Job ID = 11171279 sra ファイルのダウンロード中... Completed: 90890K bytes transferred in 5 seconds (148293K bits/sec), in 1 file. Completed: 89820K bytes transferred in 6 seconds (121160K bits/sec), in 1 file. Completed: 90056K bytes transferred in 12 seconds (58318K bits/sec), in 1 file. Completed: 89383K bytes transferred in 5 seconds (123739K 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 4699382 spots for /home/okishinya/chipatlas/results/dm3/SRX3020545/SRR5850443.sra Written 4699382 spots for /home/okishinya/chipatlas/results/dm3/SRX3020545/SRR5850443.sra Read 4734714 spots for /home/okishinya/chipatlas/results/dm3/SRX3020545/SRR5850441.sra Written 4734714 spots for /home/okishinya/chipatlas/results/dm3/SRX3020545/SRR5850441.sra Read 4741663 spots for /home/okishinya/chipatlas/results/dm3/SRX3020545/SRR5850442.sra Written 4741663 spots for /home/okishinya/chipatlas/results/dm3/SRX3020545/SRR5850442.sra Read 4785913 spots for /home/okishinya/chipatlas/results/dm3/SRX3020545/SRR5850440.sra Written 4785913 spots for /home/okishinya/chipatlas/results/dm3/SRX3020545/SRR5850440.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 fastq に変換しました。 bowtie でマッピング中... Time loading reference: 00:00:01 Time loading forward index: 00:00:00 Time loading mirror index: 00:00:00 Multiseed full-index search: 00:07:08 18961672 reads; of these: 18961672 (100.00%) were unpaired; of these: 465311 (2.45%) aligned 0 times 13620460 (71.83%) aligned exactly 1 time 4875901 (25.71%) aligned >1 times 97.55% overall alignment rate Time searching: 00:07:09 Overall time: 00:07:09 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] 3019174 / 18496361 = 0.1632 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 @ Sat, 08 Sep 2018 13:37:22: # Command line: callpeak -t SRX3020545.bam -f BAM -g dm -n SRX3020545.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX3020545.10 # format = BAM # ChIP-seq file = ['SRX3020545.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 @ Sat, 08 Sep 2018 13:37:22: #1 read tag files... INFO @ Sat, 08 Sep 2018 13:37:22: #1 read treatment tags... INFO @ Sat, 08 Sep 2018 13:37:22: # Command line: callpeak -t SRX3020545.bam -f BAM -g dm -n SRX3020545.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX3020545.05 # format = BAM # ChIP-seq file = ['SRX3020545.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 @ Sat, 08 Sep 2018 13:37:22: #1 read tag files... INFO @ Sat, 08 Sep 2018 13:37:22: #1 read treatment tags... INFO @ Sat, 08 Sep 2018 13:37:22: # Command line: callpeak -t SRX3020545.bam -f BAM -g dm -n SRX3020545.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX3020545.20 # format = BAM # ChIP-seq file = ['SRX3020545.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 @ Sat, 08 Sep 2018 13:37:22: #1 read tag files... INFO @ Sat, 08 Sep 2018 13:37:22: #1 read treatment tags... INFO @ Sat, 08 Sep 2018 13:37:29: 1000000 INFO @ Sat, 08 Sep 2018 13:37:29: 1000000 INFO @ Sat, 08 Sep 2018 13:37:29: 1000000 INFO @ Sat, 08 Sep 2018 13:37:35: 2000000 INFO @ Sat, 08 Sep 2018 13:37:35: 2000000 INFO @ Sat, 08 Sep 2018 13:37:35: 2000000 INFO @ Sat, 08 Sep 2018 13:37:41: 3000000 INFO @ Sat, 08 Sep 2018 13:37:41: 3000000 INFO @ Sat, 08 Sep 2018 13:37:42: 3000000 INFO @ Sat, 08 Sep 2018 13:37:48: 4000000 INFO @ Sat, 08 Sep 2018 13:37:48: 4000000 INFO @ Sat, 08 Sep 2018 13:37:48: 4000000 INFO @ Sat, 08 Sep 2018 13:37:54: 5000000 INFO @ Sat, 08 Sep 2018 13:37:54: 5000000 INFO @ Sat, 08 Sep 2018 