Job ID = 9157406 sra ファイルのダウンロード中... Completed: 605663K bytes transferred in 7 seconds (658296K bits/sec), in 1 file, 2 directories. 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 18415218 spots for /home/okishinya/chipatlas/results/ce10/SRX208770/SRR628904.sra Written 18415218 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: 00:06:03 18415218 reads; of these: 18415218 (100.00%) were unpaired; of these: 2749355 (14.93%) aligned 0 times 13632561 (74.03%) aligned exactly 1 time 2033302 (11.04%) aligned >1 times 85.07% overall alignment rate Time searching: 00:06:03 Overall time: 00:06:03 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] 8229650 / 15665863 = 0.5253 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 @ Tue, 27 Jun 2017 11:56:22: # Command line: callpeak -t SRX208770.bam -f BAM -g ce -n SRX208770.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX208770.05 # format = BAM # ChIP-seq file = ['SRX208770.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 # Paired-End mode is off INFO @ Tue, 27 Jun 2017 11:56:22: #1 read tag files... INFO @ Tue, 27 Jun 2017 11:56:22: #1 read treatment tags... INFO @ Tue, 27 Jun 2017 11:56:22: # Command line: callpeak -t SRX208770.bam -f BAM -g ce -n SRX208770.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX208770.20 # format = BAM # ChIP-seq file = ['SRX208770.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 # Paired-End mode is off INFO @ Tue, 27 Jun 2017 11:56:22: #1 read tag files... INFO @ Tue, 27 Jun 2017 11:56:22: #1 read treatment tags... INFO @ Tue, 27 Jun 2017 11:56:22: # Command line: callpeak -t SRX208770.bam -f BAM -g ce -n SRX208770.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX208770.10 # format = BAM # ChIP-seq file = ['SRX208770.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 # Paired-End mode is off INFO @ Tue, 27 Jun 2017 11:56:22: #1 read tag files... INFO @ Tue, 27 Jun 2017 11:56:22: #1 read treatment tags... INFO @ Tue, 27 Jun 2017 11:56:29: 1000000 INFO @ Tue, 27 Jun 2017 11:56:29: 1000000 INFO @ Tue, 27 Jun 2017 11:56:29: 1000000 INFO @ Tue, 27 Jun 2017 11:56:36: 2000000 INFO @ Tue, 27 Jun 2017 11:56:36: 2000000 INFO @ Tue, 27 Jun 2017 11:56:36: 2000000 INFO @ Tue, 27 Jun 2017 11:56:43: 3000000 INFO @ Tue, 27 Jun 2017 11:56:43: 3000000 INFO @ Tue, 27 Jun 2017 11:56:43: 3000000 INFO @ Tue, 27 Jun 2017 11:56:50: 4000000 INFO @ Tue, 27 Jun 2017 11:56:50: 4000000 INFO @ Tue, 27 Jun 2017 11:56:51: 4000000 INFO @ Tue, 27 Jun 2017 11:56:57: 5000000 INFO @ Tue, 27 Jun 2017 11:56:57: 5000000 INFO @ Tue, 27 Jun 2017 11:56:58: 5000000 INFO @ Tue, 27 Jun 2017 11:57:04: 6000000 INFO @ Tue, 27 Jun 2017 11:57:04: 6000000 INFO @ Tue, 27 Jun 2017 11:57:05: 6000000 INFO @ Tue, 27 Jun 2017 11:57:11: 7000000 INFO @ Tue, 27 Jun 2017 11:57:11: 7000000 INFO @ Tue, 27 Jun 2017 11:57:12: 7000000 INFO @ Tue, 27 Jun 2017 11:57:14: #1 tag size is determined as 50 bps INFO @ Tue, 27 Jun 2017 11:57:14: #1 tag size = 50 INFO @ Tue, 27 Jun 2017 11:57:14: #1 total tags in treatment: 7436213 INFO @ Tue, 27 Jun 2017 11:57:14: #1 user defined the maximum tags... INFO @ Tue, 27 Jun 2017 11:57:14: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 27 Jun 2017 11:57:14: #1 tag size is determined as 50 bps