Job ID = 11632673 sra ファイルのダウンロード中... Completed: 992238K bytes transferred in 24 seconds (326575K 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 52773992 spots for /home/okishinya/chipatlas/results/rn6/SRX3360111/SRR6253217.sra Written 52773992 spots for /home/okishinya/chipatlas/results/rn6/SRX3360111/SRR6253217.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: 00:00:01 Time loading mirror index: 00:00:01 Multiseed full-index search: 00:15:06 52773992 reads; of these: 52773992 (100.00%) were unpaired; of these: 37532782 (71.12%) aligned 0 times 12538300 (23.76%) aligned exactly 1 time 2702910 (5.12%) aligned >1 times 28.88% overall alignment rate Time searching: 00:15:09 Overall time: 00:15:09 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] 8443484 / 15241210 = 0.5540 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 @ Fri, 15 Feb 2019 07:09:03: # Command line: callpeak -t SRX3360111.bam -f BAM -g 2.15e9 -n SRX3360111.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX3360111.10 # format = BAM # ChIP-seq file = ['SRX3360111.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 @ Fri, 15 Feb 2019 07:09:03: #1 read tag files... INFO @ Fri, 15 Feb 2019 07:09:03: #1 read treatment tags... INFO @ Fri, 15 Feb 2019 07:09:03: # Command line: callpeak -t SRX3360111.bam -f BAM -g 2.15e9 -n SRX3360111.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX3360111.05 # format = BAM # ChIP-seq file = ['SRX3360111.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 @ Fri, 15 Feb 2019 07:09:03: #1 read tag files... INFO @ Fri, 15 Feb 2019 07:09:03: #1 read treatment tags... INFO @ Fri, 15 Feb 2019 07:09:03: # Command line: callpeak -t SRX3360111.bam -f BAM -g 2.15e9 -n SRX3360111.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX3360111.20 # format = BAM # ChIP-seq file = ['SRX3360111.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 @ Fri, 15 Feb 2019 07:09:03: #1 read tag files... INFO @ Fri, 15 Feb 2019 07:09:03: #1 read treatment tags... INFO @ Fri, 15 Feb 2019 07:09:11: 1000000 INFO @ Fri, 15 Feb 2019 07:09:11: 1000000 INFO @ Fri, 15 Feb 2019 07:09:11: 1000000 INFO @ Fri, 15 Feb 2019 07:09:18: 2000000 INFO @ Fri, 15 Feb 2019 07:09:18: 2000000 INFO @ Fri, 15 Feb 2019 07:09:18: 2000000 INFO @ Fri, 15 Feb 2019 07:09:24: 3000000 INFO @ Fri, 15 Feb 2019 07:09:26: 3000000 INFO @ Fri, 15 Feb 2019 07:09:26: 3000000 INFO @ Fri, 15 Feb 2019 07:09:31: 4000000 INFO @ Fri, 15 Feb 2019 07:09:33: 4000000 INFO @ Fri, 15 Feb 2019 07:09:33: 4000000 INFO @ Fri, 15 Feb 2019 07:09:38: 5000000 INFO @ Fri, 15 Feb 2019 07:09:40: 5000000 INFO @ Fri, 15 Feb 2019 07:09:40: 5000000 INFO @ Fri, 15 Feb 2019 07:09:45: 6000000 INFO @ Fri, 15 Feb 2019 07:09:48: 6000000 INFO @ Fri, 15 Feb 2019 07:09:48: 6000000 INFO @ Fri, 15 Feb 2019 07:09:51: #1 tag size is determined as 51 bps INFO @ Fri, 15 Feb 2019 07:09:51: #1 tag size = 51 INFO @ Fri, 15 Feb 2019 07:09:51: #1 total tags in treatment: 6797726 INFO @ Fri, 15 Feb 2019 07:09:51: #1 user defined the maximum tags... INFO @ Fri, 15 Feb 2019 07:09:51: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 15 Feb 2019 07:09:52: #1 tags after filtering in treatment: 6797477 INFO @ Fri, 15 Feb 2019 07:09:52: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 15 Feb 2019 07:09:52: #1 finished! INFO @ Fri, 15 Feb 2019 07:09:52: #2 Build Peak Model... INFO @ Fri, 15 Feb 2019 07:09:52: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 15 Feb 2019 07:09:54: #2 number of paired peaks: 34780 INFO @ Fri, 15 Feb 2019 07:09:54: start model_add_line... INFO @ Fri, 15 Feb 2019 07:09:54: start X-correlation... INFO @ Fri, 15 Feb 2019 07:09:54: end of X-cor INFO @ Fri, 15 Feb 2019 07:09:54: #2 finished! INFO @ Fri, 15 Feb 2019 07:09:54: #2 predicted fragment length is 181 bps INFO @ Fri, 15 Feb 2019 07:09:54: #2 alternative fragment length(s) may be 181 bps INFO @ Fri, 15 Feb 2019 07:09:54: #2.2 Generate R script for model : SRX3360111.10_model.r INFO @ Fri, 15 Feb 2019 07:09:54: #3 Call peaks... INFO @ Fri, 15 Feb 2019 07:09:54: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 15 Feb 2019 07:09:54: #1 tag size is determined as 51 bps INFO @ Fri, 15 Feb 2019 07:09:54: #1 tag