Job ID = 9029485 sra ファイルのダウンロード中... Completed: 394412K bytes transferred in 6 seconds (531118K 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 14324 0 14324 0 0 1895 0 --:--:-- 0:00:07 --:--:-- 14843 100 54603 0 54603 0 0 6480 0 --:--:-- 0:00:08 --:--:-- 29772 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 11251283 spots for /home/okishinya/chipatlas/results/dm3/SRX1794238/SRR3575280.sra Written 11251283 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: 00:03:48 11251283 reads; of these: 11251283 (100.00%) were unpaired; of these: 478779 (4.26%) aligned 0 times 8789093 (78.12%) aligned exactly 1 time 1983411 (17.63%) aligned >1 times 95.74% overall alignment rate Time searching: 00:03:48 Overall time: 00:03:48 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] 1222197 / 10772504 = 0.1135 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 14:00:46: # Command line: callpeak -t SRX1794238.bam -f BAM -g dm -n SRX1794238.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX1794238.05 # format = BAM # ChIP-seq file = ['SRX1794238.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 14:00:46: #1 read tag files... INFO @ Sat, 03 Jun 2017 14:00:46: #1 read treatment tags... INFO @ Sat, 03 Jun 2017 14:00:46: # Command line: callpeak -t SRX1794238.bam -f BAM -g dm -n SRX1794238.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX1794238.10 # format = BAM # ChIP-seq file = ['SRX1794238.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 14:00:46: #1 read tag files... INFO @ Sat, 03 Jun 2017 14:00:46: #1 read treatment tags... INFO @ Sat, 03 Jun 2017 14:00:46: # Command line: callpeak -t SRX1794238.bam -f BAM -g dm -n SRX1794238.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX1794238.20 # format = BAM # ChIP-seq file = ['SRX1794238.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 14:00:46: #1 read tag files... INFO @ Sat, 03 Jun 2017 14:00:46: #1 read treatment tags... INFO @ Sat, 03 Jun 2017 14:00:54: 1000000 INFO @ Sat, 03 Jun 2017 14:00:54: 1000000 INFO @ Sat, 03 Jun 2017 14:00:55: 1000000 INFO @ Sat, 03 Jun 2017 14:01:00: 2000000 INFO @ Sat, 03 Jun 2017 14:01:00: 2000000 INFO @ Sat, 03 Jun 2017 14:01:03: 2000000 INFO @ Sat, 03 Jun 2017 14:01:07: 3000000 INFO @ Sat, 03 Jun 2017 14:01:07: 3000000 INFO @ Sat, 03 Jun 2017 14:01:09: 3000000 INFO @ Sat, 03 Jun 2017 14:01:13: 4000000 INFO @ Sat, 03 Jun 2017 14:01:13: 4000000 INFO @ Sat, 03 Jun 2017 14:01:15: 4000000 INFO @ Sat, 03 Jun 2017 14:01:20: 5000000 INFO @ Sat, 03 Jun 2017 14:01:20: 5000000 INFO @ Sat, 03 Jun 2017 14:01:21: 5000000 INFO @ Sat, 03 Jun 2017 14:01:27: 6000000 INFO @ Sat, 03 Jun 2017 14:01:27: 6000000 INFO @ Sat, 03 Jun 2017 14:01:28: 6000000 INFO @ Sat, 03 Jun 2017 14:01:34: 7000000 INFO @ Sat, 03 Jun 2017 14:01:34: 7000000 INFO @ Sat, 03 Jun 2017 14:01:34: 7000000 INFO @ Sat, 03 Jun 2017 14:01:41: 8000000 INFO @ Sat, 03 Jun 2017 14:01:41: 8000000 INFO @ Sat, 03 Jun 2017 14:01:41: 8000000 INFO @ Sat, 03 Jun 2017 14:01:47: 9000000 INFO @ Sat, 03 Jun 2017 14:01:47: 9000000 INFO @ Sat, 03 Jun 2017 14:01:47: 9000000 INFO @ Sat, 03 Jun 2017 14:01:50: #1 tag size is determined as 51 bps INFO @ Sat, 03 Jun 2017 14:01:50: #1 tag size = 51 INFO @ Sat, 03 Jun 2017 14:01:50: #1 total tags in treatment: 9550307 INFO @ Sat, 03 Jun 2017 14:01:50: #1 user defined the maximum tags... INFO @ Sat, 03 Jun 2017 14:01:50: #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 14:01:51: #1 tag size is determined as 51 bps INFO @ Sat, 03 Jun 2017 14:01:51: #1 tag size = 51 INFO @ Sat, 03 Jun 2017 14:01:51: #1 total tags in treatment: 9550307 INFO @ Sat, 03 Jun 2017 14:01:51: #1 user defined the maximum tags... INFO @ Sat, 03 Jun 2017 14:01:51: #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 14:01:51: #1 tag size is determined as 51 bps INFO @ Sat, 03 Jun 2017 14:01:51: #1 tag size = 51 INFO @ Sat, 03 Jun 2017 14:01:51: #1 total tags in treatment: 9550307 INFO @ Sat, 03 Jun 2017 14:01:51: #1 user defined the maximum tags... INFO @ Sat, 03 Jun 2017 14:01:51: #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 14:01:52: #1 tags after filtering in treatment: 9548299 INFO @ Sat, 03 Jun 2017 14:01:52: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 03 Jun 2017 