Job ID = 10450887 sra ファイルのダウンロード中... Completed: 177638K bytes transferred in 5 seconds (252132K 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 8780963 spots for /home/okishinya/chipatlas/results/dm3/SRX3404029/SRR6303506.sra Written 8780963 spots total rm: cannot remove `[DSE]RX*': No such file or directory rm: cannot remove `[DSE]RR*.fastq': No such file or directory 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: 00:06:30 8780963 reads; of these: 8780963 (100.00%) were unpaired; of these: 698479 (7.95%) aligned 0 times 5920909 (67.43%) aligned exactly 1 time 2161575 (24.62%) aligned >1 times 92.05% overall alignment rate Time searching: 00:06:30 Overall time: 00:06:30 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_rmdupse_core] 1438016 / 8082484 = 0.1779 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 @ Wed, 07 Feb 2018 13:05:01: # Command line: callpeak -t SRX3404029.bam -f BAM -g dm -n SRX3404029.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX3404029.10 # format = BAM # ChIP-seq file = ['SRX3404029.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 @ Wed, 07 Feb 2018 13:05:01: #1 read tag files... INFO @ Wed, 07 Feb 2018 13:05:01: #1 read treatment tags... INFO @ Wed, 07 Feb 2018 13:05:01: # Command line: callpeak -t SRX3404029.bam -f BAM -g dm -n SRX3404029.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX3404029.20 # format = BAM # ChIP-seq file = ['SRX3404029.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 @ Wed, 07 Feb 2018 13:05:01: #1 read tag files... INFO @ Wed, 07 Feb 2018 13:05:01: #1 read treatment tags... INFO @ Wed, 07 Feb 2018 13:05:01: # Command line: callpeak -t SRX3404029.bam -f BAM -g dm -n SRX3404029.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX3404029.05 # format = BAM # ChIP-seq file = ['SRX3404029.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 @ Wed, 07 Feb 2018 13:05:01: #1 read tag files... INFO @ Wed, 07 Feb 2018 13:05:01: #1 read treatment tags... INFO @ Wed, 07 Feb 2018 13:05:20: 1000000 INFO @ Wed, 07 Feb 2018 13:05:20: 1000000 INFO @ Wed, 07 Feb 2018 13:05:20: 1000000 INFO @ Wed, 07 Feb 2018 13:05:35: 2000000 INFO @ Wed, 07 Feb 2018 13:05:35: 2000000 INFO @ Wed, 07 Feb 2018 13:05:40: 2000000 INFO @ Wed, 07 Feb 2018 13:05:51: 3000000 INFO @ Wed, 07 Feb 2018 13:05:51: 3000000 INFO @ Wed, 07 Feb 2018 13:05:59: 3000000 INFO @ Wed, 07 Feb 2018 13:06:07: 4000000 INFO @ Wed, 07 Feb 2018 13:06:07: 4000000 INFO @ Wed, 07 Feb 2018 13:06:18: 4000000 INFO @ Wed, 07 Feb 2018 13:06:24: 5000000 INFO @ Wed, 07 Feb 2018 13:06:24: 5000000 INFO @ Wed, 07 Feb 2018 13:06:36: 5000000 INFO @ Wed, 07 Feb 2018 13:06:42: 6000000 INFO @ Wed, 07 Feb 2018 13:06:42: 6000000 INFO @ Wed, 07 Feb 2018 13:06:53: #1 tag size is determined as 51 bps INFO @ Wed, 07 Feb 2018 13:06:53: #1 tag size = 51 INFO @ Wed, 07 Feb 2018 13:06:53: #1 total tags in treatment: 6644468 INFO @ Wed, 07 Feb 2018 13:06:53: #1 user defined the maximum tags... INFO @ Wed, 07 Feb 2018 13:06:53: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Wed, 07 Feb 2018 13:06:53: #1 tag size is determined as 51 bps INFO @ Wed, 07 Feb 2018 13:06:53: #1 tag size = 51 INFO @ Wed, 07 Feb 2018 13:06:53: #1 total tags in treatment: 6644468 INFO @ Wed, 07 Feb 2018 13:06:53: #1 user defined the maximum tags... INFO @ Wed, 07 Feb 2018 13:06:53: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Wed, 07 Feb 2018 13:06:53: #1 tags after filtering in treatment: 6644468 INFO @ Wed, 07 Feb 2018 13:06:53: #1 Redundant rate of treatment: 0.00 INFO @ Wed, 07 Feb 2018 13:06:53: #1 finished! INFO @ Wed, 07 Feb 2018 13:06:53: #2 Build Peak Model... INFO @ Wed, 07 Feb 2018 13:06:53: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 07 Feb 2018 13:06:53: #1 tags after filtering in treatment: 6644468 INFO @ Wed, 07 Feb 2018 13:06:53: #1 Redundant rate of treatment: 0.00 INFO @ Wed, 07 Feb 2018 13:06:53: #1 finished! INFO @ Wed, 07 Feb 2018 13:06:53: #2 Build Peak Model... INFO @ Wed, 07 Feb 2018 13:06:53: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 07 Feb 2018 13:06:54: #2 number of paired peaks: 3079 INFO @ Wed, 07 Feb 2018 13:06:54: start model_add_line... INFO @ Wed, 07 Feb 