13:37:55: 5000000 INFO @ Sat, 08 Sep 2018 13:38:00: 6000000 INFO @ Sat, 08 Sep 2018 13:38:00: 6000000 INFO @ Sat, 08 Sep 2018 13:38:02: 6000000 INFO @ Sat, 08 Sep 2018 13:38:06: 7000000 INFO @ Sat, 08 Sep 2018 13:38:07: 7000000 INFO @ Sat, 08 Sep 2018 13:38:08: 7000000 INFO @ Sat, 08 Sep 2018 13:38:13: 8000000 INFO @ Sat, 08 Sep 2018 13:38:13: 8000000 INFO @ Sat, 08 Sep 2018 13:38:14: 8000000 INFO @ Sat, 08 Sep 2018 13:38:19: 9000000 INFO @ Sat, 08 Sep 2018 13:38:20: 9000000 INFO @ Sat, 08 Sep 2018 13:38:21: 9000000 INFO @ Sat, 08 Sep 2018 13:38:25: 10000000 INFO @ Sat, 08 Sep 2018 13:38:26: 10000000 INFO @ Sat, 08 Sep 2018 13:38:27: 10000000 INFO @ Sat, 08 Sep 2018 13:38:31: 11000000 INFO @ Sat, 08 Sep 2018 13:38:32: 11000000 INFO @ Sat, 08 Sep 2018 13:38:33: 11000000 INFO @ Sat, 08 Sep 2018 13:38:37: 12000000 INFO @ Sat, 08 Sep 2018 13:38:39: 12000000 INFO @ Sat, 08 Sep 2018 13:38:40: 12000000 INFO @ Sat, 08 Sep 2018 13:38:44: 13000000 INFO @ Sat, 08 Sep 2018 13:38:45: 13000000 INFO @ Sat, 08 Sep 2018 13:38:46: 13000000 INFO @ Sat, 08 Sep 2018 13:38:50: 14000000 INFO @ Sat, 08 Sep 2018 13:38:52: 14000000 INFO @ Sat, 08 Sep 2018 13:38:52: 14000000 INFO @ Sat, 08 Sep 2018 13:38:56: 15000000 INFO @ Sat, 08 Sep 2018 13:38:58: 15000000 INFO @ Sat, 08 Sep 2018 13:38:59: 15000000 INFO @ Sat, 08 Sep 2018 13:38:59: #1 tag size is determined as 50 bps INFO @ Sat, 08 Sep 2018 13:38:59: #1 tag size = 50 INFO @ Sat, 08 Sep 2018 13:38:59: #1 total tags in treatment: 15477187 INFO @ Sat, 08 Sep 2018 13:38:59: #1 user defined the maximum tags... INFO @ Sat, 08 Sep 2018 13:38:59: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 08 Sep 2018 13:38:59: #1 tags after filtering in treatment: 15477187 INFO @ Sat, 08 Sep 2018 13:38:59: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 08 Sep 2018 13:38:59: #1 finished! INFO @ Sat, 08 Sep 2018 13:38:59: #2 Build Peak Model... INFO @ Sat, 08 Sep 2018 13:38:59: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 08 Sep 2018 13:39:01: #2 number of paired peaks: 2212 INFO @ Sat, 08 Sep 2018 13:39:01: start model_add_line... INFO @ Sat, 08 Sep 2018 13:39:01: start X-correlation... INFO @ Sat, 08 Sep 2018 13:39:01: end of X-cor INFO @ Sat, 08 Sep 2018 13:39:01: #2 finished! INFO @ Sat, 08 Sep 2018 13:39:01: #2 predicted fragment length is 139 bps INFO @ Sat, 08 Sep 2018 13:39:01: #2 alternative fragment length(s) may be 139 bps INFO @ Sat, 08 Sep 2018 13:39:01: #2.2 Generate R script for model : SRX3020545.05_model.r INFO @ Sat, 08 Sep 2018 13:39:01: #3 Call peaks... INFO @ Sat, 08 Sep 2018 13:39:01: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 08 Sep 2018 13:39:01: #1 tag size is determined as 50 bps INFO @ Sat, 08 Sep 2018 13:39:01: #1 tag size = 50 INFO @ Sat, 08 Sep 2018 13:39:01: #1 total tags in treatment: 15477187 INFO @ Sat, 08 Sep 2018 13:39:01: #1 user defined the maximum tags... INFO @ Sat, 08 Sep 2018 13:39:01: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 08 Sep 2018 13:39:01: #1 tags after filtering in treatment: 15477187 INFO @ Sat, 08 Sep 2018 13:39:01: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 08 Sep 2018 13:39:01: #1 finished! INFO @ Sat, 08 Sep 2018 13:39:01: #2 Build Peak Model... INFO @ Sat, 08 Sep 2018 13:39:01: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 08 Sep 2018 13:39:02: #1 tag size is determined as 50 bps INFO @ Sat, 08 Sep 2018 13:39:02: #1 tag size = 50 INFO @ Sat, 08 Sep 2018 13:39:02: #1 total tags