size = 51 INFO @ Fri, 15 Feb 2019 07:09:54: #1 total tags in treatment: 6797726 INFO @ Fri, 15 Feb 2019 07:09:54: #1 user defined the maximum tags... INFO @ Fri, 15 Feb 2019 07:09:54: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 15 Feb 2019 07:09:54: #1 tag size is determined as 51 bps INFO @ Fri, 15 Feb 2019 07:09:54: #1 tag size = 51 INFO @ Fri, 15 Feb 2019 07:09:54: #1 total tags in treatment: 6797726 INFO @ Fri, 15 Feb 2019 07:09:54: #1 user defined the maximum tags... INFO @ Fri, 15 Feb 2019 07:09:54: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 15 Feb 2019 07:09:54: #1 tags after filtering in treatment: 6797477 INFO @ Fri, 15 Feb 2019 07:09:54: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 15 Feb 2019 07:09:54: #1 finished! INFO @ Fri, 15 Feb 2019 07:09:54: #2 Build Peak Model... INFO @ Fri, 15 Feb 2019 07:09:54: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 15 Feb 2019 07:09:54: #1 tags after filtering in treatment: 6797477 INFO @ Fri, 15 Feb 2019 07:09:54: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 15 Feb 2019 07:09:54: #1 finished! INFO @ Fri, 15 Feb 2019 07:09:54: #2 Build Peak Model... INFO @ Fri, 15 Feb 2019 07:09:54: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 15 Feb 2019 07:09:56: #2 number of paired peaks: 34780 INFO @ Fri, 15 Feb 2019 07:09:56: start model_add_line... INFO @ Fri, 15 Feb 2019 07:09:56: #2 number of paired peaks: 34780 INFO @ Fri, 15 Feb 2019 07:09:56: start model_add_line... INFO @ Fri, 15 Feb 2019 07:09:56: start X-correlation... INFO @ Fri, 15 Feb 2019 07:09:56: end of X-cor INFO @ Fri, 15 Feb 2019 07:09:56: #2 finished! INFO @ Fri, 15 Feb 2019 07:09:56: #2 predicted fragment length is 181 bps INFO @ Fri, 15 Feb 2019 07:09:56: #2 alternative fragment length(s) may be 181 bps INFO @ Fri, 15 Feb 2019 07:09:56: #2.2 Generate R script for model : SRX3360111.05_model.r INFO @ Fri, 15 Feb 2019 07:09:56: #3 Call peaks... INFO @ Fri, 15 Feb 2019 07:09:56: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 15 Feb 2019 07:09:56: start X-correlation... INFO @ Fri, 15 Feb 2019 07:09:56: end of X-cor INFO @ Fri, 15 Feb 2019 07:09:56: #2 finished! INFO @ Fri, 15 Feb 2019 07:09:56: #2 predicted fragment length is 181 bps INFO @ Fri, 15 Feb 2019 07:09:56: #2 alternative fragment length(s) may be 181 bps INFO @ Fri, 15 Feb 2019 07:09:56: #2.2 Generate R script for model : SRX3360111.20_model.r INFO @ Fri, 15 Feb 2019 07:09:56: #3 Call peaks... INFO @ Fri, 15 Feb 2019 07:09:56: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 15 Feb 2019 07:10:11: #3 Call peaks for each chromosome... INFO @ Fri, 15 Feb 2019 07:10:14: #3 Call peaks for each chromosome... INFO @ Fri, 15 Feb 2019 07:10:15: #3 Call peaks for each chromosome... INFO @ Fri, 15 Feb 2019 07:10:24: #4 Write output xls file... SRX3360111.10_peaks.xls INFO @ Fri, 15 Feb 2019 07:10:24: #4 Write peak in narrowPeak format file... SRX3360111.10_peaks.narrowPeak INFO @ Fri, 15 Feb 2019 07:10:24: #4 Write summits bed file... SRX3360111.10_summits.bed INFO @ Fri, 15 Feb 2019 07:10:24: Done! pass1 - making usageList (99 chroms): 6 millis pass2 - checking and writing primary data (15086 records, 4 fields): 24 millis CompletedMACS2peakCalling INFO @ Fri, 15 Feb 2019 07:10:25: #4 Write output xls file... SRX3360111.20_peaks.xls INFO @ Fri, 15 Feb 2019 07:10:25: #4 Write peak in narrowPeak format file... SRX3360111.20_peaks.narrowPeak INFO @ Fri, 15 Feb 2019 07:10:25: #4 Write summits bed file... SRX3360111.20_summits.bed INFO @ Fri, 15 Feb 2019 07:10:25: Done! pass1 - making usageList (68 chroms): 4 millis pass2 - checking and writing primary data (8407 records, 4 fields): 16 millis CompletedMACS2peakCalling INFO @ Fri, 15 Feb 2019 07:10:25: #4 Write output xls file... SRX3360111.05_peaks.xls INFO @ Fri, 15 Feb 2019 07:10:25: #4 Write peak in narrowPeak format file... SRX3360111.05_peaks.narrowPeak INFO @ Fri, 15 Feb 2019 07:10:26: #4 Write summits bed file... SRX3360111.05_summits.bed INFO @ Fri, 15 Feb 2019 07:10:26: Done! pass1 - making usageList (122 chroms): 7 millis pass2 - checking and writing primary data (19732 records, 4 fields): 40 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。