Job ID = 2237055 sra ファイルのダウンロード中... Completed: 384450K bytes transferred in 8 seconds (370095K 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 --:--:-- --:--:-- --:--:-- 0 100 9082 0 9082 0 0 16483 0 --:--:-- --:--:-- --:--:-- 25227 100 35221 0 35221 0 0 47537 0 --:--:-- --:--:-- --:--:-- 64038 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 17659150 spots for /home/okishinya/chipatlas/results/ce10/SRX094514/SRR340088.sra Written 17659150 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: 00:03:32 17659150 reads; of these: 17659150 (100.00%) were unpaired; of these: 1071535 (6.07%) aligned 0 times 13654657 (77.32%) aligned exactly 1 time 2932958 (16.61%) aligned >1 times 93.93% overall alignment rate Time searching: 00:03:32 Overall time: 00:03:32 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_sort_core] merging from 8 files... [bam_rmdupse_core] 8207924 / 16587615 = 0.4948 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 @ Thu, 30 Apr 2015 11:32:49: # Command line: callpeak -t SRX094514.bam -f BAM -g ce -n SRX094514.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX094514.05 # format = BAM # ChIP-seq file = ['SRX094514.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 @ Thu, 30 Apr 2015 11:32:49: #1 read tag files... INFO @ Thu, 30 Apr 2015 11:32:49: # Command line: callpeak -t SRX094514.bam -f BAM -g ce -n SRX094514.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX094514.20 # format = BAM # ChIP-seq file = ['SRX094514.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 @ Thu, 30 Apr 2015 11:32:49: #1 read treatment tags... INFO @ Thu, 30 Apr 2015 11:32:49: #1 read tag files... INFO @ Thu, 30 Apr 2015 11:32:49: # Command line: callpeak -t SRX094514.bam -f BAM -g ce -n SRX094514.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX094514.10 # format = BAM # ChIP-seq file = ['SRX094514.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 @ Thu, 30 Apr 2015 11:32:49: #1 read treatment tags... INFO @ Thu, 30 Apr 2015 11:32:49: #1 read tag files... INFO @ Thu, 30 Apr 2015 11:32:49: #1 read treatment tags... INFO @ Thu, 30 Apr 2015 11:32:56: 1000000 INFO @ Thu, 30 Apr 2015 11:32:56: 1000000 INFO @ Thu, 30 Apr 2015 11:32:56: 1000000 INFO @ Thu, 30 Apr 2015 11:33:03: 2000000 INFO @ Thu, 30 Apr 2015 11:33:03: 2000000 INFO @ Thu, 30 Apr 2015 11:33:03: 2000000 INFO @ Thu, 30 Apr 2015 11:33:09: 3000000 INFO @ Thu, 30 Apr 2015 11:33:09: 3000000 INFO @ Thu, 30 Apr 2015 11:33:09: 3000000 INFO @ Thu, 30 Apr 2015 11:33:16: 4000000 INFO @ Thu, 30 Apr 2015 11:33:16: 4000000 INFO @ Thu, 30 Apr 2015 11:33:16: 4000000 INFO @ Thu, 30 Apr 2015 11:33:22: 5000000 INFO @ Thu, 30 Apr 2015 11:33:22: 5000000 INFO @ Thu, 30 Apr 2015 11:33:22: 5000000 INFO @ Thu, 30 Apr 2015 11:33:28: 6000000 INFO @ Thu, 30 Apr 2015 11:33:28: 6000000 INFO @ Thu, 30 Apr 2015 11:33:28: 6000000 INFO @ Thu, 30 Apr 2015 11:33:34: 7000000 INFO @ Thu, 30 Apr 2015 11:33:34: 7000000 INFO @ Thu, 30 Apr 2015 11:33:34: 7000000 INFO @ Thu, 30 Apr 2015 11:33:40: 8000000 INFO @ Thu, 30 Apr 2015 11:33:40: 8000000 INFO @ Thu, 30 Apr 2015 11:33:40: 8000000 INFO @ Thu, 30 Apr 2015 11:33:42: #1 tag size is determined as 36 bps INFO @ Thu, 30 Apr 2015 11:33:42: #1 tag