Job ID = 10714384 sra ファイルのダウンロード中... Completed: 367859K bytes transferred in 11 seconds (255081K 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 16780662 spots for /home/okishinya/chipatlas/results/ce10/SRX4082344/SRR7164162.sra Written 16780662 spots for /home/okishinya/chipatlas/results/ce10/SRX4082344/SRR7164162.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: 00:00:01 Multiseed full-index search: 00:03:52 16780662 reads; of these: 16780662 (100.00%) were unpaired; of these: 500956 (2.99%) aligned 0 times 14876259 (88.65%) aligned exactly 1 time 1403447 (8.36%) aligned >1 times 97.01% overall alignment rate Time searching: 00:03:53 Overall time: 00:03:53 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] 4772410 / 16279706 = 0.2932 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 12:36:32: # Command line: callpeak -t SRX4082344.bam -f BAM -g ce -n SRX4082344.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX4082344.10 # format = BAM # ChIP-seq file = ['SRX4082344.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 12:36:32: #1 read tag files... INFO @ Sun, 03 Jun 2018 12:36:32: #1 read treatment tags... INFO @ Sun, 03 Jun 2018 12:36:32: # Command line: callpeak -t SRX4082344.bam -f BAM -g ce -n SRX4082344.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX4082344.20 # format = BAM # ChIP-seq file = ['SRX4082344.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 12:36:32: #1 read tag files... INFO @ Sun, 03 Jun 2018 12:36:32: #1 read treatment tags... INFO @ Sun, 03 Jun 2018 12:36:32: # Command line: callpeak -t SRX4082344.bam -f BAM -g ce -n SRX4082344.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX4082344.05 # format = BAM # ChIP-seq file = ['SRX4082344.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 12:36:32: #1 read tag files... INFO @ Sun, 03 Jun 2018 12:36:32: #1 read treatment tags... INFO @ Sun, 03 Jun 2018 12:36:38: 1000000 INFO @ Sun, 03 Jun 2018 12:36:38: 1000000 INFO @ Sun, 03 Jun 2018 12:36:38: 1000000 INFO @ Sun, 03 Jun 2018 12:36:45: 2000000 INFO @ Sun, 03 Jun 2018 12:36:45: 2000000 INFO @ Sun, 03 Jun 2018 12:36:45: 2000000 INFO @ Sun, 03 Jun 2018 12:36:51: 3000000 INFO @ Sun, 03 Jun 2018 12:36:51: 3000000 INFO @ Sun, 03 Jun 2018 12:36:52: 3000000 INFO @ Sun, 03 Jun 2018 12:36:57: 4000000 INFO @ Sun, 03 Jun 2018 12:36:58: 4000000 INFO @ Sun, 03 Jun 2018 12:36:58: 4000000 INFO @ Sun, 03 Jun 2018 12:37:04: 5000000 INFO @ Sun, 03 Jun 2018 12:37:04: 5000000 INFO @ Sun, 03 Jun 2018 12:37:05: 5000000 INFO @ Sun, 03 Jun 2018 12:37:10: 6000000 INFO @ Sun, 03 Jun 2018 12:37:11: 6000000 INFO @ Sun, 03 Jun 2018 12:37:11: 6000000 INFO @ Sun, 03 Jun 2018 12:37:16: 7000000 INFO @ Sun, 03 Jun 2018 12:37:18: 7000000 INFO @ Sun, 03 Jun 2018 12:37:18: 7000000 INFO @ Sun, 03 Jun 2018 12:37:23: 8000000 INFO @ Sun, 03 Jun 2018 12:37:24: 8000000 INFO @ Sun, 03 Jun 2018 12:37:25: 8000000 INFO @ Sun, 03 Jun 2018 12:37:29: 9000000 INFO @ Sun, 03 Jun 2018 12:37:31: 9000000 INFO @ Sun, 03 Jun 2018 12:37:32: 9000000 INFO @ Sun, 03 Jun 2018 12:37:35: 10000000 INFO @ Sun, 03 Jun 2018 12:37:38: 10000000 INFO @ Sun, 03 Jun 2018 12:37:39: 10000000 INFO @ Sun, 03 Jun 2018 12:37:42: 11000000 INFO @ Sun, 03 Jun 2018 12:37:44: 11000000 INFO @ Sun, 03 Jun 2018 12:37:45: #1 tag size is determined as 50 bps INFO @ Sun, 03 Jun 2018 12:37:45: #1 tag size = 50 INFO @ Sun, 03 Jun 2018 12:37:45: #1 total tags in treatment: 11507296 INFO @ Sun, 03 Jun 2018 12:37:45: #1 user defined the maximum tags... INFO @ Sun, 03 Jun 2018 12:37:45: #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 12:37:45: #1 tags after filtering in treatment: 11507296 INFO @ Sun, 03 Jun 2018 12:37:45: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 03 Jun 2018 12:37:45: #1 finished! INFO @ Sun, 03 Jun 2018 12:37:45: #2 Build Peak Model... INFO @ Sun, 03 Jun 2018 12:37:45: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 03 Jun 2018 12:37:46: 11000000 INFO @ Sun, 03 Jun 2018 12:37:46: #2 number of paired peaks: 5406 INFO @ Sun, 03 Jun 2018 12:37:46: start model_add_line... INFO @ Sun, 03 Jun 2018 12:37:47: start X-correlation... INFO @ Sun, 03 Jun 2018 12:37:47: end of X-cor INFO @ Sun, 03 Jun 2018 12:37:47: #2 finished! INFO @ Sun, 03 Jun 2018 12:37:47: #2 predicted fragment length is 149 bps INFO @ Sun, 03 Jun 2018 12:37:47: #2 alternative fragment length(s) may be 149 bps INFO @ Sun, 03 Jun 2018 12:37:47: #2.2 Generate R script for model : SRX4082344.05_model.r INFO @ Sun, 03 Jun 2018 12:37:47: #3 Call peaks... INFO @ Sun, 03 Jun 2018 12:37:47: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 03 Jun 2018 12:37:48: #1 tag size is determined as 50 bps INFO @ Sun, 03 Jun 2018 12:37:48: #1 tag size = 50 INFO @ Sun, 03 Jun 2018 12:37:48: #1 total tags in treatment: 11507296 INFO @ Sun, 03 Jun 2018 12:37:48: #1 user defined the maximum tags... INFO @ Sun, 03 Jun 2018 12:37:48: #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 12:37:48: #1 tags after filtering in treatment: 11507296 INFO @ Sun, 03 Jun 2018 12:37:48: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 03 Jun 2018 12:37:48: #1 finished! INFO @ Sun, 03 Jun 2018 12:37:48: #2 Build Peak Model... INFO @ Sun, 03 Jun 2018 12:37:48: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 03 Jun 2018 12:37:49: #1 tag size is determined as 50 bps INFO @ Sun, 03 Jun 2018 12:37:49: #1 tag size = 50 INFO @ Sun, 03 Jun 2018 12:37:49: #1 total tags in treatment: 11507296 INFO @ Sun, 03 Jun 2018 12:37:49: #1 user defined the maximum tags... INFO @ Sun, 03 Jun 2018 12:37:49: #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 12:37:49: #1 tags after filtering in treatment: 11507296 INFO @ Sun, 03 Jun 2018 12:37:49: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 03 Jun 2018 12:37:49: #1 finished! INFO @ Sun, 03 Jun 2018 12:37:49: #2 Build Peak Model... INFO @ Sun, 03 Jun 2018 12:37:49: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 03 Jun 2018 12:37:50: #2 number of paired peaks: 5406 INFO @ Sun, 03 Jun 2018 12:37:50: start model_add_line... INFO @ Sun, 03 Jun 2018 12:37:50: start X-correlation... INFO @ Sun, 03 Jun 2018 12:37:50: end of X-cor INFO @ Sun, 03 Jun 2018 12:37:50: #2 finished! INFO @ Sun, 03 Jun 2018 12:37:50: #2 predicted fragment length is 149 bps INFO @ Sun, 03 Jun 2018 12:37:50: #2 alternative fragment length(s) may be 149 bps INFO @ Sun, 03 Jun 2018 12:37:50: #2.2 Generate R script for model : SRX4082344.10_model.r INFO @ Sun, 03 Jun 2018 12:37:50: #3 Call peaks... INFO @ Sun, 03 Jun 2018 12:37:50: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 03 Jun 2018 12:37:51: #2 number of paired peaks: 5406 INFO @ Sun, 03 Jun 2018 12:37:51: start model_add_line... INFO @ Sun, 03 Jun 2018 12:37:51: start X-correlation... INFO @ Sun, 03 Jun 2018 12:37:51: end of X-cor INFO @ Sun, 03 Jun 2018 12:37:51: #2 finished! INFO @ Sun, 03 Jun 2018 12:37:51: #2 predicted fragment length is 149 bps INFO @ Sun, 03 Jun 2018 12:37:51: #2 alternative fragment length(s) may be 149 bps INFO @ Sun, 03 Jun 2018 12:37:51: #2.2 Generate R script for model : SRX4082344.20_model.r INFO @ Sun, 03 Jun 2018 12:37:51: #3 Call peaks... INFO @ Sun, 03 Jun 2018 12:37:51: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 03 Jun 2018 12:38:20: #3 Call peaks for each chromosome... INFO @ Sun, 03 Jun 2018 12:38:23: #3 Call peaks for each chromosome... INFO @ Sun, 03 Jun 2018 12:38:24: #3 Call peaks for each chromosome... INFO @ Sun, 03 Jun 2018 12:38:35: #4 Write output xls file... SRX4082344.05_peaks.xls INFO @ Sun, 03 Jun 2018 12:38:35: #4 Write peak in narrowPeak format file... SRX4082344.05_peaks.narrowPeak INFO @ Sun, 03 Jun 2018 12:38:35: #4 Write summits bed file... SRX4082344.05_summits.bed INFO @ Sun, 03 Jun 2018 12:38:35: Done! pass1 - making usageList (7 chroms): 2 millis pass2 - checking and writing primary data (7364 records, 4 fields): 10 millis CompletedMACS2peakCalling INFO @ Sun, 03 Jun 2018 12:38:37: #4 Write output xls file... SRX4082344.10_peaks.xls INFO @ Sun, 03 Jun 2018 12:38:37: #4 Write peak in narrowPeak format file... SRX4082344.10_peaks.narrowPeak INFO @ Sun, 03 Jun 2018 12:38:37: #4 Write summits bed file... SRX4082344.10_summits.bed INFO @ Sun, 03 Jun 2018 12:38:37: Done! pass1 - making usageList (6 chroms): 2 millis pass2 - checking and writing primary data (5715 records, 4 fields): 8 millis CompletedMACS2peakCalling INFO @ Sun, 03 Jun 2018 12:38:39: #4 Write output xls file... SRX4082344.20_peaks.xls INFO @ Sun, 03 Jun 2018 12:38:39: #4 Write peak in narrowPeak format file... SRX4082344.20_peaks.narrowPeak INFO @ Sun, 03 Jun 2018 12:38:39: #4 Write summits bed file... SRX4082344.20_summits.bed INFO @ Sun, 03 Jun 2018 12:38:39: Done! pass1 - making usageList (6 chroms): 2 millis pass2 - checking and writing primary data (4188 records, 4 fields): 6 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。