Job ID = 9025529 sra ファイルのダウンロード中... Completed: 172991K bytes transferred in 4 seconds (298365K 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 --:--:-- 0 100 7663 0 7663 0 0 881 0 --:--:-- 0:00:08 --:--:-- 3392 100 33142 0 33142 0 0 3422 0 --:--:-- 0:00:09 --:--:-- 10181 100 47241 0 47241 0 0 4795 0 --:--:-- 0:00:09 --:--:-- 13809 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 7341639 spots for /home/okishinya/chipatlas/results/ce10/SRX1388778/SRR2832494.sra Written 7341639 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: 00:02:06 7341639 reads; of these: 7341639 (100.00%) were unpaired; of these: 269759 (3.67%) aligned 0 times 5450766 (74.24%) aligned exactly 1 time 1621114 (22.08%) aligned >1 times 96.33% overall alignment rate Time searching: 00:02:06 Overall time: 00:02:06 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] 596670 / 7071880 = 0.0844 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 04:18:33: # Command line: callpeak -t SRX1388778.bam -f BAM -g ce -n SRX1388778.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX1388778.10 # format = BAM # ChIP-seq file = ['SRX1388778.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 04:18:33: #1 read tag files... INFO @ Sat, 03 Jun 2017 04:18:33: #1 read treatment tags... INFO @ Sat, 03 Jun 2017 04:18:33: # Command line: callpeak -t SRX1388778.bam -f BAM -g ce -n SRX1388778.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX1388778.05 # format = BAM # ChIP-seq file = ['SRX1388778.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 04:18:33: #1 read tag files... INFO @ Sat, 03 Jun 2017 04:18:33: #1 read treatment tags... INFO @ Sat, 03 Jun 2017 04:18:33: # Command line: callpeak -t SRX1388778.bam -f BAM -g ce -n SRX1388778.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX1388778.20 # format = BAM # ChIP-seq file = ['SRX1388778.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 04:18:33: #1 read tag files... INFO @ Sat, 03 Jun 2017 04:18:33: #1 read treatment tags... INFO @ Sat, 03 Jun 2017 04:18:39: 1000000 INFO @ Sat, 03 Jun 2017 04:18:39: 1000000 INFO @ Sat, 03 Jun 2017 04:18:40: 1000000 INFO @ Sat, 03 Jun 2017 04:18:46: 2000000 INFO @ Sat, 03 Jun 2017 04:18:46: 2000000 INFO @ Sat, 03 Jun 2017 04:18:48: 2000000 INFO @ Sat, 03 Jun 2017 04:18:53: 3000000 INFO @ Sat, 03 Jun 2017 04:18:53: 3000000 INFO @ Sat, 03 Jun 2017 04:18:56: 3000000 INFO @ Sat, 03 Jun 2017 04:19:00: 4000000 INFO @ Sat, 03 Jun 2017 04:19:00: 4000000 INFO @ Sat, 03 Jun 2017 04:19:04: 4000000 INFO @ Sat, 03 Jun 2017 04:19:06: 5000000 INFO @ Sat, 03 Jun 2017 04:19:07: 5000000 INFO @ Sat, 03 Jun 2017 04:19:12: 5000000 INFO @ Sat, 03 Jun 2017 04:19:13: 6000000 INFO @ Sat, 03 Jun 2017 04:19:14: 6000000 INFO @ Sat, 03 Jun 2017 04:19:16: #1 tag size is determined as 50 bps INFO @ Sat, 03 Jun 2017 04:19:16: #1 tag size = 50 INFO @ Sat, 03 Jun 2017 04:19:16: #1 total tags in treatment: 6475210 INFO @ Sat, 03 Jun 2017 04:19:16: #1 user defined the maximum tags... INFO @ Sat, 03 Jun 2017 04:19:16: #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 04:19:17: #1 tag size is determined as 50 bps INFO @ Sat, 03 Jun 2017 04:19:17: #1 tag size = 50 INFO @ Sat, 03 Jun 2017 04:19:17: #1 total tags in treatment: 6475210 INFO @ Sat, 03 Jun 2017 04:19:17: #1 user defined the maximum tags... INFO @ Sat, 03 Jun 2017 04:19:17: #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 04:19:18: #1 tags after filtering in treatment: 6474012 INFO @ Sat, 03 Jun 2017 04:19:18: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 03 Jun 2017 04:19:18: #1 finished! INFO @ Sat, 03 Jun 2017 04:19:18: #2 Build Peak Model... INFO @ Sat, 03 Jun 2017 04:19:18: #1 tags after filtering in treatment: 6474012 INFO @ Sat, 03 Jun 2017 04:19:18: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 03 Jun 2017 04:19:18: #1 finished! INFO @ Sat, 03 Jun 2017 04:19:18: #2 Build Peak Model... INFO @ Sat, 03 Jun 2017 04:19:19: #2 number of paired peaks: 516 WARNING @ Sat, 03 Jun 2017 04:19:19: Fewer paired peaks (516) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 516 pairs to build model! INFO @ Sat, 03 Jun 2017 04:19:19: start model_add_line... INFO @ Sat, 03 Jun 2017 04:19:19: 6000000 INFO @ Sat, 03 Jun 2017 04:19:20: #2 number of paired peaks: 516 WARNING @ Sat, 03 Jun 2017 04:19:20: Fewer paired peaks (516) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 516 pairs to build model! INFO @ Sat, 03 Jun 2017 04:19:20: start model_add_line... INFO @ Sat, 03 Jun 2017 04:19:22: #1 tag size is determined as 50 bps INFO @ Sat, 03 Jun 2017 04:19:22: #1 tag size = 50 INFO @ Sat, 03 Jun 2017 