Job ID = 9025668 sra ファイルのダウンロード中... Completed: 88550K bytes transferred in 4 seconds (177689K 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 7663 0 7663 0 0 943 0 --:--:-- 0:00:08 --:--:-- 4463 100 31694 0 31694 0 0 3541 0 --:--:-- 0:00:08 --:--:-- 12443 100 46315 0 46315 0 0 4902 0 --:--:-- 0:00:09 --:--:-- 15215 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 3823058 spots for /home/okishinya/chipatlas/results/ce10/SRX2144194/SRR4188798.sra Written 3823058 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: 00:01:21 3823058 reads; of these: 3823058 (100.00%) were unpaired; of these: 123446 (3.23%) aligned 0 times 2795669 (73.13%) aligned exactly 1 time 903943 (23.64%) aligned >1 times 96.77% overall alignment rate Time searching: 00:01:21 Overall time: 00:01:21 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] 299701 / 3699612 = 0.0810 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 04:52:01: # Command line: callpeak -t SRX2144194.bam -f BAM -g ce -n SRX2144194.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX2144194.05 # format = BAM # ChIP-seq file = ['SRX2144194.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 04:52:01: #1 read tag files... INFO @ Sat, 03 Jun 2017 04:52:01: #1 read treatment tags... INFO @ Sat, 03 Jun 2017 04:52:01: # Command line: callpeak -t SRX2144194.bam -f BAM -g ce -n SRX2144194.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX2144194.20 # format = BAM # ChIP-seq file = ['SRX2144194.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 04:52:01: #1 read tag files... INFO @ Sat, 03 Jun 2017 04:52:01: #1 read treatment tags... INFO @ Sat, 03 Jun 2017 04:52:01: # Command line: callpeak -t SRX2144194.bam -f BAM -g ce -n SRX2144194.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX2144194.10 # format = BAM # ChIP-seq file = ['SRX2144194.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 04:52:01: #1 read tag files... INFO @ Sat, 03 Jun 2017 04:52:01: #1 read treatment tags... INFO @ Sat, 03 Jun 2017 04:52:07: 1000000 INFO @ Sat, 03 Jun 2017 04:52:08: 1000000 INFO @ Sat, 03 Jun 2017 04:52:08: 1000000 INFO @ Sat, 03 Jun 2017 04:52:14: 2000000 INFO @ Sat, 03 Jun 2017 04:52:14: 2000000 INFO @ Sat, 03 Jun 2017 04:52:15: 2000000 INFO @ Sat, 03 Jun 2017 04:52:21: 3000000 INFO @ Sat, 03 Jun 2017 04:52:21: 3000000 INFO @ Sat, 03 Jun 2017 04:52:23: 3000000 INFO @ Sat, 03 Jun 2017 04:52:23: #1 tag size is determined as 50 bps INFO @ Sat, 03 Jun 2017 04:52:23: #1 tag size = 50 INFO @ Sat, 03 Jun 2017 04:52:23: #1 total tags in treatment: 3399911 INFO @ Sat, 03 Jun 2017 04:52:23: #1 user defined the maximum tags... INFO @ Sat, 03 Jun 2017 04:52:23: #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 04:52:23: #1 tag size is determined as 50 bps INFO @ Sat, 03 Jun 2017 04:52:23: #1 tag size = 50 INFO @ Sat, 03 Jun 2017 04:52:23: #1 total tags in treatment: 3399911 INFO @ Sat, 03 Jun 2017 04:52:23: #1 user defined the maximum tags... INFO @ Sat, 03 Jun 2017 04:52:23: #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 04:52:24: #1 tags after filtering in treatment: 3399291 INFO @ Sat, 03 Jun 2017 04:52:24: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 03 Jun 2017 04:52:24: #1 finished! INFO @ Sat, 03 Jun 2017 04:52:24: #2 Build Peak Model... INFO @ Sat, 03 Jun 2017 04:52:24: #1 tags after filtering in treatment: 3399291 INFO @ Sat, 03 Jun 2017 04:52:24: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 03 Jun 2017 04:52:24: #1 finished! INFO @ Sat, 03 Jun 2017 04:52:24: #2 Build Peak Model... INFO @ Sat, 03 Jun 2017 04:52:24: #2 number of paired peaks: 626 WARNING @ Sat, 03 Jun 2017 04:52:24: Fewer paired peaks (626) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 626 pairs to build model! INFO @ Sat, 03 Jun 2017 04:52:24: start model_add_line... INFO @ Sat, 03 Jun 2017 04:52:25: #2 number of paired peaks: 626 WARNING @ Sat, 03 Jun 2017 04:52:25: Fewer paired peaks (626) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 626 pairs to build model! INFO @ Sat, 03 Jun 2017 04:52:25: start model_add_line... INFO @ Sat, 03 Jun 2017 04:52:25: #1 tag size is determined as 50 bps INFO @ Sat, 03 Jun 2017 04:52:25: #1 tag size = 50 INFO @ Sat, 03 Jun 2017 04:52:25: #1 total tags in treatment: 3399911 INFO @ Sat, 03 Jun 2017 04:52:25: #1 user defined the maximum tags... INFO @ Sat, 03 Jun 2017 04:52:25: #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 04:52:26: #1 tags after filtering in treatment: 3399291 INFO @ Sat, 03 Jun 2017 04:52:26: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 03 Jun 2017 04:52:26: #1 finished! INFO @ Sat, 03 Jun 2017 04:52:26: #2 Build Peak Model... INFO @ Sat, 03 Jun 2017 04:52:26: #2 number of paired peaks: 626 WARNING @ Sat, 03 Jun 2017 04:52:26: Fewer paired peaks (626) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 626 pairs to build model! INFO @ Sat, 03 Jun 2017 04:52:26: start model_add_line... INFO @ Sat, 03 Jun 2017 04:52:28: start X-correlation... INFO @ Sat, 03 Jun 2017 04:52:28: end of X-cor INFO @ Sat, 03 Jun 2017 04:52:28: #2 finished! INFO @ Sat, 03 Jun 2017 04:52:28: #2 predicted fragment length is 50 bps INFO @ Sat, 03 Jun 2017 04:52:28: #2 alternative fragment length(s) may be 4,50 bps INFO @ Sat, 03 Jun 2017 04:52:28: #2.2 Generate R script for model : SRX2144194.10_model.r WARNING @ Sat, 03 Jun 2017 04:52:28: #2 Since the d (50) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 03 Jun 2017 04:52:28: #2 You may need to consider one of the other alternative d(s): 4,50 WARNING @ Sat, 03 Jun 2017 04:52:28: #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 04:52:28: #3 Call peaks... INFO @ Sat, 03 Jun 2017 04:52:28: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Jun 2017 04:52:29: start X-correlation... INFO @ Sat, 03 Jun 2017 04:52:29: end of X-cor INFO @ Sat, 03 Jun 2017 04:52:29: #2 finished! INFO @ Sat, 03 Jun 2017 04:52:29: #2 predicted fragment length is 50 bps INFO @ Sat, 03 Jun 2017 04:52:29: #2 alternative fragment length(s) may be 4,50 bps INFO @ Sat, 03 Jun 2017 04:52:29: #2.2 Generate R script for model : SRX2144194.05_model.r WARNING @ Sat, 03 Jun 2017 04:52:29: #2 Since the d (50) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 03 Jun 2017 04:52:29: #2 You may need to consider one of the other alternative d(s): 4,50 WARNING @ Sat, 03 Jun 2017 04:52:29: #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 04:52:29: #3 Call peaks... INFO @ Sat, 03 Jun 2017 04:52:29: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Jun 2017 04:52:30: start X-correlation... INFO @ Sat, 03 Jun 2017 04:52:30: end of X-cor INFO @ Sat, 03 Jun 2017 04:52:30: #2 finished! INFO @ Sat, 03 Jun 2017 04:52:30: #2 predicted fragment length is 50 bps INFO @ Sat, 03 Jun 2017 04:52:30: #2 alternative fragment length(s) may be 4,50 bps INFO @ Sat, 03 Jun 2017 04:52:30: #2.2 Generate R script for model : SRX2144194.20_model.r WARNING @ Sat, 03 Jun 2017 04:52:30: #2 Since the d (50) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 03 Jun 2017 04:52:30: #2 You may need to consider one of the other alternative d(s): 4,50 WARNING @ Sat, 03 Jun 2017 04:52:30: #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 04:52:30: #3 Call peaks... INFO @ Sat, 03 Jun 2017 04:52:30: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Jun 2017 04:52:50: #3 Call peaks for each chromosome... INFO @ Sat, 03 Jun 2017 04:52:50: #3 Call peaks for each chromosome... INFO @ Sat, 03 Jun 2017 04:52:51: #3 Call peaks for each chromosome... INFO @ Sat, 03 Jun 2017 04:53:03: #4 Write output xls file... SRX2144194.05_peaks.xls INFO @ Sat, 03 Jun 2017 04:53:03: #4 Write peak in narrowPeak format file... SRX2144194.05_peaks.narrowPeak INFO @ Sat, 03 Jun 2017 04:53:03: #4 Write summits bed file... SRX2144194.05_summits.bed INFO @ Sat, 03 Jun 2017 04:53:03: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (501 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Sat, 03 Jun 2017 04:53:04: #4 Write output xls file... SRX2144194.10_peaks.xls INFO @ Sat, 03 Jun 2017 04:53:04: #4 Write peak in narrowPeak format file... SRX2144194.10_peaks.narrowPeak INFO @ Sat, 03 Jun 2017 04:53:04: #4 Write summits bed file... SRX2144194.10_summits.bed INFO @ Sat, 03 Jun 2017 04:53:04: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (315 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Sat, 03 Jun 2017 04:53:05: #4 Write output xls file... SRX2144194.20_peaks.xls INFO @ Sat, 03 Jun 2017 04:53:05: #4 Write peak in narrowPeak format file... SRX2144194.20_peaks.narrowPeak INFO @ Sat, 03 Jun 2017 04:53:05: #4 Write summits bed file... SRX2144194.20_summits.bed INFO @ Sat, 03 Jun 2017 04:53:05: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (125 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。