size = 36 INFO @ Thu, 30 Apr 2015 11:33:42: #1 total tags in treatment: 8379691 INFO @ Thu, 30 Apr 2015 11:33:42: #1 user defined the maximum tags... INFO @ Thu, 30 Apr 2015 11:33:42: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Thu, 30 Apr 2015 11:33:42: #1 tag size is determined as 36 bps INFO @ Thu, 30 Apr 2015 11:33:42: #1 tag size = 36 INFO @ Thu, 30 Apr 2015 11:33:42: #1 total tags in treatment: 8379691 INFO @ Thu, 30 Apr 2015 11:33:42: #1 user defined the maximum tags... INFO @ Thu, 30 Apr 2015 11:33:42: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Thu, 30 Apr 2015 11:33:42: #1 tag size is determined as 36 bps INFO @ Thu, 30 Apr 2015 11:33:42: #1 tag size = 36 INFO @ Thu, 30 Apr 2015 11:33:42: #1 total tags in treatment: 8379691 INFO @ Thu, 30 Apr 2015 11:33:42: #1 user defined the maximum tags... INFO @ Thu, 30 Apr 2015 11:33:42: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Thu, 30 Apr 2015 11:33:44: #1 tags after filtering in treatment: 8379186 INFO @ Thu, 30 Apr 2015 11:33:44: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 30 Apr 2015 11:33:44: #1 finished! INFO @ Thu, 30 Apr 2015 11:33:44: #2 Build Peak Model... INFO @ Thu, 30 Apr 2015 11:33:44: #1 tags after filtering in treatment: 8379186 INFO @ Thu, 30 Apr 2015 11:33:44: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 30 Apr 2015 11:33:44: #1 finished! INFO @ Thu, 30 Apr 2015 11:33:44: #2 Build Peak Model... INFO @ Thu, 30 Apr 2015 11:33:44: #1 tags after filtering in treatment: 8379186 INFO @ Thu, 30 Apr 2015 11:33:44: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 30 Apr 2015 11:33:44: #1 finished! INFO @ Thu, 30 Apr 2015 11:33:44: #2 Build Peak Model... INFO @ Thu, 30 Apr 2015 11:33:45: #2 number of paired peaks: 579 WARNING @ Thu, 30 Apr 2015 11:33:45: Fewer paired peaks (579) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 579 pairs to build model! INFO @ Thu, 30 Apr 2015 11:33:45: start model_add_line... INFO @ Thu, 30 Apr 2015 11:33:45: #2 number of paired peaks: 579 WARNING @ Thu, 30 Apr 2015 11:33:45: Fewer paired peaks (579) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 579 pairs to build model! INFO @ Thu, 30 Apr 2015 11:33:45: start model_add_line... INFO @ Thu, 30 Apr 2015 11:33:45: #2 number of paired peaks: 579 WARNING @ Thu, 30 Apr 2015 11:33:45: Fewer paired peaks (579) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 579 pairs to build model! INFO @ Thu, 30 Apr 2015 11:33:45: start model_add_line... INFO @ Thu, 30 Apr 2015 11:33:52: start X-correlation... INFO @ Thu, 30 Apr 2015 11:33:52: end of X-cor INFO @ Thu, 30 Apr 2015 11:33:52: #2 finished! INFO @ Thu, 30 Apr 2015 11:33:52: #2 predicted fragment length is 38 bps INFO @ Thu, 30 Apr 2015 11:33:52: #2 alternative fragment length(s) may be 3,38 bps INFO @ Thu, 30 Apr 2015 11:33:52: #2.2 Generate R script for model : SRX094514.10_model.r WARNING @ Thu, 30 Apr 2015 11:33:52: #2 Since the d (38) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 30 Apr 2015 11:33:52: #2 You may need to consider one of the other alternative d(s): 3,38 WARNING @ Thu, 30 Apr 2015 11:33:52: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Thu, 30 Apr 2015 11:33:52: #3 Call