Job ID = 11598012 sra ファイルのダウンロード中... Completed: 724003K bytes transferred in 10 seconds (584377K 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 30166481 spots for /home/okishinya/chipatlas/results/dm3/SRX4664667/SRR7813094.sra Written 30166481 spots for /home/okishinya/chipatlas/results/dm3/SRX4664667/SRR7813094.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: 00:12:12 30166481 reads; of these: 30166481 (100.00%) were unpaired; of these: 1104781 (3.66%) aligned 0 times 19934295 (66.08%) aligned exactly 1 time 9127405 (30.26%) aligned >1 times 96.34% overall alignment rate Time searching: 00:12:12 Overall time: 00:12:12 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] 8445160 / 29061700 = 0.2906 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 17:16:03: # Command line: callpeak -t SRX4664667.bam -f BAM -g dm -n SRX4664667.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX4664667.05 # format = BAM # ChIP-seq file = ['SRX4664667.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 17:16:03: # Command line: callpeak -t SRX4664667.bam -f BAM -g dm -n SRX4664667.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX4664667.10 # format = BAM # ChIP-seq file = ['SRX4664667.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 17:16:03: # Command line: callpeak -t SRX4664667.bam -f BAM -g dm -n SRX4664667.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX4664667.20 # format = BAM # ChIP-seq file = ['SRX4664667.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 17:16:03: #1 read tag files... INFO @ Wed, 30 Jan 2019 17:16:03: #1 read tag files... INFO @ Wed, 30 Jan 2019 17:16:03: #1 read tag files... INFO @ Wed, 30 Jan 2019 17:16:03: #1 read treatment tags... INFO @ Wed, 30 Jan 2019 17:16:03: #1 read treatment tags... INFO @ Wed, 30 Jan 2019 17:16:03: #1 read treatment tags... INFO @ Wed, 30 Jan 2019 17:16:09: 1000000 INFO @ Wed, 30 Jan 2019 17:16:10: 1000000 INFO @ Wed, 30 Jan 2019 17:16:10: 1000000 INFO @ Wed, 30 Jan 2019 17:16:16: 2000000 INFO @ Wed, 30 Jan 2019 17:16:16: 2000000 INFO @ Wed, 30 Jan 2019 17:16:16: 2000000 INFO @ Wed, 30 Jan 2019 17:16:23: 3000000 INFO @ Wed, 30 Jan 2019 17:16:23: 3000000 INFO @ Wed, 30 Jan 2019 17:16:23: 3000000 INFO @ Wed, 30 Jan 2019 17:16:29: 4000000 INFO @ Wed, 30 Jan 2019 17:16:30: 4000000 INFO @ Wed, 30 Jan 2019 17:16:30: 4000000 INFO @ Wed, 30 Jan 2019 17:16:36: 5000000 INFO @ Wed, 30 Jan 2019 17:16:37: 5000000 INFO @ Wed, 30 Jan 2019 17:16:37: 5000000 INFO @ Wed, 30 Jan 2019 17:16:43: 6000000 INFO @ Wed, 30 Jan 2019 17:16:44: 6000000 INFO @ Wed, 30 Jan 2019 17:16:44: 6000000 INFO @ Wed, 30 Jan 2019 17:16:49: 7000000 INFO @ Wed, 30 Jan 2019 17:16:51: 7000000 INFO @ Wed, 30 Jan 2019 17:16:51: 7000000 INFO @ Wed, 30 Jan 2019 17:16:56: 8000000 INFO @ Wed, 30 Jan 2019 17:16:58: 8000000 INFO @ Wed, 30 Jan 2019 17:16:58: 8000000 INFO @ Wed, 30 Jan 2019 17:17:03: 9000000 INFO @ Wed, 30 Jan 2019 17:17:05: 9000000 INFO @ Wed, 30 Jan 2019 17:17:05: 9000000 INFO @ Wed, 30 Jan 2019 17:17:09: 10000000 INFO @ Wed, 30 Jan 2019 17:17:12: 10000000 INFO @ Wed, 30 Jan 2019 17:17:12: 10000000 INFO @ Wed, 30 Jan 2019 17:17:16: 11000000 INFO @ Wed, 30 Jan 2019 17:17:19: 11000000 INFO @ Wed, 30 Jan 2019 17:17:19: 11000000 INFO @ Wed, 30 Jan 2019 17:17:23: 12000000 INFO @ Wed, 30 Jan 