Job ID = 10450980 sra ファイルのダウンロード中... Completed: 138683K bytes transferred in 9 seconds (123402K bits/sec), in 1 file. 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 6525567 spots for /home/okishinya/chipatlas/results/dm3/SRX3404041/SRR6303518.sra Written 6525567 spots total rm: cannot remove `[DSE]RX*': そのようなファイルやディレクトリはありません 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: 00:06:02 6525567 reads; of these: 6525567 (100.00%) were unpaired; of these: 659986 (10.11%) aligned 0 times 1690384 (25.90%) aligned exactly 1 time 4175197 (63.98%) aligned >1 times 89.89% overall alignment rate Time searching: 00:06:02 Overall time: 00:06:02 マッピングが完了しました。 samtools でBAM に変換中... [samopen] SAM header is present: 15 sequences. [bam_rmdupse_core] 3136814 / 5865581 = 0.5348 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 @ Wed, 07 Feb 2018 16:05:00: # Command line: callpeak -t SRX3404041.bam -f BAM -g dm -n SRX3404041.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX3404041.20 # format = BAM # ChIP-seq file = ['SRX3404041.bam'] # control file = None # effective genome size = 1.20e+08 # 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 @ Wed, 07 Feb 2018 16:05:00: #1 read tag files... INFO @ Wed, 07 Feb 2018 16:05:00: #1 read treatment tags... INFO @ Wed, 07 Feb 2018 16:05:00: # Command line: callpeak -t SRX3404041.bam -f BAM -g dm -n SRX3404041.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX3404041.10 # format = BAM # ChIP-seq file = ['SRX3404041.bam'] # control file = None # effective genome size = 1.20e+08 # 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 @ Wed, 07 Feb 2018 16:05:00: #1 read tag files... INFO @ Wed, 07 Feb 2018 16:05:00: #1 read treatment tags... INFO @ Wed, 07 Feb 2018 16:05:00: # Command line: callpeak -t SRX3404041.bam -f BAM -g dm -n SRX3404041.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX3404041.05 # format = BAM # ChIP-seq file = ['SRX3404041.bam'] # control file = None # effective genome size = 1.20e+08 # 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 @ Wed, 07 Feb 2018 16:05:00: #1 read tag files... INFO @ Wed, 07 Feb 2018 16:05:00: #1 read treatment tags... INFO @ Wed, 07 Feb 2018 16:05:08: 1000000 INFO @ Wed, 07 Feb 2018 16:05:08: 1000000 INFO @ Wed, 07 Feb 2018 16:05:09: 1000000 INFO @ Wed, 07 Feb 2018 16:05:17: 2000000 INFO @ Wed, 07 Feb 2018 16:05:17: 2000000 INFO @ Wed, 07 Feb 2018 16:05:19: 2000000 INFO @ Wed, 07 Feb 2018 16:05:23: #1 tag size is determined as 51 bps INFO @ Wed, 07 Feb 2018 16:05:23: #1 tag size = 51 INFO @ Wed, 07 Feb 2018 16:05:23: #1 total tags in treatment: 2728767 INFO @ Wed, 07 Feb 2018 16:05:23: #1 user defined the maximum tags... INFO @ Wed, 07 Feb 2018 16:05:23: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Wed, 07 Feb 2018 16:05:23: #1 tags after filtering in treatment: 2728767 INFO @ Wed, 07 Feb 2018 16:05:23: #1 Redundant rate of treatment: 0.00 INFO @ Wed, 07 Feb 2018 16:05:23: #1 finished! INFO @ Wed, 07 Feb 2018 16:05:23: #2 Build Peak Model... INFO @ Wed, 07 Feb 2018 16:05:23: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 07 Feb 2018 16:05:23: #2 number of paired peaks: 2128 INFO @ Wed, 07 Feb 2018 16:05:23: start model_add_line... INFO @ Wed, 07 Feb 2018 16:05:23: start X-correlation... INFO @ Wed, 07 Feb 2018 16:05:23: end of X-cor INFO @ Wed, 07 Feb 2018 16:05:23: #2 finished! INFO @ Wed, 07 Feb 2018 16:05:23: #2 predicted fragment length is 53 bps INFO @ Wed, 07 Feb 2018 16:05:23: #2 alternative fragment length(s) may be 53 bps INFO @ Wed, 07 Feb 2018 16:05:23: #2.2 Generate R script for model : SRX3404041.10_model.r WARNING @ Wed, 07 Feb 2018 16:05:23: #2 Since the d (53) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Wed, 07 Feb 2018 16:05:23: #2 You may need to consider one of the other alternative d(s): 53 WARNING @ Wed, 07 Feb 2018 16:05:23: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Wed, 07 Feb 2018 16:05:23: #3 Call peaks... INFO @ Wed, 07 Feb 2018 16:05:23: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 07 Feb 2018 16:05:23: #1 tag size is determined as 51 bps INFO @ Wed, 07 Feb 2018 16:05:23: #1 tag size = 51 INFO @ Wed, 07 Feb 2018 16:05:23: #1 total tags in treatment: 2728767 INFO @ Wed, 07 Feb 2018 16:05:23: #1 user defined the maximum tags... INFO @ Wed, 07 Feb 2018 16:05:23: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Wed, 07 Feb 2018 16:05:23: #1 tags