Job ID = 10480752 sra ファイルのダウンロード中... Completed: 571852K bytes transferred in 41 seconds (113406K 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... Written 21661140 spots for /home/okishinya/chipatlas/results/dm3/SRX3380811/SRR6278174.sra Written 21661140 spots total 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: 00:06:03 21661140 reads; of these: 21661140 (100.00%) were unpaired; of these: 1479727 (6.83%) aligned 0 times 18286389 (84.42%) aligned exactly 1 time 1895024 (8.75%) aligned >1 times 93.17% overall alignment rate Time searching: 00:06:03 Overall time: 00:06:03 マッピングが完了しました。 samtools でBAM に変換中... [samopen] SAM header is present: 15 sequences. [bam_sort_core] merging from 12 files... [bam_rmdupse_core] 15821000 / 20181413 = 0.7839 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 @ Fri, 16 Mar 2018 07:59:03: # Command line: callpeak -t SRX3380811.bam -f BAM -g dm -n SRX3380811.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX3380811.10 # format = BAM # ChIP-seq file = ['SRX3380811.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 @ Fri, 16 Mar 2018 07:59:03: #1 read tag files... INFO @ Fri, 16 Mar 2018 07:59:03: #1 read treatment tags... INFO @ Fri, 16 Mar 2018 07:59:03: # Command line: callpeak -t SRX3380811.bam -f BAM -g dm -n SRX3380811.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX3380811.20 # format = BAM # ChIP-seq file = ['SRX3380811.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 @ Fri, 16 Mar 2018 07:59:03: #1 read tag files... INFO @ Fri, 16 Mar 2018 07:59:03: #1 read treatment tags... INFO @ Fri, 16 Mar 2018 07:59:03: # Command line: callpeak -t SRX3380811.bam -f BAM -g dm -n SRX3380811.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX3380811.05 # format = BAM # ChIP-seq file = ['SRX3380811.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 @ Fri, 16 Mar 2018 07:59:03: #1 read tag files... INFO @ Fri, 16 Mar 2018 07:59:03: #1 read treatment tags... INFO @ Fri, 16 Mar 2018 07:59:10: 1000000 INFO @ Fri, 16 Mar 2018 07:59:10: 1000000 INFO @ Fri, 16 Mar 2018 07:59:10: 1000000 INFO @ Fri, 16 Mar 2018 07:59:16: 2000000 INFO @ Fri, 16 Mar 2018 07:59:17: 2000000 INFO @ Fri, 16 Mar 2018 07:59:17: 2000000 INFO @ Fri, 16 Mar 2018 07:59:23: 3000000 INFO @ Fri, 16 Mar 2018 07:59:24: 3000000 INFO @ Fri, 16 Mar 2018 07:59:24: 3000000 INFO @ Fri, 16 Mar 2018 07:59:30: 4000000 INFO @ Fri, 16 Mar 2018 07:59:30: 4000000 INFO @ Fri, 16 Mar 2018 07:59:31: 4000000 INFO @ Fri, 16 Mar 2018 07:59:32: #1 tag size is determined as 51 bps INFO @ Fri, 16 Mar 2018 07:59:32: #1 tag size = 51 INFO @ Fri, 16 Mar 2018 07:59:32: #1 total tags in treatment: 4360413 INFO @ Fri, 16 Mar 2018 07:59:32: #1 user defined the maximum tags... INFO @ Fri, 16 Mar 2018 07:59:32: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 16 Mar 2018 07:59:32: #1 tags after filtering in treatment: 4360413 INFO @ Fri, 16 Mar 2018 07:59:32: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 16 Mar 2018 07:59:32: #1 finished! INFO @ Fri, 16 Mar 2018 07:59:32: #2 Build Peak Model... INFO @ Fri, 16 Mar 2018 07:59:32: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 16 Mar 2018 07:59:33: #1 tag size is determined as 51 bps INFO @ Fri, 16 Mar 2018 07:59:33: #1 tag size = 51 INFO @ Fri, 16 Mar 2018 07:59:33: #1 total tags in treatment: 4360413 INFO @ Fri, 16 Mar 2018 07:59:33: #1 user defined the maximum tags... INFO @ Fri, 16 Mar 2018 07:59:33: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 16 Mar 2018 07:59:33: #1 tags after filtering in treatment: 4360413 INFO @ Fri, 16 Mar 2018 07:59:33: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 16 Mar 2018 07:59:33: #1 finished! INFO @ Fri, 16 Mar 2018 07:59:33: #2 Build Peak Model... INFO @ Fri, 16 Mar 2018 07:59:33: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 16 Mar 2018 07:59:33: #2 number of paired peaks: 6271 INFO @ Fri, 16 Mar 2018 07:59:33: start model_add_line... INFO @ Fri, 16 Mar 2018 07:59:33: start X-correlation... INFO @ Fri, 16 Mar 2018 07:59:33: end of X-cor