Job ID = 9025625 sra ファイルのダウンロード中... Completed: 192831K bytes transferred in 4 seconds (317922K 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 --:--:-- 0:00:07 --:--:-- 0 100 14323 0 14323 0 0 1777 0 --:--:-- 0:00:08 --:--:-- 9574 100 53548 0 53548 0 0 5914 0 --:--:-- 0:00:09 --:--:-- 21487 100 55419 0 55419 0 0 6120 0 --:--:-- 0:00:09 --:--:-- 22229 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 8273591 spots for /home/okishinya/chipatlas/results/ce10/SRX208767/SRR628901.sra Written 8273591 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: 00:01:36 8273591 reads; of these: 8273591 (100.00%) were unpaired; of these: 2433254 (29.41%) aligned 0 times 4517522 (54.60%) aligned exactly 1 time 1322815 (15.99%) aligned >1 times 70.59% overall alignment rate Time searching: 00:01:36 Overall time: 00:01:36 マッピングが完了しました。 samtools でBAM に変換中... [samopen] SAM header is present: 7 sequences. [bam_rmdupse_core] 1085022 / 5840337 = 0.1858 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 04:41:57: # Command line: callpeak -t SRX208767.bam -f BAM -g ce -n SRX208767.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX208767.10 # format = BAM # ChIP-seq file = ['SRX208767.bam'] # control file = None # effective genome size = 9.00e+07 # 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 04:41:57: #1 read tag files... INFO @ Sat, 03 Jun 2017 04:41:57: #1 read treatment tags... INFO @ Sat, 03 Jun 2017 04:41:57: # Command line: callpeak -t SRX208767.bam -f BAM -g ce -n SRX208767.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX208767.05 # format = BAM # ChIP-seq file = ['SRX208767.bam'] # control file = None # effective genome size = 9.00e+07 # 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 04:41:57: #1 read tag files... INFO @ Sat, 03 Jun 2017 04:41:57: #1 read treatment tags... INFO @ Sat, 03 Jun 2017 04:41:57: # Command line: callpeak -t SRX208767.bam -f BAM -g ce -n SRX208767.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX208767.20 # format = BAM # ChIP-seq file = ['SRX208767.bam'] # control file = None # effective genome size = 9.00e+07 # 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 04:41:57: #1 read tag files... INFO @ Sat, 03 Jun 2017 04:41:57: #1 read treatment tags... INFO @ Sat, 03 Jun 2017 04:42:04: 1000000 INFO @ Sat, 03 Jun 2017 04:42:04: 1000000 INFO @ Sat, 03 Jun 2017 04:42:04: 1000000 INFO @ Sat, 03 Jun 2017 04:42:11: 2000000 INFO @ Sat, 03 Jun 2017 04:42:11: 2000000 INFO @ Sat, 03 Jun 2017 04:42:12: 2000000 INFO @ Sat, 03 Jun 2017 04:42:18: 3000000 INFO @ Sat, 03 Jun 2017 04:42:18: 3000000 INFO @ Sat, 03 Jun 2017 04:42:19: 3000000 INFO @ Sat, 03 Jun 2017 04:42:24: 4000000 INFO @ Sat, 03 Jun 2017 04:42:25: 4000000 INFO @ Sat, 03 Jun 2017 04:42:26: 4000000 INFO @ Sat, 03 Jun 2017 04:42:30: #1 tag size is determined as 36 bps INFO @ Sat, 03 Jun 2017 04:42:30: #1 tag size = 36 INFO @ Sat, 03 Jun 2017 04:42:30: #1 total tags in treatment: 4755315 INFO @ Sat, 03 Jun 2017 04:42:30: #1 user defined the maximum tags... INFO @ Sat, 03 Jun 2017 04:42:30: #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 04:42:30: #1 tag size is determined as 36 bps INFO @ Sat, 03 Jun 2017 04:42:30: #1 tag size = 36 INFO @ Sat, 03 Jun 2017 04:42:30: #1 total tags in treatment: 4755315 INFO @ Sat, 03 Jun 2017 04:42:30: #1 user defined the maximum tags... INFO @ Sat, 03 Jun 2017 04:42:30: #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 04:42:30: #1 tags after filtering in treatment: 4754897 INFO @ Sat, 03 Jun 2017 04:42:30: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 03 Jun 2017 04:42:30: #1 finished! INFO @ Sat, 03 Jun 2017 04:42:30: #2 Build Peak Model... INFO @ Sat, 03 Jun 2017 04:42:31: #1 tags after filtering in treatment: 4754897 INFO @ Sat, 03 Jun 2017 04:42:31: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 03 Jun 2017 04:42:31: #1 finished! INFO @ Sat, 03 Jun 2017 04:42:31: #2 Build Peak Model... INFO @ Sat, 03 Jun 2017 04:42:31: #2 number of paired peaks: 936 WARNING @ Sat, 03 Jun 2017 04:42:31: Fewer paired peaks (936) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 936 pairs to build model! INFO @ Sat, 03 Jun 2017 04:42:31: start model_add_line... INFO @ Sat, 03 Jun 2017 04:42:32: #1 