Job ID = 9157149 sra ファイルのダウンロード中... Completed: 439184K bytes transferred in 5 seconds (629914K bits/sec), in 1 file, 2 directories. 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 19257180 spots for /home/okishinya/chipatlas/results/ce10/SRX2228878/SRR4380334.sra Written 19257180 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: 00:02:44 19257180 reads; of these: 19257180 (100.00%) were unpaired; of these: 13224414 (68.67%) aligned 0 times 5017039 (26.05%) aligned exactly 1 time 1015727 (5.27%) aligned >1 times 31.33% overall alignment rate Time searching: 00:02:44 Overall time: 00:02:45 マッピングが完了しました。 samtools でBAM に変換中... [samopen] SAM header is present: 7 sequences. [bam_rmdupse_core] 884095 / 6032766 = 0.1465 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 @ Tue, 27 Jun 2017 10:49:58: # Command line: callpeak -t SRX2228878.bam -f BAM -g ce -n SRX2228878.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX2228878.20 # format = BAM # ChIP-seq file = ['SRX2228878.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 # Paired-End mode is off INFO @ Tue, 27 Jun 2017 10:49:58: #1 read tag files... INFO @ Tue, 27 Jun 2017 10:49:58: #1 read treatment tags... INFO @ Tue, 27 Jun 2017 10:49:58: # Command line: callpeak -t SRX2228878.bam -f BAM -g ce -n SRX2228878.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX2228878.10 # format = BAM # ChIP-seq file = ['SRX2228878.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 # Paired-End mode is off INFO @ Tue, 27 Jun 2017 10:49:58: #1 read tag files... INFO @ Tue, 27 Jun 2017 10:49:58: #1 read treatment tags... INFO @ Tue, 27 Jun 2017 10:49:58: # Command line: callpeak -t SRX2228878.bam -f BAM -g ce -n SRX2228878.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX2228878.05 # format = BAM # ChIP-seq file = ['SRX2228878.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 # Paired-End mode is off INFO @ Tue, 27 Jun 2017 10:49:58: #1 read tag files... INFO @ Tue, 27 Jun 2017 10:49:58: #1 read treatment tags... INFO @ Tue, 27 Jun 2017 10:50:06: 1000000 INFO @ Tue, 27 Jun 2017 10:50:06: 1000000 INFO @ Tue, 27 Jun 2017 10:50:06: 1000000 INFO @ Tue, 27 Jun 2017 10:50:13: 2000000 INFO @ Tue, 27 Jun 2017 10:50:13: 2000000 INFO @ Tue, 27 Jun 2017 10:50:14: 2000000 INFO @ Tue, 27 Jun 2017 10:50:20: 3000000 INFO @ Tue, 27 Jun 2017 10:50:20: 3000000 INFO @ Tue, 27 Jun 2017 10:50:21: 3000000 INFO @ Tue, 27 Jun 2017 10:50:27: 4000000 INFO @ Tue, 27 Jun 2017 10:50:27: 4000000 INFO @ Tue, 27 Jun 2017 10:50:29: 4000000 INFO @ Tue, 27 Jun 2017 10:50:34: 5000000 INFO @ Tue, 27 Jun 2017 10:50:34: 5000000 INFO @ Tue, 27 Jun 2017 10:50:35: #1 tag size is determined as 51 bps INFO @ Tue, 27 Jun 2017 10:50:35: #1 tag size = 51 INFO @ Tue, 27 Jun 2017 10:50:35: #1 total tags in treatment: 5148671 INFO @ Tue, 27 Jun 2017 10:50:35: #1 user defined the maximum tags... INFO @ Tue, 27 Jun 2017 10:50:35: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 27 Jun 2017 10:50:35: #1 tags after filtering in treatment: 5148671 INFO @ Tue, 27 Jun 2017 10:50:35: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 27 Jun 2017 10:50:35: #1 finished! INFO @ Tue, 27 Jun 2017 10:50:35: #2 Build Peak Model... INFO @ Tue, 27 Jun 2017 10:50:35: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 27 Jun 2017 10:50:35: #1 tag size is determined as 51 bps INFO @ Tue, 27 Jun 2017 10:50:35: #1 tag size = 51 INFO @ Tue, 27 Jun 2017 10:50:35: #1 total tags in treatment: 5148671 INFO @ Tue, 27 Jun 2017 10:50:35: #1 user defined the maximum tags... INFO @ Tue, 27 Jun 2017 10:50:35: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 27 Jun 2017 10:50:36: #1 tags after filtering in treatment: 5148671 INFO @ Tue, 27 Jun 2017 10:50:36: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 27 Jun 2017 10:50:36: #1 finished! INFO @ Tue, 27 Jun 2017 10:50:36: #2 Build Peak Model... INFO @ Tue, 27 Jun 2017 10:50:36: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 27 Jun 2017 10:50:36: #2 number of paired peaks: 652 WARNING @ Tue, 27 Jun 2017 10:50:36: Fewer paired peaks (652) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 652 pairs to build model! INFO @ Tue, 27 Jun 2017 10:50:36: start model_add_line... INFO @ Tue, 27 Jun 2017 10:50:36: start X-correlation... INFO @ Tue, 