Job ID = 9157120 sra ファイルのダウンロード中... Completed: 539293K bytes transferred in 7 seconds (566985K 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 11982884 spots for /home/okishinya/chipatlas/results/ce10/SRX2228863/SRR4380319.sra Written 11982884 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: 00:04:13 11982884 reads; of these: 11982884 (100.00%) were unpaired; of these: 1115219 (9.31%) aligned 0 times 9281015 (77.45%) aligned exactly 1 time 1586650 (13.24%) aligned >1 times 90.69% overall alignment rate Time searching: 00:04:13 Overall time: 00:04:13 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_sort_core] merging from 8 files... [bam_rmdupse_core] 1918044 / 10867665 = 0.1765 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 10:43:25: # Command line: callpeak -t SRX2228863.bam -f BAM -g ce -n SRX2228863.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX2228863.10 # format = BAM # ChIP-seq file = ['SRX2228863.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 10:43:25: #1 read tag files... INFO @ Tue, 27 Jun 2017 10:43:25: #1 read treatment tags... INFO @ Tue, 27 Jun 2017 10:43:25: # Command line: callpeak -t SRX2228863.bam -f BAM -g ce -n SRX2228863.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX2228863.20 # format = BAM # ChIP-seq file = ['SRX2228863.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 10:43:25: #1 read tag files... INFO @ Tue, 27 Jun 2017 10:43:25: #1 read treatment tags... INFO @ Tue, 27 Jun 2017 10:43:25: # Command line: callpeak -t SRX2228863.bam -f BAM -g ce -n SRX2228863.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX2228863.05 # format = BAM # ChIP-seq file = ['SRX2228863.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 10:43:25: #1 read tag files... INFO @ Tue, 27 Jun 2017 10:43:25: #1 read treatment tags... INFO @ Tue, 27 Jun 2017 10:43:32: 1000000 INFO @ Tue, 27 Jun 2017 10:43:32: 1000000 INFO @ Tue, 27 Jun 2017 10:43:32: 1000000 INFO @ Tue, 27 Jun 2017 10:43:39: 2000000 INFO @ Tue, 27 Jun 2017 10:43:40: 2000000 INFO @ Tue, 27 Jun 2017 10:43:40: 2000000 INFO @ Tue, 27 Jun 2017 10:43:46: 3000000 INFO @ Tue, 27 Jun 2017 10:43:47: 3000000 INFO @ Tue, 27 Jun 2017 10:43:48: 3000000 INFO @ Tue, 27 Jun 2017 10:43:53: 4000000 INFO @ Tue, 27 Jun 2017 10:43:55: 4000000 INFO @ Tue, 27 Jun 2017 10:43:56: 4000000 INFO @ Tue, 27 Jun 2017 10:44:01: 5000000 INFO @ Tue, 27 Jun 2017 10:44:03: 5000000 INFO @ Tue, 27 Jun 2017 10:44:04: 5000000 INFO @ Tue, 27 Jun 2017 10:44:08: 6000000 INFO @ Tue, 27 Jun 2017 10:44:11: 6000000 INFO @ Tue, 27 Jun 2017 10:44:12: 6000000 INFO @ Tue, 27 Jun 2017 10:44:15: 7000000 INFO @ Tue, 27 Jun 2017 10:44:18: 7000000 INFO @ Tue, 27 Jun 2017 10:44:20: 7000000 INFO @ Tue, 27 Jun 2017 10:44:22: 8000000 INFO @ Tue, 27 Jun 2017 10:44:26: 8000000 INFO @ Tue, 27 Jun 2017 10:44:28: 8000000 INFO @ Tue, 27 Jun 2017 10:44:28: #1 tag size is determined as 76 bps INFO @ Tue, 27 Jun 2017 10:44:28: #1 tag size = 76 INFO @ Tue, 27 Jun 2017 10:44:28: #1 total tags in treatment: 8949621 INFO @ Tue, 27 Jun 2017 10:44:28: #1 user defined the maximum tags... INFO @ Tue, 27 Jun 2017 10:44:28: #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 10:44:29: #1 tags after filtering in treatment: 8949621 INFO @ Tue, 27 Jun 2017 10:44:29: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 27 Jun 2017 10:44:29: #1 finished! INFO @ Tue, 27 Jun 2017 10:44:29: #2 Build Peak Model... INFO @ Tue, 27 Jun 2017 10:44:29: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 27 Jun 2017 10:44:29: #2 number of paired peaks: 801 WARNING @ Tue, 27 Jun 2017 10:44:29: Fewer paired peaks (801) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 801 pairs to build model! INFO @ Tue, 27 Jun 2017 10:44:29: start model_add_line... INFO @ Tue, 27 Jun 2017 10:44:29: start X-correlation... INFO @ Tue, 27 Jun 2017 10:44:29: end of X-cor INFO @ Tue, 27 Jun 2017 10:44:29: #2 finished! INFO @ Tue, 27 Jun 2017 10:44:29: #2 predicted fragment length is 158 bps INFO @ Tue, 27 Jun 2017 10:44:29: #2 alternative fragment length(s) may be 158 bps INFO @ Tue, 27 Jun 2017 10:44:29: #2.2 Generate R script for model : SRX2228863.20_model.r INFO @ Tue, 27 Jun 2017 10:44:29: #3 Call peaks... INFO @ Tue, 27 Jun 2017 10:44:29: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 27 Jun 2017 10:44:33: #1 tag size is determined as 76 bps INFO @ Tue, 27 Jun 2017 10:44:33: #1 tag size = 76 INFO @ Tue, 27 Jun 2017 10:44:33: #1 total tags in treatment: 8949621 INFO @ Tue, 27 Jun 2017 10:44:33: #1 user defined the maximum tags... INFO @ Tue, 27 Jun 2017 10:44:33: #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 10:44:33: #1 tags after filtering in treatment: 8949621 INFO @ Tue, 27 Jun 2017 10:44:33: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 27 Jun 2017 10:44:33: #1 finished! INFO @ Tue, 27 Jun 2017 10:44:33: #2 Build Peak Model... INFO @ Tue, 27 Jun 2017 10:44:33: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 27 Jun 2017 10:44:34: #2 number of paired peaks: 801 WARNING @ Tue, 27 Jun 2017 10:44:34: Fewer paired peaks (801) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 801 pairs to build model! INFO @ Tue, 27 Jun 2017 10:44:34: start model_add_line... INFO @ Tue, 27 Jun 2017 10:44:34: start X-correlation... INFO @ Tue, 27 Jun 2017 10:44:34: end of X-cor INFO @ Tue, 27 Jun 2017 10:44:34: #2 finished! INFO @ Tue, 27 Jun 2017 10:44:34: #2 predicted fragment length is 158 bps INFO @ Tue, 27 Jun 2017 10:44:34: #2 alternative fragment length(s) may be 158 bps INFO @ Tue, 27 Jun 2017 10:44:34: #2.2 Generate R script for model : SRX2228863.10_model.r INFO @ Tue, 27 Jun 2017 10:44:34: #3 Call peaks... INFO @ Tue, 27 Jun 2017 10:44:34: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 27 Jun 2017 10:44:35: #1 tag size is determined as 76 bps INFO @ Tue, 27 Jun 2017 10:44:35: #1 tag size = 76 INFO @ Tue, 27 Jun 2017 10:44:35: #1 total tags in treatment: 8949621 INFO @ Tue, 27 Jun 2017 10:44:35: #1 user defined the maximum tags... INFO @ Tue, 27 Jun 2017 10:44:35: #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 10:44:35: #1 tags after filtering in treatment: 8949621 INFO @ Tue, 27 Jun 2017 10:44:35: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 27 Jun 2017 10:44:35: #1 finished! INFO @ Tue, 27 Jun 2017 10:44:35: #2 Build Peak Model... INFO @ Tue, 27 Jun 2017 10:44:35: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 27 Jun 2017 10:44:36: #2 number of paired peaks: 801 WARNING @ Tue, 27 Jun 2017 10:44:36: Fewer paired peaks (801) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 801 pairs to build model! INFO @ Tue, 27 Jun 2017 10:44:36: start model_add_line... INFO @ Tue, 27 Jun 2017 10:44:36: start X-correlation... INFO @ Tue, 27 Jun 2017 10:44:36: end of X-cor INFO @ Tue, 27 Jun 2017 10:44:36: #2 finished! INFO @ Tue, 27 Jun 2017 10:44:36: #2 predicted fragment length is 158 bps INFO @ Tue, 27 Jun 2017 10:44:36: #2 alternative fragment length(s) may be 158 bps INFO @ Tue, 27 Jun 2017 10:44:36: #2.2 Generate R script for model : SRX2228863.05_model.r INFO @ Tue, 27 Jun 2017 10:44:36: #3 Call peaks... INFO @ Tue, 27 Jun 2017 10:44:36: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 27 Jun 2017 10:44:53: #3 Call peaks for each chromosome... INFO @ Tue, 27 Jun 2017 10:44:59: #3 Call peaks for each chromosome... INFO @ Tue, 27 Jun 2017 10:44:59: #3 Call peaks for each chromosome... INFO @ Tue, 27 Jun 2017 10:45:05: #4 Write output xls file... SRX2228863.20_peaks.xls INFO @ Tue, 27 Jun 2017 10:45:05: #4 Write peak in narrowPeak format file... SRX2228863.20_peaks.narrowPeak INFO @ Tue, 27 Jun 2017 10:45:05: #4 Write summits bed file... SRX2228863.20_summits.bed INFO @ Tue, 27 Jun 2017 10:45:05: Done! pass1 - making usageList (7 chroms): 0 millis pass2 - checking and writing primary data (767 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Tue, 27 Jun 2017 10:45:11: #4 Write output xls file... SRX2228863.05_peaks.xls INFO @ Tue, 27 Jun 2017 10:45:11: #4 Write peak in narrowPeak format file... SRX2228863.05_peaks.narrowPeak INFO @ Tue, 27 Jun 2017 10:45:11: #4 Write summits bed file... SRX2228863.05_summits.bed INFO @ Tue, 27 Jun 2017 10:45:11: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (1816 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Tue, 27 Jun 2017 10:45:11: #4 Write output xls file... SRX2228863.10_peaks.xls INFO @ Tue, 27 Jun 2017 10:45:11: #4 Write peak in narrowPeak format file... SRX2228863.10_peaks.narrowPeak INFO @ Tue, 27 Jun 2017 10:45:11: #4 Write summits bed file... SRX2228863.10_summits.bed INFO @ Tue, 27 Jun 2017 10:45:11: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (1216 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。