Job ID = 11597981 sra ファイルのダウンロード中... Completed: 670718K bytes transferred in 10 seconds (520475K 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 27801470 spots for /home/okishinya/chipatlas/results/dm3/SRX4664647/SRR7813074.sra Written 27801470 spots for /home/okishinya/chipatlas/results/dm3/SRX4664647/SRR7813074.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: 00:11:08 27801470 reads; of these: 27801470 (100.00%) were unpaired; of these: 739432 (2.66%) aligned 0 times 19604220 (70.52%) aligned exactly 1 time 7457818 (26.83%) aligned >1 times 97.34% overall alignment rate Time searching: 00:11:08 Overall time: 00:11:08 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] 9390138 / 27062038 = 0.3470 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 16:56:54: # Command line: callpeak -t SRX4664647.bam -f BAM -g dm -n SRX4664647.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX4664647.20 # format = BAM # ChIP-seq file = ['SRX4664647.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 16:56:54: #1 read tag files... INFO @ Wed, 30 Jan 2019 16:56:54: #1 read treatment tags... INFO @ Wed, 30 Jan 2019 16:56:54: # Command line: callpeak -t SRX4664647.bam -f BAM -g dm -n SRX4664647.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX4664647.05 # format = BAM # ChIP-seq file = ['SRX4664647.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 16:56:54: #1 read tag files... INFO @ Wed, 30 Jan 2019 16:56:54: #1 read treatment tags... INFO @ Wed, 30 Jan 2019 16:56:54: # Command line: callpeak -t SRX4664647.bam -f BAM -g dm -n SRX4664647.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX4664647.10 # format = BAM # ChIP-seq file = ['SRX4664647.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 16:56:54: #1 read tag files... INFO @ Wed, 30 Jan 2019 16:56:54: #1 read treatment tags... INFO @ Wed, 30 Jan 2019 16:57:01: 1000000 INFO @ Wed, 30 Jan 2019 16:57:01: 1000000 INFO @ Wed, 30 Jan 2019 16:57:01: 1000000 INFO @ Wed, 30 Jan 2019 16:57:08: 2000000 INFO @ Wed, 30 Jan 2019 16:57:09: 2000000 INFO @ Wed, 30 Jan 2019 16:57:09: 2000000 INFO @ Wed, 30 Jan 2019 16:57:15: 3000000 INFO @ Wed, 30 Jan 2019 16:57:16: 3000000 INFO @ Wed, 30 Jan 2019 16:57:16: 3000000 INFO @ Wed, 30 Jan 2019 16:57:22: 4000000 INFO @ Wed, 30 Jan 2019 16:57:23: 4000000 INFO @ Wed, 30 Jan 2019 16:57:23: 4000000 INFO @ Wed, 30 Jan 2019 16:57:29: 5000000 INFO @ Wed, 30 Jan 2019 16:57:30: 5000000 INFO @ Wed, 30 Jan 2019 16:57:30: 5000000 INFO @ Wed, 30 Jan 2019 16:57:36: 6000000 INFO @ Wed, 30 Jan 2019 16:57:38: 6000000 INFO @ Wed, 30 Jan 2019 16:57:38: 6000000 INFO @ Wed, 30 Jan 2019 16:57:43: 7000000 INFO @ Wed, 30 Jan 2019 16:57:45: 7000000 INFO @ Wed, 30 Jan 2019 16:57:45: 7000000 INFO @ Wed, 30 Jan 2019 16:57:50: 8000000 INFO @ Wed, 30 Jan 2019 16:57:52: 8000000 INFO @ Wed, 30 Jan 2019 16:57:52: 8000000 INFO @ Wed, 30 Jan 2019 16:57:57: 9000000 INFO @ Wed, 30 Jan 2019 16:58:00: 9000000 INFO @ Wed, 30 Jan 2019 16:58:00: 9000000 INFO @ Wed, 30 Jan 2019 16:58:04: 10000000 INFO @ Wed, 30 Jan 2019 16:58:07: 10000000 INFO @ Wed, 30 Jan 2019 16:58:07: 10000000 INFO @ Wed, 30 Jan 2019 16:58:11: 11000000 INFO @ Wed, 30 Jan 2019 16:58:14: 11000000 INFO @ Wed, 