Job ID = 11240727 sra ファイルのダウンロード中... Completed: 865414K bytes transferred in 27 seconds (258857K 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 27925816 spots for /home/okishinya/chipatlas/results/dm3/SRX4639146/SRR7784127.sra Written 27925816 spots for /home/okishinya/chipatlas/results/dm3/SRX4639146/SRR7784127.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: 00:09:40 27925816 reads; of these: 27925816 (100.00%) were unpaired; of these: 3884470 (13.91%) aligned 0 times 17640811 (63.17%) aligned exactly 1 time 6400535 (22.92%) aligned >1 times 86.09% overall alignment rate Time searching: 00:09:40 Overall time: 00:09:40 マッピングが完了しました。 samtools でBAM に変換中... [samopen] SAM header is present: 15 sequences. [bam_sort_core] merging from 12 files... [bam_rmdupse_core] 9923422 / 24041346 = 0.4128 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, 07 Oct 2018 20:45:19: # Command line: callpeak -t SRX4639146.bam -f BAM -g dm -n SRX4639146.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX4639146.05 # format = BAM # ChIP-seq file = ['SRX4639146.bam'] # control file = None # effective genome size = 1.20e+08 # 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, 07 Oct 2018 20:45:19: # Command line: callpeak -t SRX4639146.bam -f BAM -g dm -n SRX4639146.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX4639146.10 # format = BAM # ChIP-seq file = ['SRX4639146.bam'] # control file = None # effective genome size = 1.20e+08 # 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, 07 Oct 2018 20:45:19: # Command line: callpeak -t SRX4639146.bam -f BAM -g dm -n SRX4639146.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX4639146.20 # format = BAM # ChIP-seq file = ['SRX4639146.bam'] # control file = None # effective genome size = 1.20e+08 # 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, 07 Oct 2018 20:45:19: #1 read tag files... INFO @ Sun, 07 Oct 2018 20:45:19: #1 read tag files... INFO @ Sun, 07 Oct 2018 20:45:19: #1 read tag files... INFO @ Sun, 07 Oct 2018 20:45:19: #1 read treatment tags... INFO @ Sun, 07 Oct 2018 20:45:19: #1 read treatment tags... INFO @ Sun, 07 Oct 2018 20:45:19: #1 read treatment tags... INFO @ Sun, 07 Oct 2018 20:45:26: 1000000 INFO @ Sun, 07 Oct 2018 20:45:26: 1000000 INFO @ Sun, 07 Oct 2018 20:45:26: 1000000 INFO @ Sun, 07 Oct 2018 20:45:32: 2000000 INFO @ Sun, 07 Oct 2018 20:45:32: 2000000 INFO @ Sun, 07 Oct 2018 20:45:32: 2000000 INFO @ Sun, 07 Oct 2018 20:45:38: 3000000 INFO @ Sun, 07 Oct 2018 20:45:39: 3000000 INFO @ Sun, 07 Oct 2018 20:45:39: 3000000 INFO @ Sun, 07 Oct 2018 20:45:45: 4000000 INFO @ Sun, 07 Oct 2018 20:45:45: 4000000 INFO @ Sun, 07 Oct 2018 20:45:45: 4000000 INFO @ Sun, 07 Oct 2018 20:45:51: 5000000 INFO @ Sun, 07 Oct 2018 20:45:52: 5000000 INFO @ Sun, 07 Oct 2018 20:45:52: 5000000 INFO @ Sun, 07 Oct 2018 20:45:58: 6000000 INFO @ Sun, 07 Oct 2018 20:45:58: 6000000 INFO @ Sun, 07 Oct 2018 20:45:58: 6000000 INFO @ Sun, 07 Oct 2018 20:46:04: 7000000 INFO @ Sun, 07 Oct 2018 20:46:04: 7000000 INFO @ Sun, 07 Oct 2018 20:46:05: 7000000 INFO @ Sun, 07 Oct 2018 20:46:10: 8000000 INFO @ Sun, 07 Oct 2018 20:46:11: 8000000 INFO @ Sun, 07 Oct 2018 20:46:11: 8000000 INFO @ Sun, 07 Oct 2018 20:46:16: 9000000 INFO @ Sun, 07 Oct 2018 20:46:17: 9000000 INFO @ Sun, 07 Oct 2018 20:46:17: 9000000 INFO @ Sun, 07 Oct 2018 20:46:23: 10000000 INFO @ Sun, 07 Oct 2018 20:46:24: 10000000 INFO @ Sun, 07 Oct 2018 20:46:24: 10000000 INFO @ Sun, 07 Oct 2018 20:46:29: 11000000 INFO @ Sun, 07 Oct 2018 20:46:30: 11000000 INFO @ Sun, 07 Oct 2018 20:46:30: 11000000 INFO @ Sun, 07 Oct 2018 20:46:35: 12000000 INFO @ Sun, 07 Oct 2018 20:46:37: 12000000 INFO @ Sun, 07 Oct 2018 20:46:37: 12000000 INFO @ Sun, 07 Oct 2018 20:46:42: 13000000 INFO @ Sun, 07 Oct 2018 20:46:43: 13000000 INFO @ Sun, 07 Oct 2018 20:46:43: 13000000 INFO @ Sun, 07 Oct 2018 20:46:48: 14000000 INFO @ Sun, 07 Oct 2018 20:46:49: #1 tag size is determined as 51 bps INFO @ Sun, 07 Oct 2018 20:46:49: #1 tag size = 51 INFO @ Sun, 07 Oct 2018 20:46:49: #1 total tags in treatment: 14117924 INFO @ Sun, 07 Oct 2018 20:46:49: #1 user defined the maximum tags... INFO @ Sun, 07 Oct 2018 20:46:49: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sun, 07 Oct 2018 20:46:49: #1 tags after filtering in treatment: 14117924 INFO @ Sun, 07 Oct 2018 20:46:49: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 07 Oct 2018 20:46:49: #1 finished! INFO @ Sun, 07 Oct 2018 20:46:49: #2 Build Peak Model... INFO @ Sun, 07 Oct 2018 20:46:49: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 07 Oct 2018 20:46:50: 14000000 INFO @ Sun, 07 Oct 2018 20:46:50: 14000000 INFO @ Sun, 07 Oct 2018 20:46:50: #2 number of paired peaks: 295 WARNING @ Sun, 07 Oct 2018 20:46:50: Fewer paired peaks (295) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 295 pairs to build model! INFO @ Sun, 07 Oct 2018 20:46:50: start model_add_line... INFO @ Sun, 07 Oct 2018 20:46:50: #1 tag size is determined as 51 bps INFO @ Sun, 07 Oct 2018 20:46:50: #1 tag size = 51 INFO @ Sun, 07 Oct 2018 20:46:50: #1 total tags in treatment: 14117924 INFO @ Sun, 07 Oct 2018 20:46:50: #1 user defined the maximum tags... INFO @ Sun, 07 Oct 2018 20:46:50: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sun, 07 Oct 2018 20:46:50: start X-correlation... INFO @ Sun, 07 Oct 2018 20:46:51: #1 tag size is determined as 51 bps INFO @ Sun, 07 Oct 2018 20:46:51: #1 tag size = 51 INFO @ Sun, 07 Oct 2018 20:46:51: #1 total tags in treatment: 14117924 INFO @ Sun, 07 Oct 2018 20:46:51: #1 user defined the maximum tags... INFO @ Sun, 07 Oct 2018 20:46:51: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sun, 07 Oct 2018 20:46:51: #1 tags after filtering in treatment: 14117924 INFO @ Sun, 07 Oct 2018 20:46:51: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 07 Oct 2018 20:46:51: #1 finished! INFO @ Sun, 07 Oct 2018 20:46:51: #2 Build Peak Model... INFO @ Sun, 07 Oct 2018 20:46:51: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 07 Oct 2018 20:46:51: end of X-cor INFO @ Sun, 07 Oct 2018 20:46:51: #2 finished! INFO @ Sun, 07 Oct 2018 20:46:51: #2 predicted fragment length is 174 bps INFO @ Sun, 07 Oct 2018 20:46:51: #2 alternative fragment length(s) may be 174 bps INFO @ Sun, 07 Oct 2018 20:46:51: #2.2 Generate R script for model : SRX4639146.20_model.r INFO @ Sun, 07 Oct 2018 20:46:51: #3 Call peaks... INFO @ Sun, 07 Oct 2018 20:46:51: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 07 Oct 2018 20:46:51: #1 tags after filtering in treatment: 14117924 INFO @ Sun, 07 Oct 2018 20:46:51: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 07 Oct 2018 20:46:51: #1 finished! INFO @ Sun, 07 Oct 2018 20:46:51: #2 Build Peak Model... INFO @ Sun, 07 Oct 2018 20:46:51: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 07 Oct 2018 20:46:52: #2 number of paired peaks: 295 WARNING @ Sun, 07 Oct 2018 20:46:52: Fewer paired peaks (295) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 295 pairs to build model! INFO @ Sun, 07 Oct 2018 20:46:52: start model_add_line... INFO @ Sun, 07 Oct 2018 20:46:52: start X-correlation... INFO @ Sun, 07 Oct 2018 20:46:52: end of X-cor INFO @ Sun, 07 Oct 2018 20:46:52: #2 finished! INFO @ Sun, 07 Oct 2018 20:46:52: #2 predicted fragment length is 174 bps INFO @ Sun, 07 Oct 2018 20:46:52: #2 alternative fragment length(s) may be 174 bps INFO @ Sun, 07 Oct 2018 20:46:52: #2.2 Generate R script for model : SRX4639146.05_model.r INFO @ Sun, 07 Oct 2018 20:46:52: #3 Call peaks... INFO @ Sun, 07 Oct 2018 20:46:52: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 07 Oct 2018 20:46:52: #2 number of paired peaks: 295 WARNING @ Sun, 07 Oct 2018 20:46:52: Fewer paired peaks (295) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 295 pairs to build model! INFO @ Sun, 07 Oct 2018 20:46:52: start model_add_line... INFO @ Sun, 07 Oct 2018 20:46:52: start X-correlation... INFO @ Sun, 07 Oct 2018 20:46:52: end of X-cor INFO @ Sun, 07 Oct 2018 20:46:52: #2 finished! INFO @ Sun, 07 Oct 2018 20:46:52: #2 predicted fragment length is 174 bps INFO @ Sun, 07 Oct 2018 20:46:52: #2 alternative fragment length(s) may be 174 bps INFO @ Sun, 07 Oct 2018 20:46:52: #2.2 Generate R script for model : SRX4639146.10_model.r INFO @ Sun, 07 Oct 2018 20:46:52: #3 Call peaks... INFO @ Sun, 07 Oct 2018 20:46:52: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 07 Oct 2018 20:47:22: #3 Call peaks for each chromosome... INFO @ Sun, 07 Oct 2018 20:47:22: #3 Call peaks for each chromosome... INFO @ Sun, 07 Oct 2018 20:47:23: #3 Call peaks for each chromosome... INFO @ Sun, 07 Oct 2018 20:47:37: #4 Write output xls file... SRX4639146.20_peaks.xls INFO @ Sun, 07 Oct 2018 20:47:37: #4 Write peak in narrowPeak format file... SRX4639146.20_peaks.narrowPeak INFO @ Sun, 07 Oct 2018 20:47:37: #4 Write summits bed file... SRX4639146.20_summits.bed INFO @ Sun, 07 Oct 2018 20:47:37: Done! pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (1369 records, 4 fields): 91 millis CompletedMACS2peakCalling INFO @ Sun, 07 Oct 2018 20:47:39: #4 Write output xls file... SRX4639146.10_peaks.xls INFO @ Sun, 07 Oct 2018 20:47:40: #4 Write peak in narrowPeak format file... SRX4639146.10_peaks.narrowPeak INFO @ Sun, 07 Oct 2018 20:47:40: #4 Write output xls file... SRX4639146.05_peaks.xls INFO @ Sun, 07 Oct 2018 20:47:40: #4 Write peak in narrowPeak format file... SRX4639146.05_peaks.narrowPeak INFO @ Sun, 07 Oct 2018 20:47:40: #4 Write summits bed file... SRX4639146.10_summits.bed INFO @ Sun, 07 Oct 2018 20:47:40: Done! INFO @ Sun, 07 Oct 2018 20:47:40: #4 Write summits bed file... SRX4639146.05_summits.bed INFO @ Sun, 07 Oct 2018 20:47:40: Done! pass1 - making usageList (15 chroms): 2 millis pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (2578 records, 4 fields): 5 millis CompletedMACS2peakCalling pass2 - checking and writing primary data (4688 records, 4 fields): 1053 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。