Job ID = 10480657 sra ファイルのダウンロード中... Completed: 571097K bytes transferred in 15 seconds (292825K 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 17185102 spots for /home/okishinya/chipatlas/results/dm3/SRX2832093/SRR5573757.sra Written 17185102 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: 00:05:18 17185102 reads; of these: 17185102 (100.00%) were unpaired; of these: 323227 (1.88%) aligned 0 times 13353493 (77.70%) aligned exactly 1 time 3508382 (20.42%) aligned >1 times 98.12% overall alignment rate Time searching: 00:05:18 Overall time: 00:05:18 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] 4559300 / 16861875 = 0.2704 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 07:29:28: # Command line: callpeak -t SRX2832093.bam -f BAM -g dm -n SRX2832093.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX2832093.05 # format = BAM # ChIP-seq file = ['SRX2832093.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 07:29:28: # Command line: callpeak -t SRX2832093.bam -f BAM -g dm -n SRX2832093.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX2832093.20 # format = BAM # ChIP-seq file = ['SRX2832093.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 07:29:28: #1 read tag files... INFO @ Fri, 16 Mar 2018 07:29:28: #1 read tag files... INFO @ Fri, 16 Mar 2018 07:29:28: #1 read treatment tags... INFO @ Fri, 16 Mar 2018 07:29:28: #1 read treatment tags... INFO @ Fri, 16 Mar 2018 07:29:28: # Command line: callpeak -t SRX2832093.bam -f BAM -g dm -n SRX2832093.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX2832093.10 # format = BAM # ChIP-seq file = ['SRX2832093.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 07:29:28: #1 read tag files... INFO @ Fri, 16 Mar 2018 07:29:28: #1 read treatment tags... INFO @ Fri, 16 Mar 2018 07:29:35: 1000000 INFO @ Fri, 16 Mar 2018 07:29:35: 1000000 INFO @ Fri, 16 Mar 2018 07:29:36: 1000000 INFO @ Fri, 16 Mar 2018 07:29:42: 2000000 INFO @ Fri, 16 Mar 2018 07:29:43: 2000000 INFO @ Fri, 16 Mar 2018 07:29:43: 2000000 INFO @ Fri, 16 Mar 2018 07:29:48: 3000000 INFO @ Fri, 16 Mar 2018 07:29:50: 3000000 INFO @ Fri, 16 Mar 2018 07:29:50: 3000000 INFO @ Fri, 16 Mar 2018 07:29:55: 4000000 INFO @ Fri, 16 Mar 2018 07:29:58: 4000000 INFO @ Fri, 16 Mar 2018 07:29:58: 4000000 INFO @ Fri, 16 Mar 2018 07:30:02: 5000000 INFO @ Fri, 16 Mar 2018 07:30:05: 5000000 INFO @ Fri, 16 Mar 2018 07:30:05: 5000000 INFO @ Fri, 16 Mar 2018 07:30:09: 6000000 INFO @ Fri, 16 Mar 2018 07:30:13: 6000000 INFO @ Fri, 16 Mar 2018 07:30:13: 6000000 INFO @ Fri, 16 Mar 2018 07:30:15: 7000000 INFO @ Fri, 16 Mar 2018 07:30:20: 7000000 INFO @ Fri, 16 Mar 2018 07:30:21: 7000000 INFO @ Fri, 16 Mar 2018 07:30:22: 8000000 INFO @ Fri, 16 Mar 2018 07:30:28: 8000000 INFO @ Fri, 16 Mar 2018 07:30:29: 8000000 INFO @ Fri, 16 Mar 2018 07:30:29: 9000000 INFO @ Fri, 16 Mar 2018 07:30:36: 10000000 INFO @ Fri, 16 Mar 2018 07:30:36: 9000000 INFO @ Fri, 16 Mar 2018 07:30:37: 9000000 INFO @ Fri, 16 Mar 2018 07:30:42: 11000000 INFO @ Fri, 16 Mar 2018 07:30:43: 10000000 INFO @ Fri, 16 Mar 2018 07:30:44: 10000000 INFO @ Fri, 16 Mar 2018 07:30:49: 12000000 INFO @ Fri, 16 Mar 2018 07:30:51: 11000000 INFO @ Fri, 16 Mar 2018 07:30:51: #1 tag size is determined as 50 bps INFO @ Fri, 16 Mar 2018 07:30:51: #1 tag size = 50 INFO @ Fri, 16 Mar 2018 07:30:51: #1 total tags in treatment: 12302575 INFO @ Fri, 16 Mar 2018 07:30:51: #1 user defined the maximum tags... INFO @ Fri, 16 Mar 2018 07:30:51: #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 07:30:52: #1 tags after filtering in treatment: 12302575 INFO @ Fri, 16 Mar 2018 07:30:52: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 16 Mar 2018 07:30:52: #1 finished! INFO @ Fri, 16 Mar 2018 07:30:52: #2 Build Peak Model... INFO @ Fri, 16 Mar 2018 07:30:52: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 16 Mar 2018 07:30:52: 11000000 INFO @ Fri, 16 Mar 2018 07:30:53: #2 number of paired peaks: 5375 INFO @ Fri, 16 Mar 2018 07:30:53: start model_add_line... INFO @ Fri, 16 Mar 2018 07:30:53: start X-correlation... INFO @ Fri, 16 Mar 2018 07:30:54: end of X-cor INFO @ Fri, 16 Mar 2018 07:30:54: #2 finished! INFO @ Fri, 16 Mar 2018 07:30:54: #2 predicted fragment length is 181 bps INFO @ Fri, 16 Mar 2018 07:30:54: #2 alternative fragment length(s) may be 4,181 bps INFO @ Fri, 16 Mar 2018 07:30:54: #2.2 Generate R script for model : SRX2832093.10_model.r INFO @ Fri, 16 Mar 2018 07:30:54: #3 Call peaks... INFO @ Fri, 16 Mar 2018 07:30:54: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 16 Mar 2018 07:30:58: 12000000 INFO @ Fri, 16 Mar 2018 07:31:00: 12000000 INFO @ Fri, 16 Mar 2018 07:31:01: #1 tag size is determined as 50 bps INFO @ Fri, 16 Mar 2018 07:31:01: #1 tag size = 50 INFO @ Fri, 16 Mar 2018 07:31:01: #1 total tags in treatment: 12302575 INFO @ Fri, 16 Mar 2018 07:31:01: #1 user defined the maximum tags... INFO @ Fri, 16 Mar 2018 07:31:01: #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 07:31:01: #1 tags after filtering in treatment: 12302575 INFO @ Fri, 16 Mar 2018 07:31:01: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 16 Mar 2018 07:31:01: #1 finished! INFO @ Fri, 16 Mar 2018 07:31:01: #2 Build Peak Model... INFO @ Fri, 16 Mar 2018 07:31:01: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 16 Mar 2018 07:31:02: #1 tag size is determined as 50 bps INFO @ Fri, 16 Mar 2018 07:31:02: #1 tag size = 50 INFO @ Fri, 16 Mar 2018 07:31:02: #1 total tags in treatment: 12302575 INFO @ Fri, 16 Mar 2018 07:31:02: #1 user defined the maximum tags... INFO @ Fri, 16 Mar 2018 07:31:02: #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 07:31:02: #2 number of paired peaks: 5375 INFO @ Fri, 16 Mar 2018 07:31:02: start model_add_line... INFO @ Fri, 16 Mar 2018 07:31:02: #1 tags after filtering in treatment: 12302575 INFO @ Fri, 16 Mar 2018 07:31:02: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 16 Mar 2018 07:31:02: #1 finished! INFO @ Fri, 16 Mar 2018 07:31:02: #2 Build Peak Model... INFO @ Fri, 16 Mar 2018 07:31:02: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 16 Mar 2018 07:31:03: start X-correlation... INFO @ Fri, 16 Mar 2018 07:31:03: end of X-cor INFO @ Fri, 16 Mar 2018 07:31:03: #2 finished! INFO @ Fri, 16 Mar 2018 07:31:03: #2 predicted fragment length is 181 bps INFO @ Fri, 16 Mar 2018 07:31:03: #2 alternative fragment length(s) may be 4,181 bps INFO @ Fri, 16 Mar 2018 07:31:03: #2.2 Generate R script for model : SRX2832093.20_model.r INFO @ Fri, 16 Mar 2018 07:31:03: #3 Call peaks... INFO @ Fri, 16 Mar 2018 07:31:03: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 16 Mar 2018 07:31:04: #2 number of paired peaks: 5375 INFO @ Fri, 16 Mar 2018 07:31:04: start model_add_line... INFO @ Fri, 16 Mar 2018 07:31:04: start X-correlation... INFO @ Fri, 16 Mar 2018 07:31:04: end of X-cor INFO @ Fri, 16 Mar 2018 07:31:04: #2 finished! INFO @ Fri, 16 Mar 2018 07:31:04: #2 predicted fragment length is 181 bps INFO @ Fri, 16 Mar 2018 07:31:04: #2 alternative fragment length(s) may be 4,181 bps INFO @ Fri, 16 Mar 2018 07:31:04: #2.2 Generate R script for model : SRX2832093.05_model.r INFO @ Fri, 16 Mar 2018 07:31:04: #3 Call peaks... INFO @ Fri, 16 Mar 2018 07:31:04: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 16 Mar 2018 07:31:27: #3 Call peaks for each chromosome... INFO @ Fri, 16 Mar 2018 07:31:35: #3 Call peaks for each chromosome... INFO @ Fri, 16 Mar 2018 07:31:37: #3 Call peaks for each chromosome... INFO @ Fri, 16 Mar 2018 07:31:42: #4 Write output xls file... SRX2832093.10_peaks.xls INFO @ Fri, 16 Mar 2018 07:31:42: #4 Write peak in narrowPeak format file... SRX2832093.10_peaks.narrowPeak INFO @ Fri, 16 Mar 2018 07:31:42: #4 Write summits bed file... SRX2832093.10_summits.bed INFO @ Fri, 16 Mar 2018 07:31:42: Done! pass1 - making usageList (14 chroms): 2 millis pass2 - checking and writing primary data (6094 records, 4 fields): 9 millis CompletedMACS2peakCalling INFO @ Fri, 16 Mar 2018 07:31:52: #4 Write output xls file... SRX2832093.20_peaks.xls INFO @ Fri, 16 Mar 2018 07:31:52: #4 Write peak in narrowPeak format file... SRX2832093.20_peaks.narrowPeak INFO @ Fri, 16 Mar 2018 07:31:52: #4 Write summits bed file... SRX2832093.20_summits.bed INFO @ Fri, 16 Mar 2018 07:31:52: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (2261 records, 4 fields): 4 millis CompletedMACS2peakCalling INFO @ Fri, 16 Mar 2018 07:31:53: #4 Write output xls file... SRX2832093.05_peaks.xls INFO @ Fri, 16 Mar 2018 07:31:53: #4 Write peak in narrowPeak format file... SRX2832093.05_peaks.narrowPeak INFO @ Fri, 16 Mar 2018 07:31:53: #4 Write summits bed file... SRX2832093.05_summits.bed INFO @ Fri, 16 Mar 2018 07:31:53: Done! pass1 - making usageList (14 chroms): 2 millis pass2 - checking and writing primary data (11305 records, 4 fields): 14 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。