Job ID = 9028845 sra ファイルのダウンロード中... Completed: 259842K bytes transferred in 5 seconds (404764K 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 20110 0 20110 0 0 2592 0 --:--:-- 0:00:07 --:--:-- 16984 100 50486 0 50486 0 0 5768 0 --:--:-- 0:00:08 --:--:-- 23169 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 7295902 spots for /home/okishinya/chipatlas/results/ce10/SRX982074/SRR1956553.sra Written 7295902 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: 00:02:11 7295902 reads; of these: 7295902 (100.00%) were unpaired; of these: 155821 (2.14%) aligned 0 times 5788162 (79.33%) aligned exactly 1 time 1351919 (18.53%) aligned >1 times 97.86% overall alignment rate Time searching: 00:02:11 Overall time: 00:02:11 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] 596197 / 7140081 = 0.0835 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 12:05:06: # Command line: callpeak -t SRX982074.bam -f BAM -g ce -n SRX982074.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX982074.20 # format = BAM # ChIP-seq file = ['SRX982074.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 12:05:06: #1 read tag files... INFO @ Sat, 03 Jun 2017 12:05:06: #1 read treatment tags... INFO @ Sat, 03 Jun 2017 12:05:06: # Command line: callpeak -t SRX982074.bam -f BAM -g ce -n SRX982074.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX982074.05 # format = BAM # ChIP-seq file = ['SRX982074.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 12:05:06: #1 read tag files... INFO @ Sat, 03 Jun 2017 12:05:06: #1 read treatment tags... INFO @ Sat, 03 Jun 2017 12:05:06: # Command line: callpeak -t SRX982074.bam -f BAM -g ce -n SRX982074.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX982074.10 # format = BAM # ChIP-seq file = ['SRX982074.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 12:05:06: #1 read tag files... INFO @ Sat, 03 Jun 2017 12:05:06: #1 read treatment tags... INFO @ Sat, 03 Jun 2017 12:05:11: 1000000 INFO @ Sat, 03 Jun 2017 12:05:12: 1000000 INFO @ Sat, 03 Jun 2017 12:05:12: 1000000 INFO @ Sat, 03 Jun 2017 12:05:17: 2000000 INFO @ Sat, 03 Jun 2017 12:05:18: 2000000 INFO @ Sat, 03 Jun 2017 12:05:18: 2000000 INFO @ Sat, 03 Jun 2017 12:05:22: 3000000 INFO @ Sat, 03 Jun 2017 12:05:24: 3000000 INFO @ Sat, 03 Jun 2017 12:05:24: 3000000 INFO @ Sat, 03 Jun 2017 12:05:27: 4000000 INFO @ Sat, 03 Jun 2017 12:05:29: 4000000 INFO @ Sat, 03 Jun 2017 12:05:29: 4000000 INFO @ Sat, 03 Jun 2017 12:05:33: 5000000 INFO @ Sat, 03 Jun 2017 12:05:35: 5000000 INFO @ Sat, 03 Jun 2017 12:05:35: 5000000 INFO @ Sat, 03 Jun 2017 12:05:38: 6000000 INFO @ Sat, 03 Jun 2017 12:05:40: 6000000 INFO @ Sat, 03 Jun 2017 12:05:40: 6000000 INFO @ Sat, 03 Jun 2017 12:05:41: #1 tag size is determined as 51 bps INFO @ Sat, 03 Jun 2017 12:05:41: #1 tag size = 51 INFO @ Sat, 03 Jun 2017 12:05:41: #1 total tags in treatment: 6543884 INFO @ Sat, 03 Jun 2017 12:05:41: #1 user defined the maximum tags... INFO @ Sat, 03 Jun 2017 12:05:41: #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 12:05:42: #1 tags after filtering in treatment: 6543304 INFO @ Sat, 03 Jun 2017 12:05:42: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 03 Jun 2017 12:05:42: #1 finished! INFO @ Sat, 03 Jun 2017 12:05:42: #2 Build Peak Model... INFO @ Sat, 03 Jun 2017 12:05:43: #2 number of paired peaks: 426 WARNING @ Sat, 03 Jun 2017 12:05:43: Fewer paired peaks (426) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 426 pairs to build model! INFO @ Sat, 03 Jun 2017 12:05:43: start model_add_line... INFO @ Sat, 03 Jun 2017 12:05:43: #1 tag size is determined as 51 bps INFO @ Sat, 03 Jun 2017 12:05:43: #1 tag size = 51 INFO @ Sat, 03 Jun 2017 12:05:43: #1 total tags in treatment: 6543884 INFO @ Sat, 03 Jun 2017 12:05:43: #1 user defined the maximum tags... INFO @ Sat, 03 Jun 2017 12:05:43: #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 12:05:44: #1 tag size is determined as 51 bps INFO @ Sat, 03 Jun 2017 12:05:44: #1 tag size = 51 INFO @ Sat, 03 Jun 2017 12:05:44: #1 total tags in treatment: 6543884 INFO @ Sat, 03 Jun 2017 12:05:44: #1 user defined the maximum tags... INFO @ Sat, 03 Jun 2017 12:05:44: #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 12:05:45: #1 tags after filtering in treatment: 6543304 INFO @ Sat, 03 Jun 2017 12:05:45: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 03 Jun 2017 12:05:45: #1 finished! INFO @ Sat, 03 Jun 2017 12:05:45: #2 Build Peak Model... INFO @ Sat, 03 Jun 2017 12:05:45: #1 tags after filtering in treatment: 6543304 INFO @ Sat, 03 Jun 2017 