27 Jun 2017 10:50:36: end of X-cor INFO @ Tue, 27 Jun 2017 10:50:36: #2 finished! INFO @ Tue, 27 Jun 2017 10:50:36: #2 predicted fragment length is 117 bps INFO @ Tue, 27 Jun 2017 10:50:36: #2 alternative fragment length(s) may be 117 bps INFO @ Tue, 27 Jun 2017 10:50:36: #2.2 Generate R script for model : SRX2228878.05_model.r INFO @ Tue, 27 Jun 2017 10:50:36: #3 Call peaks... INFO @ Tue, 27 Jun 2017 10:50:36: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 27 Jun 2017 10:50:36: #2 number of paired peaks: 652 WARNING @ Tue, 27 Jun 2017 10:50:36: Fewer paired peaks (652) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 652 pairs to build model! INFO @ Tue, 27 Jun 2017 10:50:36: start model_add_line... INFO @ Tue, 27 Jun 2017 10:50:36: start X-correlation... INFO @ Tue, 27 Jun 2017 10:50:36: end of X-cor INFO @ Tue, 27 Jun 2017 10:50:36: #2 finished! INFO @ Tue, 27 Jun 2017 10:50:36: #2 predicted fragment length is 117 bps INFO @ Tue, 27 Jun 2017 10:50:36: #2 alternative fragment length(s) may be 117 bps INFO @ Tue, 27 Jun 2017 10:50:36: #2.2 Generate R script for model : SRX2228878.20_model.r INFO @ Tue, 27 Jun 2017 10:50:36: #3 Call peaks... INFO @ Tue, 27 Jun 2017 10:50:36: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 27 Jun 2017 10:50:36: 5000000 INFO @ Tue, 27 Jun 2017 10:50:37: #1 tag size is determined as 51 bps INFO @ Tue, 27 Jun 2017 10:50:37: #1 tag size = 51 INFO @ Tue, 27 Jun 2017 10:50:37: #1 total tags in treatment: 5148671 INFO @ Tue, 27 Jun 2017 10:50:37: #1 user defined the maximum tags... INFO @ Tue, 27 Jun 2017 10:50:37: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 27 Jun 2017 10:50:37: #1 tags after filtering in treatment: 5148671 INFO @ Tue, 27 Jun 2017 10:50:37: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 27 Jun 2017 10:50:37: #1 finished! INFO @ Tue, 27 Jun 2017 10:50:37: #2 Build Peak Model... INFO @ Tue, 27 Jun 2017 10:50:37: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 27 Jun 2017 10:50:38: #2 number of paired peaks: 652 WARNING @ Tue, 27 Jun 2017 10:50:38: Fewer paired peaks (652) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 652 pairs to build model! INFO @ Tue, 27 Jun 2017 10:50:38: start model_add_line... INFO @ Tue, 27 Jun 2017 10:50:38: start X-correlation... INFO @ Tue, 27 Jun 2017 10:50:38: end of X-cor INFO @ Tue, 27 Jun 2017 10:50:38: #2 finished! INFO @ Tue, 27 Jun 2017 10:50:38: #2 predicted fragment length is 117 bps INFO @ Tue, 27 Jun 2017 10:50:38: #2 alternative fragment length(s) may be 117 bps INFO @ Tue, 27 Jun 2017 10:50:38: #2.2 Generate R script for model : SRX2228878.10_model.r INFO @ Tue, 27 Jun 2017 10:50:38: #3 Call peaks... INFO @ Tue, 27 Jun 2017 10:50:38: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 27 Jun 2017 10:50:49: #3 Call peaks for each chromosome... INFO @ Tue, 27 Jun 2017 10:50:49: #3 Call peaks for each chromosome... INFO @ Tue, 27 Jun 2017 10:50:50: #3 Call peaks for each chromosome... INFO @ Tue, 27 Jun 2017 10:50:55: #4 Write output xls file... SRX2228878.05_peaks.xls INFO @ Tue, 27 Jun 2017 10:50:55: #4 Write output xls file... SRX2228878.20_peaks.xls INFO @ Tue, 27 Jun 2017 10:50:55: #4 Write peak in narrowPeak format file... SRX2228878.20_peaks.narrowPeak INFO @ Tue, 27 Jun 2017 10:50:55: #4 Write summits bed file... SRX2228878.20_summits.bed INFO @ Tue, 27 Jun 2017 10:50:55: #4 Write peak in narrowPeak format file... SRX2228878.05_peaks.narrowPeak INFO @ Tue, 27 Jun 2017 10:50:55: Done! INFO @ Tue, 27 Jun 2017 10:50:55: #4 Write summits bed file... SRX2228878.05_summits.bed INFO @ Tue, 27 Jun 2017 10:50:55: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (497 records, 4 fields): 2 millis CompletedMACS2peakCalling pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (1467 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Tue, 27 Jun 2017 10:50:58: #4 Write output xls file... SRX2228878.10_peaks.xls INFO @ Tue, 27 Jun 2017 10:50:58: #4 Write peak in narrowPeak format file... SRX2228878.10_peaks.narrowPeak INFO @ Tue, 27 Jun 2017 10:50:58: #4 Write summits bed file... SRX2228878.10_summits.bed INFO @ Tue, 27 Jun 2017 10:50:58: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (917 records, 4 fields): 3 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。