Job ID = 11171266 sra ファイルのダウンロード中... Completed: 102188K bytes transferred in 5 seconds (143555K bits/sec), in 1 file. Completed: 101079K bytes transferred in 6 seconds (133823K bits/sec), in 1 file. Completed: 101137K bytes transferred in 5 seconds (151750K bits/sec), in 1 file. Completed: 100317K bytes transferred in 6 seconds (131876K 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 5283560 spots for /home/okishinya/chipatlas/results/dm3/SRX3020533/SRR5850395.sra Written 5283560 spots for /home/okishinya/chipatlas/results/dm3/SRX3020533/SRR5850395.sra Read 5331319 spots for /home/okishinya/chipatlas/results/dm3/SRX3020533/SRR5850394.sra Written 5331319 spots for /home/okishinya/chipatlas/results/dm3/SRX3020533/SRR5850394.sra Read 5335105 spots for /home/okishinya/chipatlas/results/dm3/SRX3020533/SRR5850393.sra Written 5335105 spots for /home/okishinya/chipatlas/results/dm3/SRX3020533/SRR5850393.sra Read 5386233 spots for /home/okishinya/chipatlas/results/dm3/SRX3020533/SRR5850392.sra Written 5386233 spots for /home/okishinya/chipatlas/results/dm3/SRX3020533/SRR5850392.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: 00:00:00 Time loading forward index: 00:00:00 Time loading mirror index: 00:00:00 Multiseed full-index search: 00:08:20 21336217 reads; of these: 21336217 (100.00%) were unpaired; of these: 683129 (3.20%) aligned 0 times 15080285 (70.68%) aligned exactly 1 time 5572803 (26.12%) aligned >1 times 96.80% overall alignment rate Time searching: 00:08:20 Overall time: 00:08:20 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] 3156028 / 20653088 = 0.1528 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 13:34:03: # Command line: callpeak -t SRX3020533.bam -f BAM -g dm -n SRX3020533.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX3020533.05 # format = BAM # ChIP-seq file = ['SRX3020533.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 13:34:03: #1 read tag files... INFO @ Sat, 08 Sep 2018 13:34:03: #1 read treatment tags... INFO @ Sat, 08 Sep 2018 13:34:03: # Command line: callpeak -t SRX3020533.bam -f BAM -g dm -n SRX3020533.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX3020533.20 # format = BAM # ChIP-seq file = ['SRX3020533.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 13:34:03: #1 read tag files... INFO @ Sat, 08 Sep 2018 13:34:03: #1 read treatment tags... INFO @ Sat, 08 Sep 2018 13:34:03: # Command line: callpeak -t SRX3020533.bam -f BAM -g dm -n SRX3020533.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX3020533.10 # format = BAM # ChIP-seq file = ['SRX3020533.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 13:34:03: #1 read tag files... INFO @ Sat, 08 Sep 2018 13:34:03: #1 read treatment tags... INFO @ Sat, 08 Sep 2018 13:34:09: 1000000 INFO @ Sat, 08 Sep 2018 13:34:09: 1000000 INFO @ Sat, 08 Sep 2018 13:34:09: 1000000 INFO @ Sat, 08 Sep 2018 13:34:16: 2000000 INFO @ Sat, 08 Sep 2018 13:34:16: 2000000 INFO @ Sat, 08 Sep 2018 13:34:16: 2000000 INFO @ Sat, 08 Sep 2018 13:34:22: 3000000 INFO @ Sat, 08 Sep 2018 13:34:23: 3000000 INFO @ Sat, 08 Sep 2018 13:34:23: 3000000 INFO @ Sat, 08 Sep 2018 13:34:29: 4000000 INFO @ Sat, 08 Sep 2018 13:34:30: 4000000 INFO @ Sat, 08 Sep 2018 13:34:30: 4000000 INFO @ Sat, 08 Sep 2018 13:34:35: 5000000 INFO @ Sat, 08 Sep 2018 13:34:36: 5000000 INFO @ Sat, 08 Sep 2018 13:34:37: 5000000 INFO @ Sat, 08 Sep 2018 13:34:42: 6000000 INFO @ Sat, 08 Sep 2018 13:34:43: 6000000 INFO @ Sat, 08 Sep 2018 13:34:44: 6000000 INFO @ Sat, 