Job ID = 11171390 sra ファイルのダウンロード中... Completed: 337172K bytes transferred in 33 seconds (81259K 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 22674832 spots for /home/okishinya/chipatlas/results/dm3/SRX4315056/SRR7444517.sra Written 22674832 spots for /home/okishinya/chipatlas/results/dm3/SRX4315056/SRR7444517.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: 00:06:59 22674832 reads; of these: 22674832 (100.00%) were unpaired; of these: 2483 (0.01%) aligned 0 times 20378708 (89.87%) aligned exactly 1 time 2293641 (10.12%) aligned >1 times 99.99% overall alignment rate Time searching: 00:06:59 Overall time: 00:06:59 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_sort_core] merging from 12 files... [bam_rmdupse_core] 8515823 / 22672349 = 0.3756 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, 08 Sep 2018 14:22:14: # Command line: callpeak -t SRX4315056.bam -f BAM -g dm -n SRX4315056.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX4315056.05 # format = BAM # ChIP-seq file = ['SRX4315056.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 @ Sat, 08 Sep 2018 14:22:14: #1 read tag files... INFO @ Sat, 08 Sep 2018 14:22:14: #1 read treatment tags... INFO @ Sat, 08 Sep 2018 14:22:14: # Command line: callpeak -t SRX4315056.bam -f BAM -g dm -n SRX4315056.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX4315056.20 # format = BAM # ChIP-seq file = ['SRX4315056.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 @ Sat, 08 Sep 2018 14:22:14: #1 read tag files... INFO @ Sat, 08 Sep 2018 14:22:14: #1 read treatment tags... INFO @ Sat, 08 Sep 2018 14:22:14: # Command line: callpeak -t SRX4315056.bam -f BAM -g dm -n SRX4315056.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX4315056.10 # format = BAM # ChIP-seq file = ['SRX4315056.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 @ Sat, 08 Sep 2018 14:22:14: #1 read tag files... INFO @ Sat, 08 Sep 2018 14:22:14: #1 read treatment tags... INFO @ Sat, 08 Sep 2018 14:22:21: 1000000 INFO @ Sat, 08 Sep 2018 14:22:21: 1000000 INFO @ Sat, 08 Sep 2018 14:22:21: 1000000 INFO @ Sat, 08 Sep 2018 14:22:29: 2000000 INFO @ Sat, 08 Sep 2018 14:22:29: 2000000 INFO @ Sat, 08 Sep 2018 14:22:29: 2000000 INFO @ Sat, 08 Sep 2018 14:22:36: 3000000 INFO @ Sat, 08 Sep 2018 14:22:36: 3000000 INFO @ Sat, 08 Sep 2018 14:22:36: 3000000 INFO @ Sat, 08 Sep 2018 14:22:43: 4000000 INFO @ Sat, 08 Sep 2018 14:22:43: 4000000 INFO @ Sat, 08 Sep 2018 14:22:43: 4000000 INFO @ Sat, 08 Sep 2018 14:22:50: 5000000 INFO @ Sat, 08 Sep 2018 14:22:50: 5000000 INFO @ Sat, 08 Sep 2018 14:22:50: 5000000 INFO @ Sat, 08 Sep 2018 14:22:57: 6000000 INFO @ Sat, 08 Sep 2018 14:22:57: 6000000 INFO @ Sat, 08 Sep 2018 14:22:57: 6000000 INFO @ Sat, 08 Sep 2018 14:23:04: 7000000 INFO @ Sat, 08 Sep 2018 14:23:04: 7000000 INFO @ Sat, 08 Sep 2018 14:23:04: 7000000 INFO @ Sat, 08 Sep 2018 14:23:11: 8000000 INFO @ Sat, 08 Sep 2018 14:23:11: 8000000 INFO @ Sat, 08 Sep 2018 14:23:11: 8000000 INFO @ Sat, 08 Sep 2018 14:23:18: 9000000 INFO @ Sat, 08 Sep 2018 14:23:18: 9000000 INFO @ Sat, 08 Sep 2018 14:23:19: 9000000 INFO @ Sat, 08 Sep 2018 14:23:25: 10000000 INFO @ Sat, 08 Sep 2018 14:23:25: 10000000 INFO @ Sat, 08 Sep 2018 14:23:26: 10000000 INFO @ Sat, 08 Sep 2018 14:23:32: 11000000 INFO @ Sat, 08 Sep 2018 14:23:33: 11000000 INFO @ Sat, 08 Sep 2018 14:23:33: 11000000 INFO @ Sat, 08 Sep 2018 14:23:39: 12000000 INFO @ Sat, 