2018 13:06:54: #2 number of paired peaks: 3079 INFO @ Wed, 07 Feb 2018 13:06:54: start model_add_line... INFO @ Wed, 07 Feb 2018 13:06:54: start X-correlation... INFO @ Wed, 07 Feb 2018 13:06:54: start X-correlation... INFO @ Wed, 07 Feb 2018 13:06:54: end of X-cor INFO @ Wed, 07 Feb 2018 13:06:54: #2 finished! INFO @ Wed, 07 Feb 2018 13:06:54: #2 predicted fragment length is 132 bps INFO @ Wed, 07 Feb 2018 13:06:54: #2 alternative fragment length(s) may be 132 bps INFO @ Wed, 07 Feb 2018 13:06:54: #2.2 Generate R script for model : SRX3404029.10_model.r INFO @ Wed, 07 Feb 2018 13:06:54: end of X-cor INFO @ Wed, 07 Feb 2018 13:06:54: #2 finished! INFO @ Wed, 07 Feb 2018 13:06:54: #2 predicted fragment length is 132 bps INFO @ Wed, 07 Feb 2018 13:06:54: #2 alternative fragment length(s) may be 132 bps INFO @ Wed, 07 Feb 2018 13:06:54: #2.2 Generate R script for model : SRX3404029.20_model.r INFO @ Wed, 07 Feb 2018 13:06:54: #3 Call peaks... INFO @ Wed, 07 Feb 2018 13:06:54: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 07 Feb 2018 13:06:54: #3 Call peaks... INFO @ Wed, 07 Feb 2018 13:06:54: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 07 Feb 2018 13:06:55: 6000000 INFO @ Wed, 07 Feb 2018 13:07:06: #1 tag size is determined as 51 bps INFO @ Wed, 07 Feb 2018 13:07:06: #1 tag size = 51 INFO @ Wed, 07 Feb 2018 13:07:06: #1 total tags in treatment: 6644468 INFO @ Wed, 07 Feb 2018 13:07:06: #1 user defined the maximum tags... INFO @ Wed, 07 Feb 2018 13:07:06: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Wed, 07 Feb 2018 13:07:06: #1 tags after filtering in treatment: 6644468 INFO @ Wed, 07 Feb 2018 13:07:06: #1 Redundant rate of treatment: 0.00 INFO @ Wed, 07 Feb 2018 13:07:06: #1 finished! INFO @ Wed, 07 Feb 2018 13:07:06: #2 Build Peak Model... INFO @ Wed, 07 Feb 2018 13:07:06: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 07 Feb 2018 13:07:07: #2 number of paired peaks: 3079 INFO @ Wed, 07 Feb 2018 13:07:07: start model_add_line... INFO @ Wed, 07 Feb 2018 13:07:07: start X-correlation... INFO @ Wed, 07 Feb 2018 13:07:07: end of X-cor INFO @ Wed, 07 Feb 2018 13:07:07: #2 finished! INFO @ Wed, 07 Feb 2018 13:07:07: #2 predicted fragment length is 132 bps INFO @ Wed, 07 Feb 2018 13:07:07: #2 alternative fragment length(s) may be 132 bps INFO @ Wed, 07 Feb 2018 13:07:07: #2.2 Generate R script for model : SRX3404029.05_model.r INFO @ Wed, 07 Feb 2018 13:07:07: #3 Call peaks... INFO @ Wed, 07 Feb 2018 13:07:07: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 07 Feb 2018 13:07:22: #3 Call peaks for each chromosome... INFO @ Wed, 07 Feb 2018 13:07:25: #3 Call peaks for each chromosome... INFO @ Wed, 07 Feb 2018 13:07:40: #3 Call peaks for each chromosome... INFO @ Wed, 07 Feb 2018 13:07:50: #4 Write output xls file... SRX3404029.10_peaks.xls INFO @ Wed, 07 Feb 2018 13:07:51: #4 Write peak in narrowPeak format file... SRX3404029.10_peaks.narrowPeak INFO @ Wed, 07 Feb 2018 13:07:51: #4 Write summits bed file... SRX3404029.10_summits.bed INFO @ Wed, 07 Feb 2018 13:07:51: Done! pass1 - making usageList (15 chroms): 4 millis pass2 - checking and writing primary data (10872 records, 4 fields): 21 millis CompletedMACS2peakCalling INFO @ Wed, 07 Feb 2018 13:07:53: #4 Write output xls file... SRX3404029.20_peaks.xls INFO @ Wed, 07 Feb 2018 13:07:53: #4 Write peak in narrowPeak format file... SRX3404029.20_peaks.narrowPeak INFO @ Wed, 07 Feb 2018 13:07:53: #4 Write summits bed file... SRX3404029.20_summits.bed INFO @ Wed, 07 Feb 2018 13:07:53: Done! pass1 - making usageList (15 chroms): 2 millis pass2 - checking and writing primary data (4378 records, 4 fields): 9 millis CompletedMACS2peakCalling INFO @ Wed, 07 Feb 2018 13:08:14: #4 Write output xls file... SRX3404029.05_peaks.xls INFO @ Wed, 07 Feb 2018 13:08:15: #4 Write peak in narrowPeak format file... SRX3404029.05_peaks.narrowPeak INFO @ Wed, 07 Feb 2018 13:08:15: #4 Write summits bed file... SRX3404029.05_summits.bed INFO @ Wed, 07 Feb 2018 13:08:15: Done! pass1 - making usageList (15 chroms): 6 millis pass2 - checking and writing primary data (18514 records, 4 fields): 31 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。