08 Sep 2018 13:34:48: 7000000 INFO @ Sat, 08 Sep 2018 13:34:50: 7000000 INFO @ Sat, 08 Sep 2018 13:34:51: 7000000 INFO @ Sat, 08 Sep 2018 13:34:55: 8000000 INFO @ Sat, 08 Sep 2018 13:34:57: 8000000 INFO @ Sat, 08 Sep 2018 13:34:58: 8000000 INFO @ Sat, 08 Sep 2018 13:35:01: 9000000 INFO @ Sat, 08 Sep 2018 13:35:04: 9000000 INFO @ Sat, 08 Sep 2018 13:35:06: 9000000 INFO @ Sat, 08 Sep 2018 13:35:08: 10000000 INFO @ Sat, 08 Sep 2018 13:35:11: 10000000 INFO @ Sat, 08 Sep 2018 13:35:13: 10000000 INFO @ Sat, 08 Sep 2018 13:35:14: 11000000 INFO @ Sat, 08 Sep 2018 13:35:18: 11000000 INFO @ Sat, 08 Sep 2018 13:35:20: 11000000 INFO @ Sat, 08 Sep 2018 13:35:21: 12000000 INFO @ Sat, 08 Sep 2018 13:35:25: 12000000 INFO @ Sat, 08 Sep 2018 13:35:27: 13000000 INFO @ Sat, 08 Sep 2018 13:35:27: 12000000 INFO @ Sat, 08 Sep 2018 13:35:32: 13000000 INFO @ Sat, 08 Sep 2018 13:35:34: 14000000 INFO @ Sat, 08 Sep 2018 13:35:35: 13000000 INFO @ Sat, 08 Sep 2018 13:35:40: 14000000 INFO @ Sat, 08 Sep 2018 13:35:40: 15000000 INFO @ Sat, 08 Sep 2018 13:35:42: 14000000 INFO @ Sat, 08 Sep 2018 13:35:47: 15000000 INFO @ Sat, 08 Sep 2018 13:35:47: 16000000 INFO @ Sat, 08 Sep 2018 13:35:49: 15000000 INFO @ Sat, 08 Sep 2018 13:35:53: 17000000 INFO @ Sat, 08 Sep 2018 13:35:54: 16000000 INFO @ Sat, 08 Sep 2018 13:35:57: 16000000 INFO @ Sat, 08 Sep 2018 13:35:57: #1 tag size is determined as 50 bps INFO @ Sat, 08 Sep 2018 13:35:57: #1 tag size = 50 INFO @ Sat, 08 Sep 2018 13:35:57: #1 total tags in treatment: 17497060 INFO @ Sat, 08 Sep 2018 13:35:57: #1 user defined the maximum tags... INFO @ Sat, 08 Sep 2018 13:35:57: #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 13:35:57: #1 tags after filtering in treatment: 17497060 INFO @ Sat, 08 Sep 2018 13:35:57: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 08 Sep 2018 13:35:57: #1 finished! INFO @ Sat, 08 Sep 2018 13:35:57: #2 Build Peak Model... INFO @ Sat, 08 Sep 2018 13:35:57: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 08 Sep 2018 13:35:58: #2 number of paired peaks: 1363 INFO @ Sat, 08 Sep 2018 13:35:58: start model_add_line... INFO @ Sat, 08 Sep 2018 13:35:59: start X-correlation... INFO @ Sat, 08 Sep 2018 13:35:59: end of X-cor INFO @ Sat, 08 Sep 2018 13:35:59: #2 finished! INFO @ Sat, 08 Sep 2018 13:35:59: #2 predicted fragment length is 103 bps INFO @ Sat, 08 Sep 2018 13:35:59: #2 alternative fragment length(s) may be 3,103,118 bps INFO @ Sat, 08 Sep 2018 13:35:59: #2.2 Generate R script for model : SRX3020533.05_model.r INFO @ Sat, 08 Sep 2018 13:35:59: #3 Call peaks... INFO @ Sat, 08 Sep 2018 13:35:59: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 08 Sep 2018 13:36:01: 17000000 INFO @ Sat, 08 Sep 2018 13:36:04: 17000000 INFO @ Sat, 08 Sep 2018 13:36:05: #1 tag size is determined as 50 bps INFO @ Sat, 08 Sep 2018 13:36:05: #1 tag size = 50 INFO @ Sat, 08 Sep 2018 13:36:05: #1 total tags in treatment: 17497060 INFO @ Sat, 08 Sep 2018 13:36:05: #1 user defined the maximum tags... INFO @ Sat, 08 Sep 2018 13:36:05: #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 13:36:05: #1 tags after filtering in treatment: 17497060 INFO @ Sat, 08 Sep 2018 13:36:05: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 08 Sep 2018 13:36:05: #1 finished! INFO @ Sat, 08 Sep 2018 13:36:05: #2 Build Peak Model... INFO @ Sat, 08 Sep 2018 13:36:05: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 08 Sep 2018 13:36:06: #2 number of paired peaks: 1363 INFO @ Sat, 08 Sep 2018 13:36:06: start