Job ID = 9028905 sra ファイルのダウンロード中... Completed: 202893K bytes transferred in 5 seconds (328972K 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 --:--:-- 0 100 13455 0 13455 0 0 1733 0 --:--:-- 0:00:07 --:--:-- 11297 100 33142 0 33142 0 0 3857 0 --:--:-- 0:00:08 --:--:-- 16406 100 52257 0 52257 0 0 5748 0 --:--:-- 0:00:09 --:--:-- 20745 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 6259067 spots for /home/okishinya/chipatlas/results/ce10/SRX982102/SRR1956589.sra Written 6259067 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: 00:01:44 6259067 reads; of these: 6259067 (100.00%) were unpaired; of these: 291327 (4.65%) aligned 0 times 5049778 (80.68%) aligned exactly 1 time 917962 (14.67%) aligned >1 times 95.35% overall alignment rate Time searching: 00:01:44 Overall time: 00:01:44 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] 274456 / 5967740 = 0.0460 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 12:21:19: # Command line: callpeak -t SRX982102.bam -f BAM -g ce -n SRX982102.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX982102.05 # format = BAM # ChIP-seq file = ['SRX982102.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 12:21:19: #1 read tag files... INFO @ Sat, 03 Jun 2017 12:21:19: #1 read treatment tags... INFO @ Sat, 03 Jun 2017 12:21:19: # Command line: callpeak -t SRX982102.bam -f BAM -g ce -n SRX982102.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX982102.10 # format = BAM # ChIP-seq file = ['SRX982102.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 12:21:19: #1 read tag files... INFO @ Sat, 03 Jun 2017 12:21:19: #1 read treatment tags... INFO @ Sat, 03 Jun 2017 12:21:19: # Command line: callpeak -t SRX982102.bam -f BAM -g ce -n SRX982102.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX982102.20 # format = BAM # ChIP-seq file = ['SRX982102.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 12:21:19: #1 read tag files... INFO @ Sat, 03 Jun 2017 12:21:19: #1 read treatment tags... INFO @ Sat, 03 Jun 2017 12:21:24: 1000000 INFO @ Sat, 03 Jun 2017 12:21:24: 1000000 INFO @ Sat, 03 Jun 2017 12:21:25: 1000000 INFO @ Sat, 03 Jun 2017 12:21:30: 2000000 INFO @ Sat, 03 Jun 2017 12:21:30: 2000000 INFO @ Sat, 03 Jun 2017 12:21:32: 2000000 INFO @ Sat, 03 Jun 2017 12:21:35: 3000000 INFO @ Sat, 03 Jun 2017 12:21:36: 3000000 INFO @ Sat, 03 Jun 2017 12:21:39: 3000000 INFO @ Sat, 03 Jun 2017 12:21:41: 4000000 INFO @ Sat, 03 Jun 2017 12:21:42: 4000000 INFO @ Sat, 03 Jun 2017 12:21:46: 4000000 INFO @ Sat, 03 Jun 2017 12:21:46: 5000000 INFO @ Sat, 03 Jun 2017 12:21:48: 5000000 INFO @ Sat, 03 Jun 2017 12:21:50: #1 tag size is determined as 51 bps INFO @ Sat, 03 Jun 2017 12:21:50: #1 tag size = 51 INFO @ Sat, 03 Jun 2017 12:21:50: #1 total tags in treatment: 5693284 INFO @ Sat, 03 Jun 2017 12:21:50: #1 user defined the maximum tags... INFO @ Sat, 03 Jun 2017 12:21:50: #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 12:21:51: #1 tags after filtering in treatment: 5692800 INFO @ Sat, 03 Jun 2017 12:21:51: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 03 Jun 2017 12:21:51: #1 finished! INFO @ Sat, 03 Jun 2017 12:21:51: #2 Build Peak Model... INFO @ Sat, 03 Jun 2017 12:21:52: 5000000 INFO @ Sat, 03 Jun 2017 12:21:52: #1 tag size is determined as 51 bps INFO @ Sat, 03 Jun 2017 12:21:52: #1 tag size = 51 INFO @ Sat, 03 Jun 2017 12:21:52: #1 total tags in treatment: 5693284 INFO @ Sat, 03 Jun 2017 12:21:52: #1 user defined the maximum tags... INFO @ Sat, 03 Jun 2017 12:21:52: #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 12:21:52: #2 number of paired peaks: 311 WARNING @ Sat, 03 Jun 2017 12:21:52: Fewer paired peaks (311) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 311 pairs to build model! INFO @ Sat, 03 Jun 2017 12:21:52: start model_add_line... INFO @ Sat, 03 Jun 2017 12:21:53: #1 tags after filtering in treatment: 5692800 INFO @ Sat, 03 Jun 2017 12:21:53: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 03 Jun 2017 12:21:53: #1 finished! INFO @ Sat, 03 Jun 2017 12:21:53: #2 Build Peak Model... INFO @ Sat, 03 Jun 2017 12:21:54: #2 number of paired peaks: 311 WARNING @ Sat, 03 Jun 2017 12:21:54: Fewer paired peaks (311) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 311 pairs to build model! INFO @ Sat, 03 Jun 2017 12:21:54: start model_add_line... INFO @ Sat, 03 Jun 2017 12:21:55: start X-correlation... INFO @ Sat, 03 Jun 2017 12:21:55: end of X-cor INFO @ Sat, 03 Jun 2017 12:21:55: #2 finished! INFO @ Sat, 03 Jun 2017 