INFO @ Tue, 27 Jun 2017 11:57:14: #1 tag size = 50 INFO @ Tue, 27 Jun 2017 11:57:14: #1 total tags in treatment: 7436213 INFO @ Tue, 27 Jun 2017 11:57:14: #1 user defined the maximum tags... INFO @ Tue, 27 Jun 2017 11:57:14: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 27 Jun 2017 11:57:14: #1 tags after filtering in treatment: 7436213 INFO @ Tue, 27 Jun 2017 11:57:14: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 27 Jun 2017 11:57:14: #1 finished! INFO @ Tue, 27 Jun 2017 11:57:14: #2 Build Peak Model... INFO @ Tue, 27 Jun 2017 11:57:14: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 27 Jun 2017 11:57:14: #1 tags after filtering in treatment: 7436213 INFO @ Tue, 27 Jun 2017 11:57:14: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 27 Jun 2017 11:57:14: #1 finished! INFO @ Tue, 27 Jun 2017 11:57:14: #2 Build Peak Model... INFO @ Tue, 27 Jun 2017 11:57:14: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 27 Jun 2017 11:57:15: #2 number of paired peaks: 128 WARNING @ Tue, 27 Jun 2017 11:57:15: Fewer paired peaks (128) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 128 pairs to build model! INFO @ Tue, 27 Jun 2017 11:57:15: start model_add_line... INFO @ Tue, 27 Jun 2017 11:57:15: start X-correlation... INFO @ Tue, 27 Jun 2017 11:57:15: end of X-cor INFO @ Tue, 27 Jun 2017 11:57:15: #2 finished! INFO @ Tue, 27 Jun 2017 11:57:15: #2 predicted fragment length is 55 bps INFO @ Tue, 27 Jun 2017 11:57:15: #2 alternative fragment length(s) may be 1,55,110,144,157,232,253,513,569,574 bps INFO @ Tue, 27 Jun 2017 11:57:15: #2.2 Generate R script for model : SRX208770.10_model.r WARNING @ Tue, 27 Jun 2017 11:57:15: #2 Since the d (55) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 27 Jun 2017 11:57:15: #2 You may need to consider one of the other alternative d(s): 1,55,110,144,157,232,253,513,569,574 WARNING @ Tue, 27 Jun 2017 11:57:15: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 27 Jun 2017 11:57:15: #3 Call peaks... INFO @ Tue, 27 Jun 2017 11:57:15: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 27 Jun 2017 11:57:15: #1 tag size is determined as 50 bps INFO @ Tue, 27 Jun 2017 11:57:15: #1 tag size = 50 INFO @ Tue, 27 Jun 2017 11:57:15: #1 total tags in treatment: 7436213 INFO @ Tue, 27 Jun 2017 11:57:15: #1 user defined the maximum tags... INFO @ Tue, 27 Jun 2017 11:57:15: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 27 Jun 2017 11:57:15: #2 number of paired peaks: 128 WARNING @ Tue, 27 Jun 2017 11:57:15: Fewer paired peaks (128) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 128 pairs to build model! INFO @ Tue, 27 Jun 2017 11:57:15: start model_add_line... INFO @ Tue, 27 Jun 2017 11:57:15: #1 tags after filtering in treatment: 7436213 INFO @ Tue, 27 Jun 2017 11:57:15: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 27 Jun 2017 11:57:15: #1 finished! INFO @ Tue, 27 Jun 2017 11:57:15: #2 Build Peak Model... INFO @ Tue, 27 Jun 2017 11:57:15: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 27 Jun 2017 11:57:15: start X-correlation... INFO @ Tue, 27 Jun 2017 11:57:15: end of X-cor INFO @ Tue, 27 Jun 2017 11:57:15: #2 finished! INFO @ Tue, 27 Jun 2017 11:57:15: #2 predicted fragment length is 55 bps INFO @ Tue, 27 Jun 