2019 17:17:26: 12000000 INFO @ Wed, 30 Jan 2019 17:17:26: 12000000 INFO @ Wed, 30 Jan 2019 17:17:29: 13000000 INFO @ Wed, 30 Jan 2019 17:17:33: 13000000 INFO @ Wed, 30 Jan 2019 17:17:33: 13000000 INFO @ Wed, 30 Jan 2019 17:17:36: 14000000 INFO @ Wed, 30 Jan 2019 17:17:40: 14000000 INFO @ Wed, 30 Jan 2019 17:17:40: 14000000 INFO @ Wed, 30 Jan 2019 17:17:43: 15000000 INFO @ Wed, 30 Jan 2019 17:17:47: 15000000 INFO @ Wed, 30 Jan 2019 17:17:47: 15000000 INFO @ Wed, 30 Jan 2019 17:17:49: 16000000 INFO @ Wed, 30 Jan 2019 17:17:54: 16000000 INFO @ Wed, 30 Jan 2019 17:17:54: 16000000 INFO @ Wed, 30 Jan 2019 17:17:56: 17000000 INFO @ Wed, 30 Jan 2019 17:18:01: 17000000 INFO @ Wed, 30 Jan 2019 17:18:01: 17000000 INFO @ Wed, 30 Jan 2019 17:18:03: 18000000 INFO @ Wed, 30 Jan 2019 17:18:08: 18000000 INFO @ Wed, 30 Jan 2019 17:18:08: 18000000 INFO @ Wed, 30 Jan 2019 17:18:10: 19000000 INFO @ Wed, 30 Jan 2019 17:18:14: 19000000 INFO @ Wed, 30 Jan 2019 17:18:14: 19000000 INFO @ Wed, 30 Jan 2019 17:18:16: 20000000 INFO @ Wed, 30 Jan 2019 17:18:20: #1 tag size is determined as 50 bps INFO @ Wed, 30 Jan 2019 17:18:20: #1 tag size = 50 INFO @ Wed, 30 Jan 2019 17:18:20: #1 total tags in treatment: 20616540 INFO @ Wed, 30 Jan 2019 17:18:20: #1 user defined the maximum tags... INFO @ Wed, 30 Jan 2019 17:18:20: #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 17:18:21: #1 tags after filtering in treatment: 20616540 INFO @ Wed, 30 Jan 2019 17:18:21: #1 Redundant rate of treatment: 0.00 INFO @ Wed, 30 Jan 2019 17:18:21: #1 finished! INFO @ Wed, 30 Jan 2019 17:18:21: #2 Build Peak Model... INFO @ Wed, 30 Jan 2019 17:18:21: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 30 Jan 2019 17:18:21: 20000000 INFO @ Wed, 30 Jan 2019 17:18:21: 20000000 INFO @ Wed, 30 Jan 2019 17:18:22: #2 number of paired peaks: 1082 INFO @ Wed, 30 Jan 2019 17:18:22: start model_add_line... INFO @ Wed, 30 Jan 2019 17:18:23: start X-correlation... INFO @ Wed, 30 Jan 2019 17:18:23: end of X-cor INFO @ Wed, 30 Jan 2019 17:18:23: #2 finished! INFO @ Wed, 30 Jan 2019 17:18:23: #2 predicted fragment length is 154 bps INFO @ Wed, 30 Jan 2019 17:18:23: #2 alternative fragment length(s) may be 154 bps INFO @ Wed, 30 Jan 2019 17:18:23: #2.2 Generate R script for model : SRX4664667.10_model.r INFO @ Wed, 30 Jan 2019 17:18:23: #3 Call peaks... INFO @ Wed, 30 Jan 2019 17:18:23: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 30 Jan 2019 17:18:26: #1 tag size is determined as 50 bps INFO @ Wed, 30 Jan 2019 17:18:26: #1 tag size = 50 INFO @ Wed, 30 Jan 2019 17:18:26: #1 total tags in treatment: 20616540 INFO @ Wed, 30 Jan 2019 17:18:26: #1 user defined the maximum tags... INFO @ Wed, 30 Jan 2019 17:18:26: #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 17:18:26: #1 tag size is determined as 50 bps INFO @ Wed, 30 Jan 2019 17:18:26: #1 tag size = 50 INFO @ Wed, 30 Jan 2019 17:18:26: #1 total tags in treatment: 20616540 INFO @ Wed, 30 Jan 2019 17:18:26: #1 user defined the maximum tags... INFO @ Wed, 30 Jan 2019 17:18:26: #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 17:18:26: #1 tags after filtering in treatment: 20616540 INFO @ Wed, 30 Jan 2019 17:18:26: #1 Redundant rate of treatment: 0.00 INFO @ Wed, 30 Jan 2019 17:18:26: #1 finished! INFO @ Wed, 30 Jan 2019 17:18:26: #2 Build Peak Model... INFO @ Wed, 30 Jan 2019 17:18:26: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 30 Jan 2019 17:18:26: #1 tags after filtering in treatment: 20616540 INFO @ Wed, 30 Jan 2019 17:18:26: #1 Redundant rate of treatment: 0.00 INFO @ Wed, 30 Jan 2019 17:18:26: #1 finished! INFO @ Wed, 30 Jan 2019 17:18:26: #2 Build Peak Model... INFO @ Wed, 30 Jan 2019 17:18:26: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 30 Jan 2019 17:18:27: #2 number of paired peaks: 1082 INFO @ Wed, 30 Jan 2019 17:18:27: start model_add_line... INFO @ Wed, 30 Jan 2019 17:18:28: #2 number of paired peaks: 1082 INFO @ Wed, 30 Jan 2019 17:18:28: start model_add_line... INFO @ Wed, 30 Jan 2019 17:18:28: start X-correlation... INFO @ Wed, 30 Jan 2019 17:18:28: end of X-cor INFO @ Wed, 30 Jan 2019 17:18:28: #2 finished! INFO @ Wed, 30 Jan 2019 17:18:28: #2 predicted fragment length is 154 bps INFO @ Wed, 30 Jan 2019 17:18:28: #2 alternative fragment length(s) may be 154 bps INFO @ Wed, 30 Jan 2019 17:18:28: #2.2 Generate R script for model : SRX4664667.05_model.r INFO @ Wed, 30 Jan 2019 17:18:28: #3 Call peaks... INFO @ Wed, 30 Jan 2019 17:18:28: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 30 Jan 2019 17:18:28: start X-correlation... INFO @ Wed, 30 Jan 2019 17:18:28: end of X-cor INFO @ Wed, 30 Jan 2019 17:18:28: #2 finished! INFO @ Wed, 30 Jan 2019 17:18:28: #2 predicted fragment length is 154 bps INFO @ Wed, 30 Jan 2019 17:18:28: #2 alternative fragment length(s) may be 154 bps INFO @ Wed, 30 Jan 2019 17:18:28: #2.2 Generate R script for model : SRX4664667.20_model.r INFO @ Wed, 30 Jan 2019 17:18:28: #3 Call peaks... INFO @ Wed, 30 Jan 2019 17:18:28: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 30 Jan 2019 17:19:08: #3 Call peaks for each chromosome... INFO @ Wed, 30 Jan 2019 17:19:14: #3 Call peaks for each chromosome... INFO @ Wed, 30 Jan 2019 17:19:15: #3 Call peaks for each chromosome... INFO @ Wed, 30 Jan 2019 17:19:31: #4 Write output xls file... SRX4664667.10_peaks.xls INFO @ Wed, 30 Jan 2019 17:19:31: #4 Write peak in narrowPeak format file... SRX4664667.10_peaks.narrowPeak INFO @ Wed, 30 Jan 2019 17:19:31: #4 Write summits bed file... SRX4664667.10_summits.bed INFO @ Wed, 30 Jan 2019 17:19:31: Done! pass1 - making usageList (15 chroms): 2 millis pass2 - checking and writing primary data (4420 records, 4 fields): 6 millis CompletedMACS2peakCalling INFO @ Wed, 30 Jan 2019 17:19:36: #4 Write output xls file... SRX4664667.20_peaks.xls INFO @ Wed, 30 Jan 2019 17:19:36: #4 Write peak in narrowPeak format file... SRX4664667.20_peaks.narrowPeak INFO @ Wed, 30 Jan 2019 17:19:36: #4 Write summits bed file... SRX4664667.20_summits.bed INFO @ Wed, 30 Jan 2019 17:19:36: Done! pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (2654 records, 4 fields): 5 millis CompletedMACS2peakCalling INFO @ Wed, 30 Jan 2019 17:19:39: #4 Write output xls file... SRX4664667.05_peaks.xls INFO @ Wed, 30 Jan 2019 17:19:39: #4 Write peak in narrowPeak format file... SRX4664667.05_peaks.narrowPeak INFO @ Wed, 30 Jan 2019 17:19:39: #4 Write summits bed file... SRX4664667.05_summits.bed INFO @ Wed, 30 Jan 2019 17:19:39: Done! pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (6545 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。