Job ID = 11240742 sra ファイルのダウンロード中... Completed: 337454K bytes transferred in 17 seconds (156224K 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 19191421 spots for /home/okishinya/chipatlas/results/dm3/SRX4669026/SRR7817551.sra Written 19191421 spots for /home/okishinya/chipatlas/results/dm3/SRX4669026/SRR7817551.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: 00:05:30 19191421 reads; of these: 19191421 (100.00%) were unpaired; of these: 675978 (3.52%) aligned 0 times 16721639 (87.13%) aligned exactly 1 time 1793804 (9.35%) aligned >1 times 96.48% overall alignment rate Time searching: 00:05:30 Overall time: 00:05:30 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 8 files... [bam_rmdupse_core] 3787496 / 18515443 = 0.2046 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 20:39:34: # Command line: callpeak -t SRX4669026.bam -f BAM -g dm -n SRX4669026.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX4669026.10 # format = BAM # ChIP-seq file = ['SRX4669026.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 20:39:34: #1 read tag files... INFO @ Sun, 07 Oct 2018 20:39:34: #1 read treatment tags... INFO @ Sun, 07 Oct 2018 20:39:34: # Command line: callpeak -t SRX4669026.bam -f BAM -g dm -n SRX4669026.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX4669026.20 # format = BAM # ChIP-seq file = ['SRX4669026.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 20:39:34: #1 read tag files... INFO @ Sun, 07 Oct 2018 20:39:34: #1 read treatment tags... INFO @ Sun, 07 Oct 2018 20:39:34: # Command line: callpeak -t SRX4669026.bam -f BAM -g dm -n SRX4669026.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX4669026.05 # format = BAM # ChIP-seq file = ['SRX4669026.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 20:39:34: #1 read tag files... INFO @ Sun, 07 Oct 2018 20:39:34: #1 read treatment tags... INFO @ Sun, 07 Oct 2018 20:39:41: 1000000 INFO @ Sun, 07 Oct 2018 20:39:42: 1000000 INFO @ Sun, 07 Oct 2018 20:39:42: 1000000 INFO @ Sun, 07 Oct 2018 20:39:48: 2000000 INFO @ Sun, 07 Oct 2018 20:39:49: 2000000 INFO @ Sun, 07 Oct 2018 20:39:49: 2000000 INFO @ Sun, 07 Oct 2018 20:39:55: 3000000 INFO @ Sun, 07 Oct 2018 20:39:57: 3000000 INFO @ Sun, 07 Oct 2018 20:39:57: 3000000 INFO @ Sun, 07 Oct 2018 20:40:02: 4000000 INFO @ Sun, 07 Oct 2018 20:40:06: 4000000 INFO @ Sun, 07 Oct 2018 20:40:06: 4000000 INFO @ Sun, 07 Oct 2018 20:40:10: 5000000 INFO @ Sun, 07 Oct 2018 20:40:14: 5000000 INFO @ Sun, 07 Oct 2018 20:40:14: 5000000 INFO @ Sun, 07 Oct 2018 20:40:17: 6000000 INFO @ Sun, 07 Oct 2018 20:40:22: 6000000 INFO @ Sun, 07 Oct 2018 20:40:22: 6000000 INFO @ Sun, 07 Oct 2018 20:40:25: 7000000 INFO @ Sun, 07 Oct 2018 20:40:30: 7000000 INFO @ Sun, 07 Oct 2018 20:40:30: 7000000 INFO @ Sun, 07 Oct 2018 20:40:32: 8000000 INFO @ Sun, 07 Oct 2018 20:40:36: 8000000 INFO @ Sun, 07 Oct 2018 20:40:36: 8000000 INFO @ Sun, 07 Oct 2018 20:40:38: 9000000 INFO @ Sun, 07 Oct 2018 20:40:44: 9000000 INFO @ Sun, 07 Oct 2018 20:40:44: 9000000 INFO @ Sun, 07 Oct 2018 20:40:45: 10000000 INFO @ Sun, 07 Oct 2018 20:40:50: 10000000 INFO @ Sun, 07 Oct 2018 20:40:50: 10000000 INFO @ Sun, 07 Oct 2018 20:40:51: 11000000 INFO @ Sun, 07 Oct 2018 20:40:57: 11000000 INFO @ Sun, 07 Oct 2018 20:40:57: 11000000 INFO @ Sun, 07 Oct 2018 20:40:57: 12000000 INFO @ Sun, 07 Oct 2018 20:41:04: 13000000 INFO @ Sun, 07 Oct 2018 20:41:05: 12000000 INFO @ Sun, 07 Oct 2018 20:41:05: 12000000 INFO @ Sun, 07 Oct 2018 20:41:10: 14000000 INFO @ Sun, 07 Oct 2018 20:41:11: 13000000 INFO @ Sun, 07 Oct 2018 20:41:11: 13000000 INFO @ Sun, 07 Oct 2018 20:41:14: #1 tag size is determined as 50 bps INFO @ Sun, 07 Oct 2018 20:41:14: #1 tag size = 50 INFO @ Sun, 07 Oct 2018 20:41:14: #1 total tags in treatment: 14727947 INFO @ Sun, 07 Oct 2018 20:41:14: #1 user defined the maximum tags... INFO @ Sun, 07 Oct 2018 20:41:14: #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 20:41:14: #1 tags after filtering in treatment: 14727947 INFO @ Sun, 07 Oct 2018 20:41:14: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 07 Oct 2018 20:41:14: #1 finished! INFO @ Sun, 07 Oct 2018 20:41:14: #2 Build Peak Model... INFO @ Sun, 07 Oct 2018 20:41:14: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 07 Oct 2018 20:41:16: #2 number of paired peaks: 653 WARNING @ Sun, 07 Oct 2018 20:41:16: Fewer paired peaks (653) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 653 pairs to build model! INFO @ Sun, 07 Oct 2018 20:41:16: start model_add_line... INFO @ Sun, 07 Oct 2018 20:41:16: start X-correlation... INFO @ Sun, 07 Oct 2018 20:41:16: end of X-cor INFO @ Sun, 07 Oct 2018 20:41:16: #2 finished! INFO @ Sun, 07 Oct 2018 20:41:16: #2 predicted fragment length is 118 bps INFO @ Sun, 07 Oct 2018 20:41:16: #2 alternative fragment length(s) may be 118 bps INFO @ Sun, 07 Oct 2018 20:41:16: #2.2 Generate R script for model : SRX4669026.10_model.r INFO @ Sun, 07 Oct 2018 20:41:16: #3 Call peaks... INFO @ Sun, 07 Oct 2018 20:41:16: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 07 Oct 2018 20:41:18: 14000000 INFO @ Sun, 07 Oct 2018 20:41:18: 14000000 INFO @ Sun, 07 Oct 2018 20:41:23: #1 tag size is determined as 50 bps INFO @ Sun, 07 Oct 2018 20:41:23: #1 tag size = 50 INFO @ Sun, 07 Oct 2018 20:41:23: #1 total tags in treatment: 14727947 INFO @ Sun, 07 Oct 2018 20:41:23: #1 user defined the maximum tags... INFO @ Sun, 07 Oct 2018 20:41:23: #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 20:41:23: #1 tag size is determined as 50 bps INFO @ Sun, 07 Oct 2018 20:41:23: #1 tag size = 50 INFO @ Sun, 07 Oct 2018 20:41:23: #1 total tags in treatment: 14727947 INFO @ Sun, 07 Oct 2018 20:41:23: #1 user defined the maximum tags... INFO @ Sun, 07 Oct 2018 20:41:23: #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 20:41:23: #1 tags after filtering in treatment: 14727947 INFO @ Sun, 07 Oct 2018 20:41:23: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 07 Oct 2018 20:41:23: #1 finished! INFO @ Sun, 07 Oct 2018 20:41:23: #2 Build Peak Model... INFO @ Sun, 07 Oct 2018 20:41:23: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 07 Oct 2018 20:41:23: #1 tags after filtering in treatment: 14727947 INFO @ Sun, 07 Oct 2018 20:41:23: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 07 Oct 2018 20:41:23: #1 finished! INFO @ Sun, 07 Oct 2018 20:41:23: #2 Build Peak Model... INFO @ Sun, 07 Oct 2018 20:41:23: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 07 