Job ID = 11597977 sra ファイルのダウンロード中... Completed: 747965K bytes transferred in 12 seconds (510002K 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 31198743 spots for /home/okishinya/chipatlas/results/dm3/SRX4664644/SRR7813071.sra Written 31198743 spots for /home/okishinya/chipatlas/results/dm3/SRX4664644/SRR7813071.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: 00:12:25 31198743 reads; of these: 31198743 (100.00%) were unpaired; of these: 818128 (2.62%) aligned 0 times 21789841 (69.84%) aligned exactly 1 time 8590774 (27.54%) aligned >1 times 97.38% overall alignment rate Time searching: 00:12:25 Overall time: 00:12:25 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 16 files... [bam_rmdupse_core] 8641589 / 30380615 = 0.2844 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 16:58:23: # Command line: callpeak -t SRX4664644.bam -f BAM -g dm -n SRX4664644.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX4664644.05 # format = BAM # ChIP-seq file = ['SRX4664644.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 16:58:23: #1 read tag files... INFO @ Wed, 30 Jan 2019 16:58:23: #1 read treatment tags... INFO @ Wed, 30 Jan 2019 16:58:23: # Command line: callpeak -t SRX4664644.bam -f BAM -g dm -n SRX4664644.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX4664644.10 # format = BAM # ChIP-seq file = ['SRX4664644.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 16:58:23: #1 read tag files... INFO @ Wed, 30 Jan 2019 16:58:23: #1 read treatment tags... INFO @ Wed, 30 Jan 2019 16:58:23: # Command line: callpeak -t SRX4664644.bam -f BAM -g dm -n SRX4664644.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX4664644.20 # format = BAM # ChIP-seq file = ['SRX4664644.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 16:58:23: #1 read tag files... INFO @ Wed, 30 Jan 2019 16:58:23: #1 read treatment tags... INFO @ Wed, 30 Jan 2019 16:58:29: 1000000 INFO @ Wed, 30 Jan 2019 16:58:29: 1000000 INFO @ Wed, 30 Jan 2019 16:58:30: 1000000 INFO @ Wed, 30 Jan 2019 16:58:35: 2000000 INFO @ Wed, 30 Jan 2019 16:58:36: 2000000 INFO @ Wed, 30 Jan 2019 16:58:36: 2000000 INFO @ Wed, 30 Jan 2019 16:58:41: 3000000 INFO @ Wed, 30 Jan 2019 16:58:42: 3000000 INFO @ Wed, 30 Jan 2019 16:58:43: 3000000 INFO @ Wed, 30 Jan 2019 16:58:47: 4000000 INFO @ Wed, 30 Jan 2019 16:58:49: 4000000 INFO @ Wed, 30 Jan 2019 16:58:49: 4000000 INFO @ Wed, 30 Jan 2019 16:58:53: 5000000 INFO @ Wed, 30 Jan 2019 16:58:55: 5000000 INFO @ Wed, 30 Jan 2019 16:58:56: 5000000 INFO @ Wed, 30 Jan 2019 16:58:59: 6000000 INFO @ Wed, 30 Jan 2019 16:59:02: 6000000 INFO @ Wed, 30 Jan 2019 16:59:02: 6000000 INFO @ Wed, 30 Jan 2019 16:59:05: 7000000 INFO @ Wed, 30 Jan 2019 16:59:09: 7000000 INFO @ Wed, 30 Jan 2019 16:59:09: 7000000 INFO @ Wed, 30 Jan 2019 16:59:11: 8000000 INFO @ Wed, 30 Jan 2019 16:59:15: 8000000 INFO @ Wed, 30 Jan 2019 16:59:15: 8000000 INFO @ Wed, 30 Jan 2019 16:59:17: 9000000 INFO @ Wed, 30 Jan 2019 16:59:22: 9000000 INFO @ Wed, 30 Jan 2019 16:59:22: 9000000 INFO @ Wed, 30 Jan 2019 16:59:23: 10000000 INFO @ Wed, 30 Jan 2019 16:59:28: 10000000 INFO @ Wed, 30 Jan 2019 16:59:29: 10000000 INFO @ Wed, 30 Jan 2019 16:59:29: 11000000 INFO @ Wed, 30 Jan 2019 16:59:35: 12000000 INFO @ Wed, 30 Jan 2019 16:59:35: 11000000 INFO @ Wed, 30 Jan 2019 16:59:35: 11000000 INFO @ Wed, 30 Jan 2019 16:59:41: 13000000 INFO @ Wed, 30 Jan 2019 16:59:41: 