30 Jan 2019 16:58:14: 11000000 INFO @ Wed, 30 Jan 2019 16:58:18: 12000000 INFO @ Wed, 30 Jan 2019 16:58:21: 12000000 INFO @ Wed, 30 Jan 2019 16:58:21: 12000000 INFO @ Wed, 30 Jan 2019 16:58:25: 13000000 INFO @ Wed, 30 Jan 2019 16:58:29: 13000000 INFO @ Wed, 30 Jan 2019 16:58:29: 13000000 INFO @ Wed, 30 Jan 2019 16:58:32: 14000000 INFO @ Wed, 30 Jan 2019 16:58:36: 14000000 INFO @ Wed, 30 Jan 2019 16:58:36: 14000000 INFO @ Wed, 30 Jan 2019 16:58:38: 15000000 INFO @ Wed, 30 Jan 2019 16:58:43: 15000000 INFO @ Wed, 30 Jan 2019 16:58:43: 15000000 INFO @ Wed, 30 Jan 2019 16:58:45: 16000000 INFO @ Wed, 30 Jan 2019 16:58:50: 16000000 INFO @ Wed, 30 Jan 2019 16:58:50: 16000000 INFO @ Wed, 30 Jan 2019 16:58:52: 17000000 INFO @ Wed, 30 Jan 2019 16:58:57: #1 tag size is determined as 50 bps INFO @ Wed, 30 Jan 2019 16:58:57: #1 tag size = 50 INFO @ Wed, 30 Jan 2019 16:58:57: #1 total tags in treatment: 17671900 INFO @ Wed, 30 Jan 2019 16:58:57: #1 user defined the maximum tags... INFO @ Wed, 30 Jan 2019 16:58:57: #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 16:58:57: #1 tags after filtering in treatment: 17671900 INFO @ Wed, 30 Jan 2019 16:58:57: #1 Redundant rate of treatment: 0.00 INFO @ Wed, 30 Jan 2019 16:58:57: #1 finished! INFO @ Wed, 30 Jan 2019 16:58:57: #2 Build Peak Model... INFO @ Wed, 30 Jan 2019 16:58:57: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 30 Jan 2019 16:58:58: 17000000 INFO @ Wed, 30 Jan 2019 16:58:58: 17000000 INFO @ Wed, 30 Jan 2019 16:58:59: #2 number of paired peaks: 2371 INFO @ Wed, 30 Jan 2019 16:58:59: start model_add_line... INFO @ Wed, 30 Jan 2019 16:58:59: start X-correlation... INFO @ Wed, 30 Jan 2019 16:58:59: end of X-cor INFO @ Wed, 30 Jan 2019 16:58:59: #2 finished! INFO @ Wed, 30 Jan 2019 16:58:59: #2 predicted fragment length is 166 bps INFO @ Wed, 30 Jan 2019 16:58:59: #2 alternative fragment length(s) may be 166 bps INFO @ Wed, 30 Jan 2019 16:58:59: #2.2 Generate R script for model : SRX4664647.10_model.r INFO @ Wed, 30 Jan 2019 16:58:59: #3 Call peaks... INFO @ Wed, 30 Jan 2019 16:58:59: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 30 Jan 2019 16:59:03: #1 tag size is determined as 50 bps INFO @ Wed, 30 Jan 2019 16:59:03: #1 tag size = 50 INFO @ Wed, 30 Jan 2019 16:59:03: #1 total tags in treatment: 17671900 INFO @ Wed, 30 Jan 2019 16:59:03: #1 user defined the maximum tags... INFO @ Wed, 30 Jan 2019 16:59:03: #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 16:59:03: #1 tag size is determined as 50 bps INFO @ Wed, 30 Jan 2019 16:59:03: #1 tag size = 50 INFO @ Wed, 30 Jan 2019 16:59:03: #1 total tags in treatment: 17671900 INFO @ Wed, 30 Jan 2019 16:59:03: #1 user defined the maximum tags... INFO @ Wed, 30 Jan 2019 16:59:03: #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 16:59:03: #1 tags after filtering in treatment: 17671900 INFO @ Wed, 30 Jan 2019 16:59:03: #1 Redundant rate of treatment: 0.00 INFO @ Wed, 30 Jan 2019 16:59:03: #1 finished! INFO @ Wed, 30 Jan 2019 16:59:03: #2 Build Peak Model... INFO @ Wed, 30 Jan 2019 16:59:03: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 30 Jan 2019 16:59:03: #1 tags after filtering in treatment: 17671900 INFO @ Wed, 