in treatment: 15477187 INFO @ Sat, 08 Sep 2018 13:39:02: #1 user defined the maximum tags... INFO @ Sat, 08 Sep 2018 13:39:02: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 08 Sep 2018 13:39:02: #1 tags after filtering in treatment: 15477187 INFO @ Sat, 08 Sep 2018 13:39:02: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 08 Sep 2018 13:39:02: #1 finished! INFO @ Sat, 08 Sep 2018 13:39:02: #2 Build Peak Model... INFO @ Sat, 08 Sep 2018 13:39:02: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 08 Sep 2018 13:39:03: #2 number of paired peaks: 2212 INFO @ Sat, 08 Sep 2018 13:39:03: start model_add_line... INFO @ Sat, 08 Sep 2018 13:39:03: start X-correlation... INFO @ Sat, 08 Sep 2018 13:39:03: end of X-cor INFO @ Sat, 08 Sep 2018 13:39:03: #2 finished! INFO @ Sat, 08 Sep 2018 13:39:03: #2 predicted fragment length is 139 bps INFO @ Sat, 08 Sep 2018 13:39:03: #2 alternative fragment length(s) may be 139 bps INFO @ Sat, 08 Sep 2018 13:39:03: #2.2 Generate R script for model : SRX3020545.10_model.r INFO @ Sat, 08 Sep 2018 13:39:03: #3 Call peaks... INFO @ Sat, 08 Sep 2018 13:39:03: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 08 Sep 2018 13:39:03: #2 number of paired peaks: 2212 INFO @ Sat, 08 Sep 2018 13:39:03: start model_add_line... INFO @ Sat, 08 Sep 2018 13:39:04: start X-correlation... INFO @ Sat, 08 Sep 2018 13:39:04: end of X-cor INFO @ Sat, 08 Sep 2018 13:39:04: #2 finished! INFO @ Sat, 08 Sep 2018 13:39:04: #2 predicted fragment length is 139 bps INFO @ Sat, 08 Sep 2018 13:39:04: #2 alternative fragment length(s) may be 139 bps INFO @ Sat, 08 Sep 2018 13:39:04: #2.2 Generate R script for model : SRX3020545.20_model.r INFO @ Sat, 08 Sep 2018 13:39:04: #3 Call peaks... INFO @ Sat, 08 Sep 2018 13:39:04: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 08 Sep 2018 13:39:36: #3 Call peaks for each chromosome... INFO @ Sat, 08 Sep 2018 13:39:39: #3 Call peaks for each chromosome... INFO @ Sat, 08 Sep 2018 13:39:40: #3 Call peaks for each chromosome... INFO @ Sat, 08 Sep 2018 13:39:55: #4 Write output xls file... SRX3020545.05_peaks.xls INFO @ Sat, 08 Sep 2018 13:39:55: #4 Write peak in narrowPeak format file... SRX3020545.05_peaks.narrowPeak INFO @ Sat, 08 Sep 2018 13:39:55: #4 Write summits bed file... SRX3020545.05_summits.bed INFO @ Sat, 08 Sep 2018 13:39:55: Done! pass1 - making usageList (15 chroms): 3 millis pass2 - checking and writing primary data (8886 records, 4 fields): 12 millis CompletedMACS2peakCalling INFO @ Sat, 08 Sep 2018 13:39:59: #4 Write output xls file... SRX3020545.10_peaks.xls INFO @ Sat, 08 Sep 2018 13:39:59: #4 Write peak in narrowPeak format file... SRX3020545.10_peaks.narrowPeak INFO @ Sat, 08 Sep 2018 13:39:59: #4 Write summits bed file... SRX3020545.10_summits.bed INFO @ Sat, 08 Sep 2018 13:39:59: Done! pass1 - making usageList (15 chroms): 2 millis pass2 - checking and writing primary data (7192 records, 4 fields): 15 millis CompletedMACS2peakCalling INFO @ Sat, 08 Sep 2018 13:40:00: #4 Write output xls file... SRX3020545.20_peaks.xls INFO @ Sat, 08 Sep 2018 13:40:00: #4 Write peak in narrowPeak format file... SRX3020545.20_peaks.narrowPeak INFO @ Sat, 08 Sep 2018 13:40:00: #4 Write summits bed file... SRX3020545.20_summits.bed INFO @ Sat, 08 Sep 2018 13:40:00: Done! pass1 - making usageList (15 chroms): 4 millis pass2 - checking and writing primary data (4539 records, 4 fields): 17 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。