Job ID = 10714406 sra ファイルのダウンロード中... Completed: 278098K bytes transferred in 9 seconds (235304K 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 12616786 spots for /home/okishinya/chipatlas/results/ce10/SRX4082366/SRR7164184.sra Written 12616786 spots for /home/okishinya/chipatlas/results/ce10/SRX4082366/SRR7164184.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: 00:03:03 12616786 reads; of these: 12616786 (100.00%) were unpaired; of these: 501888 (3.98%) aligned 0 times 11104059 (88.01%) aligned exactly 1 time 1010839 (8.01%) aligned >1 times 96.02% overall alignment rate Time searching: 00:03:03 Overall time: 00:03:03 マッピングが完了しました。 samtools でBAM に変換中... [samopen] SAM header is present: 7 sequences. [bam_sort_core] merging from 8 files... [bam_rmdupse_core] 5936999 / 12114898 = 0.4901 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 12:34:52: # Command line: callpeak -t SRX4082366.bam -f BAM -g ce -n SRX4082366.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX4082366.05 # format = BAM # ChIP-seq file = ['SRX4082366.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 12:34:52: #1 read tag files... INFO @ Sun, 03 Jun 2018 12:34:52: #1 read treatment tags... INFO @ Sun, 03 Jun 2018 12:34:52: # Command line: callpeak -t SRX4082366.bam -f BAM -g ce -n SRX4082366.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX4082366.20 # format = BAM # ChIP-seq file = ['SRX4082366.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 12:34:52: #1 read tag files... INFO @ Sun, 03 Jun 2018 12:34:52: #1 read treatment tags... INFO @ Sun, 03 Jun 2018 12:34:52: # Command line: callpeak -t SRX4082366.bam -f BAM -g ce -n SRX4082366.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX4082366.10 # format = BAM # ChIP-seq file = ['SRX4082366.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 12:34:52: #1 read tag files... INFO @ Sun, 03 Jun 2018 12:34:52: #1 read treatment tags... INFO @ Sun, 03 Jun 2018 12:34:58: 1000000 INFO @ Sun, 03 Jun 2018 12:34:58: 1000000 INFO @ Sun, 03 Jun 2018 12:34:58: 1000000 INFO @ Sun, 03 Jun 2018 12:35:04: 2000000 INFO @ Sun, 03 Jun 2018 12:35:04: 2000000 INFO @ Sun, 03 Jun 2018 12:35:05: 2000000 INFO @ Sun, 03 Jun 2018 12:35:10: 3000000 INFO @ Sun, 03 Jun 2018 12:35:11: 3000000 INFO @ Sun, 03 Jun 2018 12:35:11: 3000000 INFO @ Sun, 03 Jun 2018 12:35:17: 4000000 INFO @ Sun, 03 Jun 2018 12:35:18: 4000000 INFO @ Sun, 03 Jun 2018 12:35:18: 4000000 INFO @ Sun, 03 Jun 2018 12:35:24: 5000000 INFO @ Sun, 03 Jun 2018 12:35:26: 5000000 INFO @ Sun, 03 Jun 2018 12:35:26: 5000000 INFO @ Sun, 03 Jun 2018 12:35:31: 6000000 INFO @ Sun, 03 Jun 2018 12:35:32: #1 tag size is determined as 50 bps INFO @ Sun, 03 Jun 2018 12:35:32: #1 tag size = 50 INFO @ Sun, 03 Jun 2018 12:35:32: #1 total tags in treatment: 6177899 INFO @ Sun, 03 Jun 2018 12:35:32: #1 user defined the maximum tags... INFO @ Sun, 03 Jun 2018 12:35:32: #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 12:35:32: #1 tags after filtering in treatment: 6177899 INFO @ Sun, 03 Jun 2018 12:35:32: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 03 Jun 2018 12:35:32: #1 finished! INFO @ Sun, 03 Jun 2018 12:35:32: #2 Build Peak Model... INFO @ Sun, 03 Jun 2018 12:35:32: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 03 Jun 2018 12:35:33: #2 number of paired peaks: 5893 INFO @ Sun, 03 Jun 2018 12:35:33: start model_add_line... INFO @ Sun, 03 Jun 2018 12:35:33: start X-correlation... INFO @ Sun, 03 Jun 2018 12:35:33: end of X-cor INFO @ Sun, 03 Jun 2018 12:35:33: #2 finished! INFO @ Sun, 03 Jun 2018 12:35:33: #2 predicted fragment length is 151 bps INFO @ Sun, 03 Jun 2018 12:35:33: #2 alternative fragment length(s) may be 4,151 bps INFO @ Sun, 03 Jun 2018 12:35:33: #2.2 Generate R script for model : SRX4082366.10_model.r INFO @ Sun, 03 Jun 2018 12:35:33: #3 Call peaks... INFO @ Sun, 03 Jun 2018 12:35:33: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 03 Jun 2018 12:35:33: 6000000 INFO @ Sun, 03 Jun 2018 12:35:34: 6000000 INFO @ Sun, 03 Jun 2018 12:35:35: #1 tag size is determined as 50 bps INFO @ Sun, 03 