30 Jan 2019 16:59:03: #1 Redundant rate of treatment: 0.00 INFO @ Wed, 30 Jan 2019 16:59:03: #1 finished! INFO @ Wed, 30 Jan 2019 16:59:03: #2 Build Peak Model... INFO @ Wed, 30 Jan 2019 16:59:03: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 30 Jan 2019 16:59:04: #2 number of paired peaks: 2371 INFO @ Wed, 30 Jan 2019 16:59:04: start model_add_line... INFO @ Wed, 30 Jan 2019 16:59:04: #2 number of paired peaks: 2371 INFO @ Wed, 30 Jan 2019 16:59:04: start model_add_line... INFO @ Wed, 30 Jan 2019 16:59:05: start X-correlation... INFO @ Wed, 30 Jan 2019 16:59:05: start X-correlation... INFO @ Wed, 30 Jan 2019 16:59:05: end of X-cor INFO @ Wed, 30 Jan 2019 16:59:05: #2 finished! INFO @ Wed, 30 Jan 2019 16:59:05: #2 predicted fragment length is 166 bps INFO @ Wed, 30 Jan 2019 16:59:05: #2 alternative fragment length(s) may be 166 bps INFO @ Wed, 30 Jan 2019 16:59:05: #2.2 Generate R script for model : SRX4664647.05_model.r INFO @ Wed, 30 Jan 2019 16:59:05: end of X-cor INFO @ Wed, 30 Jan 2019 16:59:05: #2 finished! INFO @ Wed, 30 Jan 2019 16:59:05: #2 predicted fragment length is 166 bps INFO @ Wed, 30 Jan 2019 16:59:05: #2 alternative fragment length(s) may be 166 bps INFO @ Wed, 30 Jan 2019 16:59:05: #2.2 Generate R script for model : SRX4664647.20_model.r INFO @ Wed, 30 Jan 2019 16:59:05: #3 Call peaks... INFO @ Wed, 30 Jan 2019 16:59:05: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 30 Jan 2019 16:59:05: #3 Call peaks... INFO @ Wed, 30 Jan 2019 16:59:05: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 30 Jan 2019 16:59:46: #3 Call peaks for each chromosome... INFO @ Wed, 30 Jan 2019 16:59:51: #3 Call peaks for each chromosome... INFO @ Wed, 30 Jan 2019 16:59:51: #3 Call peaks for each chromosome... INFO @ Wed, 30 Jan 2019 17:00:08: #4 Write output xls file... SRX4664647.10_peaks.xls INFO @ Wed, 30 Jan 2019 17:00:09: #4 Write peak in narrowPeak format file... SRX4664647.10_peaks.narrowPeak INFO @ Wed, 30 Jan 2019 17:00:09: #4 Write summits bed file... SRX4664647.10_summits.bed INFO @ Wed, 30 Jan 2019 17:00:09: Done! pass1 - making usageList (15 chroms): 2 millis pass2 - checking and writing primary data (9267 records, 4 fields): 13 millis CompletedMACS2peakCalling INFO @ Wed, 30 Jan 2019 17:00:11: #4 Write output xls file... SRX4664647.20_peaks.xls INFO @ Wed, 30 Jan 2019 17:00:11: #4 Write peak in narrowPeak format file... SRX4664647.20_peaks.narrowPeak INFO @ Wed, 30 Jan 2019 17:00:12: #4 Write summits bed file... SRX4664647.20_summits.bed INFO @ Wed, 30 Jan 2019 17:00:12: Done! pass1 - making usageList (15 chroms): 2 millis pass2 - checking and writing primary data (6479 records, 4 fields): 9 millis CompletedMACS2peakCalling INFO @ Wed, 30 Jan 2019 17:00:13: #4 Write output xls file... SRX4664647.05_peaks.xls INFO @ Wed, 30 Jan 2019 17:00:13: #4 Write peak in narrowPeak format file... SRX4664647.05_peaks.narrowPeak INFO @ Wed, 30 Jan 2019 17:00:13: #4 Write summits bed file... SRX4664647.05_summits.bed INFO @ Wed, 30 Jan 2019 17:00:13: Done! pass1 - making usageList (15 chroms): 3 millis pass2 - checking and writing primary data (11747 records, 4 fields): 15 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。