Job ID = 10450996 sra ファイルのダウンロード中... Completed: 427499K bytes transferred in 26 seconds (133988K 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 22527570 spots for /home/okishinya/chipatlas/results/dm3/SRX3404047/SRR6303524.sra Written 22527570 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: 00:19:18 22527570 reads; of these: 22527570 (100.00%) were unpaired; of these: 582955 (2.59%) aligned 0 times 15861559 (70.41%) aligned exactly 1 time 6083056 (27.00%) aligned >1 times 97.41% overall alignment rate Time searching: 00:19:19 Overall time: 00:19:19 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] 5322420 / 21944615 = 0.2425 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 14:58:43: # Command line: callpeak -t SRX3404047.bam -f BAM -g dm -n SRX3404047.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX3404047.20 # format = BAM # ChIP-seq file = ['SRX3404047.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 14:58:43: #1 read tag files... INFO @ Wed, 07 Feb 2018 14:58:43: #1 read treatment tags... INFO @ Wed, 07 Feb 2018 14:58:43: # Command line: callpeak -t SRX3404047.bam -f BAM -g dm -n SRX3404047.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX3404047.10 # format = BAM # ChIP-seq file = ['SRX3404047.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 14:58:43: #1 read tag files... INFO @ Wed, 07 Feb 2018 14:58:43: #1 read treatment tags... INFO @ Wed, 07 Feb 2018 14:58:43: # Command line: callpeak -t SRX3404047.bam -f BAM -g dm -n SRX3404047.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX3404047.05 # format = BAM # ChIP-seq file = ['SRX3404047.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 14:58:43: #1 read tag files... INFO @ Wed, 07 Feb 2018 14:58:43: #1 read treatment tags... INFO @ Wed, 07 Feb 2018 14:58:56: 1000000 INFO @ Wed, 07 Feb 2018 14:58:59: 1000000 INFO @ Wed, 07 Feb 2018 14:59:02: 1000000 INFO @ Wed, 07 Feb 2018 14:59:05: 2000000 INFO @ Wed, 07 Feb 2018 14:59:16: 3000000 INFO @ Wed, 07 Feb 2018 14:59:18: 2000000 INFO @ Wed, 07 Feb 2018 14:59:21: 2000000 INFO @ Wed, 07 Feb 2018 14:59:27: 4000000 INFO @ Wed, 07 Feb 2018 14:59:34: 3000000 INFO @ Wed, 07 Feb 2018 14:59:37: 5000000 INFO @ Wed, 07 Feb 2018 14:59:39: 3000000 INFO @ Wed, 07 Feb 2018 14:59:46: 6000000 INFO @ Wed, 07 Feb 2018 14:59:50: 4000000 INFO @ Wed, 07 Feb 2018 14:59:56: 7000000 INFO @ Wed, 07 Feb 2018 14:59:58: 4000000 INFO @ Wed, 07 Feb 2018 15:00:05: 8000000 INFO @ Wed, 07 Feb 2018 15:00:06: 5000000 INFO @ Wed, 07 Feb 2018 15:00:14: 9000000 INFO @ Wed, 07 Feb 2018 15:00:15: 5000000 INFO @ Wed, 07 Feb 2018 15:00:17: 6000000 INFO @ Wed, 07 Feb 2018 15:00:22: 10000000 INFO @ Wed, 07 Feb 2018 15:00:26: 7000000 INFO @ Wed, 07 Feb 2018 15:00:30: 6000000 INFO @ Wed, 07 Feb 2018 15:00:30: 11000000 INFO @ Wed, 07 Feb 2018 15:00:35: 8000000 INFO @ Wed, 07 Feb 2018 15:00:38: 12000000 INFO @ Wed, 07 Feb 2018 15:00:43: 7000000 INFO @ Wed, 07 Feb 2018 15:00:46: 9000000 INFO @ Wed, 07 Feb 2018 15:00:46: 13000000 INFO @ Wed, 07 Feb 2018 15:00:54: 14000000 INFO @ Wed, 07 Feb 2018 15:00:55: 10000000 INFO @ Wed, 07 Feb 2018 15:00:57: 8000000 INFO @ Wed, 