Job ID = 10714382 sra ファイルのダウンロード中... Completed: 452299K bytes transferred in 12 seconds (301996K 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 20737442 spots for /home/okishinya/chipatlas/results/ce10/SRX4082342/SRR7164160.sra Written 20737442 spots for /home/okishinya/chipatlas/results/ce10/SRX4082342/SRR7164160.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: 00:00:00 Time loading mirror index: 00:00:00 Multiseed full-index search: 00:05:01 20737442 reads; of these: 20737442 (100.00%) were unpaired; of these: 501850 (2.42%) aligned 0 times 18576553 (89.58%) aligned exactly 1 time 1659039 (8.00%) aligned >1 times 97.58% overall alignment rate Time searching: 00:05:01 Overall time: 00:05:01 マッピングが完了しました。 samtools でBAM に変換中... [samopen] SAM header is present: 7 sequences. [bam_sort_core] merging from 12 files... [bam_rmdupse_core] 6187706 / 20235592 = 0.3058 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 @ Sun, 03 Jun 2018 12:38:49: # Command line: callpeak -t SRX4082342.bam -f BAM -g ce -n SRX4082342.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX4082342.05 # format = BAM # ChIP-seq file = ['SRX4082342.bam'] # control file = None # effective genome size = 9.00e+07 # 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 @ Sun, 03 Jun 2018 12:38:49: #1 read tag files... INFO @ Sun, 03 Jun 2018 12:38:49: #1 read treatment tags... INFO @ Sun, 03 Jun 2018 12:38:49: # Command line: callpeak -t SRX4082342.bam -f BAM -g ce -n SRX4082342.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX4082342.10 # format = BAM # ChIP-seq file = ['SRX4082342.bam'] # control file = None # effective genome size = 9.00e+07 # 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 @ Sun, 03 Jun 2018 12:38:49: #1 read tag files... INFO @ Sun, 03 Jun 2018 12:38:49: #1 read treatment tags... INFO @ Sun, 03 Jun 2018 12:38:49: # Command line: callpeak -t SRX4082342.bam -f BAM -g ce -n SRX4082342.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX4082342.20 # format = BAM # ChIP-seq file = ['SRX4082342.bam'] # control file = None # effective genome size = 9.00e+07 # 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 @ Sun, 03 Jun 2018 12:38:49: #1 read tag files... INFO @ Sun, 03 Jun 2018 12:38:49: #1 read treatment tags... INFO @ Sun, 03 Jun 2018 12:38:56: 1000000 INFO @ Sun, 03 Jun 2018 12:38:57: 1000000 INFO @ Sun, 03 Jun 2018 12:38:57: 1000000 INFO @ Sun, 03 Jun 2018 12:39:03: 2000000 INFO @ Sun, 03 Jun 2018 12:39:04: 2000000 INFO @ Sun, 03 Jun 2018 12:39:04: 2000000 INFO @ Sun, 03 Jun 2018 12:39:10: 3000000 INFO @ Sun, 03 Jun 2018 12:39:11: 3000000 INFO @ Sun, 03 Jun 2018 12:39:11: 3000000 INFO @ Sun, 03 Jun 2018 12:39:16: 4000000 INFO @ Sun, 03 Jun 2018 12:39:18: 4000000 INFO @ Sun, 03 Jun 2018 12:39:18: 4000000 INFO @ Sun, 03 Jun 2018 12:39:23: 5000000 INFO @ Sun, 03 Jun 2018 12:39:25: 5000000 INFO @ Sun, 03 Jun 2018 12:39:25: 5000000 INFO @ Sun, 03 Jun 2018 12:39:29: 6000000 INFO @ Sun, 03 Jun 2018 12:39:32: 6000000 INFO @ Sun, 03 Jun 2018 12:39:32: 6000000 INFO @ Sun, 03 Jun 2018 12:39:36: 7000000 INFO @ Sun, 03 Jun 2018 12:39:39: 7000000 INFO @ Sun, 03 Jun 2018 12:39:39: 7000000 INFO @ Sun, 03 Jun 2018 12:39:42: 8000000 INFO @ Sun, 03 Jun 