Job ID = 11597776 sra ファイルのダウンロード中... Completed: 337842K bytes transferred in 6 seconds (454457K 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 13476376 spots for /home/okishinya/chipatlas/results/dm3/ERX1430244/ERR1358769.sra Written 13476376 spots for /home/okishinya/chipatlas/results/dm3/ERX1430244/ERR1358769.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: 00:00:00 Time loading forward index: 00:00:00 Time loading mirror index: 00:00:00 Multiseed full-index search: 00:05:07 13476376 reads; of these: 13476376 (100.00%) were unpaired; of these: 661671 (4.91%) aligned 0 times 9484929 (70.38%) aligned exactly 1 time 3329776 (24.71%) aligned >1 times 95.09% overall alignment rate Time searching: 00:05:07 Overall time: 00:05:07 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] 8540596 / 12814705 = 0.6665 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, 30 Jan 2019 14:48:00: # Command line: callpeak -t ERX1430244.bam -f BAM -g dm -n ERX1430244.10 -q 1e-10 # ARGUMENTS LIST: # name = ERX1430244.10 # format = BAM # ChIP-seq file = ['ERX1430244.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, 30 Jan 2019 14:48:00: #1 read tag files... INFO @ Wed, 30 Jan 2019 14:48:00: #1 read treatment tags... INFO @ Wed, 30 Jan 2019 14:48:00: # Command line: callpeak -t ERX1430244.bam -f BAM -g dm -n ERX1430244.20 -q 1e-20 # ARGUMENTS LIST: # name = ERX1430244.20 # format = BAM # ChIP-seq file = ['ERX1430244.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, 30 Jan 2019 14:48:00: #1 read tag files... INFO @ Wed, 30 Jan 2019 14:48:00: #1 read treatment tags... INFO @ Wed, 30 Jan 2019 14:48:00: # Command line: callpeak -t ERX1430244.bam -f BAM -g dm -n ERX1430244.05 -q 1e-05 # ARGUMENTS LIST: # name = ERX1430244.05 # format = BAM # ChIP-seq file = ['ERX1430244.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, 30 Jan 2019 14:48:00: #1 read tag files... INFO @ Wed, 30 Jan 2019 14:48:00: #1 read treatment tags... INFO @ Wed, 30 Jan 2019 14:48:06: 1000000 INFO @ Wed, 30 Jan 2019 14:48:06: 1000000 INFO @ Wed, 30 Jan 2019 14:48:06: 1000000 INFO @ Wed, 30 Jan 2019 14:48:12: 2000000 INFO @ Wed, 30 Jan 2019 14:48:12: 2000000 INFO @ Wed, 30 Jan 2019 14:48:12: 2000000 INFO @ Wed, 30 Jan 2019 14:48:18: 3000000 INFO @ Wed, 30 Jan 2019 14:48:18: 3000000 INFO @ Wed, 30 Jan 2019 14:48:18: 3000000 INFO @ Wed, 30 Jan 2019 14:48:24: 4000000 INFO @ Wed, 30 Jan 2019 14:48:24: 4000000 INFO @ Wed, 30 Jan 2019 14:48:24: 4000000 INFO @ Wed, 30 Jan 2019 14:48:25: #1 tag size is determined as 44 bps INFO @ Wed, 30 Jan 2019 14:48:25: #1 tag size = 44 INFO @ Wed, 30 Jan 2019 14:48:25: #1 total tags in treatment: 4274109 INFO @ Wed, 30 Jan 2019 14:48:25: #1 user defined the maximum tags... INFO @ Wed, 30 Jan 2019 14:48:25: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Wed, 30 Jan 2019 14:48:25: #1 tags after filtering in treatment: 4274109 INFO @ Wed, 30 Jan 2019 14:48:25: #1 Redundant rate of treatment: 0.00 INFO @ Wed, 30 Jan 2019 14:48:25: #1 finished! INFO @ Wed, 30 Jan 2019 14:48:25: #2 Build Peak Model... INFO @ Wed, 30 Jan 2019 14:48:25: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 30 Jan 2019 14:48:26: #2 number of paired peaks: 1235 INFO @ Wed, 30 Jan 2019 14:48:26: start model_add_line... INFO @ Wed, 30 Jan 2019 14:48:26: start X-correlation... INFO @ Wed, 30 Jan 2019 14:48:26: end of X-cor INFO @ Wed, 30 Jan 2019 14:48:26: #2 finished! INFO @ Wed, 30 Jan 2019 14:48:26: #2 predicted fragment length is 50 bps INFO @ Wed, 30 Jan 2019 14:48:26: #2 alternative fragment length(s) may be 50 bps INFO @ Wed, 30 Jan 2019 14:48:26: #2.2 Generate R script for model : ERX1430244.10_model.r WARNING @ Wed, 30 Jan 2019 14:48:26: #2 Since the d (50) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Wed, 30 Jan 2019 14:48:26: #2 You may need to consider one of the other alternative d(s): 50 WARNING @ Wed, 30 Jan 2019 14:48:26: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Wed, 30 Jan 2019 14:48:26: #3 Call peaks... INFO @ Wed, 30 Jan 2019 14:48:26: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 30 Jan 2019 14:48:26: #1 tag size is determined as 44 bps INFO @ Wed, 30 Jan 2019 14:48:26: #1 tag size = 44 INFO @ Wed, 30 Jan 2019 14:48:26: #1 total tags in treatment: 4274109 INFO @ Wed, 30 Jan 2019 14:48:26: #1 user defined the maximum tags... INFO @ Wed, 30 Jan 2019 14:48:26: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Wed, 30 Jan 2019 14:48:26: #1 tag size is determined as 44 bps INFO @ Wed, 30 Jan 2019 14:48:26: #1 tag size = 44 INFO @ Wed, 30 Jan 2019 14:48:26: #1 total tags in treatment: 4274109 INFO @ Wed, 30 Jan 2019 14:48:26: #1 user defined the maximum tags... INFO @ Wed, 30 Jan 2019 14:48:26: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Wed, 30 Jan 2019 14:48:26: #1 tags after filtering in treatment: 4274109 INFO @ Wed, 30 Jan 2019 14:48:26: #1 Redundant rate of treatment: 0.00 INFO @ Wed, 30 Jan 2019 14:48:26: #1 finished! INFO @ Wed, 30 Jan 2019 14:48:26: #2 Build Peak Model... INFO @ Wed, 30 Jan 2019 14:48:26: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 30 Jan 2019 14:48:26: #1 tags after filtering in treatment: 4274109 INFO @ Wed, 30 Jan 2019 14:48:26: #1 Redundant rate of treatment: 0.00 INFO @ Wed, 30 Jan 2019 14:48:26: #1 finished! INFO @ Wed, 30 Jan 2019 14:48:26: #2 Build Peak Model... INFO @ Wed, 30 Jan 2019 14:48:26: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 30 Jan 2019 14:48:27: #2 number of paired peaks: 1235 INFO @ Wed, 30 Jan 2019 14:48:27: start model_add_line... INFO @ Wed, 30 Jan 2019 14:48:27: #2 number of paired peaks: 1235 INFO @ Wed, 30 Jan 2019 14:48:27: start model_add_line... INFO @ Wed, 30 Jan 2019 14:48:27: start X-correlation... INFO @ Wed, 30 Jan 2019 14:48:27: end of X-cor INFO @ Wed, 30 Jan 2019 14:48:27: #2 finished! INFO @ Wed, 30 Jan 2019 14:48:27: #2 predicted fragment length is 50 bps INFO @ Wed, 30 Jan 2019 14:48:27: #2 alternative fragment length(s) may be 50 bps INFO @ Wed, 30 Jan 2019 14:48:27: #2.2 Generate R script for model : ERX1430244.20_model.r INFO @ Wed, 30 Jan 2019 14:48:27: start X-correlation... INFO @ Wed, 30 Jan 2019 14:48:27: end of X-cor INFO @ Wed, 30 Jan 2019 14:48:27: #2 finished! INFO @ Wed, 30 Jan 2019 14:48:27: #2 predicted fragment length is 50 bps INFO @ Wed, 30 Jan 2019 14:48:27: #2 alternative fragment length(s) may be 50 bps INFO @ Wed, 30 Jan 2019 14:48:27: #2.2 Generate R script for model : ERX1430244.05_model.r WARNING @ Wed, 30 Jan 2019 14:48:27: #2 Since the d (50) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Wed, 30 Jan 2019 14:48:27: #2 You may need to consider one of the other alternative d(s): 50 WARNING @ Wed, 30 Jan 2019 14:48:27: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Wed, 30 Jan 2019 14:48:27: #3 Call peaks... INFO @ Wed, 30 Jan 2019 14:48:27: #3 Pre-compute pvalue-qvalue table... WARNING @ Wed, 30 Jan 2019 14:48:27: #2 Since the d (50) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Wed, 30 Jan 2019 14:48:27: #2 You may need to consider one of the other alternative d(s): 50 WARNING @ Wed, 30 Jan 2019 14:48:27: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Wed, 30 Jan 2019 14:48:27: #3 Call peaks... INFO @ Wed, 30 Jan 2019 14:48:27: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 30 Jan 2019 14:48:37: #3 Call peaks for each chromosome... INFO @ Wed, 30 Jan 2019 14:48:37: #3 Call peaks for each chromosome... INFO @ Wed, 30 Jan 2019 14:48:37: #3 Call peaks for each chromosome... INFO @ Wed, 30 Jan 2019 14:48:42: #4 Write output xls file... ERX1430244.10_peaks.xls INFO @ Wed, 30 Jan 2019 14:48:42: #4 Write output xls file... ERX1430244.20_peaks.xls INFO @ Wed, 30 Jan 2019 14:48:42: #4 Write peak in narrowPeak format file... ERX1430244.20_peaks.narrowPeak INFO @ Wed, 30 Jan 2019 14:48:42: #4 Write peak in narrowPeak format file... ERX1430244.10_peaks.narrowPeak INFO @ Wed, 30 Jan 2019 14:48:42: #4 Write summits bed file... ERX1430244.20_summits.bed INFO @ Wed, 30 Jan 2019 14:48:42: #4 Write summits bed file... ERX1430244.10_summits.bed INFO @ Wed, 30 Jan 2019 14:48:42: Done! INFO @ Wed, 30 Jan 2019 14:48:42: Done! pass1 - making usageList (12 chroms): 1 millis pass2 - checking and writing primary data (1052 records, 4 fields): 3 millis CompletedMACS2peakCalling pass1 - making usageList (12 chroms): 0 millis pass2 - checking and writing primary data (1425 records, 4 fields): 4 millis CompletedMACS2peakCalling INFO @ Wed, 30 Jan 2019 14:48:42: #4 Write output xls file... ERX1430244.05_peaks.xls INFO @ Wed, 30 Jan 2019 14:48:42: #4 Write peak in narrowPeak format file... ERX1430244.05_peaks.narrowPeak INFO @ Wed, 30 Jan 2019 14:48:42: #4 Write summits bed file... ERX1430244.05_summits.bed INFO @ Wed, 30 Jan 2019 14:48:43: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (2161 records, 4 fields): 4 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。