Job ID = 11632685 sra ファイルのダウンロード中... Completed: 1438876K bytes transferred in 16 seconds (721040K 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 57191909 spots for /home/okishinya/chipatlas/results/rn6/SRX3782445/SRR6826263.sra Written 57191909 spots for /home/okishinya/chipatlas/results/rn6/SRX3782445/SRR6826263.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: 00:00:01 Time loading mirror index: 00:00:00 Multiseed full-index search: 00:23:01 57191909 reads; of these: 57191909 (100.00%) were unpaired; of these: 12752264 (22.30%) aligned 0 times 37857708 (66.19%) aligned exactly 1 time 6581937 (11.51%) aligned >1 times 77.70% overall alignment rate Time searching: 00:23:03 Overall time: 00:23:03 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 16 files... [bam_rmdupse_core] 26197325 / 44439645 = 0.5895 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 07:37:13: # Command line: callpeak -t SRX3782445.bam -f BAM -g 2.15e9 -n SRX3782445.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX3782445.05 # format = BAM # ChIP-seq file = ['SRX3782445.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 07:37:13: #1 read tag files... INFO @ Fri, 15 Feb 2019 07:37:13: #1 read treatment tags... INFO @ Fri, 15 Feb 2019 07:37:13: # Command line: callpeak -t SRX3782445.bam -f BAM -g 2.15e9 -n SRX3782445.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX3782445.20 # format = BAM # ChIP-seq file = ['SRX3782445.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 07:37:13: #1 read tag files... INFO @ Fri, 15 Feb 2019 07:37:13: #1 read treatment tags... INFO @ Fri, 15 Feb 2019 07:37:13: # Command line: callpeak -t SRX3782445.bam -f BAM -g 2.15e9 -n SRX3782445.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX3782445.10 # format = BAM # ChIP-seq file = ['SRX3782445.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 07:37:13: #1 read tag files... INFO @ Fri, 15 Feb 2019 07:37:13: #1 read treatment tags... INFO @ Fri, 15 Feb 2019 07:37:22: 1000000 INFO @ Fri, 15 Feb 2019 07:37:22: 1000000 INFO @ Fri, 15 Feb 2019 07:37:22: 1000000 INFO @ Fri, 15 Feb 2019 07:37:30: 2000000 INFO @ Fri, 15 Feb 2019 07:37:30: 2000000 INFO @ Fri, 15 Feb 2019 07:37:30: 2000000 INFO @ Fri, 15 Feb 2019 07:37:39: 3000000 INFO @ Fri, 15 Feb 2019 07:37:39: 3000000 INFO @ Fri, 15 Feb 2019 07:37:39: 3000000 INFO @ Fri, 15 Feb 2019 07:37:47: 4000000 INFO @ Fri, 15 Feb 2019 07:37:47: 4000000 INFO @ Fri, 15 Feb 2019 07:37:47: 4000000 INFO @ Fri, 15 Feb 2019 07:37:56: 5000000 INFO @ Fri, 15 Feb 2019 07:37:56: 5000000 INFO @ Fri, 15 Feb 2019 07:37:56: 5000000 INFO @ Fri, 15 Feb 2019 07:38:05: 6000000 INFO @ Fri, 15 Feb 2019 07:38:05: 6000000 INFO @ Fri, 15 Feb 2019 07:38:05: 6000000 INFO @ Fri, 15 Feb 2019 07:38:14: 7000000 INFO @ Fri, 15 Feb 2019 07:38:14: 7000000 INFO @ Fri, 15 Feb 2019 07:38:14: 7000000 INFO @ Fri, 15 Feb 2019 07:38:22: 8000000 INFO @ Fri, 15 Feb 2019 07:38:22: 8000000 INFO @ Fri, 15 Feb 2019 07:38:22: 8000000 INFO @ Fri, 15 Feb 2019 07:38:31: 9000000 INFO @ Fri, 15 Feb 2019 07:38:31: 9000000 INFO @ Fri, 15 Feb 2019 07:38:31: 9000000 INFO @ Fri, 15 Feb 2019 07:38:40: 10000000 INFO @ Fri, 15 Feb 2019 07:38:40: 10000000 INFO @ Fri, 15 Feb 2019 07:38:40: 10000000 INFO @ Fri, 15 Feb 2019 07:38:48: 11000000 INFO @ Fri, 15 Feb 2019 