Jun 2018 12:35:35: #1 tag size = 50 INFO @ Sun, 03 Jun 2018 12:35:35: #1 total tags in treatment: 6177899 INFO @ Sun, 03 Jun 2018 12:35:35: #1 user defined the maximum tags... INFO @ Sun, 03 Jun 2018 12:35:35: #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 12:35:35: #1 tags after filtering in treatment: 6177899 INFO @ Sun, 03 Jun 2018 12:35:35: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 03 Jun 2018 12:35:35: #1 finished! INFO @ Sun, 03 Jun 2018 12:35:35: #2 Build Peak Model... INFO @ Sun, 03 Jun 2018 12:35:35: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 03 Jun 2018 12:35:35: #1 tag size is determined as 50 bps INFO @ Sun, 03 Jun 2018 12:35:35: #1 tag size = 50 INFO @ Sun, 03 Jun 2018 12:35:35: #1 total tags in treatment: 6177899 INFO @ Sun, 03 Jun 2018 12:35:35: #1 user defined the maximum tags... INFO @ Sun, 03 Jun 2018 12:35:35: #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 12:35:35: #1 tags after filtering in treatment: 6177899 INFO @ Sun, 03 Jun 2018 12:35:35: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 03 Jun 2018 12:35:35: #1 finished! INFO @ Sun, 03 Jun 2018 12:35:35: #2 Build Peak Model... INFO @ Sun, 03 Jun 2018 12:35:35: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 03 Jun 2018 12:35:36: #2 number of paired peaks: 5893 INFO @ Sun, 03 Jun 2018 12:35:36: start model_add_line... INFO @ Sun, 03 Jun 2018 12:35:36: start X-correlation... INFO @ Sun, 03 Jun 2018 12:35:36: end of X-cor INFO @ Sun, 03 Jun 2018 12:35:36: #2 finished! INFO @ Sun, 03 Jun 2018 12:35:36: #2 predicted fragment length is 151 bps INFO @ Sun, 03 Jun 2018 12:35:36: #2 alternative fragment length(s) may be 4,151 bps INFO @ Sun, 03 Jun 2018 12:35:36: #2.2 Generate R script for model : SRX4082366.05_model.r INFO @ Sun, 03 Jun 2018 12:35:36: #3 Call peaks... INFO @ Sun, 03 Jun 2018 12:35:36: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 03 Jun 2018 12:35:36: #2 number of paired peaks: 5893 INFO @ Sun, 03 Jun 2018 12:35:36: start model_add_line... INFO @ Sun, 03 Jun 2018 12:35:37: start X-correlation... INFO @ Sun, 03 Jun 2018 12:35:37: end of X-cor INFO @ Sun, 03 Jun 2018 12:35:37: #2 finished! INFO @ Sun, 03 Jun 2018 12:35:37: #2 predicted fragment length is 151 bps INFO @ Sun, 03 Jun 2018 12:35:37: #2 alternative fragment length(s) may be 4,151 bps INFO @ Sun, 03 Jun 2018 12:35:37: #2.2 Generate R script for model : SRX4082366.20_model.r INFO @ Sun, 03 Jun 2018 12:35:37: #3 Call peaks... INFO @ Sun, 03 Jun 2018 12:35:37: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 03 Jun 2018 12:35:49: #3 Call peaks for each chromosome... INFO @ Sun, 03 Jun 2018 12:35:53: #3 Call peaks for each chromosome... INFO @ Sun, 03 Jun 2018 12:35:53: #3 Call peaks for each chromosome... INFO @ Sun, 03 Jun 2018 12:35:58: #4 Write output xls file... SRX4082366.10_peaks.xls INFO @ Sun, 03 Jun 2018 12:35:58: #4 Write peak in narrowPeak format file... SRX4082366.10_peaks.narrowPeak INFO @ Sun, 03 Jun 2018 12:35:58: #4 Write summits bed file... SRX4082366.10_summits.bed INFO @ Sun, 03 Jun 2018 12:35:58: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (3550 records, 4 fields): 6 millis CompletedMACS2peakCalling INFO @ Sun, 03 Jun 2018 12:36:02: #4 Write output xls file... SRX4082366.20_peaks.xls INFO @ Sun, 03 Jun 2018 12:36:02: #4 Write peak in narrowPeak format file... SRX4082366.20_peaks.narrowPeak INFO @ Sun, 03 Jun 2018 12:36:02: #4 Write summits bed file... SRX4082366.20_summits.bed INFO @ Sun, 03 Jun 2018 12:36:02: Done! INFO @ Sun, 03 Jun 2018 12:36:02: #4 Write output xls file... SRX4082366.05_peaks.xls INFO @ Sun, 03 Jun 2018 12:36:03: #4 Write peak in narrowPeak format file... SRX4082366.05_peaks.narrowPeak INFO @ Sun, 03 Jun 2018 12:36:03: #4 Write summits bed file... SRX4082366.05_summits.bed INFO @ Sun, 03 Jun 2018 12:36:03: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (577 records, 4 fields): 2 millis CompletedMACS2peakCalling pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (7999 records, 4 fields): 10 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。