12:21:55: #2 predicted fragment length is 49 bps INFO @ Sat, 03 Jun 2017 12:21:55: #2 alternative fragment length(s) may be 49 bps INFO @ Sat, 03 Jun 2017 12:21:55: #2.2 Generate R script for model : SRX982102.10_model.r WARNING @ Sat, 03 Jun 2017 12:21:55: #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 12:21:55: #2 You may need to consider one of the other alternative d(s): 49 WARNING @ Sat, 03 Jun 2017 12:21:55: #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 12:21:55: #3 Call peaks... INFO @ Sat, 03 Jun 2017 12:21:55: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Jun 2017 12:21:56: #1 tag size is determined as 51 bps INFO @ Sat, 03 Jun 2017 12:21:56: #1 tag size = 51 INFO @ Sat, 03 Jun 2017 12:21:56: #1 total tags in treatment: 5693284 INFO @ Sat, 03 Jun 2017 12:21:56: #1 user defined the maximum tags... INFO @ Sat, 03 Jun 2017 12:21:56: #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 12:21:57: #1 tags after filtering in treatment: 5692800 INFO @ Sat, 03 Jun 2017 12:21:57: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 03 Jun 2017 12:21:57: #1 finished! INFO @ Sat, 03 Jun 2017 12:21:57: #2 Build Peak Model... INFO @ Sat, 03 Jun 2017 12:21:57: start X-correlation... INFO @ Sat, 03 Jun 2017 12:21:57: end of X-cor INFO @ Sat, 03 Jun 2017 12:21:57: #2 finished! INFO @ Sat, 03 Jun 2017 12:21:57: #2 predicted fragment length is 49 bps INFO @ Sat, 03 Jun 2017 12:21:57: #2 alternative fragment length(s) may be 49 bps INFO @ Sat, 03 Jun 2017 12:21:57: #2.2 Generate R script for model : SRX982102.05_model.r WARNING @ Sat, 03 Jun 2017 12:21:57: #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 12:21:57: #2 You may need to consider one of the other alternative d(s): 49 WARNING @ Sat, 03 Jun 2017 12:21:57: #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 12:21:57: #3 Call peaks... INFO @ Sat, 03 Jun 2017 12:21:57: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Jun 2017 12:21:58: #2 number of paired peaks: 311 WARNING @ Sat, 03 Jun 2017 12:21:58: Fewer paired peaks (311) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 311 pairs to build model! INFO @ Sat, 03 Jun 2017 12:21:58: start model_add_line... INFO @ Sat, 03 Jun 2017 12:22:01: start X-correlation... INFO @ Sat, 03 Jun 2017 12:22:01: end of X-cor INFO @ Sat, 03 Jun 2017 12:22:01: #2 finished! INFO @ Sat, 03 Jun 2017 12:22:01: #2 predicted fragment length is 49 bps INFO @ Sat, 03 Jun 2017 12:22:01: #2 alternative fragment length(s) may be 49 bps INFO @ Sat, 03 Jun 2017 12:22:01: #2.2 Generate R script for model : SRX982102.20_model.r WARNING @ Sat, 03 Jun 2017 12:22:01: #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 12:22:01: #2 You may need to consider one of the other alternative d(s): 49 WARNING @ Sat, 03 Jun 2017 12:22:01: #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 12:22:01: #3 Call peaks... INFO @ Sat, 03 Jun 2017 12:22:01: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Jun 2017 12:22:29: #3 Call peaks for each chromosome... INFO @ Sat, 03 Jun 2017 12:22:31: #3 Call peaks for each chromosome... INFO @ Sat, 03 Jun 2017 12:22:34: #3 Call peaks for each chromosome... INFO @ Sat, 03 Jun 2017 12:22:53: #4 Write output xls file... SRX982102.10_peaks.xls INFO @ Sat, 03 Jun 2017 12:22:53: #4 Write peak in narrowPeak format file... SRX982102.10_peaks.narrowPeak INFO @ Sat, 03 Jun 2017 12:22:53: #4 Write summits bed file... SRX982102.10_summits.bed INFO @ Sat, 03 Jun 2017 12:22:53: Done! pass1 - making usageList (6 chroms): 6 millis pass2 - checking and writing primary data (257 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Sat, 03 Jun 2017 12:22:54: #4 Write output xls file... SRX982102.05_peaks.xls INFO @ Sat, 03 Jun 2017 12:22:54: #4 Write peak in narrowPeak format file... SRX982102.05_peaks.narrowPeak INFO @ Sat, 03 Jun 2017 12:22:54: #4 Write summits bed file... SRX982102.05_summits.bed INFO @ Sat, 03 Jun 2017 12:22:54: Done! pass1 - making usageList (7 chroms): 0 millis pass2 - checking and writing primary data (438 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Sat, 03 Jun 2017 12:22:59: #4 Write output xls file... SRX982102.20_peaks.xls INFO @ Sat, 03 Jun 2017 12:22:59: #4 Write peak in narrowPeak format file... SRX982102.20_peaks.narrowPeak INFO @ Sat, 03 Jun 2017 12:22:59: #4 Write summits bed file... SRX982102.20_summits.bed INFO @ Sat, 03 Jun 2017 12:22:59: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (102 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。