Job ID = 10450717 sra ファイルのダウンロード中... Completed: 377258K bytes transferred in 22 seconds (139456K 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... Written 19411300 spots for /home/okishinya/chipatlas/results/dm3/SRX3404011/SRR6303488.sra Written 19411300 spots total 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: 00:00:01 Multiseed full-index search: 00:07:09 19411300 reads; of these: 19411300 (100.00%) were unpaired; of these: 450477 (2.32%) aligned 0 times 14405473 (74.21%) aligned exactly 1 time 4555350 (23.47%) aligned >1 times 97.68% overall alignment rate Time searching: 00:07:10 Overall time: 00:07:10 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] 3120213 / 18960823 = 0.1646 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, 07 Feb 2018 11:01:28: # Command line: callpeak -t SRX3404011.bam -f BAM -g dm -n SRX3404011.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX3404011.05 # format = BAM # ChIP-seq file = ['SRX3404011.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, 07 Feb 2018 11:01:28: #1 read tag files... INFO @ Wed, 07 Feb 2018 11:01:28: #1 read treatment tags... INFO @ Wed, 07 Feb 2018 11:01:28: # Command line: callpeak -t SRX3404011.bam -f BAM -g dm -n SRX3404011.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX3404011.10 # format = BAM # ChIP-seq file = ['SRX3404011.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, 07 Feb 2018 11:01:28: #1 read tag files... INFO @ Wed, 07 Feb 2018 11:01:28: #1 read treatment tags... INFO @ Wed, 07 Feb 2018 11:01:28: # Command line: callpeak -t SRX3404011.bam -f BAM -g dm -n SRX3404011.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX3404011.20 # format = BAM # ChIP-seq file = ['SRX3404011.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, 07 Feb 2018 11:01:28: #1 read tag files... INFO @ Wed, 07 Feb 2018 11:01:28: #1 read treatment tags... INFO @ Wed, 07 Feb 2018 11:01:35: 1000000 INFO @ Wed, 07 Feb 2018 11:01:35: 1000000 INFO @ Wed, 07 Feb 2018 11:01:36: 1000000 INFO @ Wed, 07 Feb 2018 11:01:42: 2000000 INFO @ Wed, 07 Feb 2018 11:01:42: 2000000 INFO @ Wed, 07 Feb 2018 11:01:43: 2000000 INFO @ Wed, 07 Feb 2018 11:01:49: 3000000 INFO @ Wed, 07 Feb 2018 11:01:49: 3000000 INFO @ Wed, 07 Feb 2018 11:01:50: 3000000 INFO @ Wed, 07 Feb 2018 11:01:55: 4000000 INFO @ Wed, 07 Feb 2018 11:01:55: 4000000 INFO @ Wed, 07 Feb 2018 11:01:57: 4000000 INFO @ Wed, 07 Feb 2018 11:02:02: 5000000 INFO @ Wed, 07 Feb 2018 11:02:02: 5000000 INFO @ Wed, 07 Feb 2018 11:02:04: 5000000 INFO @ Wed, 07 Feb 2018 11:02:09: 6000000 INFO @ Wed, 07 Feb 2018 11:02:09: 6000000 INFO @ Wed, 07 Feb 2018 11:02:11: 6000000 INFO @ Wed, 07 Feb 2018 11:02:15: 7000000 INFO @ Wed, 07 Feb 2018 11:02:15: 7000000 INFO @ Wed, 07 Feb 2018 11:02:19: 7000000 INFO @ Wed, 07 Feb 2018 11:02:22: 8000000 INFO @ Wed, 07 Feb 2018 11:02:22: 8000000 INFO @ Wed, 07 Feb 2018 11:02:26: 8000000 INFO @ Wed, 07 Feb 2018 11:02:29: 9000000 INFO @ Wed, 07 Feb 2018 11:02:29: 9000000 INFO @ Wed, 07 Feb 2018 11:02:33: 9000000 INFO @ Wed, 07 Feb 2018 11:02:35: 10000000 INFO @ Wed, 07 Feb 2018 11:02:36: 10000000 INFO @ Wed, 07 Feb 2018 