INFO @ Fri, 16 Mar 2018 07:59:33: #2 finished! INFO @ Fri, 16 Mar 2018 07:59:33: #2 predicted fragment length is 167 bps INFO @ Fri, 16 Mar 2018 07:59:33: #2 alternative fragment length(s) may be 167 bps INFO @ Fri, 16 Mar 2018 07:59:33: #2.2 Generate R script for model : SRX3380811.10_model.r INFO @ Fri, 16 Mar 2018 07:59:33: #3 Call peaks... INFO @ Fri, 16 Mar 2018 07:59:33: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 16 Mar 2018 07:59:33: #1 tag size is determined as 51 bps INFO @ Fri, 16 Mar 2018 07:59:33: #1 tag size = 51 INFO @ Fri, 16 Mar 2018 07:59:33: #1 total tags in treatment: 4360413 INFO @ Fri, 16 Mar 2018 07:59:33: #1 user defined the maximum tags... INFO @ Fri, 16 Mar 2018 07:59:33: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 16 Mar 2018 07:59:33: #1 tags after filtering in treatment: 4360413 INFO @ Fri, 16 Mar 2018 07:59:33: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 16 Mar 2018 07:59:33: #1 finished! INFO @ Fri, 16 Mar 2018 07:59:33: #2 Build Peak Model... INFO @ Fri, 16 Mar 2018 07:59:33: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 16 Mar 2018 07:59:34: #2 number of paired peaks: 6271 INFO @ Fri, 16 Mar 2018 07:59:34: start model_add_line... INFO @ Fri, 16 Mar 2018 07:59:34: start X-correlation... INFO @ Fri, 16 Mar 2018 07:59:34: end of X-cor INFO @ Fri, 16 Mar 2018 07:59:34: #2 finished! INFO @ Fri, 16 Mar 2018 07:59:34: #2 predicted fragment length is 167 bps INFO @ Fri, 16 Mar 2018 07:59:34: #2 alternative fragment length(s) may be 167 bps INFO @ Fri, 16 Mar 2018 07:59:34: #2.2 Generate R script for model : SRX3380811.05_model.r INFO @ Fri, 16 Mar 2018 07:59:34: #3 Call peaks... INFO @ Fri, 16 Mar 2018 07:59:34: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 16 Mar 2018 07:59:34: #2 number of paired peaks: 6271 INFO @ Fri, 16 Mar 2018 07:59:34: start model_add_line... INFO @ Fri, 16 Mar 2018 07:59:34: start X-correlation... INFO @ Fri, 16 Mar 2018 07:59:34: end of X-cor INFO @ Fri, 16 Mar 2018 07:59:34: #2 finished! INFO @ Fri, 16 Mar 2018 07:59:34: #2 predicted fragment length is 167 bps INFO @ Fri, 16 Mar 2018 07:59:34: #2 alternative fragment length(s) may be 167 bps INFO @ Fri, 16 Mar 2018 07:59:34: #2.2 Generate R script for model : SRX3380811.20_model.r INFO @ Fri, 16 Mar 2018 07:59:34: #3 Call peaks... INFO @ Fri, 16 Mar 2018 07:59:34: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 16 Mar 2018 07:59:45: #3 Call peaks for each chromosome... INFO @ Fri, 16 Mar 2018 07:59:45: #3 Call peaks for each chromosome... INFO @ Fri, 16 Mar 2018 07:59:46: #3 Call peaks for each chromosome... INFO @ Fri, 16 Mar 2018 07:59:51: #4 Write output xls file... SRX3380811.10_peaks.xls INFO @ Fri, 16 Mar 2018 07:59:51: #4 Write peak in narrowPeak format file... SRX3380811.10_peaks.narrowPeak INFO @ Fri, 16 Mar 2018 07:59:51: #4 Write summits bed file... SRX3380811.10_summits.bed INFO @ Fri, 16 Mar 2018 07:59:51: Done! pass1 - making usageList (14 chroms): 2 millis pass2 - checking and writing primary data (6312 records, 4 fields): 9 millis CompletedMACS2peakCalling INFO @ Fri, 16 Mar 2018 07:59:52: #4 Write output xls file... SRX3380811.05_peaks.xls INFO @ Fri, 16 Mar 2018 07:59:52: #4 Write output xls file... SRX3380811.20_peaks.xls INFO @ Fri, 16 Mar 2018 07:59:52: #4 Write peak in narrowPeak format file... SRX3380811.05_peaks.narrowPeak INFO @ Fri, 16 Mar 2018 07:59:52: #4 Write peak in narrowPeak format file... SRX3380811.20_peaks.narrowPeak INFO @ Fri, 16 Mar 2018 07:59:52: #4 Write summits bed file... SRX3380811.20_summits.bed INFO @ Fri, 16 Mar 2018 07:59:52: Done! INFO @ Fri, 16 Mar 2018 07:59:52: #4 Write summits bed file... SRX3380811.05_summits.bed pass1 - making usageList (14 chroms): 1 millis INFO @ Fri, 16 Mar 2018 07:59:52: Done! pass2 - checking and writing primary data (2826 records, 4 fields): 5 millis CompletedMACS2peakCalling pass1 - making usageList (14 chroms): 2 millis pass2 - checking and writing primary data (9790 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。