Job ID = 10845161 sra ファイルのダウンロード中... Completed: 134647K bytes transferred in 14 seconds (77669K 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... Read 2751401 spots for /home/okishinya/chipatlas/results/dm3/SRX2642377/SRR5345717.sra Written 2751401 spots for /home/okishinya/chipatlas/results/dm3/SRX2642377/SRR5345717.sra 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: 00:00:01 Time loading forward index: 00:00:00 Time loading mirror index: 00:00:00 Multiseed full-index search: 00:01:40 2751401 reads; of these: 2751401 (100.00%) were unpaired; of these: 436832 (15.88%) aligned 0 times 1723949 (62.66%) aligned exactly 1 time 590620 (21.47%) aligned >1 times 84.12% overall alignment rate Time searching: 00:01:41 Overall time: 00:01:41 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] 112813 / 2314569 = 0.0487 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, 04 Jul 2018 09:28:39: # Command line: callpeak -t SRX2642377.bam -f BAM -g dm -n SRX2642377.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX2642377.05 # format = BAM # ChIP-seq file = ['SRX2642377.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, 04 Jul 2018 09:28:39: # Command line: callpeak -t SRX2642377.bam -f BAM -g dm -n SRX2642377.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX2642377.10 # format = BAM # ChIP-seq file = ['SRX2642377.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, 04 Jul 2018 09:28:39: # Command line: callpeak -t SRX2642377.bam -f BAM -g dm -n SRX2642377.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX2642377.20 # format = BAM # ChIP-seq file = ['SRX2642377.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, 04 Jul 2018 09:28:39: #1 read tag files... INFO @ Wed, 04 Jul 2018 09:28:39: #1 read tag files... INFO @ Wed, 04 Jul 2018 09:28:39: #1 read tag files... INFO @ Wed, 04 Jul 2018 09:28:39: #1 read treatment tags... INFO @ Wed, 04 Jul 2018 09:28:39: #1 read treatment tags... INFO @ Wed, 04 Jul 2018 09:28:39: #1 read treatment tags... INFO @ Wed, 04 Jul 2018 09:28:47: 1000000 INFO @ Wed, 04 Jul 2018 09:28:47: 1000000 INFO @ Wed, 04 Jul 2018 09:28:47: 1000000 INFO @ Wed, 04 Jul 2018 09:28:55: 2000000 INFO @ Wed, 04 Jul 2018 09:28:55: 2000000 INFO @ Wed, 04 Jul 2018 09:28:55: 2000000 INFO @ Wed, 04 Jul 2018 09:28:56: #1 tag size is determined as 99 bps INFO @ Wed, 04 Jul 2018 09:28:56: #1 tag size = 99 INFO @ Wed, 04 Jul 2018 09:28:56: #1 total tags in treatment: 2201756 INFO @ Wed, 04 Jul 2018 09:28:56: #1 user defined the maximum tags... INFO @ Wed, 04 Jul 2018 09:28:56: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Wed, 04 Jul 2018 09:28:56: #1 tags after filtering in treatment: 2201756 INFO @ Wed, 04 Jul 2018 09:28:56: #1 Redundant rate of treatment: 0.00 INFO @ Wed, 04 Jul 2018 09:28:56: #1 finished! INFO @ Wed, 04 Jul 2018 09:28:56: #2 Build Peak Model... INFO @ Wed, 04 Jul 2018 09:28:56: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 04 Jul 2018 09:28:56: #1 tag size is determined as 99 bps INFO @ Wed, 04 Jul 2018 09:28:56: #1 tag size = 99 INFO @ Wed, 04 Jul 2018 09:28:56: #1 total tags in treatment: 2201756 INFO @ Wed, 04 Jul 2018 09:28:56: #1 user defined the maximum tags... INFO @ Wed, 04 Jul 2018 09:28:56: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Wed, 04 Jul 2018 09:28:56: #1 tags after filtering in treatment: 2201756 INFO @ Wed, 04 Jul 2018 09:28:56: #1 Redundant rate of treatment: 0.00 INFO @ Wed, 04 Jul 2018 09:28:56: #1 finished! INFO @ Wed, 04 Jul 2018 09:28:56: #2 Build Peak Model... INFO @ Wed, 04 Jul 2018 09:28:56: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 04 Jul 2018 09:28:57: #1 tag size is determined as 99 bps INFO @ Wed, 04 Jul 2018 09:28:57: #1 tag size = 99 INFO @ Wed, 04 Jul 2018 09:28:57: #1 total tags in treatment: 2201756 INFO @ Wed, 04 Jul 2018 09:28:57: #1 user defined the maximum tags... INFO @ Wed, 04 Jul 2018 09:28:57: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Wed, 04 Jul 2018 09:28:57: #1 tags after filtering in treatment: 2201756 INFO @ Wed, 04 Jul 2018 09:28:57: #1 Redundant rate of treatment: 0.00 INFO @ Wed, 04 Jul 2018 09:28:57: #1 finished! INFO @ Wed, 04 Jul 2018 09:28:57: #2 Build Peak Model... INFO @ Wed, 04 Jul 2018 09:28:57: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 04 Jul 2018 09:28:57: #2 number of paired peaks: 1939 INFO @ Wed, 04 Jul 2018 09:28:57: start model_add_line... INFO @ Wed, 04 Jul 2018 09:28:57: start X-correlation... INFO @ Wed, 04 Jul 2018 09:28:57: #2 number of paired peaks: 1939 INFO @ Wed, 04 Jul 2018 09:28:57: start model_add_line... INFO @ Wed, 04 Jul 2018 09:28:57: start X-correlation... INFO @ Wed, 04 Jul 2018 09:28:57: #2 number of paired peaks: 1939 INFO @ Wed, 04 Jul 2018 09:28:57: start model_add_line... INFO @ Wed, 04 Jul 2018 09:28:57: start X-correlation... INFO @ Wed, 04 Jul 2018 09:28:57: end of X-cor INFO @ Wed, 04 Jul 2018 09:28:57: end of X-cor INFO @ Wed, 04 Jul 2018 09:28:57: end of X-cor INFO @ Wed, 04 Jul 2018 09:28:57: #2 finished! INFO @ Wed, 04 Jul 2018 09:28:57: #2 finished! INFO @ Wed, 04 Jul 2018 09:28:57: #2 finished! INFO @ Wed, 04 Jul 2018 09:28:57: #2 predicted fragment length is 109 bps INFO @ Wed, 04 Jul 2018 09:28:57: #2 predicted fragment length is 109 bps INFO @ Wed, 04 Jul 2018 09:28:57: #2 predicted fragment length is 109 bps INFO @ Wed, 04 Jul 2018 09:28:57: #2 alternative fragment length(s) may be 109 bps INFO @ Wed, 04 Jul 2018 09:28:57: #2 alternative fragment length(s) may be 109 bps INFO @ Wed, 04 Jul 2018 09:28:57: #2 alternative fragment length(s) may be 109 bps INFO @ Wed, 04 Jul 2018 09:28:57: #2.2 Generate R script for model : SRX2642377.05_model.r INFO @ Wed, 04 Jul 2018 09:28:57: #2.2 Generate R script for model : SRX2642377.10_model.r INFO @ Wed, 04 Jul 2018 09:28:57: #2.2 Generate R script for model : SRX2642377.20_model.r WARNING @ Wed, 04 Jul 2018 09:28:57: #2 Since the d (109) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Wed, 04 Jul 2018 09:28:57: #2 You may need to consider one of the other alternative d(s): 109 WARNING @ Wed, 04 Jul 2018 09:28:57: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Wed, 04 Jul 2018 09:28:57: #3 Call peaks... WARNING @ Wed, 04 Jul 2018 09:28:57: #2 Since the d (109) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Wed, 04 Jul 2018 09:28:57: #2 You may need to consider one of the other alternative d(s): 109 WARNING @ Wed, 04 Jul 2018 09:28:57: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Wed, 04 Jul 2018 09:28:57: #3 Call peaks... WARNING @ Wed, 04 Jul 2018 09:28:57: #2 Since the d (109) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Wed, 04 Jul 2018 09:28:57: #2 You may need to consider one of the other alternative d(s): 109 WARNING @ Wed, 04 Jul 2018 09:28:57: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Wed, 04 Jul 2018 09:28:57: #3 Call peaks... INFO @ Wed, 04 Jul 2018 09:28:57: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 04 Jul 2018 09:28:57: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 04 Jul 2018 09:28:57: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 04 Jul 2018 09:29:02: #3 Call peaks for each chromosome... INFO @ Wed, 04 Jul 2018 09:29:02: #3 Call peaks for each chromosome... INFO @ Wed, 04 Jul 2018 09:29:03: #3 Call peaks for each chromosome... INFO @ Wed, 04 Jul 2018 09:29:05: #4 Write output xls file... SRX2642377.20_peaks.xls INFO @ Wed, 04 Jul 2018 09:29:05: #4 Write peak in narrowPeak format file... SRX2642377.20_peaks.narrowPeak INFO @ Wed, 04 Jul 2018 09:29:05: #4 Write summits bed file... SRX2642377.20_summits.bed INFO @ Wed, 04 Jul 2018 09:29:05: Done! pass1 - making usageList (5 chroms): 1 millis pass2 - checking and writing primary data (221 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Wed, 04 Jul 2018 09:29:05: #4 Write output xls file... SRX2642377.10_peaks.xls INFO @ Wed, 04 Jul 2018 09:29:05: #4 Write peak in narrowPeak format file... SRX2642377.10_peaks.narrowPeak INFO @ Wed, 04 Jul 2018 09:29:05: #4 Write summits bed file... SRX2642377.10_summits.bed INFO @ Wed, 04 Jul 2018 09:29:05: Done! pass1 - making usageList (8 chroms): 1 millis pass2 - checking and writing primary data (365 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Wed, 04 Jul 2018 09:29:05: #4 Write output xls file... SRX2642377.05_peaks.xls INFO @ Wed, 04 Jul 2018 09:29:05: #4 Write peak in narrowPeak format file... SRX2642377.05_peaks.narrowPeak INFO @ Wed, 04 Jul 2018 09:29:05: #4 Write summits bed file... SRX2642377.05_summits.bed INFO @ Wed, 04 Jul 2018 09:29:05: Done! pass1 - making usageList (11 chroms): 1 millis pass2 - checking and writing primary data (567 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。