Job ID = 9025527 sra ファイルのダウンロード中... Completed: 84921K bytes transferred in 4 seconds (172739K 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 --:--:-- 0:00:06 --:--:-- 0 100 14324 0 14324 0 0 1887 0 --:--:-- 0:00:07 --:--:-- 12242 100 38318 0 38318 0 0 4463 0 --:--:-- 0:00:08 --:--:-- 17690 100 45087 0 45087 0 0 5152 0 --:--:-- 0:00:08 --:--:-- 19334 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 3633709 spots for /home/okishinya/chipatlas/results/ce10/SRX1388776/SRR2832492.sra Written 3633709 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: 00:00:01 Time loading mirror index: 00:00:00 Multiseed full-index search: 00:00:59 3633709 reads; of these: 3633709 (100.00%) were unpaired; of these: 173192 (4.77%) aligned 0 times 2679435 (73.74%) aligned exactly 1 time 781082 (21.50%) aligned >1 times 95.23% overall alignment rate Time searching: 00:01:00 Overall time: 00:01:00 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] 245602 / 3460517 = 0.0710 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 04:16:21: # Command line: callpeak -t SRX1388776.bam -f BAM -g ce -n SRX1388776.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX1388776.10 # format = BAM # ChIP-seq file = ['SRX1388776.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 04:16:21: #1 read tag files... INFO @ Sat, 03 Jun 2017 04:16:21: #1 read treatment tags... INFO @ Sat, 03 Jun 2017 04:16:21: # Command line: callpeak -t SRX1388776.bam -f BAM -g ce -n SRX1388776.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX1388776.05 # format = BAM # ChIP-seq file = ['SRX1388776.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 04:16:21: #1 read tag files... INFO @ Sat, 03 Jun 2017 04:16:21: #1 read treatment tags... INFO @ Sat, 03 Jun 2017 04:16:21: # Command line: callpeak -t SRX1388776.bam -f BAM -g ce -n SRX1388776.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX1388776.20 # format = BAM # ChIP-seq file = ['SRX1388776.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 04:16:21: #1 read tag files... INFO @ Sat, 03 Jun 2017 04:16:21: #1 read treatment tags... INFO @ Sat, 03 Jun 2017 04:16:27: 1000000 INFO @ Sat, 03 Jun 2017 04:16:27: 1000000 INFO @ Sat, 03 Jun 2017 04:16:27: 1000000 INFO @ Sat, 03 Jun 2017 04:16:32: 2000000 INFO @ Sat, 03 Jun 2017 04:16:33: 2000000 INFO @ Sat, 03 Jun 2017 04:16:34: 2000000 INFO @ Sat, 03 Jun 2017 04:16:38: 3000000 INFO @ Sat, 03 Jun 2017 04:16:39: #1 tag size is determined as 50 bps INFO @ Sat, 03 Jun 2017 04:16:39: #1 tag size = 50 INFO @ Sat, 03 Jun 2017 04:16:39: #1 total tags in treatment: 3214915 INFO @ Sat, 03 Jun 2017 04:16:39: #1 user defined the maximum tags... INFO @ Sat, 03 Jun 2017 04:16:39: #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 04:16:40: 3000000 INFO @ Sat, 03 Jun 2017 04:16:40: 3000000 INFO @ Sat, 03 Jun 2017 04:16:40: #1 tags after filtering in treatment: 3214434 INFO @ Sat, 03 Jun 2017 04:16:40: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 03 Jun 2017 04:16:40: #1 finished! INFO @ Sat, 03 Jun 2017 04:16:40: #2 Build Peak Model... INFO @ Sat, 03 Jun 2017 04:16:40: #2 number of paired peaks: 513 WARNING @ Sat, 03 Jun 2017 04:16:40: Fewer paired peaks (513) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 513 pairs to build model! INFO @ Sat, 03 Jun 2017 04:16:40: start model_add_line... INFO @ Sat, 03 Jun 2017 04:16:41: #1 tag size is determined as 50 bps INFO @ Sat, 03 Jun 2017 04:16:41: #1 tag size = 50 INFO @ Sat, 03 Jun 2017 04:16:41: #1 total tags in treatment: 3214915 INFO @ Sat, 03 Jun 2017 04:16:41: #1 user defined the maximum tags... INFO @ Sat, 03 Jun 2017 04:16:41: #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 04:16:41: #1 tag size is determined as 50 bps INFO @ Sat, 03 Jun 2017 04:16:41: #1 tag size = 50 INFO @ Sat, 03 Jun 2017 04:16:41: #1 total tags in treatment: 3214915 INFO @ Sat, 03 Jun 2017 04:16:41: #1 user defined the maximum tags... INFO @ Sat, 03 Jun 2017 04:16:41: #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 04:16:42: #1 tags after filtering in treatment: 3214434 INFO @ Sat, 03 Jun 2017 04:16:42: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 03 Jun 2017 04:16:42: #1 finished! INFO @ Sat, 03 Jun 2017 04:16:42: #2 Build Peak Model... INFO @ Sat, 03 Jun 2017 04:16:42: #1 tags after filtering in treatment: 3214434 INFO @ Sat, 03 Jun 2017 04:16:42: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 