Job ID = 9025663 sra ファイルのダウンロード中... Completed: 69699K bytes transferred in 3 seconds (146677K 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 0 0 0 0 0 0 0 0 --:--:-- 0:00:08 --:--:-- 0 0 0 0 0 0 0 0 0 --:--:-- 0:00:08 --:--:-- 0 100 22318 0 22318 0 0 2257 0 --:--:-- 0:00:09 --:--:-- 6437 100 43772 0 43772 0 0 4149 0 --:--:-- 0:00:10 --:--:-- 10598 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 3029738 spots for /home/okishinya/chipatlas/results/ce10/SRX2144189/SRR4188793.sra Written 3029738 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: 00:00:49 3029738 reads; of these: 3029738 (100.00%) were unpaired; of these: 147935 (4.88%) aligned 0 times 2388957 (78.85%) aligned exactly 1 time 492846 (16.27%) aligned >1 times 95.12% overall alignment rate Time searching: 00:00:49 Overall time: 00:00:49 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] 105176 / 2881803 = 0.0365 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 04:50:17: # Command line: callpeak -t SRX2144189.bam -f BAM -g ce -n SRX2144189.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX2144189.20 # format = BAM # ChIP-seq file = ['SRX2144189.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 04:50:17: #1 read tag files... INFO @ Sat, 03 Jun 2017 04:50:17: #1 read treatment tags... INFO @ Sat, 03 Jun 2017 04:50:17: # Command line: callpeak -t SRX2144189.bam -f BAM -g ce -n SRX2144189.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX2144189.05 # format = BAM # ChIP-seq file = ['SRX2144189.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 04:50:17: #1 read tag files... INFO @ Sat, 03 Jun 2017 04:50:17: #1 read treatment tags... INFO @ Sat, 03 Jun 2017 04:50:17: # Command line: callpeak -t SRX2144189.bam -f BAM -g ce -n SRX2144189.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX2144189.10 # format = BAM # ChIP-seq file = ['SRX2144189.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 04:50:17: #1 read tag files... INFO @ Sat, 03 Jun 2017 04:50:17: #1 read treatment tags... INFO @ Sat, 03 Jun 2017 04:50:22: 1000000 INFO @ Sat, 03 Jun 2017 04:50:22: 1000000 INFO @ Sat, 03 Jun 2017 04:50:22: 1000000 INFO @ Sat, 03 Jun 2017 04:50:28: 2000000 INFO @ Sat, 03 Jun 2017 04:50:28: 2000000 INFO @ Sat, 03 Jun 2017 04:50:28: 2000000 INFO @ Sat, 03 Jun 2017 04:50:32: #1 tag size is determined as 50 bps INFO @ Sat, 03 Jun 2017 04:50:32: #1 tag size = 50 INFO @ Sat, 03 Jun 2017 04:50:32: #1 total tags in treatment: 2776627 INFO @ Sat, 03 Jun 2017 04:50:32: #1 user defined the maximum tags... INFO @ Sat, 03 Jun 2017 04:50:32: #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 04:50:33: #1 tag size is determined as 50 bps INFO @ Sat, 03 Jun 2017 04:50:33: #1 tag size = 50 INFO @ Sat, 03 Jun 2017 04:50:33: #1 total tags in treatment: 2776627 INFO @ Sat, 03 Jun 2017 04:50:33: #1 user defined the maximum tags... INFO @ Sat, 03 Jun 2017 04:50:33: #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 04:50:33: #1 tag size is determined as 50 bps INFO @ Sat, 03 Jun 2017 04:50:33: #1 tag size = 50 INFO @ Sat, 03 Jun 2017 04:50:33: #1 total tags in treatment: 2776627 INFO @ Sat, 03 Jun 2017 04:50:33: #1 user defined the maximum tags... INFO @ Sat, 03 Jun 2017 04:50:33: #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 04:50:33: #1 tags after filtering in treatment: 2776327 INFO @ Sat, 03 Jun 2017 04:50:33: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 03 Jun 2017 04:50:33: #1 finished! INFO @ Sat, 03 Jun 2017 04:50:33: #2 Build Peak Model... INFO @ Sat, 03 Jun 2017 04:50:33: #1 tags after filtering in treatment: 2776327 INFO @ Sat, 03 Jun 2017 04:50:33: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 03 Jun 2017 04:50:33: #1 finished! INFO @ Sat, 03 Jun 2017 04:50:33: #2 Build Peak Model... INFO @ Sat, 03 Jun 2017 04:50:33: #1 tags after filtering in treatment: 2776327 INFO @ Sat, 03 Jun 2017 04:50:33: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 03 Jun 2017 04:50:33: #1 finished! INFO @ Sat, 03 Jun 2017 04:50:33: #2 Build Peak Model... INFO @ Sat, 03 Jun 2017 04:50:33: #2 number of paired peaks: 374 WARNING @ Sat, 03 Jun 2017 04:50:33: Fewer paired peaks (374) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 374 pairs to build model! INFO @ Sat, 03 Jun 2017 04:50:33: start model_add_line... INFO @ Sat, 03 Jun 2017 04:50:34: #2 number of paired peaks: 374 WARNING @ Sat, 03 