Job ID = 9029469 sra ファイルのダウンロード中... Completed: 278849K bytes transferred in 5 seconds (398511K 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 1068 0 --:--:-- 0:00:07 --:--:-- 11236 100 38318 0 38318 0 0 4689 0 --:--:-- 0:00:08 --:--:-- 22835 100 57836 0 57836 0 0 6771 0 --:--:-- 0:00:08 --:--:-- 28240 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 10926568 spots for /home/okishinya/chipatlas/results/dm3/SRX1794222/SRR3575256.sra Written 10926568 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: 00:03:45 10926568 reads; of these: 10926568 (100.00%) were unpaired; of these: 299410 (2.74%) aligned 0 times 8731378 (79.91%) aligned exactly 1 time 1895780 (17.35%) aligned >1 times 97.26% overall alignment rate Time searching: 00:03:45 Overall time: 00:03:45 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 8 files... [bam_rmdupse_core] 1263325 / 10627158 = 0.1189 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 13:57:33: # Command line: callpeak -t SRX1794222.bam -f BAM -g dm -n SRX1794222.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX1794222.20 # format = BAM # ChIP-seq file = ['SRX1794222.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 13:57:33: #1 read tag files... INFO @ Sat, 03 Jun 2017 13:57:33: #1 read treatment tags... INFO @ Sat, 03 Jun 2017 13:57:33: # Command line: callpeak -t SRX1794222.bam -f BAM -g dm -n SRX1794222.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX1794222.10 # format = BAM # ChIP-seq file = ['SRX1794222.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 13:57:33: #1 read tag files... INFO @ Sat, 03 Jun 2017 13:57:33: #1 read treatment tags... INFO @ Sat, 03 Jun 2017 13:57:33: # Command line: callpeak -t SRX1794222.bam -f BAM -g dm -n SRX1794222.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX1794222.05 # format = BAM # ChIP-seq file = ['SRX1794222.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 13:57:33: #1 read tag files... INFO @ Sat, 03 Jun 2017 13:57:33: #1 read treatment tags... INFO @ Sat, 03 Jun 2017 13:57:38: 1000000 INFO @ Sat, 03 Jun 2017 13:57:38: 1000000 INFO @ Sat, 03 Jun 2017 13:57:39: 1000000 INFO @ Sat, 03 Jun 2017 13:57:44: 2000000 INFO @ Sat, 03 Jun 2017 13:57:44: 2000000 INFO @ Sat, 03 Jun 2017 13:57:44: 2000000 INFO @ Sat, 03 Jun 2017 13:57:49: 3000000 INFO @ Sat, 03 Jun 2017 13:57:50: 3000000 INFO @ Sat, 03 Jun 2017 13:57:50: 3000000 INFO @ Sat, 03 Jun 2017 13:57:55: 4000000 INFO @ Sat, 03 Jun 2017 13:57:55: 4000000 INFO @ Sat, 03 Jun 2017 13:57:56: 4000000 INFO @ Sat, 03 Jun 2017 13:58:01: 5000000 INFO @ Sat, 03 Jun 2017 13:58:01: 5000000 INFO @ Sat, 03 Jun 2017 13:58:02: 5000000 INFO @ Sat, 03 Jun 2017 13:58:06: 6000000 INFO @ Sat, 03 Jun 2017 13:58:06: 6000000 INFO @ Sat, 03 Jun 2017 13:58:08: 6000000 INFO @ Sat, 03 Jun 2017 13:58:12: 7000000 INFO @ Sat, 03 Jun 2017 13:58:12: 7000000 INFO @ Sat, 03 Jun 2017 13:58:13: 7000000 INFO @ Sat, 03 Jun 2017 13:58:18: 8000000 INFO @ Sat, 03 Jun 2017 13:58:18: 8000000 INFO @ Sat, 03 Jun 2017 13:58:20: 8000000 INFO @ Sat, 03 Jun 2017 13:58:23: 9000000 INFO @ Sat, 03 Jun 2017 13:58:24: 9000000 INFO @ Sat, 03 Jun 2017 13:58:25: #1 tag size is determined as 51 bps INFO @ Sat, 03 Jun 2017 13:58:25: #1 tag size = 51 INFO @ Sat, 03 Jun 2017 13:58:25: #1 total tags in treatment: 9363833 INFO @ Sat, 03 Jun 2017 13:58:25: #1 user defined the maximum tags... INFO @ Sat, 03 Jun 2017 13:58:25: #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 13:58:25: 9000000 INFO @ Sat, 03 Jun 2017 13:58:26: #1 tag size is determined as 51 bps INFO @ Sat, 03 Jun 2017 13:58:26: #1 tag size = 51 INFO @ Sat, 03 Jun 2017 13:58:26: #1 total tags in treatment: 9363833 INFO @ Sat, 03 Jun 2017 13:58:26: #1 user defined the maximum tags... INFO @ Sat, 03 Jun 2017 13:58:26: #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 13:58:27: #1 tags after filtering in treatment: 9361937 INFO @ Sat, 03 Jun 2017 13:58:27: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 03 Jun 2017 13:58:27: #1 finished! INFO @ Sat, 03 Jun 2017 13:58:27: #2 Build Peak Model... INFO @ Sat, 03 Jun 2017 13:58:28: #1 tag size is determined as 51 bps INFO @ Sat, 03 Jun 2017 13:58:28: #1 tag size = 51 INFO @ Sat, 03 Jun 2017 13:58:28: #1 total tags in treatment: 9363833 INFO @ Sat, 03 Jun 