03 Jun 2017 04:16:42: #1 finished! INFO @ Sat, 03 Jun 2017 04:16:42: #2 Build Peak Model... INFO @ Sat, 03 Jun 2017 04:16:42: #2 number of paired peaks: 513 WARNING @ Sat, 03 Jun 2017 04:16:42: Fewer paired peaks (513) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 513 pairs to build model! INFO @ Sat, 03 Jun 2017 04:16:42: start model_add_line... INFO @ Sat, 03 Jun 2017 04:16:43: #2 number of paired peaks: 513 WARNING @ Sat, 03 Jun 2017 04:16:43: Fewer paired peaks (513) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 513 pairs to build model! INFO @ Sat, 03 Jun 2017 04:16:43: start model_add_line... INFO @ Sat, 03 Jun 2017 04:16:43: start X-correlation... INFO @ Sat, 03 Jun 2017 04:16:43: end of X-cor INFO @ Sat, 03 Jun 2017 04:16:43: #2 finished! INFO @ Sat, 03 Jun 2017 04:16:43: #2 predicted fragment length is 49 bps INFO @ Sat, 03 Jun 2017 04:16:43: #2 alternative fragment length(s) may be 49,530 bps INFO @ Sat, 03 Jun 2017 04:16:43: #2.2 Generate R script for model : SRX1388776.05_model.r WARNING @ Sat, 03 Jun 2017 04:16:43: #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 04:16:43: #2 You may need to consider one of the other alternative d(s): 49,530 WARNING @ Sat, 03 Jun 2017 04:16:43: #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 04:16:43: #3 Call peaks... INFO @ Sat, 03 Jun 2017 04:16:43: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Jun 2017 04:16:46: start X-correlation... INFO @ Sat, 03 Jun 2017 04:16:46: end of X-cor INFO @ Sat, 03 Jun 2017 04:16:46: #2 finished! INFO @ Sat, 03 Jun 2017 04:16:46: #2 predicted fragment length is 49 bps INFO @ Sat, 03 Jun 2017 04:16:46: #2 alternative fragment length(s) may be 49,530 bps INFO @ Sat, 03 Jun 2017 04:16:46: #2.2 Generate R script for model : SRX1388776.10_model.r WARNING @ Sat, 03 Jun 2017 04:16:46: #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 04:16:46: #2 You may need to consider one of the other alternative d(s): 49,530 WARNING @ Sat, 03 Jun 2017 04:16:46: #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 04:16:46: #3 Call peaks... INFO @ Sat, 03 Jun 2017 04:16:46: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Jun 2017 04:16:46: start X-correlation... INFO @ Sat, 03 Jun 2017 04:16:46: end of X-cor INFO @ Sat, 03 Jun 2017 04:16:46: #2 finished! INFO @ Sat, 03 Jun 2017 04:16:46: #2 predicted fragment length is 49 bps INFO @ Sat, 03 Jun 2017 04:16:46: #2 alternative fragment length(s) may be 49,530 bps INFO @ Sat, 03 Jun 2017 04:16:46: #2.2 Generate R script for model : SRX1388776.20_model.r WARNING @ Sat, 03 Jun 2017 04:16:46: #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 04:16:46: #2 You may need to consider one of the other alternative d(s): 49,530 WARNING @ Sat, 03 Jun 2017 04:16:46: #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 04:16:46: #3 Call peaks... INFO @ Sat, 03 Jun 2017 04:16:46: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Jun 2017 04:17:03: #3 Call peaks for each chromosome... INFO @ Sat, 03 Jun 2017 04:17:05: #3 Call peaks for each chromosome... INFO @ Sat, 03 Jun 2017 04:17:07: #3 Call peaks for each chromosome... INFO @ Sat, 03 Jun 2017 04:17:17: #4 Write output xls file... SRX1388776.05_peaks.xls INFO @ Sat, 03 Jun 2017 04:17:17: #4 Write peak in narrowPeak format file... SRX1388776.05_peaks.narrowPeak INFO @ Sat, 03 Jun 2017 04:17:17: #4 Write summits bed file... SRX1388776.05_summits.bed INFO @ Sat, 03 Jun 2017 04:17:17: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (479 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Sat, 03 Jun 2017 04:17:18: #4 Write output xls file... SRX1388776.20_peaks.xls INFO @ Sat, 03 Jun 2017 04:17:18: #4 Write peak in narrowPeak format file... SRX1388776.20_peaks.narrowPeak INFO @ Sat, 03 Jun 2017 04:17:18: #4 Write summits bed file... SRX1388776.20_summits.bed INFO @ Sat, 03 Jun 2017 04:17:18: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (118 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Sat, 03 Jun 2017 04:17:21: #4 Write output xls file... SRX1388776.10_peaks.xls INFO @ Sat, 03 Jun 2017 04:17:21: #4 Write peak in narrowPeak format file... SRX1388776.10_peaks.narrowPeak INFO @ Sat, 03 Jun 2017 04:17:21: #4 Write summits bed file... SRX1388776.10_summits.bed INFO @ Sat, 03 Jun 2017 04:17:21: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (278 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。