Oct 2018 20:41:24: #2 number of paired peaks: 653 WARNING @ Sun, 07 Oct 2018 20:41:24: Fewer paired peaks (653) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 653 pairs to build model! INFO @ Sun, 07 Oct 2018 20:41:24: start model_add_line... INFO @ Sun, 07 Oct 2018 20:41:24: #2 number of paired peaks: 653 WARNING @ Sun, 07 Oct 2018 20:41:24: Fewer paired peaks (653) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 653 pairs to build model! INFO @ Sun, 07 Oct 2018 20:41:24: start model_add_line... INFO @ Sun, 07 Oct 2018 20:41:24: start X-correlation... INFO @ Sun, 07 Oct 2018 20:41:24: end of X-cor INFO @ Sun, 07 Oct 2018 20:41:24: #2 finished! INFO @ Sun, 07 Oct 2018 20:41:24: #2 predicted fragment length is 118 bps INFO @ Sun, 07 Oct 2018 20:41:24: #2 alternative fragment length(s) may be 118 bps INFO @ Sun, 07 Oct 2018 20:41:24: #2.2 Generate R script for model : SRX4669026.20_model.r INFO @ Sun, 07 Oct 2018 20:41:24: #3 Call peaks... INFO @ Sun, 07 Oct 2018 20:41:24: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 07 Oct 2018 20:41:24: start X-correlation... INFO @ Sun, 07 Oct 2018 20:41:24: end of X-cor INFO @ Sun, 07 Oct 2018 20:41:24: #2 finished! INFO @ Sun, 07 Oct 2018 20:41:24: #2 predicted fragment length is 118 bps INFO @ Sun, 07 Oct 2018 20:41:24: #2 alternative fragment length(s) may be 118 bps INFO @ Sun, 07 Oct 2018 20:41:24: #2.2 Generate R script for model : SRX4669026.05_model.r INFO @ Sun, 07 Oct 2018 20:41:24: #3 Call peaks... INFO @ Sun, 07 Oct 2018 20:41:24: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 07 Oct 2018 20:41:50: #3 Call peaks for each chromosome... INFO @ Sun, 07 Oct 2018 20:41:57: #3 Call peaks for each chromosome... INFO @ Sun, 07 Oct 2018 20:41:59: #3 Call peaks for each chromosome... INFO @ Sun, 07 Oct 2018 20:42:08: #4 Write output xls file... SRX4669026.10_peaks.xls INFO @ Sun, 07 Oct 2018 20:42:08: #4 Write peak in narrowPeak format file... SRX4669026.10_peaks.narrowPeak INFO @ Sun, 07 Oct 2018 20:42:08: #4 Write summits bed file... SRX4669026.10_summits.bed INFO @ Sun, 07 Oct 2018 20:42:08: Done! pass1 - making usageList (13 chroms): 1 millis pass2 - checking and writing primary data (6605 records, 4 fields): 10 millis CompletedMACS2peakCalling INFO @ Sun, 07 Oct 2018 20:42:17: #4 Write output xls file... SRX4669026.20_peaks.xls INFO @ Sun, 07 Oct 2018 20:42:17: #4 Write peak in narrowPeak format file... SRX4669026.20_peaks.narrowPeak INFO @ Sun, 07 Oct 2018 20:42:17: #4 Write summits bed file... SRX4669026.20_summits.bed INFO @ Sun, 07 Oct 2018 20:42:17: Done! pass1 - making usageList (11 chroms): 1 millis pass2 - checking and writing primary data (3362 records, 4 fields): 5 millis CompletedMACS2peakCalling INFO @ Sun, 07 Oct 2018 20:42:19: #4 Write output xls file... SRX4669026.05_peaks.xls INFO @ Sun, 07 Oct 2018 20:42:19: #4 Write peak in narrowPeak format file... SRX4669026.05_peaks.narrowPeak INFO @ Sun, 07 Oct 2018 20:42:19: #4 Write summits bed file... SRX4669026.05_summits.bed INFO @ Sun, 07 Oct 2018 20:42:19: Done! pass1 - making usageList (13 chroms): 2 millis pass2 - checking and writing primary data (9842 records, 4 fields): 13 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。