2017 13:58:28: #1 user defined the maximum tags... INFO @ Sat, 03 Jun 2017 13:58:28: #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 13:58:28: #1 tags after filtering in treatment: 9361937 INFO @ Sat, 03 Jun 2017 13:58:28: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 03 Jun 2017 13:58:28: #1 finished! INFO @ Sat, 03 Jun 2017 13:58:28: #2 Build Peak Model... INFO @ Sat, 03 Jun 2017 13:58:29: #1 tags after filtering in treatment: 9361937 INFO @ Sat, 03 Jun 2017 13:58:29: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 03 Jun 2017 13:58:29: #1 finished! INFO @ Sat, 03 Jun 2017 13:58:29: #2 Build Peak Model... INFO @ Sat, 03 Jun 2017 13:58:30: #2 number of paired peaks: 8612 INFO @ Sat, 03 Jun 2017 13:58:30: start model_add_line... INFO @ Sat, 03 Jun 2017 13:58:31: #2 number of paired peaks: 8612 INFO @ Sat, 03 Jun 2017 13:58:31: start model_add_line... INFO @ Sat, 03 Jun 2017 13:58:32: #2 number of paired peaks: 8612 INFO @ Sat, 03 Jun 2017 13:58:32: start model_add_line... INFO @ Sat, 03 Jun 2017 13:59:24: start X-correlation... INFO @ Sat, 03 Jun 2017 13:59:24: end of X-cor INFO @ Sat, 03 Jun 2017 13:59:24: #2 finished! INFO @ Sat, 03 Jun 2017 13:59:24: #2 predicted fragment length is 153 bps INFO @ Sat, 03 Jun 2017 13:59:24: #2 alternative fragment length(s) may be 153 bps INFO @ Sat, 03 Jun 2017 13:59:24: #2.2 Generate R script for model : SRX1794222.20_model.r INFO @ Sat, 03 Jun 2017 13:59:24: #3 Call peaks... INFO @ Sat, 03 Jun 2017 13:59:24: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Jun 2017 13:59:24: start X-correlation... INFO @ Sat, 03 Jun 2017 13:59:24: end of X-cor INFO @ Sat, 03 Jun 2017 13:59:24: #2 finished! INFO @ Sat, 03 Jun 2017 13:59:24: #2 predicted fragment length is 153 bps INFO @ Sat, 03 Jun 2017 13:59:24: #2 alternative fragment length(s) may be 153 bps INFO @ Sat, 03 Jun 2017 13:59:24: #2.2 Generate R script for model : SRX1794222.10_model.r INFO @ Sat, 03 Jun 2017 13:59:24: #3 Call peaks... INFO @ Sat, 03 Jun 2017 13:59:24: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Jun 2017 13:59:25: start X-correlation... INFO @ Sat, 03 Jun 2017 13:59:25: end of X-cor INFO @ Sat, 03 Jun 2017 13:59:25: #2 finished! INFO @ Sat, 03 Jun 2017 13:59:25: #2 predicted fragment length is 153 bps INFO @ Sat, 03 Jun 2017 13:59:25: #2 alternative fragment length(s) may be 153 bps INFO @ Sat, 03 Jun 2017 13:59:25: #2.2 Generate R script for model : SRX1794222.05_model.r INFO @ Sat, 03 Jun 2017 13:59:25: #3 Call peaks... INFO @ Sat, 03 Jun 2017 13:59:25: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Jun 2017 14:00:22: #3 Call peaks for each chromosome... INFO @ Sat, 03 Jun 2017 14:00:23: #3 Call peaks for each chromosome... INFO @ Sat, 03 Jun 2017 14:00:24: #3 Call peaks for each chromosome... BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 03 Jun 2017 14:01:10: #4 Write output xls file... SRX1794222.20_peaks.xls INFO @ Sat, 03 Jun 2017 14:01:10: #4 Write peak in narrowPeak format file... SRX1794222.20_peaks.narrowPeak INFO @ Sat, 03 Jun 2017 14:01:10: #4 Write summits bed file... SRX1794222.20_summits.bed INFO @ Sat, 03 Jun 2017 14:01:10: Done! pass1 - making usageList (14 chroms): 2 millis pass2 - checking and writing primary data (5737 records, 4 fields): 8 millis CompletedMACS2peakCalling INFO @ Sat, 03 Jun 2017 14:01:10: #4 Write output xls file... SRX1794222.10_peaks.xls INFO @ Sat, 03 Jun 2017 14:01:11: #4 Write peak in narrowPeak format file... SRX1794222.10_peaks.narrowPeak INFO @ Sat, 03 Jun 2017 14:01:11: #4 Write summits bed file... SRX1794222.10_summits.bed INFO @ Sat, 03 Jun 2017 14:01:11: Done! pass1 - making usageList (15 chroms): 2 millis pass2 - checking and writing primary data (8503 records, 4 fields): 11 millis CompletedMACS2peakCalling BigWig に変換しました。 INFO @ Sat, 03 Jun 2017 14:01:22: #4 Write output xls file... SRX1794222.05_peaks.xls INFO @ Sat, 03 Jun 2017 14:01:22: #4 Write peak in narrowPeak format file... SRX1794222.05_peaks.narrowPeak INFO @ Sat, 03 Jun 2017 14:01:22: #4 Write summits bed file... SRX1794222.05_summits.bed INFO @ Sat, 03 Jun 2017 14:01:22: Done! pass1 - making usageList (15 chroms): 2 millis pass2 - checking and writing primary data (10316 records, 4 fields): 14 millis CompletedMACS2peakCalling