Jun 2017 04:50:34: Fewer paired peaks (374) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 374 pairs to build model! INFO @ Sat, 03 Jun 2017 04:50:34: start model_add_line... INFO @ Sat, 03 Jun 2017 04:50:34: #2 number of paired peaks: 374 WARNING @ Sat, 03 Jun 2017 04:50:34: Fewer paired peaks (374) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 374 pairs to build model! INFO @ Sat, 03 Jun 2017 04:50:34: start model_add_line... INFO @ Sat, 03 Jun 2017 04:50:35: start X-correlation... INFO @ Sat, 03 Jun 2017 04:50:35: end of X-cor INFO @ Sat, 03 Jun 2017 04:50:35: #2 finished! INFO @ Sat, 03 Jun 2017 04:50:35: #2 predicted fragment length is 49 bps INFO @ Sat, 03 Jun 2017 04:50:35: #2 alternative fragment length(s) may be 49,501 bps INFO @ Sat, 03 Jun 2017 04:50:35: #2.2 Generate R script for model : SRX2144189.20_model.r WARNING @ Sat, 03 Jun 2017 04:50:35: #2 Since the d (49) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 03 Jun 2017 04:50:35: #2 You may need to consider one of the other alternative d(s): 49,501 WARNING @ Sat, 03 Jun 2017 04:50:35: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sat, 03 Jun 2017 04:50:35: #3 Call peaks... INFO @ Sat, 03 Jun 2017 04:50:35: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Jun 2017 04:50:35: start X-correlation... INFO @ Sat, 03 Jun 2017 04:50:35: end of X-cor INFO @ Sat, 03 Jun 2017 04:50:35: #2 finished! INFO @ Sat, 03 Jun 2017 04:50:35: #2 predicted fragment length is 49 bps INFO @ Sat, 03 Jun 2017 04:50:35: #2 alternative fragment length(s) may be 49,501 bps INFO @ Sat, 03 Jun 2017 04:50:35: #2.2 Generate R script for model : SRX2144189.10_model.r WARNING @ Sat, 03 Jun 2017 04:50:36: #2 Since the d (49) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 03 Jun 2017 04:50:36: #2 You may need to consider one of the other alternative d(s): 49,501 WARNING @ Sat, 03 Jun 2017 04:50:36: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sat, 03 Jun 2017 04:50:36: #3 Call peaks... INFO @ Sat, 03 Jun 2017 04:50:36: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Jun 2017 04:50:36: start X-correlation... INFO @ Sat, 03 Jun 2017 04:50:36: end of X-cor INFO @ Sat, 03 Jun 2017 04:50:36: #2 finished! INFO @ Sat, 03 Jun 2017 04:50:36: #2 predicted fragment length is 49 bps INFO @ Sat, 03 Jun 2017 04:50:36: #2 alternative fragment length(s) may be 49,501 bps INFO @ Sat, 03 Jun 2017 04:50:36: #2.2 Generate R script for model : SRX2144189.05_model.r WARNING @ Sat, 03 Jun 2017 04:50:36: #2 Since the d (49) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 03 Jun 2017 04:50:36: #2 You may need to consider one of the other alternative d(s): 49,501 WARNING @ Sat, 03 Jun 2017 04:50:36: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sat, 03 Jun 2017 04:50:36: #3 Call peaks... INFO @ Sat, 03 Jun 2017 04:50:36: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Jun 2017 04:50:52: #3 Call peaks for each chromosome... INFO @ Sat, 03 Jun 2017 04:50:53: #3 Call peaks for each chromosome... INFO @ Sat, 03 Jun 2017 04:50:53: #3 Call peaks for each chromosome... INFO @ Sat, 03 Jun 2017 04:51:04: #4 Write output xls file... SRX2144189.05_peaks.xls INFO @ Sat, 03 Jun 2017 04:51:04: #4 Write peak in narrowPeak format file... SRX2144189.05_peaks.narrowPeak INFO @ Sat, 03 Jun 2017 04:51:04: #4 Write summits bed file... SRX2144189.05_summits.bed INFO @ Sat, 03 Jun 2017 04:51:04: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (325 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Sat, 03 Jun 2017 04:51:05: #4 Write output xls file... SRX2144189.10_peaks.xls INFO @ Sat, 03 Jun 2017 04:51:05: #4 Write peak in narrowPeak format file... SRX2144189.10_peaks.narrowPeak INFO @ Sat, 03 Jun 2017 04:51:05: #4 Write summits bed file... SRX2144189.10_summits.bed INFO @ Sat, 03 Jun 2017 04:51:05: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (198 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Sat, 03 Jun 2017 04:51:05: #4 Write output xls file... SRX2144189.20_peaks.xls INFO @ Sat, 03 Jun 2017 04:51:05: #4 Write peak in narrowPeak format file... SRX2144189.20_peaks.narrowPeak INFO @ Sat, 03 Jun 2017 04:51:05: #4 Write summits bed file... SRX2144189.20_summits.bed INFO @ Sat, 03 Jun 2017 04:51:05: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (59 records, 4 fields): 2 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。