Job ID = 10480748 sra ファイルのダウンロード中... Completed: 425859K bytes transferred in 16 seconds (211873K 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 17409242 spots for /home/okishinya/chipatlas/results/dm3/SRX3380807/SRR6278170.sra Written 17409242 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: 00:04:22 17409242 reads; of these: 17409242 (100.00%) were unpaired; of these: 6327699 (36.35%) aligned 0 times 9167638 (52.66%) aligned exactly 1 time 1913905 (10.99%) aligned >1 times 63.65% overall alignment rate Time searching: 00:04:22 Overall time: 00:04:22 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] 1688205 / 11081543 = 0.1523 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 07:54:56: # Command line: callpeak -t SRX3380807.bam -f BAM -g dm -n SRX3380807.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX3380807.20 # format = BAM # ChIP-seq file = ['SRX3380807.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 07:54:56: #1 read tag files... INFO @ Fri, 16 Mar 2018 07:54:56: #1 read treatment tags... INFO @ Fri, 16 Mar 2018 07:54:56: # Command line: callpeak -t SRX3380807.bam -f BAM -g dm -n SRX3380807.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX3380807.05 # format = BAM # ChIP-seq file = ['SRX3380807.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 07:54:56: #1 read tag files... INFO @ Fri, 16 Mar 2018 07:54:56: #1 read treatment tags... INFO @ Fri, 16 Mar 2018 07:54:56: # Command line: callpeak -t SRX3380807.bam -f BAM -g dm -n SRX3380807.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX3380807.10 # format = BAM # ChIP-seq file = ['SRX3380807.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 07:54:56: #1 read tag files... INFO @ Fri, 16 Mar 2018 07:54:56: #1 read treatment tags... INFO @ Fri, 16 Mar 2018 07:55:03: 1000000 INFO @ Fri, 16 Mar 2018 07:55:03: 1000000 INFO @ Fri, 16 Mar 2018 07:55:03: 1000000 INFO @ Fri, 16 Mar 2018 07:55:09: 2000000 INFO @ Fri, 16 Mar 2018 07:55:09: 2000000 INFO @ Fri, 16 Mar 2018 07:55:10: 2000000 INFO @ Fri, 16 Mar 2018 07:55:16: 3000000 INFO @ Fri, 16 Mar 2018 07:55:16: 3000000 INFO @ Fri, 16 Mar 2018 07:55:16: 3000000 INFO @ Fri, 16 Mar 2018 07:55:23: 4000000 INFO @ Fri, 16 Mar 2018 07:55:23: 4000000 INFO @ Fri, 16 Mar 2018 07:55:23: 4000000 INFO @ Fri, 16 Mar 2018 07:55:29: 5000000 INFO @ Fri, 16 Mar 2018 07:55:29: 5000000 INFO @ Fri, 16 Mar 2018 07:55:29: 5000000 INFO @ Fri, 16 Mar 2018 07:55:36: 6000000 INFO @ Fri, 16 Mar 2018 07:55:36: 6000000 INFO @ Fri, 16 Mar 2018 07:55:36: 6000000 INFO @ Fri, 16 Mar 2018 07:55:42: 7000000 INFO @ Fri, 16 Mar 2018 07:55:43: 7000000 INFO @ Fri, 16 Mar 2018 07:55:43: 7000000 INFO @ Fri, 16 Mar 2018 07:55:49: 8000000 INFO @ Fri, 16 Mar 2018 07:55:49: 8000000 INFO @ Fri, 16 Mar 2018 07:55:50: 8000000 INFO @ Fri, 16 Mar 2018 07:55:55: 9000000 INFO @ Fri, 16 Mar 2018 07:55:56: 9000000 INFO @ Fri, 16 Mar 2018 07:55:56: 9000000 INFO @ Fri, 16 Mar 2018 07:55:58: #1 tag size is determined as 51 bps INFO @ Fri, 16 Mar 2018 07:55:58: #1 tag size = 51 INFO @ Fri, 16 Mar 2018 07:55:58: #1 total tags in treatment: 9393338 INFO @ Fri, 16 Mar 2018 07:55:58: #1 user defined the maximum tags... INFO @ Fri, 16 Mar 2018 07:55:58: #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 07:55:58: #1 tags after filtering in treatment: 9393338 INFO @ Fri, 16 Mar 2018 07:55:58: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 16 Mar 2018 07:55:58: #1 finished! INFO @ Fri, 16 Mar 2018 07:55:58: #2 Build Peak Model... INFO @ Fri, 16 Mar 2018 07:55:58: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 16 Mar 2018 07:55:59: #1 tag size is determined as 51 bps INFO @ Fri, 16 Mar 2018 07:55:59: #1 tag size = 51 INFO @ Fri, 16 Mar 2018 07:55:59: #1 total tags in treatment: 9393338 INFO @ Fri, 16 Mar 2018 07:55:59: #1 user defined the maximum tags... INFO @ Fri, 16 Mar 2018 07:55:59: #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 07:55:59: #1 tags after filtering in treatment: 9393338 INFO @ Fri, 16 Mar 2018 07:55:59: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 16 Mar 2018 07:55:59: #1 finished! INFO @ Fri, 16 Mar 2018 07:55:59: #2 Build Peak Model... INFO @ Fri, 16 Mar 2018 07:55:59: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 16 Mar 2018 07:55:59: #1 tag size is determined as 51 bps INFO @ Fri, 16 Mar 2018 07:55:59: #1 tag size = 51 INFO @ Fri, 16 Mar 2018 07:55:59: #1 total tags in treatment: 9393338 INFO @ Fri, 16 Mar 2018 07:55:59: #1 user defined the maximum tags... INFO @ Fri, 16 Mar 2018 07:55:59: #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 07:55:59: #1 tags after filtering in treatment: 9393338 INFO @ Fri, 16 Mar 2018 07:55:59: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 16 Mar 2018 07:55:59: #1 finished! INFO @ Fri, 16 Mar 2018 07:55:59: #2 Build Peak Model... INFO @ Fri, 16 Mar 2018 07:55:59: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 16 Mar 2018 07:55:59: #2 number of paired peaks: 3255 INFO @ Fri, 16 Mar 2018 07:55:59: start model_add_line... INFO @ Fri, 16 Mar 2018 07:55:59: start X-correlation... INFO @ Fri, 16 Mar 2018 07:55:59: end of X-cor INFO @ Fri, 16 Mar 2018 07:55:59: #2 finished! INFO @ Fri, 16 Mar 2018 07:55:59: #2 predicted fragment length is 168 bps INFO @ Fri, 16 Mar 2018 07:55:59: #2 alternative fragment length(s) may be 2,168,185,593 bps INFO @ Fri, 16 Mar 2018 07:55:59: #2.2 Generate R script for model : SRX3380807.20_model.r INFO @ Fri, 16 Mar 2018 07:55:59: #3 Call peaks... INFO @ Fri, 16 Mar 2018 07:55:59: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 16 Mar 2018 07:56:00: #2 number of paired peaks: 3255 INFO @ Fri, 16 Mar 2018 07:56:00: start model_add_line... INFO @ Fri, 16 Mar 2018 07:56:00: start X-correlation... INFO @ Fri, 16 Mar 2018 07:56:00: end of X-cor INFO @ Fri, 16 Mar 2018 07:56:00: #2 finished! INFO @ Fri, 16 Mar 2018 07:56:00: #2 predicted fragment length is 168 bps INFO @ Fri, 16 Mar 2018 07:56:00: #2 alternative fragment length(s) may be 2,168,185,593 bps INFO @ Fri, 16 Mar 2018 07:56:00: #2.2 Generate R script for model : SRX3380807.05_model.r INFO @ Fri, 16 Mar 2018 07:56:00: #3 Call peaks... INFO @ Fri, 16 Mar 2018 07:56:00: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 16 Mar 2018 07:56:00: #2 number of paired peaks: 3255 INFO @ Fri, 16 Mar 2018 07:56:00: start model_add_line... INFO @ Fri, 16 Mar 2018 07:56:00: start X-correlation... INFO @ Fri, 16 Mar 2018 07:56:00: end of X-cor INFO @ Fri, 16 Mar 2018 07:56:00: #2 finished! INFO @ Fri, 16 Mar 2018 07:56:00: #2 predicted fragment length is 168 bps INFO @ Fri, 16 Mar 2018 07:56:00: #2 alternative fragment length(s) may be 2,168,185,593 bps INFO @ Fri, 16 Mar 2018 07:56:00: #2.2 Generate R script for model : SRX3380807.10_model.r INFO @ Fri, 16 Mar 2018 07:56:00: #3 Call peaks... INFO @ Fri, 16 Mar 2018 07:56:00: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 16 Mar 2018 07:56:23: #3 Call peaks for each chromosome... INFO @ Fri, 16 Mar 2018 07:56:24: #3 Call peaks for each chromosome... INFO @ Fri, 16 Mar 2018 07:56:24: #3 Call peaks for each chromosome... INFO @ Fri, 16 Mar 2018 07:56:35: #4 Write output xls file... SRX3380807.20_peaks.xls INFO @ Fri, 16 Mar 2018 07:56:35: #4 Write peak in narrowPeak format file... SRX3380807.20_peaks.narrowPeak INFO @ Fri, 16 Mar 2018 07:56:35: #4 Write summits bed file... SRX3380807.20_summits.bed INFO @ Fri, 16 Mar 2018 07:56:35: Done! pass1 - making usageList (10 chroms): 1 millis pass2 - checking and writing primary data (440 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Fri, 16 Mar 2018 07:56:36: #4 Write output xls file... SRX3380807.10_peaks.xls INFO @ Fri, 16 Mar 2018 07:56:36: #4 Write output xls file... SRX3380807.05_peaks.xls INFO @ Fri, 16 Mar 2018 07:56:36: #4 Write peak in narrowPeak format file... SRX3380807.10_peaks.narrowPeak INFO @ Fri, 16 Mar 2018 07:56:36: #4 Write summits bed file... SRX3380807.10_summits.bed INFO @ Fri, 16 Mar 2018 07:56:36: #4 Write peak in narrowPeak format file... SRX3380807.05_peaks.narrowPeak INFO @ Fri, 16 Mar 2018 07:56:36: Done! INFO @ Fri, 16 Mar 2018 07:56:36: #4 Write summits bed file... SRX3380807.05_summits.bed INFO @ Fri, 16 Mar 2018 07:56:36: Done! pass1 - making usageList (10 chroms): 1 millis pass2 - checking and writing primary data (765 records, 4 fields): 2 millis CompletedMACS2peakCalling pass1 - making usageList (11 chroms): 0 millis pass2 - checking and writing primary data (1289 records, 4 fields): 4 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。