11:02:40: 10000000 INFO @ Wed, 07 Feb 2018 11:02:42: 11000000 INFO @ Wed, 07 Feb 2018 11:02:42: 11000000 INFO @ Wed, 07 Feb 2018 11:02:47: 11000000 INFO @ Wed, 07 Feb 2018 11:02:49: 12000000 INFO @ Wed, 07 Feb 2018 11:02:49: 12000000 INFO @ Wed, 07 Feb 2018 11:02:54: 12000000 INFO @ Wed, 07 Feb 2018 11:02:56: 13000000 INFO @ Wed, 07 Feb 2018 11:02:56: 13000000 INFO @ Wed, 07 Feb 2018 11:03:01: 13000000 INFO @ Wed, 07 Feb 2018 11:03:03: 14000000 INFO @ Wed, 07 Feb 2018 11:03:03: 14000000 INFO @ Wed, 07 Feb 2018 11:03:09: 14000000 INFO @ Wed, 07 Feb 2018 11:03:10: 15000000 INFO @ Wed, 07 Feb 2018 11:03:10: 15000000 INFO @ Wed, 07 Feb 2018 11:03:16: 15000000 INFO @ Wed, 07 Feb 2018 11:03:16: #1 tag size is determined as 51 bps INFO @ Wed, 07 Feb 2018 11:03:16: #1 tag size = 51 INFO @ Wed, 07 Feb 2018 11:03:16: #1 total tags in treatment: 15840610 INFO @ Wed, 07 Feb 2018 11:03:16: #1 user defined the maximum tags... INFO @ Wed, 07 Feb 2018 11:03:16: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Wed, 07 Feb 2018 11:03:16: #1 tags after filtering in treatment: 15840610 INFO @ Wed, 07 Feb 2018 11:03:16: #1 Redundant rate of treatment: 0.00 INFO @ Wed, 07 Feb 2018 11:03:16: #1 finished! INFO @ Wed, 07 Feb 2018 11:03:16: #2 Build Peak Model... INFO @ Wed, 07 Feb 2018 11:03:16: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 07 Feb 2018 11:03:16: #1 tag size is determined as 51 bps INFO @ Wed, 07 Feb 2018 11:03:16: #1 tag size = 51 INFO @ Wed, 07 Feb 2018 11:03:16: #1 total tags in treatment: 15840610 INFO @ Wed, 07 Feb 2018 11:03:16: #1 user defined the maximum tags... INFO @ Wed, 07 Feb 2018 11:03:16: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Wed, 07 Feb 2018 11:03:17: #1 tags after filtering in treatment: 15840610 INFO @ Wed, 07 Feb 2018 11:03:17: #1 Redundant rate of treatment: 0.00 INFO @ Wed, 07 Feb 2018 11:03:17: #1 finished! INFO @ Wed, 07 Feb 2018 11:03:17: #2 Build Peak Model... INFO @ Wed, 07 Feb 2018 11:03:17: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 07 Feb 2018 11:03:17: #2 number of paired peaks: 1193 INFO @ Wed, 07 Feb 2018 11:03:17: start model_add_line... INFO @ Wed, 07 Feb 2018 11:03:17: start X-correlation... INFO @ Wed, 07 Feb 2018 11:03:17: end of X-cor INFO @ Wed, 07 Feb 2018 11:03:17: #2 finished! INFO @ Wed, 07 Feb 2018 11:03:17: #2 predicted fragment length is 188 bps INFO @ Wed, 07 Feb 2018 11:03:17: #2 alternative fragment length(s) may be 188 bps INFO @ Wed, 07 Feb 2018 11:03:17: #2.2 Generate R script for model : SRX3404011.05_model.r INFO @ Wed, 07 Feb 2018 11:03:17: #3 Call peaks... INFO @ Wed, 07 Feb 2018 11:03:17: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 07 Feb 2018 11:03:18: #2 number of paired peaks: 1193 INFO @ Wed, 07 Feb 2018 11:03:18: start model_add_line... INFO @ Wed, 07 Feb 2018 11:03:18: start X-correlation... INFO @ Wed, 07 Feb 2018 11:03:18: end of X-cor INFO @ Wed, 07 Feb 2018 11:03:18: #2 finished! INFO @ Wed, 07 Feb 2018 11:03:18: #2 predicted fragment length is 188 bps INFO @ Wed, 07 Feb 2018 11:03:18: #2 alternative fragment length(s) may be 188 bps INFO @ Wed, 07 Feb 2018 