Job ID = 11192575 sra ファイルのダウンロード中... Completed: 970146K bytes transferred in 11 seconds (686071K 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 29564392 spots for /home/okishinya/chipatlas/results/rn6/SRX2226587/SRR4374837.sra Written 29564392 spots for /home/okishinya/chipatlas/results/rn6/SRX2226587/SRR4374837.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: 00:00:01 Time loading forward index: 00:00:02 Time loading mirror index: 00:00:03 Multiseed full-index search: 00:17:34 29564392 reads; of these: 29564392 (100.00%) were unpaired; of these: 10790238 (36.50%) aligned 0 times 14514875 (49.10%) aligned exactly 1 time 4259279 (14.41%) aligned >1 times 63.50% overall alignment rate Time searching: 00:17:40 Overall time: 00:17:40 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] 9708296 / 18774154 = 0.5171 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 @ Sat, 15 Sep 2018 09:24:45: # Command line: callpeak -t SRX2226587.bam -f BAM -g 2.15e9 -n SRX2226587.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX2226587.05 # format = BAM # ChIP-seq file = ['SRX2226587.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 @ Sat, 15 Sep 2018 09:24:45: #1 read tag files... INFO @ Sat, 15 Sep 2018 09:24:45: #1 read treatment tags... INFO @ Sat, 15 Sep 2018 09:24:45: # Command line: callpeak -t SRX2226587.bam -f BAM -g 2.15e9 -n SRX2226587.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX2226587.10 # format = BAM # ChIP-seq file = ['SRX2226587.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 @ Sat, 15 Sep 2018 09:24:45: #1 read tag files... INFO @ Sat, 15 Sep 2018 09:24:45: #1 read treatment tags... INFO @ Sat, 15 Sep 2018 09:24:45: # Command line: callpeak -t SRX2226587.bam -f BAM -g 2.15e9 -n SRX2226587.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX2226587.20 # format = BAM # ChIP-seq file = ['SRX2226587.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 @ Sat, 15 Sep 2018 09:24:45: #1 read tag files... INFO @ Sat, 15 Sep 2018 09:24:45: #1 read treatment tags... INFO @ Sat, 15 Sep 2018 09:24:53: 1000000 INFO @ Sat, 15 Sep 2018 09:24:53: 1000000 INFO @ Sat, 15 Sep 2018 09:24:53: 1000000 INFO @ Sat, 15 Sep 2018 09:25:00: 2000000 INFO @ Sat, 15 Sep 2018 09:25:00: 2000000 INFO @ Sat, 15 Sep 2018 09:25:01: 2000000 INFO @ Sat, 15 Sep 2018 09:25:08: 3000000 INFO @ Sat, 15 Sep 2018 09:25:08: 3000000 INFO @ Sat, 15 Sep 2018 09:25:09: 3000000 INFO @ Sat, 15 Sep 2018 09:25:15: 4000000 INFO @ Sat, 15 Sep 2018 09:25:15: 4000000 INFO @ Sat, 15 Sep 2018 09:25:17: 4000000 INFO @ Sat, 15 Sep 2018 09:25:23: 5000000 INFO @ Sat, 15 Sep 2018 09:25:23: 5000000 INFO @ Sat, 15 Sep 2018 09:25:25: 5000000 INFO @ Sat, 15 Sep 2018 09:25:31: 6000000 INFO @ Sat, 15 Sep 2018 09:25:31: 6000000 INFO @ Sat, 15 Sep 2018 09:25:33: 6000000 INFO @ Sat, 15 Sep 2018 09:25:39: 7000000 INFO @ Sat, 15 Sep 2018 09:25:40: 7000000 INFO @ Sat, 15 Sep 2018 09:25:41: 7000000 INFO @ Sat, 15 Sep 2018 09:25:46: 8000000 INFO @ Sat, 15 Sep 2018 09:25:49: 8000000 INFO @ Sat, 15 Sep 2018 09:25:49: 8000000 INFO @ Sat, 15 Sep 2018 09:25:55: 9000000 INFO @ Sat, 15 Sep 2018 09:25:55: #1 tag size is determined as 50 bps INFO @ Sat, 15 Sep 2018 09:25:55: #1 tag size = 50 INFO @ Sat, 15 Sep 2018 09:25:55: #1 total tags in treatment: 9065858 INFO @ Sat, 15 Sep 2018 09:25:55: #1 user defined the maximum tags... INFO @ Sat, 15 Sep 2018 09:25:55: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 15 Sep 2018 09:25:56: #1 tags after filtering in treatment: 9065671 INFO @ Sat, 15 Sep 2018 09:25:56: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 15 Sep 2018 09:25:56: #1 finished! INFO @ Sat, 15 Sep 2018 09:25:56: #2 Build Peak Model... INFO @ Sat, 15 Sep 2018 09:25:56: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Sep 2018 09:25:57: 9000000 INFO @ Sat, 15 Sep 2018 09:25:58: #1 tag size is determined as 50 bps INFO @ Sat, 15 Sep 2018 09:25:58: #1 tag size = 50 INFO @ Sat, 15 Sep 2018 09:25:58: #1 total tags in treatment: 9065858 INFO @ Sat, 15 Sep 2018 09:25:58: #1 user defined the maximum tags... INFO @ Sat, 15 Sep 2018 09:25:58: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 15 Sep 2018 09:25:58: #2 number of paired peaks: 39105 INFO @ Sat, 15 Sep 2018 09:25:58: start model_add_line... INFO @ Sat, 15 Sep 2018 09:25:58: #1 tags after filtering in treatment: 9065671 INFO @ Sat, 15 Sep 2018 