12000000 INFO @ Wed, 30 Jan 2019 16:59:42: 12000000 INFO @ Wed, 30 Jan 2019 16:59:47: 14000000 INFO @ Wed, 30 Jan 2019 16:59:48: 13000000 INFO @ Wed, 30 Jan 2019 16:59:48: 13000000 INFO @ Wed, 30 Jan 2019 16:59:53: 15000000 INFO @ Wed, 30 Jan 2019 16:59:55: 14000000 INFO @ Wed, 30 Jan 2019 16:59:55: 14000000 INFO @ Wed, 30 Jan 2019 16:59:59: 16000000 INFO @ Wed, 30 Jan 2019 17:00:01: 15000000 INFO @ Wed, 30 Jan 2019 17:00:02: 15000000 INFO @ Wed, 30 Jan 2019 17:00:05: 17000000 INFO @ Wed, 30 Jan 2019 17:00:08: 16000000 INFO @ Wed, 30 Jan 2019 17:00:09: 16000000 INFO @ Wed, 30 Jan 2019 17:00:11: 18000000 INFO @ Wed, 30 Jan 2019 17:00:14: 17000000 INFO @ Wed, 30 Jan 2019 17:00:15: 17000000 INFO @ Wed, 30 Jan 2019 17:00:17: 19000000 INFO @ Wed, 30 Jan 2019 17:00:21: 18000000 INFO @ Wed, 30 Jan 2019 17:00:22: 18000000 INFO @ Wed, 30 Jan 2019 17:00:24: 20000000 INFO @ Wed, 30 Jan 2019 17:00:27: 19000000 INFO @ Wed, 30 Jan 2019 17:00:28: 19000000 INFO @ Wed, 30 Jan 2019 17:00:30: 21000000 INFO @ Wed, 30 Jan 2019 17:00:33: 20000000 INFO @ Wed, 30 Jan 2019 17:00:35: 20000000 INFO @ Wed, 30 Jan 2019 17:00:35: #1 tag size is determined as 50 bps INFO @ Wed, 30 Jan 2019 17:00:35: #1 tag size = 50 INFO @ Wed, 30 Jan 2019 17:00:35: #1 total tags in treatment: 21739026 INFO @ Wed, 30 Jan 2019 17:00:35: #1 user defined the maximum tags... INFO @ Wed, 30 Jan 2019 17:00:35: #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 17:00:35: #1 tags after filtering in treatment: 21739026 INFO @ Wed, 30 Jan 2019 17:00:35: #1 Redundant rate of treatment: 0.00 INFO @ Wed, 30 Jan 2019 17:00:35: #1 finished! INFO @ Wed, 30 Jan 2019 17:00:35: #2 Build Peak Model... INFO @ Wed, 30 Jan 2019 17:00:35: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 30 Jan 2019 17:00:37: #2 number of paired peaks: 1428 INFO @ Wed, 30 Jan 2019 17:00:37: start model_add_line... INFO @ Wed, 30 Jan 2019 17:00:37: start X-correlation... INFO @ Wed, 30 Jan 2019 17:00:37: end of X-cor INFO @ Wed, 30 Jan 2019 17:00:37: #2 finished! INFO @ Wed, 30 Jan 2019 17:00:37: #2 predicted fragment length is 171 bps INFO @ Wed, 30 Jan 2019 17:00:37: #2 alternative fragment length(s) may be 171 bps INFO @ Wed, 30 Jan 2019 17:00:37: #2.2 Generate R script for model : SRX4664644.05_model.r INFO @ Wed, 30 Jan 2019 17:00:37: #3 Call peaks... INFO @ Wed, 30 Jan 2019 17:00:37: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 30 Jan 2019 17:00:40: 21000000 INFO @ Wed, 30 Jan 2019 17:00:41: 21000000 INFO @ Wed, 30 Jan 2019 17:00:45: #1 tag size is determined as 50 bps INFO @ Wed, 30 Jan 2019 17:00:45: #1 tag size = 50 INFO @ Wed, 30 Jan 2019 17:00:45: #1 total tags in treatment: 21739026 INFO @ Wed, 30 Jan 2019 17:00:45: #1 user defined the maximum tags... INFO @ Wed, 30 Jan 2019 17:00:45: #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 17:00:45: #1 tags after filtering in treatment: 21739026 INFO @ Wed, 30 Jan 2019 17:00:45: #1 Redundant rate of treatment: 0.00 INFO @ Wed, 30 Jan 2019 17:00:45: #1 finished! INFO @ Wed, 30 Jan 2019 17:00:45: #2 Build Peak Model... INFO @ Wed, 30 Jan 2019 17:00:45: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 30 Jan 2019 17:00:46: #1 tag size is determined as 50 bps INFO @ Wed, 30 Jan 2019 17:00:46: #1 tag size = 50 INFO @ Wed, 30 Jan 2019 17:00:46: #1 total tags in treatment: 21739026 INFO @ Wed, 30 Jan 2019 17:00:46: #1 user