07:38:48: 11000000 INFO @ Fri, 15 Feb 2019 07:38:48: 11000000 INFO @ Fri, 15 Feb 2019 07:38:57: 12000000 INFO @ Fri, 15 Feb 2019 07:38:57: 12000000 INFO @ Fri, 15 Feb 2019 07:38:57: 12000000 INFO @ Fri, 15 Feb 2019 07:39:06: 13000000 INFO @ Fri, 15 Feb 2019 07:39:06: 13000000 INFO @ Fri, 15 Feb 2019 07:39:06: 13000000 INFO @ Fri, 15 Feb 2019 07:39:14: 14000000 INFO @ Fri, 15 Feb 2019 07:39:14: 14000000 INFO @ Fri, 15 Feb 2019 07:39:14: 14000000 INFO @ Fri, 15 Feb 2019 07:39:23: 15000000 INFO @ Fri, 15 Feb 2019 07:39:23: 15000000 INFO @ Fri, 15 Feb 2019 07:39:23: 15000000 INFO @ Fri, 15 Feb 2019 07:39:32: 16000000 INFO @ Fri, 15 Feb 2019 07:39:32: 16000000 INFO @ Fri, 15 Feb 2019 07:39:32: 16000000 INFO @ Fri, 15 Feb 2019 07:39:40: 17000000 INFO @ Fri, 15 Feb 2019 07:39:40: 17000000 INFO @ Fri, 15 Feb 2019 07:39:41: 17000000 INFO @ Fri, 15 Feb 2019 07:39:49: 18000000 INFO @ Fri, 15 Feb 2019 07:39:49: 18000000 INFO @ Fri, 15 Feb 2019 07:39:49: 18000000 INFO @ Fri, 15 Feb 2019 07:39:51: #1 tag size is determined as 42 bps INFO @ Fri, 15 Feb 2019 07:39:51: #1 tag size = 42 INFO @ Fri, 15 Feb 2019 07:39:51: #1 total tags in treatment: 18242320 INFO @ Fri, 15 Feb 2019 07:39:51: #1 user defined the maximum tags... INFO @ Fri, 15 Feb 2019 07:39:51: #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 07:39:52: #1 tag size is determined as 42 bps INFO @ Fri, 15 Feb 2019 07:39:52: #1 tag size = 42 INFO @ Fri, 15 Feb 2019 07:39:52: #1 total tags in treatment: 18242320 INFO @ Fri, 15 Feb 2019 07:39:52: #1 user defined the maximum tags... INFO @ Fri, 15 Feb 2019 07:39:52: #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 07:39:52: #1 tag size is determined as 42 bps INFO @ Fri, 15 Feb 2019 07:39:52: #1 tag size = 42 INFO @ Fri, 15 Feb 2019 07:39:52: #1 total tags in treatment: 18242320 INFO @ Fri, 15 Feb 2019 07:39:52: #1 user defined the maximum tags... INFO @ Fri, 15 Feb 2019 07:39:52: #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 07:39:52: #1 tags after filtering in treatment: 18242127 INFO @ Fri, 15 Feb 2019 07:39:52: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 15 Feb 2019 07:39:52: #1 finished! INFO @ Fri, 15 Feb 2019 07:39:52: #2 Build Peak Model... INFO @ Fri, 15 Feb 2019 07:39:52: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 15 Feb 2019 07:39:52: #1 tags after filtering in treatment: 18242127 INFO @ Fri, 15 Feb 2019 07:39:52: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 15 Feb 2019 07:39:52: #1 finished! INFO @ Fri, 15 Feb 2019 07:39:52: #2 Build Peak Model... INFO @ Fri, 15 Feb 2019 07:39:52: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 15 Feb 2019 07:39:52: #1 tags after filtering in treatment: 18242127 INFO @ Fri, 15 Feb 2019 07:39:52: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 15 Feb 2019 07:39:52: #1 finished! INFO @ Fri, 15 Feb 2019 07:39:52: #2 Build Peak Model... INFO @ Fri, 15 Feb 2019 07:39:52: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 15 Feb 2019 07:39:57: #2 number of paired peaks: 76472 INFO @ Fri, 15 Feb 2019 07:39:57: start model_add_line... INFO @ Fri, 15 Feb 2019 07:39:57: #2 number of paired peaks: 76472 INFO @ Fri, 15 Feb 2019 07:39:57: start model_add_line... INFO @ Fri, 15 Feb 2019 07:39:57: #2 number of paired peaks: 76472 INFO @ Fri, 