Job ID = 9025530 sra ファイルのダウンロード中... Completed: 157455K bytes transferred in 4 seconds (279141K 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 14324 0 14324 0 0 1744 0 --:--:-- 0:00:08 --:--:-- 7823 100 45626 0 45626 0 0 5046 0 --:--:-- 0:00:09 --:--:-- 17146 100 47497 0 47497 0 0 5252 0 --:--:-- 0:00:09 --:--:-- 17842 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 6755648 spots for /home/okishinya/chipatlas/results/ce10/SRX1388779/SRR2832495.sra Written 6755648 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: 00:01:52 6755648 reads; of these: 6755648 (100.00%) were unpaired; of these: 401099 (5.94%) aligned 0 times 4919557 (72.82%) aligned exactly 1 time 1434992 (21.24%) aligned >1 times 94.06% overall alignment rate Time searching: 00:01:52 Overall time: 00:01:52 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] 491603 / 6354549 = 0.0774 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 04:18:35: # Command line: callpeak -t SRX1388779.bam -f BAM -g ce -n SRX1388779.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX1388779.05 # format = BAM # ChIP-seq file = ['SRX1388779.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 04:18:35: #1 read tag files... INFO @ Sat, 03 Jun 2017 04:18:35: #1 read treatment tags... INFO @ Sat, 03 Jun 2017 04:18:35: # Command line: callpeak -t SRX1388779.bam -f BAM -g ce -n SRX1388779.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX1388779.20 # format = BAM # ChIP-seq file = ['SRX1388779.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 04:18:35: #1 read tag files... INFO @ Sat, 03 Jun 2017 04:18:35: #1 read treatment tags... INFO @ Sat, 03 Jun 2017 04:18:35: # Command line: callpeak -t SRX1388779.bam -f BAM -g ce -n SRX1388779.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX1388779.10 # format = BAM # ChIP-seq file = ['SRX1388779.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 04:18:35: #1 read tag files... INFO @ Sat, 03 Jun 2017 04:18:35: #1 read treatment tags... INFO @ Sat, 03 Jun 2017 04:18:41: 1000000 INFO @ Sat, 03 Jun 2017 04:18:41: 1000000 INFO @ Sat, 03 Jun 2017 04:18:41: 1000000 INFO @ Sat, 03 Jun 2017 04:18:47: 2000000 INFO @ Sat, 03 Jun 2017 04:18:48: 2000000 INFO @ Sat, 03 Jun 2017 04:18:48: 2000000 INFO @ Sat, 03 Jun 2017 04:18:52: 3000000 INFO @ Sat, 03 Jun 2017 04:18:54: 3000000 INFO @ Sat, 03 Jun 2017 04:18:54: 3000000 INFO @ Sat, 03 Jun 2017 04:18:58: 4000000 INFO @ Sat, 03 Jun 2017 04:19:01: 4000000 INFO @ Sat, 03 Jun 2017 04:19:01: 4000000 INFO @ Sat, 03 Jun 2017 04:19:04: 5000000 INFO @ Sat, 03 Jun 2017 04:19:07: 5000000 INFO @ Sat, 03 Jun 2017 04:19:07: 5000000 INFO @ Sat, 03 Jun 2017 04:19:09: #1 tag size is determined as 50 bps INFO @ Sat, 03 Jun 2017 04:19:09: #1 tag size = 50 INFO @ Sat, 03 Jun 2017 04:19:09: #1 total tags in treatment: 5862946 INFO @ Sat, 03 Jun 2017 04:19:09: #1 user defined the maximum tags... INFO @ Sat, 03 Jun 2017 04:19:09: #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 04:19:10: #1 tags after filtering in treatment: 5861945 INFO @ Sat, 03 Jun 2017 04:19:10: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 03 Jun 2017 04:19:10: #1 finished! INFO @ Sat, 03 Jun 2017 04:19:10: #2 Build Peak Model... INFO @ Sat, 03 Jun 2017 04:19:11: #2 number of paired peaks: 492 WARNING @ Sat, 03 Jun 2017 04:19:11: Fewer paired peaks (492) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 492 pairs to build model! INFO @ Sat, 03 Jun 2017 04:19:11: start model_add_line... INFO @ Sat, 03 Jun 2017 04:19:12: #1 tag size is determined as 50 bps INFO @ Sat, 03 Jun 2017 04:19:12: #1 tag size = 50 INFO @ Sat, 03 Jun 2017 04:19:12: #1 total tags in treatment: 5862946 INFO @ Sat, 03 Jun 2017 04:19:12: #1 user defined the maximum tags... INFO @ Sat, 03 Jun 2017 04:19:12: #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 04:19:12: #1 tag size is determined as 50 bps INFO @ Sat, 03 Jun 2017 04:19:12: #1 tag size = 50 INFO @ Sat, 03 Jun 2017 04:19:12: #1 total tags in treatment: 5862946 INFO @ Sat, 03 Jun 2017 04:19:12: #1 user defined the maximum tags... INFO @ Sat, 03 Jun 2017 04:19:12: #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 04:19:14: #1 tags after filtering in treatment: 5861945 INFO @ Sat, 03 Jun 2017 04:19:14: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 03 Jun 2017 04:19:14: #1 finished! INFO @ Sat, 03 Jun 2017 04:19:14: #2 Build Peak Model... INFO @ Sat, 03 Jun 2017 04:19:14: #1 tags after filtering in treatment: 5861945 INFO @ Sat, 03 Jun 2017 