2017 11:57:15: #2 alternative fragment length(s) may be 1,55,110,144,157,232,253,513,569,574 bps INFO @ Tue, 27 Jun 2017 11:57:15: #2.2 Generate R script for model : SRX208770.20_model.r WARNING @ Tue, 27 Jun 2017 11:57:15: #2 Since the d (55) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 27 Jun 2017 11:57:15: #2 You may need to consider one of the other alternative d(s): 1,55,110,144,157,232,253,513,569,574 WARNING @ Tue, 27 Jun 2017 11:57:15: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 27 Jun 2017 11:57:15: #3 Call peaks... INFO @ Tue, 27 Jun 2017 11:57:15: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 27 Jun 2017 11:57:16: #2 number of paired peaks: 128 WARNING @ Tue, 27 Jun 2017 11:57:16: Fewer paired peaks (128) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 128 pairs to build model! INFO @ Tue, 27 Jun 2017 11:57:16: start model_add_line... INFO @ Tue, 27 Jun 2017 11:57:16: start X-correlation... INFO @ Tue, 27 Jun 2017 11:57:16: end of X-cor INFO @ Tue, 27 Jun 2017 11:57:16: #2 finished! INFO @ Tue, 27 Jun 2017 11:57:16: #2 predicted fragment length is 55 bps INFO @ Tue, 27 Jun 2017 11:57:16: #2 alternative fragment length(s) may be 1,55,110,144,157,232,253,513,569,574 bps INFO @ Tue, 27 Jun 2017 11:57:16: #2.2 Generate R script for model : SRX208770.05_model.r WARNING @ Tue, 27 Jun 2017 11:57:16: #2 Since the d (55) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 27 Jun 2017 11:57:16: #2 You may need to consider one of the other alternative d(s): 1,55,110,144,157,232,253,513,569,574 WARNING @ Tue, 27 Jun 2017 11:57:16: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 27 Jun 2017 11:57:16: #3 Call peaks... INFO @ Tue, 27 Jun 2017 11:57:16: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 27 Jun 2017 11:57:30: #3 Call peaks for each chromosome... INFO @ Tue, 27 Jun 2017 11:57:31: #3 Call peaks for each chromosome... INFO @ Tue, 27 Jun 2017 11:57:32: #3 Call peaks for each chromosome... INFO @ Tue, 27 Jun 2017 11:57:39: #4 Write output xls file... SRX208770.10_peaks.xls INFO @ Tue, 27 Jun 2017 11:57:39: #4 Write peak in narrowPeak format file... SRX208770.10_peaks.narrowPeak INFO @ Tue, 27 Jun 2017 11:57:39: #4 Write summits bed file... SRX208770.10_summits.bed INFO @ Tue, 27 Jun 2017 11:57:39: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (60 records, 4 fields): 1 millis CompletedMACS2peakCalling INFO @ Tue, 27 Jun 2017 11:57:40: #4 Write output xls file... SRX208770.20_peaks.xls INFO @ Tue, 27 Jun 2017 11:57:40: #4 Write peak in narrowPeak format file... SRX208770.20_peaks.narrowPeak INFO @ Tue, 27 Jun 2017 11:57:40: #4 Write summits bed file... SRX208770.20_summits.bed INFO @ Tue, 27 Jun 2017 11:57:40: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (8 records, 4 fields): 1 millis CompletedMACS2peakCalling INFO @ Tue, 27 Jun 2017 11:57:42: #4 Write output xls file... SRX208770.05_peaks.xls INFO @ Tue, 27 Jun 2017 11:57:42: #4 Write peak in narrowPeak format file... SRX208770.05_peaks.narrowPeak INFO @ Tue, 27 Jun 2017 11:57:42: #4 Write summits bed file... SRX208770.05_summits.bed INFO @ Tue, 27 Jun 2017 11:57:42: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (257 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。