO @ Mon, 05 Jun 2017 02:00:19: #2 finished! INFO @ Mon, 05 Jun 2017 02:00:19: #2 predicted fragment length is 228 bps INFO @ Mon, 05 Jun 2017 02:00:19: #2 alternative fragment length(s) may be 228 bps INFO @ Mon, 05 Jun 2017 02:00:19: #2.2 Generate R script for model : SRX1361357.10_model.r INFO @ Mon, 05 Jun 2017 02:00:19: #3 Call peaks... INFO @ Mon, 05 Jun 2017 02:00:19: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 05 Jun 2017 02:00:19: start X-correlation... INFO @ Mon, 05 Jun 2017 02:00:19: end of X-cor INFO @ Mon, 05 Jun 2017 02:00:19: #2 finished! INFO @ Mon, 05 Jun 2017 02:00:19: #2 predicted fragment length is 228 bps INFO @ Mon, 05 Jun 2017 02:00:19: #2 alternative fragment length(s) may be 228 bps INFO @ Mon, 05 Jun 2017 02:00:19: #2.2 Generate R script for model : SRX1361357.20_model.r INFO @ Mon, 05 Jun 2017 02:00:20: #3 Call peaks... INFO @ Mon, 05 Jun 2017 02:00:20: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 05 Jun 2017 02:02:01: #3 Call peaks for each chromosome... INFO @ Mon, 05 Jun 2017 02:02:30: #3 Call peaks for each chromosome... INFO @ Mon, 05 Jun 2017 02:02:32: #3 Call peaks for each chromosome... INFO @ Mon, 05 Jun 2017 02:03:50: #4 Write output xls file... SRX1361357.05_peaks.xls INFO @ Mon, 05 Jun 2017 02:03:50: #4 Write peak in narrowPeak format file... SRX1361357.05_peaks.narrowPeak INFO @ Mon, 05 Jun 2017 02:03:50: #4 Write summits bed file... SRX1361357.05_summits.bed INFO @ Mon, 05 Jun 2017 02:03:50: Done! pass1 - making usageList (15 chroms): 2 millis pass2 - checking and writing primary data (8866 records, 4 fields): 12 millis CompletedMACS2peakCalling INFO @ Mon, 05 Jun 2017 02:04:08: #4 Write output xls file... SRX1361357.10_peaks.xls INFO @ Mon, 05 Jun 2017 02:04:08: #4 Write peak in narrowPeak format file... SRX1361357.10_peaks.narrowPeak INFO @ Mon, 05 Jun 2017 02:04:08: #4 Write summits bed file... SRX1361357.10_summits.bed INFO @ Mon, 05 Jun 2017 02:04:08: Done! pass1 - making usageList (15 chroms): 2 millis pass2 - checking and writing primary data (6784 records, 4 fields): 12 millis CompletedMACS2peakCalling INFO @ Mon, 05 Jun 2017 02:04:08: #4 Write output xls file... SRX1361357.20_peaks.xls INFO @ Mon, 05 Jun 2017 02:04:08: #4 Write peak in narrowPeak format file... SRX1361357.20_peaks.narrowPeak INFO @ Mon, 05 Jun 2017 02:04:08: #4 Write summits bed file... SRX1361357.20_summits.bed INFO @ Mon, 05 Jun 2017 02:04:08: Done! pass1 - making usageList (15 chroms): 2 millis pass2 - checking and writing primary data (4985 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。