2018 12:39:46: 8000000 INFO @ Sun, 03 Jun 2018 12:39:46: 8000000 INFO @ Sun, 03 Jun 2018 12:39:49: 9000000 INFO @ Sun, 03 Jun 2018 12:39:53: 9000000 INFO @ Sun, 03 Jun 2018 12:39:53: 9000000 INFO @ Sun, 03 Jun 2018 12:39:56: 10000000 INFO @ Sun, 03 Jun 2018 12:40:00: 10000000 INFO @ Sun, 03 Jun 2018 12:40:00: 10000000 INFO @ Sun, 03 Jun 2018 12:40:02: 11000000 INFO @ Sun, 03 Jun 2018 12:40:08: 11000000 INFO @ Sun, 03 Jun 2018 12:40:08: 11000000 INFO @ Sun, 03 Jun 2018 12:40:09: 12000000 INFO @ Sun, 03 Jun 2018 12:40:15: 12000000 INFO @ Sun, 03 Jun 2018 12:40:15: 12000000 INFO @ Sun, 03 Jun 2018 12:40:16: 13000000 INFO @ Sun, 03 Jun 2018 12:40:22: 14000000 INFO @ Sun, 03 Jun 2018 12:40:23: #1 tag size is determined as 50 bps INFO @ Sun, 03 Jun 2018 12:40:23: #1 tag size = 50 INFO @ Sun, 03 Jun 2018 12:40:23: #1 total tags in treatment: 14047886 INFO @ Sun, 03 Jun 2018 12:40:23: #1 user defined the maximum tags... INFO @ Sun, 03 Jun 2018 12:40:23: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sun, 03 Jun 2018 12:40:23: 13000000 INFO @ Sun, 03 Jun 2018 12:40:23: 13000000 INFO @ Sun, 03 Jun 2018 12:40:23: #1 tags after filtering in treatment: 14047886 INFO @ Sun, 03 Jun 2018 12:40:23: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 03 Jun 2018 12:40:23: #1 finished! INFO @ Sun, 03 Jun 2018 12:40:23: #2 Build Peak Model... INFO @ Sun, 03 Jun 2018 12:40:23: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 03 Jun 2018 12:40:25: #2 number of paired peaks: 5145 INFO @ Sun, 03 Jun 2018 12:40:25: start model_add_line... INFO @ Sun, 03 Jun 2018 12:40:25: start X-correlation... INFO @ Sun, 03 Jun 2018 12:40:25: end of X-cor INFO @ Sun, 03 Jun 2018 12:40:25: #2 finished! INFO @ Sun, 03 Jun 2018 12:40:25: #2 predicted fragment length is 135 bps INFO @ Sun, 03 Jun 2018 12:40:25: #2 alternative fragment length(s) may be 135 bps INFO @ Sun, 03 Jun 2018 12:40:25: #2.2 Generate R script for model : SRX4082342.20_model.r INFO @ Sun, 03 Jun 2018 12:40:25: #3 Call peaks... INFO @ Sun, 03 Jun 2018 12:40:25: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 03 Jun 2018 12:40:30: 14000000 INFO @ Sun, 03 Jun 2018 12:40:30: 14000000 INFO @ Sun, 03 Jun 2018 12:40:31: #1 tag size is determined as 50 bps INFO @ Sun, 03 Jun 2018 12:40:31: #1 tag size = 50 INFO @ Sun, 03 Jun 2018 12:40:31: #1 total tags in treatment: 14047886 INFO @ Sun, 03 Jun 2018 12:40:31: #1 user defined the maximum tags... INFO @ Sun, 03 Jun 2018 12:40:31: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sun, 03 Jun 2018 12:40:31: #1 tag size is determined as 50 bps INFO @ Sun, 03 Jun 2018 12:40:31: #1 tag size = 50 INFO @ Sun, 03 Jun 2018 12:40:31: #1 total tags in treatment: 14047886 INFO @ Sun, 03 Jun 2018 12:40:31: #1 user defined the maximum tags... INFO @ Sun, 03 Jun 2018 12:40:31: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sun, 03 Jun 2018 12:40:31: #1 tags after filtering in treatment: 14047886 INFO @ Sun, 03 Jun 2018 12:40:31: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 03 Jun 2018 12:40:31: #1 finished! INFO @ Sun, 03 Jun 2018 12:40:31: #2 Build Peak Model... INFO @ Sun, 03 Jun 2018 12:40:31: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 03 Jun 2018 12:40:31: #1 tags after filtering in treatment: 14047886 INFO @ Sun, 03 Jun 2018 12:40:31: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 03 Jun 2018 12:40:31: #1 finished! INFO @ Sun, 03 Jun 2018 12:40:31: #2 Build Peak Model... INFO @ Sun, 03 Jun 2018 12:40:31: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 03 Jun 2018 12:40:32: #2 number of paired peaks: 5145 INFO @ Sun, 03 Jun 2018 12:40:32: start model_add_line... INFO @ Sun, 03 Jun 2018 12:40:32: #2 number of paired peaks: 5145 INFO @ Sun, 03 Jun 2018 12:40:32: start model_add_line... INFO @ Sun, 03 Jun 2018 12:40:33: start X-correlation... INFO @ Sun, 03 Jun 2018 12:40:33: start X-correlation... INFO @ Sun, 03 Jun 2018 12:40:33: end of X-cor INFO @ Sun, 03 Jun 2018 12:40:33: end of X-cor INFO @ Sun, 03 Jun 2018 12:40:33: #2 finished! INFO @ Sun, 03 Jun 2018 12:40:33: #2 finished! INFO @ Sun, 03 Jun 2018 12:40:33: #2 predicted fragment length is 135 bps INFO @ Sun, 03 Jun 2018 12:40:33: #2 predicted fragment length is 135 bps INFO @ Sun, 03 Jun 2018 12:40:33: #2 alternative fragment length(s) may be 135 bps INFO @ Sun, 03 Jun 2018 12:40:33: #2 alternative fragment length(s) may be 135 bps INFO @ Sun, 03 Jun 2018 12:40:33: #2.2 Generate R script for model : SRX4082342.10_model.r INFO @ Sun, 03 Jun 2018 12:40:33: #2.2 Generate R script for model : SRX4082342.05_model.r INFO @ Sun, 03 Jun 2018 12:40:33: #3 Call peaks... INFO @ Sun, 03 Jun 2018 12:40:33: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 03 Jun 2018 12:40:33: #3 Call peaks... INFO @ Sun, 03 Jun 2018 12:40:33: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 03 Jun 2018 12:41:03: #3 Call peaks for each chromosome... INFO @ Sun, 03 Jun 2018 12:41:11: #3 Call peaks for each chromosome... INFO @ Sun, 03 Jun 2018 12:41:13: #3 Call peaks for each chromosome... INFO @ Sun, 03 Jun 2018 12:41:21: #4 Write output xls file... SRX4082342.20_peaks.xls INFO @ Sun, 03 Jun 2018 12:41:22: #4 Write peak in narrowPeak format file... SRX4082342.20_peaks.narrowPeak INFO @ Sun, 03 Jun 2018 12:41:22: #4 Write summits bed file... SRX4082342.20_summits.bed INFO @ Sun, 03 Jun 2018 12:41:22: Done! pass1 - making usageList (6 chroms): 2 millis pass2 - checking and writing primary data (4370 records, 4 fields): 6 millis CompletedMACS2peakCalling INFO @ Sun, 03 Jun 2018 12:41:28: #4 Write output xls file... SRX4082342.05_peaks.xls INFO @ Sun, 03 Jun 2018 12:41:28: #4 Write peak in narrowPeak format file... SRX4082342.05_peaks.narrowPeak INFO @ Sun, 03 Jun 2018 12:41:28: #4 Write summits bed file... SRX4082342.05_summits.bed INFO @ Sun, 03 Jun 2018 12:41:28: Done! pass1 - making usageList (6 chroms): 2 millis pass2 - checking and writing primary data (7650 records, 4 fields): 10 millis CompletedMACS2peakCalling INFO @ Sun, 03 Jun 2018 12:41:31: #4 Write output xls file... SRX4082342.10_peaks.xls INFO @ Sun, 03 Jun 2018 12:41:31: #4 Write peak in narrowPeak format file... SRX4082342.10_peaks.narrowPeak INFO @ Sun, 03 Jun 2018 12:41:31: #4 Write summits bed file... SRX4082342.10_summits.bed INFO @ Sun, 03 Jun 2018 12:41:31: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (5868 records, 4 fields): 8 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。