07 Feb 2018 15:01:03: 15000000 INFO @ Wed, 07 Feb 2018 15:01:06: 11000000 INFO @ Wed, 07 Feb 2018 15:01:11: 16000000 INFO @ Wed, 07 Feb 2018 15:01:12: 9000000 INFO @ Wed, 07 Feb 2018 15:01:16: 12000000 INFO @ Wed, 07 Feb 2018 15:01:17: #1 tag size is determined as 51 bps INFO @ Wed, 07 Feb 2018 15:01:17: #1 tag size = 51 INFO @ Wed, 07 Feb 2018 15:01:17: #1 total tags in treatment: 16622195 INFO @ Wed, 07 Feb 2018 15:01:17: #1 user defined the maximum tags... INFO @ Wed, 07 Feb 2018 15:01:17: #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 15:01:17: #1 tags after filtering in treatment: 16622195 INFO @ Wed, 07 Feb 2018 15:01:17: #1 Redundant rate of treatment: 0.00 INFO @ Wed, 07 Feb 2018 15:01:17: #1 finished! INFO @ Wed, 07 Feb 2018 15:01:17: #2 Build Peak Model... INFO @ Wed, 07 Feb 2018 15:01:17: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 07 Feb 2018 15:01:19: #2 number of paired peaks: 1961 INFO @ Wed, 07 Feb 2018 15:01:19: start model_add_line... INFO @ Wed, 07 Feb 2018 15:01:20: start X-correlation... INFO @ Wed, 07 Feb 2018 15:01:20: end of X-cor INFO @ Wed, 07 Feb 2018 15:01:20: #2 finished! INFO @ Wed, 07 Feb 2018 15:01:20: #2 predicted fragment length is 177 bps INFO @ Wed, 07 Feb 2018 15:01:20: #2 alternative fragment length(s) may be 177 bps INFO @ Wed, 07 Feb 2018 15:01:20: #2.2 Generate R script for model : SRX3404047.05_model.r INFO @ Wed, 07 Feb 2018 15:01:20: #3 Call peaks... INFO @ Wed, 07 Feb 2018 15:01:20: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 07 Feb 2018 15:01:25: 10000000 INFO @ Wed, 07 Feb 2018 15:01:28: 13000000 INFO @ Wed, 07 Feb 2018 15:01:40: 11000000 INFO @ Wed, 07 Feb 2018 15:01:45: 14000000 INFO @ Wed, 07 Feb 2018 15:01:58: 12000000 INFO @ Wed, 07 Feb 2018 15:02:04: 15000000 INFO @ Wed, 07 Feb 2018 15:02:12: 13000000 INFO @ Wed, 07 Feb 2018 15:02:16: #3 Call peaks for each chromosome... INFO @ Wed, 07 Feb 2018 15:02:19: 16000000 INFO @ Wed, 07 Feb 2018 15:02:25: 14000000 INFO @ Wed, 07 Feb 2018 15:02:29: #1 tag size is determined as 51 bps INFO @ Wed, 07 Feb 2018 15:02:29: #1 tag size = 51 INFO @ Wed, 07 Feb 2018 15:02:29: #1 total tags in treatment: 16622195 INFO @ Wed, 07 Feb 2018 15:02:29: #1 user defined the maximum tags... INFO @ Wed, 07 Feb 2018 15:02:29: #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 15:02:30: #1 tags after filtering in treatment: 16622195 INFO @ Wed, 07 Feb 2018 15:02:30: #1 Redundant rate of treatment: 0.00 INFO @ Wed, 07 Feb 2018 15:02:30: #1 finished! INFO @ Wed, 07 Feb 2018 15:02:30: #2 Build Peak Model... INFO @ Wed, 07 Feb 2018 15:02:30: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 07 Feb 2018 15:02:31: #2 number of paired peaks: 1961 INFO @ Wed, 07 Feb 2018 15:02:31: start model_add_line... INFO @ Wed, 07 Feb 2018 15:02:32: start X-correlation... INFO @ Wed, 07 Feb 2018 15:02:32: end of X-cor INFO @ Wed, 07 Feb 2018 15:02:32: #2 finished! INFO @ Wed, 07 Feb 2018 15:02:32: #2 predicted fragment length is 177 bps INFO @ Wed, 07 Feb 2018 15:02:32: #2 alternative fragment length(s) may be 177 bps INFO @ Wed, 07 Feb 2018 15:02:32: #2.2 Generate R script for model : SRX3404047.20_model.r INFO @ Wed, 07 Feb 2018 15:02:32: #3 Call peaks... INFO @ Wed, 07 Feb 2018 15:02:32: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 07 Feb 2018 15:02:38: 15000000 INFO @ Wed, 07 Feb 2018 15:02:45: #4 Write output xls file... SRX3404047.05_peaks.xls INFO @ Wed, 07 Feb 2018 15:02:45: #4 Write peak in narrowPeak format file... SRX3404047.05_peaks.narrowPeak INFO @ Wed, 07 Feb 2018 15:02:45: #4 Write summits bed file... SRX3404047.05_summits.bed INFO @ Wed, 07 Feb 2018 15:02:45: Done! pass1 - making usageList (15 chroms): 3 millis pass2 - checking and writing primary data (5957 records, 4 fields): 12 millis CompletedMACS2peakCalling INFO @ Wed, 07 Feb 2018 15:02:51: 16000000 INFO @ Wed, 07 Feb 2018 15:02:59: #1 tag size is determined as 51 bps INFO @ Wed, 07 Feb 2018 15:02:59: #1 tag size = 51 INFO @ Wed, 07 Feb 2018 15:02:59: #1 total tags in treatment: 16622195 INFO @ Wed, 07 Feb 2018 15:02:59: #1 user defined the maximum tags... INFO @ Wed, 07 Feb 2018 15:02:59: #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 15:03:00: #1 tags after filtering in treatment: 16622195 INFO @ Wed, 07 Feb 2018 15:03:00: #1 Redundant rate of treatment: 0.00 INFO @ Wed, 07 Feb 2018 15:03:00: #1 finished! INFO @ Wed, 07 Feb 2018 15:03:00: #2 Build Peak Model... INFO @ Wed, 07 Feb 2018 15:03:00: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 07 Feb 2018 15:03:02: #2 number of paired peaks: 1961 INFO @ Wed, 07 Feb 2018 15:03:02: start model_add_line... INFO @ Wed, 07 Feb 2018 15:03:02: start X-correlation... INFO @ Wed, 07 Feb 2018 15:03:02: end of X-cor INFO @ Wed, 07 Feb 2018 15:03:02: #2 finished! INFO @ Wed, 07 Feb 2018 15:03:02: #2 predicted fragment length is 177 bps INFO @ Wed, 07 Feb 2018 15:03:02: #2 alternative fragment length(s) may be 177 bps INFO @ Wed, 07 Feb 2018 15:03:02: #2.2 Generate R script for model : SRX3404047.10_model.r INFO @ Wed, 07 Feb 2018 15:03:02: #3 Call peaks... INFO @ Wed, 07 Feb 2018 15:03:02: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 07 Feb 2018 15:03:29: #3 Call peaks for each chromosome... INFO @ Wed, 07 Feb 2018 15:03:55: #3 Call peaks for each chromosome... INFO @ Wed, 07 Feb 2018 15:03:58: #4 Write output xls file... SRX3404047.20_peaks.xls INFO @ Wed, 07 Feb 2018 15:03:58: #4 Write peak in narrowPeak format file... SRX3404047.20_peaks.narrowPeak INFO @ Wed, 07 Feb 2018 15:03:58: #4 Write summits bed file... SRX3404047.20_summits.bed INFO @ Wed, 07 Feb 2018 15:03:58: Done! pass1 - making usageList (15 chroms): 2 millis pass2 - checking and writing primary data (3725 records, 4 fields): 10 millis CompletedMACS2peakCalling INFO @ Wed, 07 Feb 2018 15:04:24: #4 Write output xls file... SRX3404047.10_peaks.xls INFO @ Wed, 07 Feb 2018 15:04:25: #4 Write peak in narrowPeak format file... SRX3404047.10_peaks.narrowPeak INFO @ Wed, 07 Feb 2018 15:04:25: #4 Write summits bed file... SRX3404047.10_summits.bed INFO @ Wed, 07 Feb 2018 15:04:25: Done! pass1 - making usageList (15 chroms): 2 millis pass2 - checking and writing primary data (4778 records, 4 fields): 33 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。