08 Sep 2018 14:23:40: 12000000 INFO @ Sat, 08 Sep 2018 14:23:40: 12000000 INFO @ Sat, 08 Sep 2018 14:23:46: 13000000 INFO @ Sat, 08 Sep 2018 14:23:47: 13000000 INFO @ Sat, 08 Sep 2018 14:23:48: 13000000 INFO @ Sat, 08 Sep 2018 14:23:53: 14000000 INFO @ Sat, 08 Sep 2018 14:23:54: #1 tag size is determined as 75 bps INFO @ Sat, 08 Sep 2018 14:23:54: #1 tag size = 75 INFO @ Sat, 08 Sep 2018 14:23:54: #1 total tags in treatment: 14156526 INFO @ Sat, 08 Sep 2018 14:23:54: #1 user defined the maximum tags... INFO @ Sat, 08 Sep 2018 14:23:54: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 08 Sep 2018 14:23:54: 14000000 INFO @ Sat, 08 Sep 2018 14:23:55: #1 tags after filtering in treatment: 14156526 INFO @ Sat, 08 Sep 2018 14:23:55: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 08 Sep 2018 14:23:55: #1 finished! INFO @ Sat, 08 Sep 2018 14:23:55: #2 Build Peak Model... INFO @ Sat, 08 Sep 2018 14:23:55: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 08 Sep 2018 14:23:55: 14000000 INFO @ Sat, 08 Sep 2018 14:23:55: #1 tag size is determined as 75 bps INFO @ Sat, 08 Sep 2018 14:23:55: #1 tag size = 75 INFO @ Sat, 08 Sep 2018 14:23:55: #1 total tags in treatment: 14156526 INFO @ Sat, 08 Sep 2018 14:23:55: #1 user defined the maximum tags... INFO @ Sat, 08 Sep 2018 14:23:55: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 08 Sep 2018 14:23:56: #1 tags after filtering in treatment: 14156526 INFO @ Sat, 08 Sep 2018 14:23:56: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 08 Sep 2018 14:23:56: #1 finished! INFO @ Sat, 08 Sep 2018 14:23:56: #2 Build Peak Model... INFO @ Sat, 08 Sep 2018 14:23:56: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 08 Sep 2018 14:23:56: #2 number of paired peaks: 3915 INFO @ Sat, 08 Sep 2018 14:23:56: start model_add_line... INFO @ Sat, 08 Sep 2018 14:23:56: #1 tag size is determined as 75 bps INFO @ Sat, 08 Sep 2018 14:23:56: #1 tag size = 75 INFO @ Sat, 08 Sep 2018 14:23:56: #1 total tags in treatment: 14156526 INFO @ Sat, 08 Sep 2018 14:23:56: #1 user defined the maximum tags... INFO @ Sat, 08 Sep 2018 14:23:56: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 08 Sep 2018 14:23:56: start X-correlation... INFO @ Sat, 08 Sep 2018 14:23:56: end of X-cor INFO @ Sat, 08 Sep 2018 14:23:56: #2 finished! INFO @ Sat, 08 Sep 2018 14:23:56: #2 predicted fragment length is 130 bps INFO @ Sat, 08 Sep 2018 14:23:56: #2 alternative fragment length(s) may be 130 bps INFO @ Sat, 08 Sep 2018 14:23:56: #2.2 Generate R script for model : SRX4315056.10_model.r WARNING @ Sat, 08 Sep 2018 14:23:56: #2 Since the d (130) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 08 Sep 2018 14:23:56: #2 You may need to consider one of the other alternative d(s): 130 WARNING @ Sat, 08 Sep 2018 14:23:56: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sat, 08 Sep 2018 14:23:56: #3 Call peaks... INFO @ Sat, 08 Sep 2018 14:23:56: #1 tags after filtering in treatment: 14156526 INFO @ Sat, 08 Sep 2018 14:23:56: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 08 Sep 2018 14:23:56: #1 finished! INFO @ Sat, 08 Sep 2018 14:23:56: #2 Build Peak Model... INFO @ Sat, 08 Sep 2018 14:23:56: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 08 Sep 2018 14:23:56: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 08 Sep 2018 14:23:57: #2 number of paired peaks: 3915 INFO @ Sat, 08 Sep 2018 14:23:57: start model_add_line... INFO @ Sat, 08 Sep 2018 14:23:57: start X-correlation... INFO @ Sat, 08 Sep 2018 14:23:57: end of X-cor INFO @ Sat, 08 Sep 2018 14:23:57: #2 finished! INFO @ Sat, 08 Sep 2018 14:23:57: #2 predicted fragment length is 130 bps INFO @ Sat, 08 Sep 2018 14:23:57: #2 alternative fragment length(s) may be 130 bps INFO @ Sat, 08 Sep 2018 14:23:57: #2.2 Generate R script for model : SRX4315056.20_model.r WARNING @ Sat, 08 Sep 2018 14:23:57: #2 Since the d (130) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 08 Sep 2018 14:23:57: #2 You may need to consider one of the other alternative d(s): 130 WARNING @ Sat, 08 Sep 2018 14:23:57: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sat, 08 Sep 2018 14:23:57: #3 Call peaks... INFO @ Sat, 08 Sep 2018 14:23:57: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 08 Sep 2018 14:23:58: #2 number of paired peaks: 3915 INFO @ Sat, 08 Sep 2018 14:23:58: start model_add_line... INFO @ Sat, 08 Sep 2018 14:23:58: start X-correlation... INFO @ Sat, 08 Sep 2018 14:23:58: end of X-cor INFO @ Sat, 08 Sep 2018 14:23:58: #2 finished! INFO @ Sat, 08 Sep 2018 14:23:58: #2 predicted fragment length is 130 bps INFO @ Sat, 08 Sep 2018 14:23:58: #2 alternative fragment length(s) may be 130 bps INFO @ Sat, 08 Sep 2018 14:23:58: #2.2 Generate R script for model : SRX4315056.05_model.r WARNING @ Sat, 08 Sep 2018 14:23:58: #2 Since the d (130) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 08 Sep 2018 14:23:58: #2 You may need to consider one of the other alternative d(s): 130 WARNING @ Sat, 08 Sep 2018 14:23:58: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sat, 08 Sep 2018 14:23:58: #3 Call peaks... INFO @ Sat, 08 Sep 2018 14:23:58: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 08 Sep 2018 14:24:34: #3 Call peaks for each chromosome... INFO @ Sat, 08 Sep 2018 14:24:35: #3 Call peaks for each chromosome... INFO @ Sat, 08 Sep 2018 14:24:35: #3 Call peaks for each chromosome... INFO @ Sat, 08 Sep 2018 14:24:55: #4 Write output xls file... SRX4315056.10_peaks.xls INFO @ Sat, 08 Sep 2018 14:24:55: #4 Write peak in narrowPeak format file... SRX4315056.10_peaks.narrowPeak INFO @ Sat, 08 Sep 2018 14:24:55: #4 Write summits bed file... SRX4315056.10_summits.bed INFO @ Sat, 08 Sep 2018 14:24:55: Done! pass1 - making usageList (14 chroms): 2 millis pass2 - checking and writing primary data (8211 records, 4 fields): 13 millis CompletedMACS2peakCalling INFO @ Sat, 08 Sep 2018 14:24:55: #4 Write output xls file... SRX4315056.20_peaks.xls INFO @ Sat, 08 Sep 2018 14:24:56: #4 Write peak in narrowPeak format file... SRX4315056.20_peaks.narrowPeak INFO @ Sat, 08 Sep 2018 14:24:56: #4 Write output xls file... SRX4315056.05_peaks.xls INFO @ Sat, 08 Sep 2018 14:24:56: #4 Write summits bed file... SRX4315056.20_summits.bed INFO @ Sat, 08 Sep 2018 14:24:56: Done! INFO @ Sat, 08 Sep 2018 14:24:56: #4 Write peak in narrowPeak format file... SRX4315056.05_peaks.narrowPeak INFO @ Sat, 08 Sep 2018 14:24:56: #4 Write summits bed file... SRX4315056.05_summits.bed INFO @ Sat, 08 Sep 2018 14:24:56: Done! pass1 - making usageList (14 chroms): 5 millis pass2 - checking and writing primary data (5971 records, 4 fields): 9 millis CompletedMACS2peakCalling pass1 - making usageList (14 chroms): 8 millis pass2 - checking and writing primary data (10255 records, 4 fields): 22 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。