after filtering in treatment: 2728767 INFO @ Wed, 07 Feb 2018 16:05:23: #1 Redundant rate of treatment: 0.00 INFO @ Wed, 07 Feb 2018 16:05:23: #1 finished! INFO @ Wed, 07 Feb 2018 16:05:23: #2 Build Peak Model... INFO @ Wed, 07 Feb 2018 16:05:23: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 07 Feb 2018 16:05:24: #2 number of paired peaks: 2128 INFO @ Wed, 07 Feb 2018 16:05:24: start model_add_line... INFO @ Wed, 07 Feb 2018 16:05:24: start X-correlation... INFO @ Wed, 07 Feb 2018 16:05:24: end of X-cor INFO @ Wed, 07 Feb 2018 16:05:24: #2 finished! INFO @ Wed, 07 Feb 2018 16:05:24: #2 predicted fragment length is 53 bps INFO @ Wed, 07 Feb 2018 16:05:24: #2 alternative fragment length(s) may be 53 bps INFO @ Wed, 07 Feb 2018 16:05:24: #2.2 Generate R script for model : SRX3404041.20_model.r WARNING @ Wed, 07 Feb 2018 16:05:24: #2 Since the d (53) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Wed, 07 Feb 2018 16:05:24: #2 You may need to consider one of the other alternative d(s): 53 WARNING @ Wed, 07 Feb 2018 16:05:24: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Wed, 07 Feb 2018 16:05:24: #3 Call peaks... INFO @ Wed, 07 Feb 2018 16:05:24: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 07 Feb 2018 16:05:25: #1 tag size is determined as 51 bps INFO @ Wed, 07 Feb 2018 16:05:25: #1 tag size = 51 INFO @ Wed, 07 Feb 2018 16:05:25: #1 total tags in treatment: 2728767 INFO @ Wed, 07 Feb 2018 16:05:25: #1 user defined the maximum tags... INFO @ Wed, 07 Feb 2018 16:05:25: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Wed, 07 Feb 2018 16:05:25: #1 tags after filtering in treatment: 2728767 INFO @ Wed, 07 Feb 2018 16:05:25: #1 Redundant rate of treatment: 0.00 INFO @ Wed, 07 Feb 2018 16:05:25: #1 finished! INFO @ Wed, 07 Feb 2018 16:05:25: #2 Build Peak Model... INFO @ Wed, 07 Feb 2018 16:05:25: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 07 Feb 2018 16:05:25: #2 number of paired peaks: 2128 INFO @ Wed, 07 Feb 2018 16:05:25: start model_add_line... INFO @ Wed, 07 Feb 2018 16:05:25: start X-correlation... INFO @ Wed, 07 Feb 2018 16:05:25: end of X-cor INFO @ Wed, 07 Feb 2018 16:05:25: #2 finished! INFO @ Wed, 07 Feb 2018 16:05:25: #2 predicted fragment length is 53 bps INFO @ Wed, 07 Feb 2018 16:05:25: #2 alternative fragment length(s) may be 53 bps INFO @ Wed, 07 Feb 2018 16:05:25: #2.2 Generate R script for model : SRX3404041.05_model.r WARNING @ Wed, 07 Feb 2018 16:05:25: #2 Since the d (53) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Wed, 07 Feb 2018 16:05:25: #2 You may need to consider one of the other alternative d(s): 53 WARNING @ Wed, 07 Feb 2018 16:05:25: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Wed, 07 Feb 2018 16:05:25: #3 Call peaks... INFO @ Wed, 07 Feb 2018 16:05:25: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 07 Feb 2018 16:05:30: #3 Call peaks for each chromosome... INFO @ Wed, 07 Feb 2018 16:05:31: #3 Call peaks for each chromosome... INFO @ Wed, 07 Feb 2018 16:05:32: #3 Call peaks for each chromosome... INFO @ Wed, 07 Feb 2018 16:05:34: #4 Write output xls file... SRX3404041.10_peaks.xls INFO @ Wed, 07 Feb 2018 16:05:34: #4 Write peak in narrowPeak format file... SRX3404041.10_peaks.narrowPeak INFO @ Wed, 07 Feb 2018 16:05:34: #4 Write summits bed file... SRX3404041.10_summits.bed INFO @ Wed, 07 Feb 2018 16:05:34: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (1844 records, 4 fields): 4 millis CompletedMACS2peakCalling INFO @ Wed, 07 Feb 2018 16:05:35: #4 Write output xls file... SRX3404041.20_peaks.xls INFO @ Wed, 07 Feb 2018 16:05:35: #4 Write peak in narrowPeak format file... SRX3404041.20_peaks.narrowPeak INFO @ Wed, 07 Feb 2018 16:05:35: #4 Write summits bed file... SRX3404041.20_summits.bed INFO @ Wed, 07 Feb 2018 16:05:35: Done! pass1 - making usageList (12 chroms): 1 millis pass2 - checking and writing primary data (1276 records, 4 fields): 4 millis CompletedMACS2peakCalling INFO @ Wed, 07 Feb 2018 16:05:36: #4 Write output xls file... SRX3404041.05_peaks.xls INFO @ Wed, 07 Feb 2018 16:05:36: #4 Write peak in narrowPeak format file... SRX3404041.05_peaks.narrowPeak INFO @ Wed, 07 Feb 2018 16:05:36: #4 Write summits bed file... SRX3404041.05_summits.bed INFO @ Wed, 07 Feb 2018 16:05:36: Done! pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (2607 records, 4 fields): 6 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。