15 Feb 2019 07:39:57: start model_add_line... INFO @ Fri, 15 Feb 2019 07:39:57: start X-correlation... INFO @ Fri, 15 Feb 2019 07:39:57: end of X-cor INFO @ Fri, 15 Feb 2019 07:39:57: #2 finished! INFO @ Fri, 15 Feb 2019 07:39:57: #2 predicted fragment length is 171 bps INFO @ Fri, 15 Feb 2019 07:39:57: #2 alternative fragment length(s) may be 171 bps INFO @ Fri, 15 Feb 2019 07:39:57: #2.2 Generate R script for model : SRX3782445.10_model.r INFO @ Fri, 15 Feb 2019 07:39:57: #3 Call peaks... INFO @ Fri, 15 Feb 2019 07:39:57: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 15 Feb 2019 07:39:57: start X-correlation... INFO @ Fri, 15 Feb 2019 07:39:57: end of X-cor INFO @ Fri, 15 Feb 2019 07:39:57: #2 finished! INFO @ Fri, 15 Feb 2019 07:39:57: #2 predicted fragment length is 171 bps INFO @ Fri, 15 Feb 2019 07:39:57: #2 alternative fragment length(s) may be 171 bps INFO @ Fri, 15 Feb 2019 07:39:57: #2.2 Generate R script for model : SRX3782445.20_model.r INFO @ Fri, 15 Feb 2019 07:39:57: #3 Call peaks... INFO @ Fri, 15 Feb 2019 07:39:57: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 15 Feb 2019 07:39:57: start X-correlation... INFO @ Fri, 15 Feb 2019 07:39:57: end of X-cor INFO @ Fri, 15 Feb 2019 07:39:57: #2 finished! INFO @ Fri, 15 Feb 2019 07:39:57: #2 predicted fragment length is 171 bps INFO @ Fri, 15 Feb 2019 07:39:57: #2 alternative fragment length(s) may be 171 bps INFO @ Fri, 15 Feb 2019 07:39:57: #2.2 Generate R script for model : SRX3782445.05_model.r INFO @ Fri, 15 Feb 2019 07:39:57: #3 Call peaks... INFO @ Fri, 15 Feb 2019 07:39:57: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 15 Feb 2019 07:40:49: #3 Call peaks for each chromosome... INFO @ Fri, 15 Feb 2019 07:40:51: #3 Call peaks for each chromosome... INFO @ Fri, 15 Feb 2019 07:40:52: #3 Call peaks for each chromosome... INFO @ Fri, 15 Feb 2019 07:41:25: #4 Write output xls file... SRX3782445.05_peaks.xls INFO @ Fri, 15 Feb 2019 07:41:25: #4 Write peak in narrowPeak format file... SRX3782445.05_peaks.narrowPeak INFO @ Fri, 15 Feb 2019 07:41:26: #4 Write summits bed file... SRX3782445.05_summits.bed INFO @ Fri, 15 Feb 2019 07:41:26: #4 Write output xls file... SRX3782445.20_peaks.xls INFO @ Fri, 15 Feb 2019 07:41:26: Done! INFO @ Fri, 15 Feb 2019 07:41:26: #4 Write peak in narrowPeak format file... SRX3782445.20_peaks.narrowPeak INFO @ Fri, 15 Feb 2019 07:41:26: #4 Write summits bed file... SRX3782445.20_summits.bed INFO @ Fri, 15 Feb 2019 07:41:26: Done! pass1 - making usageList (134 chroms): 7 millis pass1 - making usageList (77 chroms): 4 millis pass2 - checking and writing primary data (13265 records, 4 fields): 20 millis pass2 - checking and writing primary data (31466 records, 4 fields): 44 millis CompletedMACS2peakCalling CompletedMACS2peakCalling INFO @ Fri, 15 Feb 2019 07:41:30: #4 Write output xls file... SRX3782445.10_peaks.xls INFO @ Fri, 15 Feb 2019 07:41:30: #4 Write peak in narrowPeak format file... SRX3782445.10_peaks.narrowPeak INFO @ Fri, 15 Feb 2019 07:41:30: #4 Write summits bed file... SRX3782445.10_summits.bed INFO @ Fri, 15 Feb 2019 07:41:30: Done! pass1 - making usageList (105 chroms): 7 millis pass2 - checking and writing primary data (21152 records, 4 fields): 30 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。