Job ID = 11597982 sra ファイルのダウンロード中... Completed: 475336K bytes transferred in 7 seconds (510119K 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 20216769 spots for /home/okishinya/chipatlas/results/dm3/SRX4664648/SRR7813075.sra Written 20216769 spots for /home/okishinya/chipatlas/results/dm3/SRX4664648/SRR7813075.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: 00:07:28 20216769 reads; of these: 20216769 (100.00%) were unpaired; of these: 1194869 (5.91%) aligned 0 times 14131561 (69.90%) aligned exactly 1 time 4890339 (24.19%) aligned >1 times 94.09% overall alignment rate Time searching: 00:07:28 Overall time: 00:07:28 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 8 files... [bam_rmdupse_core] 4157107 / 19021900 = 0.2185 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 16:52:14: # Command line: callpeak -t SRX4664648.bam -f BAM -g dm -n SRX4664648.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX4664648.10 # format = BAM # ChIP-seq file = ['SRX4664648.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 16:52:14: #1 read tag files... INFO @ Wed, 30 Jan 2019 16:52:14: #1 read treatment tags... INFO @ Wed, 30 Jan 2019 16:52:14: # Command line: callpeak -t SRX4664648.bam -f BAM -g dm -n SRX4664648.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX4664648.05 # format = BAM # ChIP-seq file = ['SRX4664648.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 16:52:14: #1 read tag files... INFO @ Wed, 30 Jan 2019 16:52:14: #1 read treatment tags... INFO @ Wed, 30 Jan 2019 16:52:14: # Command line: callpeak -t SRX4664648.bam -f BAM -g dm -n SRX4664648.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX4664648.20 # format = BAM # ChIP-seq file = ['SRX4664648.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 16:52:14: #1 read tag files... INFO @ Wed, 30 Jan 2019 16:52:14: #1 read treatment tags... INFO @ Wed, 30 Jan 2019 16:52:22: 1000000 INFO @ Wed, 30 Jan 2019 16:52:22: 1000000 INFO @ Wed, 30 Jan 2019 16:52:23: 1000000 INFO @ Wed, 30 Jan 2019 16:52:29: 2000000 INFO @ Wed, 30 Jan 2019 16:52:30: 2000000 INFO @ Wed, 30 Jan 2019 16:52:32: 2000000 INFO @ Wed, 30 Jan 2019 16:52:37: 3000000 INFO @ Wed, 30 Jan 2019 16:52:39: 3000000 INFO @ Wed, 30 Jan 2019 16:52:41: 3000000 INFO @ Wed, 30 Jan 2019 16:52:44: 4000000 INFO @ Wed, 30 Jan 2019 16:52:47: 4000000 INFO @ Wed, 30 Jan 2019 16:52:50: 4000000 INFO @ Wed, 30 Jan 2019 16:52:52: 5000000 INFO @ Wed, 30 Jan 2019 16:52:55: 5000000 INFO @ Wed, 30 Jan 2019 16:52:58: 5000000 INFO @ Wed, 30 Jan 2019 16:52:59: 6000000 INFO @ Wed, 30 Jan 2019 16:53:03: 6000000 INFO @ Wed, 30 Jan 2019 16:53:07: 7000000 INFO @ Wed, 30 Jan 2019 16:53:07: 6000000 INFO @ Wed, 30 Jan 2019 16:53:11: 7000000 INFO @ Wed, 30 Jan 2019 16:53:14: 8000000 INFO @ Wed, 30 Jan 2019 16:53:16: 7000000 INFO @ Wed, 30 Jan 2019 16:53:20: 8000000 INFO @ Wed, 30 Jan 2019 16:53:21: 9000000 INFO @ Wed, 30 Jan 2019 16:53:25: 8000000 INFO @ Wed, 30 Jan 2019 16:53:28: 9000000 INFO @ Wed, 30 Jan 2019 16:53:28: 10000000 INFO @ Wed, 30 Jan 2019 16:53:34: 9000000 INFO @ Wed, 30 