tag size is determined as 36 bps INFO @ Sat, 03 Jun 2017 04:42:32: #1 tag size = 36 INFO @ Sat, 03 Jun 2017 04:42:32: #1 total tags in treatment: 4755315 INFO @ Sat, 03 Jun 2017 04:42:32: #1 user defined the maximum tags... INFO @ Sat, 03 Jun 2017 04:42:32: #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 04:42:32: #2 number of paired peaks: 936 WARNING @ Sat, 03 Jun 2017 04:42:32: Fewer paired peaks (936) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 936 pairs to build model! INFO @ Sat, 03 Jun 2017 04:42:32: start model_add_line... INFO @ Sat, 03 Jun 2017 04:42:32: #1 tags after filtering in treatment: 4754897 INFO @ Sat, 03 Jun 2017 04:42:32: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 03 Jun 2017 04:42:32: #1 finished! INFO @ Sat, 03 Jun 2017 04:42:32: #2 Build Peak Model... INFO @ Sat, 03 Jun 2017 04:42:33: #2 number of paired peaks: 936 WARNING @ Sat, 03 Jun 2017 04:42:33: Fewer paired peaks (936) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 936 pairs to build model! INFO @ Sat, 03 Jun 2017 04:42:33: start model_add_line... INFO @ Sat, 03 Jun 2017 04:42:36: start X-correlation... INFO @ Sat, 03 Jun 2017 04:42:36: end of X-cor INFO @ Sat, 03 Jun 2017 04:42:36: #2 finished! INFO @ Sat, 03 Jun 2017 04:42:36: #2 predicted fragment length is 177 bps INFO @ Sat, 03 Jun 2017 04:42:36: #2 alternative fragment length(s) may be 177 bps INFO @ Sat, 03 Jun 2017 04:42:36: #2.2 Generate R script for model : SRX208767.20_model.r INFO @ Sat, 03 Jun 2017 04:42:36: #3 Call peaks... INFO @ Sat, 03 Jun 2017 04:42:36: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Jun 2017 04:42:37: start X-correlation... INFO @ Sat, 03 Jun 2017 04:42:37: end of X-cor INFO @ Sat, 03 Jun 2017 04:42:37: #2 finished! INFO @ Sat, 03 Jun 2017 04:42:37: #2 predicted fragment length is 177 bps INFO @ Sat, 03 Jun 2017 04:42:37: #2 alternative fragment length(s) may be 177 bps INFO @ Sat, 03 Jun 2017 04:42:37: #2.2 Generate R script for model : SRX208767.05_model.r INFO @ Sat, 03 Jun 2017 04:42:37: #3 Call peaks... INFO @ Sat, 03 Jun 2017 04:42:37: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Jun 2017 04:42:38: start X-correlation... INFO @ Sat, 03 Jun 2017 04:42:38: end of X-cor INFO @ Sat, 03 Jun 2017 04:42:38: #2 finished! INFO @ Sat, 03 Jun 2017 04:42:38: #2 predicted fragment length is 177 bps INFO @ Sat, 03 Jun 2017 04:42:38: #2 alternative fragment length(s) may be 177 bps INFO @ Sat, 03 Jun 2017 04:42:38: #2.2 Generate R script for model : SRX208767.10_model.r INFO @ Sat, 03 Jun 2017 04:42:38: #3 Call peaks... INFO @ Sat, 03 Jun 2017 04:42:38: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Jun 2017 04:43:05: #3 Call peaks for each chromosome... INFO @ Sat, 03 Jun 2017 04:43:05: #3 Call peaks for each chromosome... INFO @ Sat, 03 Jun 2017 04:43:10: #3 Call peaks for each chromosome... INFO @ Sat, 03 Jun 2017 04:43:26: #4 Write output xls file... SRX208767.20_peaks.xls INFO @ Sat, 03 Jun 2017 04:43:26: #4 Write peak in narrowPeak format file... SRX208767.20_peaks.narrowPeak INFO @ Sat, 03 Jun 2017 04:43:26: #4 Write summits bed file... SRX208767.20_summits.bed INFO @ Sat, 03 Jun 2017 04:43:26: Done! pass1 - making usageList (7 chroms): 3 millis pass2 - checking and writing primary data (685 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Sat, 03 Jun 2017 04:43:34: #4 Write output xls file... SRX208767.10_peaks.xls INFO @ Sat, 03 Jun 2017 04:43:34: #4 Write peak in narrowPeak format file... SRX208767.10_peaks.narrowPeak INFO @ Sat, 03 Jun 2017 04:43:34: #4 Write summits bed file... SRX208767.10_summits.bed INFO @ Sat, 03 Jun 2017 04:43:34: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (2968 records, 4 fields): 5 millis CompletedMACS2peakCalling INFO @ Sat, 03 Jun 2017 04:43:35: #4 Write output xls file... SRX208767.05_peaks.xls INFO @ Sat, 03 Jun 2017 04:43:35: #4 Write peak in narrowPeak format file... SRX208767.05_peaks.narrowPeak INFO @ Sat, 03 Jun 2017 04:43:35: #4 Write summits bed file... SRX208767.05_summits.bed INFO @ Sat, 03 Jun 2017 04:43:35: Done! pass1 - making usageList (7 chroms): 2 millis pass2 - checking and writing primary data (9824 records, 4 fields): 12 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。