04:19:22: #1 total tags in treatment: 6475210 INFO @ Sat, 03 Jun 2017 04:19:22: #1 user defined the maximum tags... INFO @ Sat, 03 Jun 2017 04:19:22: #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 04:19:23: #1 tags after filtering in treatment: 6474012 INFO @ Sat, 03 Jun 2017 04:19:23: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 03 Jun 2017 04:19:23: #1 finished! INFO @ Sat, 03 Jun 2017 04:19:23: #2 Build Peak Model... INFO @ Sat, 03 Jun 2017 04:19:24: start X-correlation... INFO @ Sat, 03 Jun 2017 04:19:24: end of X-cor INFO @ Sat, 03 Jun 2017 04:19:24: #2 finished! INFO @ Sat, 03 Jun 2017 04:19:24: #2 predicted fragment length is 46 bps INFO @ Sat, 03 Jun 2017 04:19:24: #2 alternative fragment length(s) may be 3,46,520,565 bps INFO @ Sat, 03 Jun 2017 04:19:24: #2.2 Generate R script for model : SRX1388778.20_model.r WARNING @ Sat, 03 Jun 2017 04:19:24: #2 Since the d (46) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 03 Jun 2017 04:19:24: #2 You may need to consider one of the other alternative d(s): 3,46,520,565 WARNING @ Sat, 03 Jun 2017 04:19:24: #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 04:19:24: #3 Call peaks... INFO @ Sat, 03 Jun 2017 04:19:24: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Jun 2017 04:19:24: #2 number of paired peaks: 516 WARNING @ Sat, 03 Jun 2017 04:19:24: Fewer paired peaks (516) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 516 pairs to build model! INFO @ Sat, 03 Jun 2017 04:19:24: start model_add_line... INFO @ Sat, 03 Jun 2017 04:19:25: start X-correlation... INFO @ Sat, 03 Jun 2017 04:19:25: end of X-cor INFO @ Sat, 03 Jun 2017 04:19:25: #2 finished! INFO @ Sat, 03 Jun 2017 04:19:25: #2 predicted fragment length is 46 bps INFO @ Sat, 03 Jun 2017 04:19:25: #2 alternative fragment length(s) may be 3,46,520,565 bps INFO @ Sat, 03 Jun 2017 04:19:25: #2.2 Generate R script for model : SRX1388778.10_model.r WARNING @ Sat, 03 Jun 2017 04:19:25: #2 Since the d (46) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 03 Jun 2017 04:19:25: #2 You may need to consider one of the other alternative d(s): 3,46,520,565 WARNING @ Sat, 03 Jun 2017 04:19:25: #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 04:19:25: #3 Call peaks... INFO @ Sat, 03 Jun 2017 04:19:25: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Jun 2017 04:19:30: start X-correlation... INFO @ Sat, 03 Jun 2017 04:19:30: end of X-cor INFO @ Sat, 03 Jun 2017 04:19:30: #2 finished! INFO @ Sat, 03 Jun 2017 04:19:30: #2 predicted fragment length is 46 bps INFO @ Sat, 03 Jun 2017 04:19:30: #2 alternative fragment length(s) may be 3,46,520,565 bps INFO @ Sat, 03 Jun 2017 04:19:30: #2.2 Generate R script for model : SRX1388778.05_model.r WARNING @ Sat, 03 Jun 2017 04:19:30: #2 Since the d (46) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 03 Jun 2017 04:19:30: #2 You may need to consider one of the other alternative d(s): 3,46,520,565 WARNING @ Sat, 03 Jun 2017 04:19:30: #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 04:19:30: #3 Call peaks... INFO @ Sat, 03 Jun 2017 04:19:30: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Jun 2017 04:20:01: #3 Call peaks for each chromosome... INFO @ Sat, 03 Jun 2017 04:20:02: #3 Call peaks for each chromosome... INFO @ Sat, 03 Jun 2017 04:20:06: #3 Call peaks for each chromosome... INFO @ Sat, 03 Jun 2017 04:20:27: #4 Write output xls file... SRX1388778.10_peaks.xls INFO @ Sat, 03 Jun 2017 04:20:27: #4 Write peak in narrowPeak format file... SRX1388778.10_peaks.narrowPeak INFO @ Sat, 03 Jun 2017 04:20:27: #4 Write summits bed file... SRX1388778.10_summits.bed INFO @ Sat, 03 Jun 2017 04:20:27: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (418 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Sat, 03 Jun 2017 04:20:28: #4 Write output xls file... SRX1388778.20_peaks.xls INFO @ Sat, 03 Jun 2017 04:20:28: #4 Write peak in narrowPeak format file... SRX1388778.20_peaks.narrowPeak INFO @ Sat, 03 Jun 2017 04:20:28: #4 Write summits bed file... SRX1388778.20_summits.bed INFO @ Sat, 03 Jun 2017 04:20:28: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (163 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Sat, 03 Jun 2017 04:20:31: #4 Write output xls file... SRX1388778.05_peaks.xls INFO @ Sat, 03 Jun 2017 04:20:31: #4 Write peak in narrowPeak format file... SRX1388778.05_peaks.narrowPeak INFO @ Sat, 03 Jun 2017 04:20:31: #4 Write summits bed file... SRX1388778.05_summits.bed INFO @ Sat, 03 Jun 2017 04:20:31: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (639 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。