Jan 2019 16:53:34: 11000000 INFO @ Wed, 30 Jan 2019 16:53:36: 10000000 INFO @ Wed, 30 Jan 2019 16:53:41: 12000000 INFO @ Wed, 30 Jan 2019 16:53:43: 10000000 INFO @ Wed, 30 Jan 2019 16:53:44: 11000000 INFO @ Wed, 30 Jan 2019 16:53:47: 13000000 INFO @ Wed, 30 Jan 2019 16:53:50: 11000000 INFO @ Wed, 30 Jan 2019 16:53:51: 12000000 INFO @ Wed, 30 Jan 2019 16:53:54: 14000000 INFO @ Wed, 30 Jan 2019 16:53:57: 12000000 INFO @ Wed, 30 Jan 2019 16:53:58: 13000000 INFO @ Wed, 30 Jan 2019 16:54:00: #1 tag size is determined as 50 bps INFO @ Wed, 30 Jan 2019 16:54:00: #1 tag size = 50 INFO @ Wed, 30 Jan 2019 16:54:00: #1 total tags in treatment: 14864793 INFO @ Wed, 30 Jan 2019 16:54:00: #1 user defined the maximum tags... INFO @ Wed, 30 Jan 2019 16:54:00: #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 16:54:00: #1 tags after filtering in treatment: 14864793 INFO @ Wed, 30 Jan 2019 16:54:00: #1 Redundant rate of treatment: 0.00 INFO @ Wed, 30 Jan 2019 16:54:00: #1 finished! INFO @ Wed, 30 Jan 2019 16:54:00: #2 Build Peak Model... INFO @ Wed, 30 Jan 2019 16:54:00: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 30 Jan 2019 16:54:01: #2 number of paired peaks: 2153 INFO @ Wed, 30 Jan 2019 16:54:01: start model_add_line... INFO @ Wed, 30 Jan 2019 16:54:02: start X-correlation... INFO @ Wed, 30 Jan 2019 16:54:02: end of X-cor INFO @ Wed, 30 Jan 2019 16:54:02: #2 finished! INFO @ Wed, 30 Jan 2019 16:54:02: #2 predicted fragment length is 132 bps INFO @ Wed, 30 Jan 2019 16:54:02: #2 alternative fragment length(s) may be 132 bps INFO @ Wed, 30 Jan 2019 16:54:02: #2.2 Generate R script for model : SRX4664648.20_model.r INFO @ Wed, 30 Jan 2019 16:54:02: #3 Call peaks... INFO @ Wed, 30 Jan 2019 16:54:02: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 30 Jan 2019 16:54:04: 13000000 INFO @ Wed, 30 Jan 2019 16:54:04: 14000000 INFO @ Wed, 30 Jan 2019 16:54:10: 14000000 INFO @ Wed, 30 Jan 2019 16:54:10: #1 tag size is determined as 50 bps INFO @ Wed, 30 Jan 2019 16:54:10: #1 tag size = 50 INFO @ Wed, 30 Jan 2019 16:54:10: #1 total tags in treatment: 14864793 INFO @ Wed, 30 Jan 2019 16:54:10: #1 user defined the maximum tags... INFO @ Wed, 30 Jan 2019 16:54:10: #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 16:54:10: #1 tags after filtering in treatment: 14864793 INFO @ Wed, 30 Jan 2019 16:54:10: #1 Redundant rate of treatment: 0.00 INFO @ Wed, 30 Jan 2019 16:54:10: #1 finished! INFO @ Wed, 30 Jan 2019 16:54:10: #2 Build Peak Model... INFO @ Wed, 30 Jan 2019 16:54:10: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 30 Jan 2019 16:54:12: #2 number of paired peaks: 2153 INFO @ Wed, 30 Jan 2019 16:54:12: start model_add_line... INFO @ Wed, 30 Jan 2019 16:54:12: start X-correlation... INFO @ Wed, 30 Jan 2019 16:54:12: end of X-cor INFO @ Wed, 30 Jan 2019 16:54:12: #2 finished! INFO @ Wed, 30 Jan 2019 16:54:12: #2 predicted fragment length is 132 bps INFO @ Wed, 30 Jan 2019 16:54:12: #2 alternative fragment length(s) may be 132 bps INFO @ Wed, 30 Jan 2019 16:54:12: #2.2 Generate R script for model : SRX4664648.10_model.r INFO @ Wed, 30 Jan 2019 16:54:12: #3 Call peaks... INFO @ Wed, 30 Jan 2019 16:54:12: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 30 Jan 2019 16:54:15: #1 tag size is determined as 50 bps INFO @ Wed, 30 Jan 2019 16:54:15: #1 tag size = 50 INFO @ Wed, 30 Jan 2019 16:54:15: #1 total tags in treatment: 14864793 INFO @ Wed, 30 Jan 2019 16:54:15: #1 user defined the maximum tags... INFO @ Wed, 30 Jan 2019 16:54:15: #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 16:54:16: #1 tags after filtering in treatment: 14864793 INFO @ Wed, 30 Jan 2019 16:54:16: #1 Redundant rate of treatment: 0.00 INFO @ Wed, 30 Jan 2019 16:54:16: #1 finished! INFO @ Wed, 30 Jan 2019 16:54:16: #2 Build Peak Model... INFO @ Wed, 30 Jan 2019 16:54:16: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 30 Jan 2019 16:54:17: #2 number of paired peaks: 2153 INFO @ Wed, 30 Jan 2019 16:54:17: start model_add_line... INFO @ Wed, 30 Jan 2019 16:54:17: start X-correlation... INFO @ Wed, 30 Jan 2019 16:54:17: end of X-cor INFO @ Wed, 30 Jan 2019 16:54:17: #2 finished! INFO @ Wed, 30 Jan 2019 16:54:17: #2 predicted fragment length is 132 bps INFO @ Wed, 30 Jan 2019 16:54:17: #2 alternative fragment length(s) may be 132 bps INFO @ Wed, 30 Jan 2019 16:54:17: #2.2 Generate R script for model : SRX4664648.05_model.r INFO @ Wed, 30 Jan 2019 16:54:17: #3 Call peaks... INFO @ Wed, 30 Jan 2019 16:54:17: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 30 Jan 2019 16:54:38: #3 Call peaks for each chromosome... INFO @ Wed, 30 Jan 2019 16:54:50: #3 Call peaks for each chromosome... INFO @ Wed, 30 Jan 2019 16:54:55: #3 Call peaks for each chromosome... INFO @ Wed, 30 Jan 2019 16:54:57: #4 Write output xls file... SRX4664648.20_peaks.xls INFO @ Wed, 30 Jan 2019 16:54:57: #4 Write peak in narrowPeak format file... SRX4664648.20_peaks.narrowPeak INFO @ Wed, 30 Jan 2019 16:54:57: #4 Write summits bed file... SRX4664648.20_summits.bed INFO @ Wed, 30 Jan 2019 16:54:57: Done! pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (6123 records, 4 fields): 9 millis CompletedMACS2peakCalling INFO @ Wed, 30 Jan 2019 16:55:10: #4 Write output xls file... SRX4664648.10_peaks.xls INFO @ Wed, 30 Jan 2019 16:55:10: #4 Write peak in narrowPeak format file... SRX4664648.10_peaks.narrowPeak INFO @ Wed, 30 Jan 2019 16:55:10: #4 Write summits bed file... SRX4664648.10_summits.bed INFO @ Wed, 30 Jan 2019 16:55:10: Done! pass1 - making usageList (15 chroms): 2 millis pass2 - checking and writing primary data (8897 records, 4 fields): 11 millis CompletedMACS2peakCalling INFO @ Wed, 30 Jan 2019 16:55:14: #4 Write output xls file... SRX4664648.05_peaks.xls INFO @ Wed, 30 Jan 2019 16:55:14: #4 Write peak in narrowPeak format file... SRX4664648.05_peaks.narrowPeak INFO @ Wed, 30 Jan 2019 16:55:14: #4 Write summits bed file... SRX4664648.05_summits.bed INFO @ Wed, 30 Jan 2019 16:55:15: Done! pass1 - making usageList (15 chroms): 2 millis pass2 - checking and writing primary data (11789 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。