Job ID = 9028859 sra ファイルのダウンロード中... Completed: 315309K bytes transferred in 6 seconds (426872K bits/sec), in 2 files, 3 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 1778 0 --:--:-- 0:00:08 --:--:-- 8869 100 55622 0 55622 0 0 6145 0 --:--:-- 0:00:09 --:--:-- 21311 100 61167 0 61167 0 0 6757 0 --:--:-- 0:00:09 --:--:-- 23426 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 5330567 spots for /home/okishinya/chipatlas/results/ce10/SRX982081/SRR1956565.sra Written 5330567 spots total Written 6203332 spots for /home/okishinya/chipatlas/results/ce10/SRX982081/SRR1956566.sra Written 6203332 spots total 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: 00:02:48 11533899 reads; of these: 11533899 (100.00%) were unpaired; of these: 3837054 (33.27%) aligned 0 times 6277485 (54.43%) aligned exactly 1 time 1419360 (12.31%) aligned >1 times 66.73% overall alignment rate Time searching: 00:02:48 Overall time: 00:02:48 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] 554768 / 7696845 = 0.0721 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 12:08:55: # Command line: callpeak -t SRX982081.bam -f BAM -g ce -n SRX982081.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX982081.05 # format = BAM # ChIP-seq file = ['SRX982081.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 12:08:55: #1 read tag files... INFO @ Sat, 03 Jun 2017 12:08:55: #1 read treatment tags... INFO @ Sat, 03 Jun 2017 12:08:55: # Command line: callpeak -t SRX982081.bam -f BAM -g ce -n SRX982081.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX982081.10 # format = BAM # ChIP-seq file = ['SRX982081.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 12:08:55: #1 read tag files... INFO @ Sat, 03 Jun 2017 12:08:55: #1 read treatment tags... INFO @ Sat, 03 Jun 2017 12:08:55: # Command line: callpeak -t SRX982081.bam -f BAM -g ce -n SRX982081.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX982081.20 # format = BAM # ChIP-seq file = ['SRX982081.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 12:08:55: #1 read tag files... INFO @ Sat, 03 Jun 2017 12:08:55: #1 read treatment tags... INFO @ Sat, 03 Jun 2017 12:09:02: 1000000 INFO @ Sat, 03 Jun 2017 12:09:02: 1000000 INFO @ Sat, 03 Jun 2017 12:09:02: 1000000 INFO @ Sat, 03 Jun 2017 12:09:08: 2000000 INFO @ Sat, 03 Jun 2017 12:09:09: 2000000 INFO @ Sat, 03 Jun 2017 12:09:09: 2000000 INFO @ Sat, 03 Jun 2017 12:09:16: 3000000 INFO @ Sat, 03 Jun 2017 12:09:17: 3000000 INFO @ Sat, 03 Jun 2017 12:09:17: 3000000 INFO @ Sat, 03 Jun 2017 12:09:25: 4000000 INFO @ Sat, 03 Jun 2017 12:09:25: 4000000 INFO @ Sat, 03 Jun 2017 12:09:25: 4000000 INFO @ Sat, 03 Jun 2017 12:09:33: 5000000 INFO @ Sat, 03 Jun 2017 12:09:34: 5000000 INFO @ Sat, 03 Jun 2017 12:09:34: 5000000 INFO @ Sat, 03 Jun 2017 12:09:41: 6000000 INFO @ Sat, 03 Jun 2017 12:09:42: 6000000 INFO @ Sat, 03 Jun 2017 12:09:42: 6000000 INFO @ Sat, 03 Jun 2017 12:09:49: 7000000 INFO @ Sat, 03 Jun 2017 12:09:50: 7000000 INFO @ Sat, 03 Jun 2017 12:09:50: 7000000 INFO @ Sat, 03 Jun 2017 12:09:51: #1 tag size is determined as 51 bps INFO @ Sat, 03 Jun 2017 12:09:51: #1 tag size = 51 INFO @ Sat, 03 Jun 2017 12:09:51: #1 total tags in treatment: 7142077 INFO @ Sat, 03 Jun 2017 12:09:51: #1 user defined the maximum tags... INFO @ Sat, 03 Jun 2017 12:09:51: #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 12:09:51: #1 tag size is determined as 51 bps INFO @ Sat, 03 Jun 2017 12:09:51: #1 tag size = 51 INFO @ Sat, 03 Jun 2017 12:09:51: #1 total tags in treatment: 7142077 INFO @ Sat, 03 Jun 2017 12:09:51: #1 user defined the maximum tags... INFO @ Sat, 03 Jun 2017 12:09:51: #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 12:09:51: #1 tag size is determined as 51 bps INFO @ Sat, 03 Jun 2017 12:09:51: #1 tag size = 51 INFO @ Sat, 03 Jun 2017 12:09:51: #1 total tags in treatment: 7142077 INFO @ Sat, 03 Jun 2017 12:09:51: #1 user defined the maximum tags... INFO @ Sat, 03 Jun 2017 12:09:51: #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 12:09:52: #1 tags after filtering in treatment: 7140153 INFO @ Sat, 03 Jun 2017 12:09:52: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 03 Jun 2017 12:09:52: #1 finished! INFO @ Sat, 03 Jun 2017 12:09:52: #2 Build Peak Model... INFO @ Sat, 03 Jun 2017 12:09:53: #1 tags after filtering in treatment: 7140153 INFO @ Sat, 03 Jun 2017 12:09:53: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 03 Jun 2017 12:09:53: #1 finished! INFO @ Sat, 03 Jun 2017 12:09:53: #2 Build Peak Model... INFO @ Sat, 03 Jun 2017 12:09:53: #1 tags after filtering in treatment: 7140153 INFO @ Sat, 03 Jun 2017 12:09:53: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 03 Jun 2017 12:09:53: #1 finished! INFO @ Sat, 03 Jun 2017 12:09:53: #2 Build Peak Model... INFO @ Sat, 03 Jun 2017 12:09:53: #2 number of paired peaks: 374 WARNING @ Sat, 03 Jun 2017 12:09:53: Fewer paired peaks (374) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 374 pairs to build model! INFO @ Sat, 03 Jun 2017 12:09:53: start model_add_line... INFO @ Sat, 03 Jun 2017 12:09:54: #2 number of paired peaks: 374 WARNING @ Sat, 03 Jun 2017 12:09:54: Fewer paired peaks (374) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 374 pairs to build model! INFO @ Sat, 03 Jun 2017 12:09:54: start model_add_line... INFO @ Sat, 03 Jun 2017 12:09:54: #2 number of paired peaks: 374 WARNING @ Sat, 03 Jun 2017 12:09:54: Fewer paired peaks (374) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 374 pairs to build model! INFO @ Sat, 03 Jun 2017 12:09:54: start model_add_line... INFO @ Sat, 03 Jun 2017 12:09:57: start X-correlation... INFO @ Sat, 03 Jun 2017 12:09:57: end of X-cor INFO @ Sat, 03 Jun 2017 12:09:57: #2 finished! INFO @ Sat, 03 Jun 2017 12:09:57: #2 predicted fragment length is 51 bps INFO @ Sat, 03 Jun 2017 12:09:57: #2 alternative fragment length(s) may be 4,51,510,544,577 bps INFO @ Sat, 03 Jun 2017 12:09:57: #2.2 Generate R script for model : SRX982081.20_model.r WARNING @ Sat, 03 Jun 2017 12:09:57: #2 Since the d (51) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 03 Jun 2017 12:09:57: #2 You may need to consider one of the other alternative d(s): 4,51,510,544,577 WARNING @ Sat, 03 Jun 2017 12:09:57: #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 12:09:57: #3 Call peaks... INFO @ Sat, 03 Jun 2017 12:09:57: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Jun 2017 12:09:58: start X-correlation... INFO @ Sat, 03 Jun 2017 12:09:58: end of X-cor INFO @ Sat, 03 Jun 2017 12:09:58: #2 finished! INFO @ Sat, 03 Jun 2017 12:09:58: #2 predicted fragment length is 51 bps INFO @ Sat, 03 Jun 2017 12:09:58: #2 alternative fragment length(s) may be 4,51,510,544,577 bps INFO @ Sat, 03 Jun 2017 12:09:58: #2.2 Generate R script for model : SRX982081.05_model.r WARNING @ Sat, 03 Jun 2017 12:09:58: #2 Since the d (51) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 03 Jun 2017 12:09:58: #2 You may need to consider one of the other alternative d(s): 4,51,510,544,577 WARNING @ Sat, 03 Jun 2017 12:09:58: #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 12:09:58: #3 Call peaks... INFO @ Sat, 03 Jun 2017 12:09:58: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Jun 2017 12:09:58: start X-correlation... INFO @ Sat, 03 Jun 2017 12:09:58: end of X-cor INFO @ Sat, 03 Jun 2017 12:09:58: #2 finished! INFO @ Sat, 03 Jun 2017 12:09:58: #2 predicted fragment length is 51 bps INFO @ Sat, 03 Jun 2017 12:09:58: #2 alternative fragment length(s) may be 4,51,510,544,577 bps INFO @ Sat, 03 Jun 2017 12:09:58: #2.2 Generate R script for model : SRX982081.10_model.r WARNING @ Sat, 03 Jun 2017 12:09:58: #2 Since the d (51) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 03 Jun 2017 12:09:58: #2 You may need to consider one of the other alternative d(s): 4,51,510,544,577 WARNING @ Sat, 03 Jun 2017 12:09:58: #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 12:09:58: #3 Call peaks... INFO @ Sat, 03 Jun 2017 12:09:58: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Jun 2017 12:10:38: #3 Call peaks for each chromosome... INFO @ Sat, 03 Jun 2017 12:10:40: #3 Call peaks for each chromosome... INFO @ Sat, 03 Jun 2017 12:10:43: #3 Call peaks for each chromosome... INFO @ Sat, 03 Jun 2017 12:11:06: #4 Write output xls file... SRX982081.05_peaks.xls INFO @ Sat, 03 Jun 2017 12:11:06: #4 Write peak in narrowPeak format file... SRX982081.05_peaks.narrowPeak INFO @ Sat, 03 Jun 2017 12:11:06: #4 Write summits bed file... SRX982081.05_summits.bed INFO @ Sat, 03 Jun 2017 12:11:06: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (597 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Sat, 03 Jun 2017 12:11:10: #4 Write output xls file... SRX982081.10_peaks.xls INFO @ Sat, 03 Jun 2017 12:11:10: #4 Write peak in narrowPeak format file... SRX982081.10_peaks.narrowPeak INFO @ Sat, 03 Jun 2017 12:11:10: #4 Write summits bed file... SRX982081.10_summits.bed INFO @ Sat, 03 Jun 2017 12:11:10: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (361 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Sat, 03 Jun 2017 12:11:15: #4 Write output xls file... SRX982081.20_peaks.xls INFO @ Sat, 03 Jun 2017 12:11:15: #4 Write peak in narrowPeak format file... SRX982081.20_peaks.narrowPeak INFO @ Sat, 03 Jun 2017 12:11:15: #4 Write summits bed file... SRX982081.20_summits.bed INFO @ Sat, 03 Jun 2017 12:11:15: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (160 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。