defined the maximum tags... INFO @ Wed, 30 Jan 2019 17:00:46: #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 17:00:46: #1 tags after filtering in treatment: 21739026 INFO @ Wed, 30 Jan 2019 17:00:46: #1 Redundant rate of treatment: 0.00 INFO @ Wed, 30 Jan 2019 17:00:46: #1 finished! INFO @ Wed, 30 Jan 2019 17:00:46: #2 Build Peak Model... INFO @ Wed, 30 Jan 2019 17:00:46: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 30 Jan 2019 17:00:47: #2 number of paired peaks: 1428 INFO @ Wed, 30 Jan 2019 17:00:47: start model_add_line... INFO @ Wed, 30 Jan 2019 17:00:47: start X-correlation... INFO @ Wed, 30 Jan 2019 17:00:47: end of X-cor INFO @ Wed, 30 Jan 2019 17:00:47: #2 finished! INFO @ Wed, 30 Jan 2019 17:00:47: #2 predicted fragment length is 171 bps INFO @ Wed, 30 Jan 2019 17:00:47: #2 alternative fragment length(s) may be 171 bps INFO @ Wed, 30 Jan 2019 17:00:47: #2.2 Generate R script for model : SRX4664644.10_model.r INFO @ Wed, 30 Jan 2019 17:00:47: #3 Call peaks... INFO @ Wed, 30 Jan 2019 17:00:47: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 30 Jan 2019 17:00:48: #2 number of paired peaks: 1428 INFO @ Wed, 30 Jan 2019 17:00:48: start model_add_line... INFO @ Wed, 30 Jan 2019 17:00:48: start X-correlation... INFO @ Wed, 30 Jan 2019 17:00:48: end of X-cor INFO @ Wed, 30 Jan 2019 17:00:48: #2 finished! INFO @ Wed, 30 Jan 2019 17:00:48: #2 predicted fragment length is 171 bps INFO @ Wed, 30 Jan 2019 17:00:48: #2 alternative fragment length(s) may be 171 bps INFO @ Wed, 30 Jan 2019 17:00:48: #2.2 Generate R script for model : SRX4664644.20_model.r INFO @ Wed, 30 Jan 2019 17:00:48: #3 Call peaks... INFO @ Wed, 30 Jan 2019 17:00:48: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 30 Jan 2019 17:01:32: #3 Call peaks for each chromosome... INFO @ Wed, 30 Jan 2019 17:01:39: #3 Call peaks for each chromosome... INFO @ Wed, 30 Jan 2019 17:01:43: #3 Call peaks for each chromosome... INFO @ Wed, 30 Jan 2019 17:01:59: #4 Write output xls file... SRX4664644.05_peaks.xls INFO @ Wed, 30 Jan 2019 17:01:59: #4 Write peak in narrowPeak format file... SRX4664644.05_peaks.narrowPeak INFO @ Wed, 30 Jan 2019 17:01:59: #4 Write summits bed file... SRX4664644.05_summits.bed INFO @ Wed, 30 Jan 2019 17:01:59: Done! pass1 - making usageList (15 chroms): 3 millis pass2 - checking and writing primary data (11674 records, 4 fields): 15 millis CompletedMACS2peakCalling INFO @ Wed, 30 Jan 2019 17:02:04: #4 Write output xls file... SRX4664644.10_peaks.xls INFO @ Wed, 30 Jan 2019 17:02:04: #4 Write peak in narrowPeak format file... SRX4664644.10_peaks.narrowPeak INFO @ Wed, 30 Jan 2019 17:02:05: #4 Write summits bed file... SRX4664644.10_summits.bed INFO @ Wed, 30 Jan 2019 17:02:05: Done! pass1 - making usageList (15 chroms): 2 millis pass2 - checking and writing primary data (9053 records, 4 fields): 13 millis CompletedMACS2peakCalling INFO @ Wed, 30 Jan 2019 17:02:06: #4 Write output xls file... SRX4664644.20_peaks.xls INFO @ Wed, 30 Jan 2019 17:02:06: #4 Write peak in narrowPeak format file... SRX4664644.20_peaks.narrowPeak INFO @ Wed, 30 Jan 2019 17:02:06: #4 Write summits bed file... SRX4664644.20_summits.bed INFO @ Wed, 30 Jan 2019 17:02:06: Done! pass1 - making usageList (15 chroms): 2 millis pass2 - checking and writing primary data (6240 records, 4 fields): 9 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。