09:25:58: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 15 Sep 2018 09:25:58: #1 finished! INFO @ Sat, 15 Sep 2018 09:25:58: #2 Build Peak Model... INFO @ Sat, 15 Sep 2018 09:25:58: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Sep 2018 09:25:58: 9000000 INFO @ Sat, 15 Sep 2018 09:25:58: start X-correlation... INFO @ Sat, 15 Sep 2018 09:25:58: end of X-cor INFO @ Sat, 15 Sep 2018 09:25:58: #2 finished! INFO @ Sat, 15 Sep 2018 09:25:58: #2 predicted fragment length is 131 bps INFO @ Sat, 15 Sep 2018 09:25:58: #2 alternative fragment length(s) may be 131 bps INFO @ Sat, 15 Sep 2018 09:25:58: #2.2 Generate R script for model : SRX2226587.20_model.r INFO @ Sat, 15 Sep 2018 09:25:58: #3 Call peaks... INFO @ Sat, 15 Sep 2018 09:25:58: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 15 Sep 2018 09:25:59: #1 tag size is determined as 50 bps INFO @ Sat, 15 Sep 2018 09:25:59: #1 tag size = 50 INFO @ Sat, 15 Sep 2018 09:25:59: #1 total tags in treatment: 9065858 INFO @ Sat, 15 Sep 2018 09:25:59: #1 user defined the maximum tags... INFO @ Sat, 15 Sep 2018 09:25:59: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 15 Sep 2018 09:25:59: #1 tags after filtering in treatment: 9065671 INFO @ Sat, 15 Sep 2018 09:25:59: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 15 Sep 2018 09:25:59: #1 finished! INFO @ Sat, 15 Sep 2018 09:25:59: #2 Build Peak Model... INFO @ Sat, 15 Sep 2018 09:25:59: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Sep 2018 09:26:01: #2 number of paired peaks: 39105 INFO @ Sat, 15 Sep 2018 09:26:01: start model_add_line... INFO @ Sat, 15 Sep 2018 09:26:01: start X-correlation... INFO @ Sat, 15 Sep 2018 09:26:01: end of X-cor INFO @ Sat, 15 Sep 2018 09:26:01: #2 finished! INFO @ Sat, 15 Sep 2018 09:26:01: #2 predicted fragment length is 131 bps INFO @ Sat, 15 Sep 2018 09:26:01: #2 alternative fragment length(s) may be 131 bps INFO @ Sat, 15 Sep 2018 09:26:01: #2.2 Generate R script for model : SRX2226587.10_model.r INFO @ Sat, 15 Sep 2018 09:26:01: #3 Call peaks... INFO @ Sat, 15 Sep 2018 09:26:01: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 15 Sep 2018 09:26:02: #2 number of paired peaks: 39105 INFO @ Sat, 15 Sep 2018 09:26:02: start model_add_line... INFO @ Sat, 15 Sep 2018 09:26:02: start X-correlation... INFO @ Sat, 15 Sep 2018 09:26:02: end of X-cor INFO @ Sat, 15 Sep 2018 09:26:02: #2 finished! INFO @ Sat, 15 Sep 2018 09:26:02: #2 predicted fragment length is 131 bps INFO @ Sat, 15 Sep 2018 09:26:02: #2 alternative fragment length(s) may be 131 bps INFO @ Sat, 15 Sep 2018 09:26:02: #2.2 Generate R script for model : SRX2226587.05_model.r INFO @ Sat, 15 Sep 2018 09:26:02: #3 Call peaks... INFO @ Sat, 15 Sep 2018 09:26:02: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 15 Sep 2018 09:26:21: #3 Call peaks for each chromosome... INFO @ Sat, 15 Sep 2018 09:26:25: #3 Call peaks for each chromosome... INFO @ Sat, 15 Sep 2018 09:26:25: #3 Call peaks for each chromosome... INFO @ Sat, 15 Sep 2018 09:26:34: #4 Write output xls file... SRX2226587.20_peaks.xls INFO @ Sat, 15 Sep 2018 09:26:34: #4 Write peak in narrowPeak format file... SRX2226587.20_peaks.narrowPeak INFO @ Sat, 15 Sep 2018 09:26:34: #4 Write summits bed file... SRX2226587.20_summits.bed INFO @ Sat, 15 Sep 2018 09:26:34: Done! pass1 - making usageList (37 chroms): 1 millis pass2 - checking and writing primary data (1249 records, 4 fields): 6 millis CompletedMACS2peakCalling INFO @ Sat, 15 Sep 2018 09:26:39: #4 Write output xls file... SRX2226587.10_peaks.xls INFO @ Sat, 15 Sep 2018 09:26:39: #4 Write peak in narrowPeak format file... SRX2226587.10_peaks.narrowPeak INFO @ Sat, 15 Sep 2018 09:26:39: #4 Write summits bed file... SRX2226587.10_summits.bed INFO @ Sat, 15 Sep 2018 09:26:39: Done! pass1 - making usageList (55 chroms): 1 millis pass2 - checking and writing primary data (2775 records, 4 fields): 12 millis INFO @ Sat, 15 Sep 2018 09:26:39: #4 Write output xls file... SRX2226587.05_peaks.xls CompletedMACS2peakCalling INFO @ Sat, 15 Sep 2018 09:26:39: #4 Write peak in narrowPeak format file... SRX2226587.05_peaks.narrowPeak INFO @ Sat, 15 Sep 2018 09:26:39: #4 Write summits bed file... SRX2226587.05_summits.bed INFO @ Sat, 15 Sep 2018 09:26:39: Done! pass1 - making usageList (74 chroms): 2 millis pass2 - checking and writing primary data (5628 records, 4 fields): 12 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。