14:01:52: #1 finished! INFO @ Sat, 03 Jun 2017 14:01:52: #2 Build Peak Model... INFO @ Sat, 03 Jun 2017 14:01:53: #1 tags after filtering in treatment: 9548299 INFO @ Sat, 03 Jun 2017 14:01:53: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 03 Jun 2017 14:01:53: #1 finished! INFO @ Sat, 03 Jun 2017 14:01:53: #2 Build Peak Model... INFO @ Sat, 03 Jun 2017 14:01:53: #1 tags after filtering in treatment: 9548299 INFO @ Sat, 03 Jun 2017 14:01:53: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 03 Jun 2017 14:01:53: #1 finished! INFO @ Sat, 03 Jun 2017 14:01:53: #2 Build Peak Model... INFO @ Sat, 03 Jun 2017 14:01:55: #2 number of paired peaks: 8531 INFO @ Sat, 03 Jun 2017 14:01:55: start model_add_line... INFO @ Sat, 03 Jun 2017 14:01:55: #2 number of paired peaks: 8531 INFO @ Sat, 03 Jun 2017 14:01:55: start model_add_line... INFO @ Sat, 03 Jun 2017 14:01:56: #2 number of paired peaks: 8531 INFO @ Sat, 03 Jun 2017 14:01:56: start model_add_line... INFO @ Sat, 03 Jun 2017 14:02:49: start X-correlation... INFO @ Sat, 03 Jun 2017 14:02:49: end of X-cor INFO @ Sat, 03 Jun 2017 14:02:49: #2 finished! INFO @ Sat, 03 Jun 2017 14:02:49: #2 predicted fragment length is 159 bps INFO @ Sat, 03 Jun 2017 14:02:49: #2 alternative fragment length(s) may be 159 bps INFO @ Sat, 03 Jun 2017 14:02:49: #2.2 Generate R script for model : SRX1794238.10_model.r INFO @ Sat, 03 Jun 2017 14:02:49: #3 Call peaks... INFO @ Sat, 03 Jun 2017 14:02:49: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Jun 2017 14:02:50: start X-correlation... INFO @ Sat, 03 Jun 2017 14:02:50: end of X-cor INFO @ Sat, 03 Jun 2017 14:02:50: #2 finished! INFO @ Sat, 03 Jun 2017 14:02:50: #2 predicted fragment length is 159 bps INFO @ Sat, 03 Jun 2017 14:02:50: #2 alternative fragment length(s) may be 159 bps INFO @ Sat, 03 Jun 2017 14:02:50: #2.2 Generate R script for model : SRX1794238.05_model.r INFO @ Sat, 03 Jun 2017 14:02:50: #3 Call peaks... INFO @ Sat, 03 Jun 2017 14:02:50: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Jun 2017 14:02:50: start X-correlation... INFO @ Sat, 03 Jun 2017 14:02:50: end of X-cor INFO @ Sat, 03 Jun 2017 14:02:50: #2 finished! INFO @ Sat, 03 Jun 2017 14:02:50: #2 predicted fragment length is 159 bps INFO @ Sat, 03 Jun 2017 14:02:50: #2 alternative fragment length(s) may be 159 bps INFO @ Sat, 03 Jun 2017 14:02:50: #2.2 Generate R script for model : SRX1794238.20_model.r INFO @ Sat, 03 Jun 2017 14:02:50: #3 Call peaks... INFO @ Sat, 03 Jun 2017 14:02:50: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Jun 2017 14:03:44: #3 Call peaks for each chromosome... INFO @ Sat, 03 Jun 2017 14:03:46: #3 Call peaks for each chromosome... INFO @ Sat, 03 Jun 2017 14:03:50: #3 Call peaks for each chromosome... BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。 INFO @ Sat, 03 Jun 2017 14:04:27: #4 Write output xls file... SRX1794238.20_peaks.xls INFO @ Sat, 03 Jun 2017 14:04:27: #4 Write peak in narrowPeak format file... SRX1794238.20_peaks.narrowPeak INFO @ Sat, 03 Jun 2017 14:04:27: #4 Write summits bed file... SRX1794238.20_summits.bed INFO @ Sat, 03 Jun 2017 14:04:27: Done! pass1 - making usageList (13 chroms): 2 millis pass2 - checking and writing primary data (4426 records, 4 fields): 6 millis CompletedMACS2peakCalling INFO @ Sat, 03 Jun 2017 14:04:38: #4 Write output xls file... SRX1794238.05_peaks.xls INFO @ Sat, 03 Jun 2017 14:04:38: #4 Write peak in narrowPeak format file... SRX1794238.05_peaks.narrowPeak INFO @ Sat, 03 Jun 2017 14:04:38: #4 Write summits bed file... SRX1794238.05_summits.bed INFO @ Sat, 03 Jun 2017 14:04:38: Done! pass1 - making usageList (15 chroms): 3 millis pass2 - checking and writing primary data (10310 records, 4 fields): 13 millis CompletedMACS2peakCalling INFO @ Sat, 03 Jun 2017 14:04:39: #4 Write output xls file... SRX1794238.10_peaks.xls INFO @ Sat, 03 Jun 2017 14:04:39: #4 Write peak in narrowPeak format file... SRX1794238.10_peaks.narrowPeak INFO @ Sat, 03 Jun 2017 14:04:39: #4 Write summits bed file... SRX1794238.10_summits.bed INFO @ Sat, 03 Jun 2017 14:04:39: Done! pass1 - making usageList (14 chroms): 2 millis pass2 - checking and writing primary data (8011 records, 4 fields): 10 millis CompletedMACS2peakCalling