Job ID = 10608884 sra ファイルのダウンロード中... Completed: 518703K bytes transferred in 55 seconds (76533K 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 15890225 spots for /home/okishinya/chipatlas/results/rn6/SRX3145023/SRR5989256.sra Written 15890225 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: 00:00:01 Time loading forward index: 00:00:01 Time loading mirror index: 00:00:01 Multiseed full-index search: 00:09:57 15890225 reads; of these: 15890225 (100.00%) were unpaired; of these: 308563 (1.94%) aligned 0 times 13121482 (82.58%) aligned exactly 1 time 2460180 (15.48%) aligned >1 times 98.06% overall alignment rate Time searching: 00:10:00 Overall time: 00:10:00 マッピングが完了しました。 samtools でBAM に変換中... [samopen] SAM header is present: 953 sequences. [bam_sort_core] merging from 8 files... [bam_rmdupse_core] 467832 / 15581662 = 0.0300 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 @ Thu, 03 May 2018 22:38:02: # Command line: callpeak -t SRX3145023.bam -f BAM -g 2.15e9 -n SRX3145023.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX3145023.05 # format = BAM # ChIP-seq file = ['SRX3145023.bam'] # control file = None # effective genome size = 2.15e+09 # 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 @ Thu, 03 May 2018 22:38:02: #1 read tag files... INFO @ Thu, 03 May 2018 22:38:02: #1 read treatment tags... INFO @ Thu, 03 May 2018 22:38:02: # Command line: callpeak -t SRX3145023.bam -f BAM -g 2.15e9 -n SRX3145023.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX3145023.20 # format = BAM # ChIP-seq file = ['SRX3145023.bam'] # control file = None # effective genome size = 2.15e+09 # 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 @ Thu, 03 May 2018 22:38:02: #1 read tag files... INFO @ Thu, 03 May 2018 22:38:02: #1 read treatment tags... INFO @ Thu, 03 May 2018 22:38:02: # Command line: callpeak -t SRX3145023.bam -f BAM -g 2.15e9 -n SRX3145023.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX3145023.10 # format = BAM # ChIP-seq file = ['SRX3145023.bam'] # control file = None # effective genome size = 2.15e+09 # 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 @ Thu, 03 May 2018 22:38:02: #1 read tag files... INFO @ Thu, 03 May 2018 22:38:02: #1 read treatment tags... INFO @ Thu, 03 May 2018 22:38:08: 1000000 INFO @ Thu, 03 May 2018 22:38:09: 1000000 INFO @ Thu, 03 May 2018 22:38:09: 1000000 INFO @ Thu, 03 May 2018 22:38:14: 2000000 INFO @ Thu, 03 May 2018 22:38:15: 2000000 INFO @ Thu, 03 May 2018 22:38:15: 2000000 INFO @ Thu, 03 May 2018 22:38:20: 3000000 INFO @ Thu, 03 May 2018 22:38:21: 3000000 INFO @ Thu, 03 May 2018 22:38:22: 3000000 INFO @ Thu, 03 May 2018 22:38:27: 4000000 INFO @ Thu, 03 May 2018 22:38:28: 4000000 INFO @ Thu, 03 May 2018 22:38:28: 4000000 INFO @ Thu, 03 May 2018 22:38:33: 5000000 INFO @ Thu, 03 May 2018 22:38:34: 5000000 INFO @ Thu, 03 May 2018 22:38:35: 5000000 INFO @ Thu, 03 May 2018 22:38:39: 6000000 INFO @ Thu, 03 May 2018 22:38:40: 6000000 INFO @ Thu, 03 May 2018 22:38:42: 6000000 INFO @ Thu, 03 May 2018 22:38:45: 7000000 INFO @ Thu, 03 May 2018 22:38:46: 7000000 INFO @ Thu, 03 May 2018 22:38:48: 7000000 INFO @ Thu, 03 May 2018 22:38:52: 8000000 INFO @ Thu, 03 May 2018 22:38:53: 8000000 INFO @ Thu, 03 May 2018 22:38:55: 8000000 INFO @ Thu, 03 May 2018 22:38:58: 9000000 INFO @ Thu, 03 May 2018 22:38:59: 9000000 INFO @ Thu, 03 May 2018 22:39:02: 9000000 INFO @ Thu, 03 May 2018 22:39:04: 10000000 INFO @ Thu, 03 May 2018 22:39:05: 10000000 INFO @ Thu, 03 May 2018 22:39:09: 10000000 INFO @ Thu, 03 May 2018 22:39:11: 11000000 INFO @ Thu, 03 May 2018 22:39:11: 11000000 INFO @ Thu, 03 May 2018 22:39:15: 11000000 INFO @ Thu, 03 May 2018 22:39:17: 12000000 INFO @ Thu, 03 May 2018 22:39:18: 12000000 INFO @ Thu, 03 May 2018 22:39:22: 12000000 INFO @ Thu, 03 May 2018 22:39:23: 13000000 INFO @ Thu, 03 May 2018 22:39:24: 13000000 INFO @ Thu, 03 May 2018 22:39:29: 13000000 INFO @ Thu, 03 May 2018 22:39:30: 14000000 INFO @ Thu, 03 May 2018 22:39:30: 14000000 INFO @ Thu, 03 May 2018 22:39:36: 14000000 INFO @ Thu, 03 May 2018 22:39:36: 15000000 INFO @ Thu, 03 May 2018 22:39:37: 15000000 INFO @ Thu, 03 May 2018 22:39:37: #1 tag size is determined as 51 bps INFO @ Thu, 03 May 2018 22:39:37: #1 tag size = 51 INFO @ Thu, 03 May 2018 22:39:37: #1 total tags in treatment: 15113830 INFO @ Thu, 03 May 2018 22:39:37: #1 user defined the maximum tags... INFO @ Thu, 03 May 2018 22:39:37: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Thu, 03 May 2018 22:39:37: #1 tags after filtering in treatment: 15113618 INFO @ Thu, 03 May 2018 22:39:37: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 03 May 2018 22:39:37: #1 finished! INFO @ Thu, 03 May 2018 22:39:37: #2 Build Peak Model... INFO @ Thu, 03 May 2018 22:39:37: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 03 May 2018 22:39:38: #1 tag size is determined as 51 bps INFO @ Thu, 03 May 2018 22:39:38: #1 tag size = 51 INFO @ Thu, 03 May 2018 22:39:38: #1 total tags in treatment: 15113830 INFO @ Thu, 03 May 2018 22:39:38: #1 user defined the maximum tags... INFO @ Thu, 03 May 2018 22:39:38: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Thu, 03 May 2018 22:39:38: #1 tags after filtering in treatment: 15113618 INFO @ Thu, 03 May 2018 22:39:38: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 03 May 2018 22:39:38: #1 finished! INFO @ Thu, 03 May 2018 22:39:38: #2 Build Peak Model... INFO @ Thu, 03 May 2018 22:39:38: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 03 May 2018 22:39:41: #2 number of paired peaks: 51620 INFO @ Thu, 03 May 2018 22:39:41: start model_add_line... INFO @ Thu, 03 May 2018 22:39:41: start X-correlation... INFO @ Thu, 03 May 2018 22:39:41: end of X-cor INFO @ Thu, 03 May 2018 22:39:41: #2 finished! INFO @ Thu, 03 May 2018 22:39:41: #2 predicted fragment length is 292 bps INFO @ Thu, 03 May 2018 22:39:41: #2 alternative fragment length(s) may be 292 bps INFO @ Thu, 03 May 2018 22:39:41: #2.2 Generate R script for model : SRX3145023.10_model.r INFO @ Thu, 03 May 2018 22:39:41: #3 Call peaks... INFO @ Thu, 03 May 2018 22:39:41: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 03 May 2018 22:39:42: 15000000 INFO @ Thu, 03 May 2018 22:39:42: #2 number of paired peaks: 51620 INFO @ Thu, 03 May 2018 22:39:42: start model_add_line... INFO @ Thu, 03 May 2018 22:39:42: start X-correlation... INFO @ Thu, 03 May 2018 22:39:42: end of X-cor INFO @ Thu, 03 May 2018 22:39:42: #2 finished! INFO @ Thu, 03 May 2018 22:39:42: #2 predicted fragment length is 292 bps INFO @ Thu, 03 May 2018 22:39:42: #2 alternative fragment length(s) may be 292 bps INFO @ Thu, 03 May 2018 22:39:42: #2.2 Generate R script for model : SRX3145023.20_model.r INFO @ Thu, 03 May 2018 22:39:42: #3 Call peaks... INFO @ Thu, 03 May 2018 22:39:42: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 03 May 2018 22:39:43: #1 tag size is determined as 51 bps INFO @ Thu, 03 May 2018 22:39:43: #1 tag size = 51 INFO @ Thu, 03 May 2018 22:39:43: #1 total tags in treatment: 15113830 INFO @ Thu, 03 May 2018 22:39:43: #1 user defined the maximum tags... INFO @ Thu, 03 May 2018 22:39:43: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Thu, 03 May 2018 22:39:43: #1 tags after filtering in treatment: 15113618 INFO @ Thu, 03 May 2018 22:39:43: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 03 May 2018 22:39:43: #1 finished! INFO @ Thu, 03 May 2018 22:39:43: #2 Build Peak Model... INFO @ Thu, 03 May 2018 22:39:43: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 03 May 2018 22:39:47: #2 number of paired peaks: 51620 INFO @ Thu, 03 May 2018 22:39:47: start model_add_line... INFO @ Thu, 03 May 2018 22:39:47: start X-correlation... INFO @ Thu, 03 May 2018 22:39:47: end of X-cor INFO @ Thu, 03 May 2018 22:39:47: #2 finished! INFO @ Thu, 03 May 2018 22:39:47: #2 predicted fragment length is 292 bps INFO @ Thu, 03 May 2018 22:39:47: #2 alternative fragment length(s) may be 292 bps INFO @ Thu, 03 May 2018 22:39:47: #2.2 Generate R script for model : SRX3145023.05_model.r INFO @ Thu, 03 May 2018 22:39:47: #3 Call peaks... INFO @ Thu, 03 May 2018 22:39:47: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 03 May 2018 22:40:18: #3 Call peaks for each chromosome... INFO @ Thu, 03 May 2018 22:40:23: #3 Call peaks for each chromosome... INFO @ Thu, 03 May 2018 22:40:25: #3 Call peaks for each chromosome... INFO @ Thu, 03 May 2018 22:40:41: #4 Write output xls file... SRX3145023.10_peaks.xls INFO @ Thu, 03 May 2018 22:40:41: #4 Write peak in narrowPeak format file... SRX3145023.10_peaks.narrowPeak INFO @ Thu, 03 May 2018 22:40:41: #4 Write summits bed file... SRX3145023.10_summits.bed INFO @ Thu, 03 May 2018 22:40:41: Done! pass1 - making usageList (28 chroms): 1 millis pass2 - checking and writing primary data (264 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Thu, 03 May 2018 22:40:45: #4 Write output xls file... SRX3145023.20_peaks.xls INFO @ Thu, 03 May 2018 22:40:45: #4 Write peak in narrowPeak format file... SRX3145023.20_peaks.narrowPeak INFO @ Thu, 03 May 2018 22:40:45: #4 Write summits bed file... SRX3145023.20_summits.bed INFO @ Thu, 03 May 2018 22:40:45: Done! pass1 - making usageList (18 chroms): 0 millis pass2 - checking and writing primary data (129 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Thu, 03 May 2018 22:40:46: #4 Write output xls file... SRX3145023.05_peaks.xls INFO @ Thu, 03 May 2018 22:40:46: #4 Write peak in narrowPeak format file... SRX3145023.05_peaks.narrowPeak INFO @ Thu, 03 May 2018 22:40:46: #4 Write summits bed file... SRX3145023.05_summits.bed INFO @ Thu, 03 May 2018 22:40:46: Done! pass1 - making usageList (38 chroms): 1 millis pass2 - checking and writing primary data (650 records, 4 fields): 4 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。