peaks... INFO @ Thu, 30 Apr 2015 11:33:52: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 30 Apr 2015 11:33:52: start X-correlation... INFO @ Thu, 30 Apr 2015 11:33:52: end of X-cor INFO @ Thu, 30 Apr 2015 11:33:52: #2 finished! INFO @ Thu, 30 Apr 2015 11:33:52: #2 predicted fragment length is 38 bps INFO @ Thu, 30 Apr 2015 11:33:52: #2 alternative fragment length(s) may be 3,38 bps INFO @ Thu, 30 Apr 2015 11:33:52: #2.2 Generate R script for model : SRX094514.05_model.r WARNING @ Thu, 30 Apr 2015 11:33:52: #2 Since the d (38) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 30 Apr 2015 11:33:52: #2 You may need to consider one of the other alternative d(s): 3,38 WARNING @ Thu, 30 Apr 2015 11:33:52: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Thu, 30 Apr 2015 11:33:52: #3 Call peaks... INFO @ Thu, 30 Apr 2015 11:33:52: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 30 Apr 2015 11:33:52: start X-correlation... INFO @ Thu, 30 Apr 2015 11:33:52: end of X-cor INFO @ Thu, 30 Apr 2015 11:33:52: #2 finished! INFO @ Thu, 30 Apr 2015 11:33:52: #2 predicted fragment length is 38 bps INFO @ Thu, 30 Apr 2015 11:33:52: #2 alternative fragment length(s) may be 3,38 bps INFO @ Thu, 30 Apr 2015 11:33:52: #2.2 Generate R script for model : SRX094514.20_model.r WARNING @ Thu, 30 Apr 2015 11:33:52: #2 Since the d (38) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 30 Apr 2015 11:33:52: #2 You may need to consider one of the other alternative d(s): 3,38 WARNING @ Thu, 30 Apr 2015 11:33:52: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Thu, 30 Apr 2015 11:33:52: #3 Call peaks... INFO @ Thu, 30 Apr 2015 11:33:52: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 30 Apr 2015 11:34:38: #3 Call peaks for each chromosome... INFO @ Thu, 30 Apr 2015 11:34:38: #3 Call peaks for each chromosome... INFO @ Thu, 30 Apr 2015 11:34:39: #3 Call peaks for each chromosome... INFO @ Thu, 30 Apr 2015 11:35:10: #4 Write output xls file... SRX094514.20_peaks.xls INFO @ Thu, 30 Apr 2015 11:35:10: #4 Write peak in narrowPeak format file... SRX094514.20_peaks.narrowPeak INFO @ Thu, 30 Apr 2015 11:35:10: #4 Write summits bed file... SRX094514.20_summits.bed INFO @ Thu, 30 Apr 2015 11:35:10: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (171 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Thu, 30 Apr 2015 11:35:10: #4 Write output xls file... SRX094514.05_peaks.xls INFO @ Thu, 30 Apr 2015 11:35:10: #4 Write peak in narrowPeak format file... SRX094514.05_peaks.narrowPeak INFO @ Thu, 30 Apr 2015 11:35:10: #4 Write summits bed file... SRX094514.05_summits.bed INFO @ Thu, 30 Apr 2015 11:35:10: Done! pass1 - making usageList (7 chroms): 0 millis pass2 - checking and writing primary data (852 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Thu, 30 Apr 2015 11:35:11: #4 Write output xls file... SRX094514.10_peaks.xls INFO @ Thu, 30 Apr 2015 11:35:11: #4 Write peak in narrowPeak format file... SRX094514.10_peaks.narrowPeak INFO @ Thu, 30 Apr 2015 11:35:11: #4 Write summits bed file... SRX094514.10_summits.bed INFO @ Thu, 30 Apr 2015 11:35:11: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (514 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。