04:19:14: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 03 Jun 2017 04:19:14: #1 finished! INFO @ Sat, 03 Jun 2017 04:19:14: #2 Build Peak Model... INFO @ Sat, 03 Jun 2017 04:19:15: #2 number of paired peaks: 492 WARNING @ Sat, 03 Jun 2017 04:19:15: Fewer paired peaks (492) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 492 pairs to build model! INFO @ Sat, 03 Jun 2017 04:19:15: start model_add_line... INFO @ Sat, 03 Jun 2017 04:19:15: #2 number of paired peaks: 492 WARNING @ Sat, 03 Jun 2017 04:19:15: Fewer paired peaks (492) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 492 pairs to build model! INFO @ Sat, 03 Jun 2017 04:19:15: start model_add_line... INFO @ Sat, 03 Jun 2017 04:19:16: start X-correlation... INFO @ Sat, 03 Jun 2017 04:19:16: end of X-cor INFO @ Sat, 03 Jun 2017 04:19:16: #2 finished! INFO @ Sat, 03 Jun 2017 04:19:16: #2 predicted fragment length is 48 bps INFO @ Sat, 03 Jun 2017 04:19:16: #2 alternative fragment length(s) may be 4,48 bps INFO @ Sat, 03 Jun 2017 04:19:16: #2.2 Generate R script for model : SRX1388779.20_model.r WARNING @ Sat, 03 Jun 2017 04:19:16: #2 Since the d (48) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 03 Jun 2017 04:19:16: #2 You may need to consider one of the other alternative d(s): 4,48 WARNING @ Sat, 03 Jun 2017 04:19:16: #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 04:19:16: #3 Call peaks... INFO @ Sat, 03 Jun 2017 04:19:16: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Jun 2017 04:19:19: start X-correlation... INFO @ Sat, 03 Jun 2017 04:19:19: end of X-cor INFO @ Sat, 03 Jun 2017 04:19:19: #2 finished! INFO @ Sat, 03 Jun 2017 04:19:19: #2 predicted fragment length is 48 bps INFO @ Sat, 03 Jun 2017 04:19:19: #2 alternative fragment length(s) may be 4,48 bps INFO @ Sat, 03 Jun 2017 04:19:19: #2.2 Generate R script for model : SRX1388779.05_model.r WARNING @ Sat, 03 Jun 2017 04:19:19: #2 Since the d (48) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 03 Jun 2017 04:19:19: #2 You may need to consider one of the other alternative d(s): 4,48 WARNING @ Sat, 03 Jun 2017 04:19:19: #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 04:19:19: #3 Call peaks... INFO @ Sat, 03 Jun 2017 04:19:19: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Jun 2017 04:19:20: start X-correlation... INFO @ Sat, 03 Jun 2017 04:19:20: end of X-cor INFO @ Sat, 03 Jun 2017 04:19:20: #2 finished! INFO @ Sat, 03 Jun 2017 04:19:20: #2 predicted fragment length is 48 bps INFO @ Sat, 03 Jun 2017 04:19:20: #2 alternative fragment length(s) may be 4,48 bps INFO @ Sat, 03 Jun 2017 04:19:20: #2.2 Generate R script for model : SRX1388779.10_model.r WARNING @ Sat, 03 Jun 2017 04:19:20: #2 Since the d (48) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 03 Jun 2017 04:19:20: #2 You may need to consider one of the other alternative d(s): 4,48 WARNING @ Sat, 03 Jun 2017 04:19:20: #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 04:19:20: #3 Call peaks... INFO @ Sat, 03 Jun 2017 04:19:20: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Jun 2017 04:19:50: #3 Call peaks for each chromosome... INFO @ Sat, 03 Jun 2017 04:19:53: #3 Call peaks for each chromosome... INFO @ Sat, 03 Jun 2017 04:19:54: #3 Call peaks for each chromosome... INFO @ Sat, 03 Jun 2017 04:20:14: #4 Write output xls file... SRX1388779.20_peaks.xls INFO @ Sat, 03 Jun 2017 04:20:14: #4 Write peak in narrowPeak format file... SRX1388779.20_peaks.narrowPeak INFO @ Sat, 03 Jun 2017 04:20:14: #4 Write summits bed file... SRX1388779.20_summits.bed INFO @ Sat, 03 Jun 2017 04:20:14: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (164 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Sat, 03 Jun 2017 04:20:16: #4 Write output xls file... SRX1388779.10_peaks.xls INFO @ Sat, 03 Jun 2017 04:20:16: #4 Write peak in narrowPeak format file... SRX1388779.10_peaks.narrowPeak INFO @ Sat, 03 Jun 2017 04:20:16: #4 Write summits bed file... SRX1388779.10_summits.bed INFO @ Sat, 03 Jun 2017 04:20:16: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (388 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Sat, 03 Jun 2017 04:20:19: #4 Write output xls file... SRX1388779.05_peaks.xls INFO @ Sat, 03 Jun 2017 04:20:19: #4 Write peak in narrowPeak format file... SRX1388779.05_peaks.narrowPeak INFO @ Sat, 03 Jun 2017 04:20:19: #4 Write summits bed file... SRX1388779.05_summits.bed INFO @ Sat, 03 Jun 2017 04:20:19: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (599 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。