11:03:18: #2.2 Generate R script for model : SRX3404011.10_model.r INFO @ Wed, 07 Feb 2018 11:03:18: #3 Call peaks... INFO @ Wed, 07 Feb 2018 11:03:18: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 07 Feb 2018 11:03:22: #1 tag size is determined as 51 bps INFO @ Wed, 07 Feb 2018 11:03:22: #1 tag size = 51 INFO @ Wed, 07 Feb 2018 11:03:22: #1 total tags in treatment: 15840610 INFO @ Wed, 07 Feb 2018 11:03:22: #1 user defined the maximum tags... INFO @ Wed, 07 Feb 2018 11:03:22: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Wed, 07 Feb 2018 11:03:22: #1 tags after filtering in treatment: 15840610 INFO @ Wed, 07 Feb 2018 11:03:22: #1 Redundant rate of treatment: 0.00 INFO @ Wed, 07 Feb 2018 11:03:22: #1 finished! INFO @ Wed, 07 Feb 2018 11:03:22: #2 Build Peak Model... INFO @ Wed, 07 Feb 2018 11:03:22: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 07 Feb 2018 11:03:23: #2 number of paired peaks: 1193 INFO @ Wed, 07 Feb 2018 11:03:23: start model_add_line... INFO @ Wed, 07 Feb 2018 11:03:24: start X-correlation... INFO @ Wed, 07 Feb 2018 11:03:24: end of X-cor INFO @ Wed, 07 Feb 2018 11:03:24: #2 finished! INFO @ Wed, 07 Feb 2018 11:03:24: #2 predicted fragment length is 188 bps INFO @ Wed, 07 Feb 2018 11:03:24: #2 alternative fragment length(s) may be 188 bps INFO @ Wed, 07 Feb 2018 11:03:24: #2.2 Generate R script for model : SRX3404011.20_model.r INFO @ Wed, 07 Feb 2018 11:03:24: #3 Call peaks... INFO @ Wed, 07 Feb 2018 11:03:24: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 07 Feb 2018 11:03:57: #3 Call peaks for each chromosome... INFO @ Wed, 07 Feb 2018 11:03:59: #3 Call peaks for each chromosome... INFO @ Wed, 07 Feb 2018 11:04:06: #3 Call peaks for each chromosome... INFO @ Wed, 07 Feb 2018 11:04:18: #4 Write output xls file... SRX3404011.05_peaks.xls INFO @ Wed, 07 Feb 2018 11:04:18: #4 Write peak in narrowPeak format file... SRX3404011.05_peaks.narrowPeak INFO @ Wed, 07 Feb 2018 11:04:18: #4 Write summits bed file... SRX3404011.05_summits.bed INFO @ Wed, 07 Feb 2018 11:04:18: Done! pass1 - making usageList (14 chroms): 2 millis pass2 - checking and writing primary data (5586 records, 4 fields): 8 millis CompletedMACS2peakCalling INFO @ Wed, 07 Feb 2018 11:04:21: #4 Write output xls file... SRX3404011.10_peaks.xls INFO @ Wed, 07 Feb 2018 11:04:21: #4 Write peak in narrowPeak format file... SRX3404011.10_peaks.narrowPeak INFO @ Wed, 07 Feb 2018 11:04:21: #4 Write summits bed file... SRX3404011.10_summits.bed INFO @ Wed, 07 Feb 2018 11:04:21: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (3672 records, 4 fields): 7 millis CompletedMACS2peakCalling INFO @ Wed, 07 Feb 2018 11:04:27: #4 Write output xls file... SRX3404011.20_peaks.xls INFO @ Wed, 07 Feb 2018 11:04:27: #4 Write peak in narrowPeak format file... SRX3404011.20_peaks.narrowPeak INFO @ Wed, 07 Feb 2018 11:04:27: #4 Write summits bed file... SRX3404011.20_summits.bed INFO @ Wed, 07 Feb 2018 11:04:27: Done! pass1 - making usageList (13 chroms): 1 millis pass2 - checking and writing primary data (2581 records, 4 fields): 5 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。