model_add_line... INFO @ Sat, 08 Sep 2018 13:36:06: start X-correlation... INFO @ Sat, 08 Sep 2018 13:36:06: end of X-cor INFO @ Sat, 08 Sep 2018 13:36:06: #2 finished! INFO @ Sat, 08 Sep 2018 13:36:06: #2 predicted fragment length is 103 bps INFO @ Sat, 08 Sep 2018 13:36:06: #2 alternative fragment length(s) may be 3,103,118 bps INFO @ Sat, 08 Sep 2018 13:36:06: #2.2 Generate R script for model : SRX3020533.10_model.r INFO @ Sat, 08 Sep 2018 13:36:06: #3 Call peaks... INFO @ Sat, 08 Sep 2018 13:36:06: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 08 Sep 2018 13:36:07: #1 tag size is determined as 50 bps INFO @ Sat, 08 Sep 2018 13:36:07: #1 tag size = 50 INFO @ Sat, 08 Sep 2018 13:36:07: #1 total tags in treatment: 17497060 INFO @ Sat, 08 Sep 2018 13:36:07: #1 user defined the maximum tags... INFO @ Sat, 08 Sep 2018 13:36:07: #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 13:36:08: #1 tags after filtering in treatment: 17497060 INFO @ Sat, 08 Sep 2018 13:36:08: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 08 Sep 2018 13:36:08: #1 finished! INFO @ Sat, 08 Sep 2018 13:36:08: #2 Build Peak Model... INFO @ Sat, 08 Sep 2018 13:36:08: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 08 Sep 2018 13:36:09: #2 number of paired peaks: 1363 INFO @ Sat, 08 Sep 2018 13:36:09: start model_add_line... INFO @ Sat, 08 Sep 2018 13:36:09: start X-correlation... INFO @ Sat, 08 Sep 2018 13:36:09: end of X-cor INFO @ Sat, 08 Sep 2018 13:36:09: #2 finished! INFO @ Sat, 08 Sep 2018 13:36:09: #2 predicted fragment length is 103 bps INFO @ Sat, 08 Sep 2018 13:36:09: #2 alternative fragment length(s) may be 3,103,118 bps INFO @ Sat, 08 Sep 2018 13:36:09: #2.2 Generate R script for model : SRX3020533.20_model.r INFO @ Sat, 08 Sep 2018 13:36:09: #3 Call peaks... INFO @ Sat, 08 Sep 2018 13:36:09: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 08 Sep 2018 13:36:39: #3 Call peaks for each chromosome... INFO @ Sat, 08 Sep 2018 13:36:47: #3 Call peaks for each chromosome... INFO @ Sat, 08 Sep 2018 13:36:50: #3 Call peaks for each chromosome... INFO @ Sat, 08 Sep 2018 13:37:00: #4 Write output xls file... SRX3020533.05_peaks.xls INFO @ Sat, 08 Sep 2018 13:37:00: #4 Write peak in narrowPeak format file... SRX3020533.05_peaks.narrowPeak INFO @ Sat, 08 Sep 2018 13:37:00: #4 Write summits bed file... SRX3020533.05_summits.bed INFO @ Sat, 08 Sep 2018 13:37:00: Done! pass1 - making usageList (15 chroms): 2 millis pass2 - checking and writing primary data (6375 records, 4 fields): 9 millis CompletedMACS2peakCalling INFO @ Sat, 08 Sep 2018 13:37:09: #4 Write output xls file... SRX3020533.10_peaks.xls INFO @ Sat, 08 Sep 2018 13:37:09: #4 Write peak in narrowPeak format file... SRX3020533.10_peaks.narrowPeak INFO @ Sat, 08 Sep 2018 13:37:09: #4 Write summits bed file... SRX3020533.10_summits.bed INFO @ Sat, 08 Sep 2018 13:37:09: Done! pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (2657 records, 4 fields): 5 millis CompletedMACS2peakCalling INFO @ Sat, 08 Sep 2018 13:37:14: #4 Write output xls file... SRX3020533.20_peaks.xls INFO @ Sat, 08 Sep 2018 13:37:14: #4 Write peak in narrowPeak format file... SRX3020533.20_peaks.narrowPeak INFO @ Sat, 08 Sep 2018 13:37:14: #4 Write summits bed file... SRX3020533.20_summits.bed INFO @ Sat, 08 Sep 2018 13:37:14: Done! pass1 - making usageList (13 chroms): 1 millis pass2 - checking and writing primary data (926 records, 4 fields): 3 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。