Job ID = 10714376 sra ファイルのダウンロード中... Completed: 321168K bytes transferred in 23 seconds (114372K 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 14229371 spots for /home/okishinya/chipatlas/results/ce10/SRX4082336/SRR7164154.sra Written 14229371 spots for /home/okishinya/chipatlas/results/ce10/SRX4082336/SRR7164154.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: 00:03:29 14229371 reads; of these: 14229371 (100.00%) were unpaired; of these: 1512824 (10.63%) aligned 0 times 11628355 (81.72%) aligned exactly 1 time 1088192 (7.65%) aligned >1 times 89.37% overall alignment rate Time searching: 00:03:29 Overall time: 00:03:29 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] 3427753 / 12716547 = 0.2696 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 12:35:01: # Command line: callpeak -t SRX4082336.bam -f BAM -g ce -n SRX4082336.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX4082336.20 # format = BAM # ChIP-seq file = ['SRX4082336.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 12:35:01: # Command line: callpeak -t SRX4082336.bam -f BAM -g ce -n SRX4082336.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX4082336.10 # format = BAM # ChIP-seq file = ['SRX4082336.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 12:35:01: # Command line: callpeak -t SRX4082336.bam -f BAM -g ce -n SRX4082336.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX4082336.05 # format = BAM # ChIP-seq file = ['SRX4082336.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 12:35:01: #1 read tag files... INFO @ Sun, 03 Jun 2018 12:35:01: #1 read tag files... INFO @ Sun, 03 Jun 2018 12:35:01: #1 read tag files... INFO @ Sun, 03 Jun 2018 12:35:01: #1 read treatment tags... INFO @ Sun, 03 Jun 2018 12:35:01: #1 read treatment tags... INFO @ Sun, 03 Jun 2018 12:35:01: #1 read treatment tags... INFO @ Sun, 03 Jun 2018 12:35:07: 1000000 INFO @ Sun, 03 Jun 2018 12:35:08: 1000000 INFO @ Sun, 03 Jun 2018 12:35:08: 1000000 INFO @ Sun, 03 Jun 2018 12:35:14: 2000000 INFO @ Sun, 03 Jun 2018 12:35:14: 2000000 INFO @ Sun, 03 Jun 2018 12:35:15: 2000000 INFO @ Sun, 03 Jun 2018 12:35:21: 3000000 INFO @ Sun, 03 Jun 2018 12:35:21: 3000000 INFO @ Sun, 03 Jun 2018 12:35:21: 3000000 INFO @ Sun, 03 Jun 2018 12:35:27: 4000000 INFO @ Sun, 03 Jun 2018 12:35:27: 4000000 INFO @ Sun, 03 Jun 2018 12:35:28: 4000000 INFO @ Sun, 03 Jun 2018 12:35:34: 5000000 INFO @ Sun, 03 Jun 2018 12:35:34: 5000000 INFO @ Sun, 03 Jun 2018 12:35:35: 5000000 INFO @ Sun, 03 Jun 2018 12:35:41: 6000000 INFO @ Sun, 03 Jun 2018 12:35:42: 6000000 INFO @ Sun, 03 Jun 2018 12:35:42: 6000000 INFO @ Sun, 03 Jun 2018 12:35:49: 7000000 INFO @ Sun, 03 Jun 2018 12:35:50: 7000000 INFO @ Sun, 03 Jun 2018 12:35:50: 7000000 INFO @ Sun, 03 Jun 2018 12:35:56: 8000000 INFO @ Sun, 03 Jun 2018 12:35:57: 8000000 INFO @ Sun, 03 Jun 2018 12:35:57: 8000000 INFO @ Sun, 03 Jun 2018 12:36:03: 9000000 INFO @ Sun, 03 Jun 2018 12:36:05: 9000000 INFO @ Sun, 03 Jun 2018 12:36:05: #1 tag size is determined as 50 bps INFO @ Sun, 03 Jun 2018 12:36:05: #1 tag size = 50 INFO @ Sun, 03 Jun 2018 12:36:05: #1 total tags in treatment: 9288794 INFO @ Sun, 03 Jun 2018 12:36:05: #1 user defined the maximum tags... INFO @ Sun, 03 Jun 2018 12:36:05: #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 12:36:05: #1 tags after filtering in treatment: 9288794 INFO @ Sun, 03 Jun 2018 12:36:05: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 03 Jun 2018 12:36:05: #1 finished! INFO @ Sun, 03 Jun 2018 12:36:05: #2 Build Peak Model... INFO @ Sun, 03 Jun 2018 12:36:05: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 03 Jun 2018 12:36:06: 9000000 INFO @ Sun, 03 Jun 2018 12:36:07: #2 number of paired peaks: 5070 INFO @ Sun, 03 Jun 2018 12:36:07: start model_add_line... INFO @ Sun, 03 Jun 2018 12:36:07: #1 tag size is determined as 50 bps INFO @ Sun, 03 Jun 2018 12:36:07: #1 tag size = 50 INFO @ Sun, 03 Jun 2018 12:36:07: #1 total tags in treatment: 9288794 INFO @ Sun, 03 Jun 2018 12:36:07: #1 user defined the maximum tags... INFO @ Sun, 03 Jun 2018 12:36:07: #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 12:36:07: start X-correlation... INFO @ Sun, 03 Jun 2018 12:36:07: end of X-cor INFO @ Sun, 03 Jun 2018 12:36:07: #2 finished! INFO @ Sun, 03 Jun 2018 12:36:07: #2 predicted fragment length is 154 bps INFO @ Sun, 03 Jun 2018 12:36:07: #2 alternative fragment length(s) may be 154 bps INFO @ Sun, 03 Jun 2018 12:36:07: #2.2 Generate R script for model : SRX4082336.20_model.r INFO @ Sun, 03 Jun 2018 12:36:07: #3 Call peaks... INFO @ Sun, 03 Jun 2018 12:36:07: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 03 Jun 2018 12:36:07: #1 tags after filtering in treatment: 9288794 INFO @ Sun, 03 Jun 2018 12:36:07: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 03 Jun 2018 12:36:07: #1 finished! INFO @ Sun, 03 Jun 2018 12:36:07: #2 Build Peak Model... INFO @ Sun, 03 Jun 2018 12:36:07: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 03 Jun 2018 12:36:08: #1 tag size is determined as 50 bps INFO @ Sun, 03 Jun 2018 12:36:08: #1 tag size = 50 INFO @ Sun, 03 Jun 2018 12:36:08: #1 total tags in treatment: 9288794 INFO @ Sun, 03 Jun 2018 12:36:08: #1 user defined the maximum tags... INFO @ Sun, 03 Jun 2018 12:36:08: #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 12:36:08: #2 number of paired peaks: 5070 INFO @ Sun, 03 Jun 2018 12:36:08: start model_add_line... INFO @ Sun, 03 Jun 2018 12:36:08: #1 tags after filtering in treatment: 9288794 INFO @ Sun, 03 Jun 2018 12:36:08: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 03 Jun 2018 12:36:08: #1 finished! INFO @ Sun, 03 Jun 2018 12:36:08: #2 Build Peak Model... INFO @ Sun, 03 Jun 2018 12:36:08: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 03 Jun 2018 12:36:08: start X-correlation... INFO @ Sun, 03 Jun 2018 12:36:08: end of X-cor INFO @ Sun, 03 Jun 2018 12:36:08: #2 finished! INFO @ Sun, 03 Jun 2018 12:36:08: #2 predicted fragment length is 154 bps INFO @ Sun, 03 Jun 2018 12:36:08: #2 alternative fragment length(s) may be 154 bps INFO @ Sun, 03 Jun 2018 12:36:08: #2.2 Generate R script for model : SRX4082336.10_model.r INFO @ Sun, 03 Jun 2018 12:36:08: #3 Call peaks... INFO @ Sun, 03 Jun 2018 12:36:08: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 03 Jun 2018 12:36:09: #2 number of paired peaks: 5070 INFO @ Sun, 03 Jun 2018 12:36:09: start model_add_line... INFO @ Sun, 03 Jun 2018 12:36:09: start X-correlation... INFO @ Sun, 03 Jun 2018 12:36:09: end of X-cor INFO @ Sun, 03 Jun 2018 12:36:09: #2 finished! INFO @ Sun, 03 Jun 2018 12:36:09: #2 predicted fragment length is 154 bps INFO @ Sun, 03 Jun 2018 12:36:09: #2 alternative fragment length(s) may be 154 bps INFO @ Sun, 03 Jun 2018 12:36:09: #2.2 Generate R script for model : SRX4082336.05_model.r INFO @ Sun, 03 Jun 2018 12:36:09: #3 Call peaks... INFO @ Sun, 03 Jun 2018 12:36:09: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 03 Jun 2018 12:36:33: #3 Call peaks for each chromosome... INFO @ Sun, 03 Jun 2018 12:36:34: #3 Call peaks for each chromosome... INFO @ Sun, 03 Jun 2018 12:36:37: #3 Call peaks for each chromosome... INFO @ Sun, 03 Jun 2018 12:36:45: #4 Write output xls file... SRX4082336.20_peaks.xls INFO @ Sun, 03 Jun 2018 12:36:45: #4 Write peak in narrowPeak format file... SRX4082336.20_peaks.narrowPeak INFO @ Sun, 03 Jun 2018 12:36:45: #4 Write summits bed file... SRX4082336.20_summits.bed INFO @ Sun, 03 Jun 2018 12:36:45: Done! pass1 - making usageList (6 chroms): 2 millis pass2 - checking and writing primary data (4205 records, 4 fields): 7 millis CompletedMACS2peakCalling INFO @ Sun, 03 Jun 2018 12:36:47: #4 Write output xls file... SRX4082336.10_peaks.xls INFO @ Sun, 03 Jun 2018 12:36:47: #4 Write peak in narrowPeak format file... SRX4082336.10_peaks.narrowPeak INFO @ Sun, 03 Jun 2018 12:36:47: #4 Write summits bed file... SRX4082336.10_summits.bed INFO @ Sun, 03 Jun 2018 12:36:47: Done! pass1 - making usageList (6 chroms): 2 millis pass2 - checking and writing primary data (5348 records, 4 fields): 7 millis CompletedMACS2peakCalling INFO @ Sun, 03 Jun 2018 12:36:52: #4 Write output xls file... SRX4082336.05_peaks.xls INFO @ Sun, 03 Jun 2018 12:36:52: #4 Write peak in narrowPeak format file... SRX4082336.05_peaks.narrowPeak INFO @ Sun, 03 Jun 2018 12:36:52: #4 Write summits bed file... SRX4082336.05_summits.bed INFO @ Sun, 03 Jun 2018 12:36:52: Done! pass1 - making usageList (6 chroms): 2 millis pass2 - checking and writing primary data (6731 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。