12:05:45: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 03 Jun 2017 12:05:45: #1 finished! INFO @ Sat, 03 Jun 2017 12:05:45: #2 Build Peak Model... INFO @ Sat, 03 Jun 2017 12:05:46: #2 number of paired peaks: 426 WARNING @ Sat, 03 Jun 2017 12:05:46: Fewer paired peaks (426) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 426 pairs to build model! INFO @ Sat, 03 Jun 2017 12:05:46: start model_add_line... INFO @ Sat, 03 Jun 2017 12:05:46: #2 number of paired peaks: 426 WARNING @ Sat, 03 Jun 2017 12:05:46: Fewer paired peaks (426) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 426 pairs to build model! INFO @ Sat, 03 Jun 2017 12:05:46: start model_add_line... INFO @ Sat, 03 Jun 2017 12:05:47: start X-correlation... INFO @ Sat, 03 Jun 2017 12:05:47: end of X-cor INFO @ Sat, 03 Jun 2017 12:05:47: #2 finished! INFO @ Sat, 03 Jun 2017 12:05:47: #2 predicted fragment length is 56 bps INFO @ Sat, 03 Jun 2017 12:05:47: #2 alternative fragment length(s) may be 4,56,593 bps INFO @ Sat, 03 Jun 2017 12:05:47: #2.2 Generate R script for model : SRX982074.10_model.r WARNING @ Sat, 03 Jun 2017 12:05:47: #2 Since the d (56) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 03 Jun 2017 12:05:47: #2 You may need to consider one of the other alternative d(s): 4,56,593 WARNING @ Sat, 03 Jun 2017 12:05:47: #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 12:05:47: #3 Call peaks... INFO @ Sat, 03 Jun 2017 12:05:47: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Jun 2017 12:05:50: start X-correlation... INFO @ Sat, 03 Jun 2017 12:05:50: end of X-cor INFO @ Sat, 03 Jun 2017 12:05:50: #2 finished! INFO @ Sat, 03 Jun 2017 12:05:50: #2 predicted fragment length is 56 bps INFO @ Sat, 03 Jun 2017 12:05:50: #2 alternative fragment length(s) may be 4,56,593 bps INFO @ Sat, 03 Jun 2017 12:05:50: #2.2 Generate R script for model : SRX982074.20_model.r WARNING @ Sat, 03 Jun 2017 12:05:50: #2 Since the d (56) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 03 Jun 2017 12:05:50: #2 You may need to consider one of the other alternative d(s): 4,56,593 WARNING @ Sat, 03 Jun 2017 12:05:50: #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 12:05:50: #3 Call peaks... INFO @ Sat, 03 Jun 2017 12:05:50: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Jun 2017 12:05:50: start X-correlation... INFO @ Sat, 03 Jun 2017 12:05:50: end of X-cor INFO @ Sat, 03 Jun 2017 12:05:50: #2 finished! INFO @ Sat, 03 Jun 2017 12:05:50: #2 predicted fragment length is 56 bps INFO @ Sat, 03 Jun 2017 12:05:50: #2 alternative fragment length(s) may be 4,56,593 bps INFO @ Sat, 03 Jun 2017 12:05:50: #2.2 Generate R script for model : SRX982074.05_model.r WARNING @ Sat, 03 Jun 2017 12:05:50: #2 Since the d (56) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 03 Jun 2017 12:05:50: #2 You may need to consider one of the other alternative d(s): 4,56,593 WARNING @ Sat, 03 Jun 2017 12:05:50: #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 12:05:50: #3 Call peaks... INFO @ Sat, 03 Jun 2017 12:05:50: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Jun 2017 12:06:22: #3 Call peaks for each chromosome... INFO @ Sat, 03 Jun 2017 12:06:25: #3 Call peaks for each chromosome... INFO @ Sat, 03 Jun 2017 12:06:31: #3 Call peaks for each chromosome... INFO @ Sat, 03 Jun 2017 12:06:48: #4 Write output xls file... SRX982074.10_peaks.xls INFO @ Sat, 03 Jun 2017 12:06:48: #4 Write peak in narrowPeak format file... SRX982074.10_peaks.narrowPeak INFO @ Sat, 03 Jun 2017 12:06:48: #4 Write summits bed file... SRX982074.10_summits.bed INFO @ Sat, 03 Jun 2017 12:06:48: Done! pass1 - making usageList (7 chroms): 0 millis pass2 - checking and writing primary data (333 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Sat, 03 Jun 2017 12:06:51: #4 Write output xls file... SRX982074.20_peaks.xls INFO @ Sat, 03 Jun 2017 12:06:51: #4 Write peak in narrowPeak format file... SRX982074.20_peaks.narrowPeak INFO @ Sat, 03 Jun 2017 12:06:51: #4 Write summits bed file... SRX982074.20_summits.bed INFO @ Sat, 03 Jun 2017 12:06:51: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (136 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Sat, 03 Jun 2017 12:06:59: #4 Write output xls file... SRX982074.05_peaks.xls INFO @ Sat, 03 Jun 2017 12:06:59: #4 Write peak in narrowPeak format file... SRX982074.05_peaks.narrowPeak INFO @ Sat, 03 Jun 2017 12:06:59: #4 Write summits bed file... SRX982074.05_summits.bed INFO @ Sat, 03 Jun 2017 12:06:59: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (1011 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。