Job ID = 11192571 sra ファイルのダウンロード中... Completed: 815423K bytes transferred in 13 seconds (501729K 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 25357497 spots for /home/okishinya/chipatlas/results/rn6/SRX2226583/SRR4374833.sra Written 25357497 spots for /home/okishinya/chipatlas/results/rn6/SRX2226583/SRR4374833.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 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: 00:00:02 Time loading mirror index: 00:00:01 Multiseed full-index search: 00:15:57 25357497 reads; of these: 25357497 (100.00%) were unpaired; of these: 3736904 (14.74%) aligned 0 times 16308897 (64.32%) aligned exactly 1 time 5311696 (20.95%) aligned >1 times 85.26% overall alignment rate Time searching: 00:16:00 Overall time: 00:16:00 マッピングが完了しました。 samtools でBAM に変換中... [samopen] SAM header is present: 953 sequences. [bam_sort_core] merging from 12 files... [bam_rmdupse_core] 7503745 / 21620593 = 0.3471 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, 15 Sep 2018 09:20:34: # Command line: callpeak -t SRX2226583.bam -f BAM -g 2.15e9 -n SRX2226583.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX2226583.20 # format = BAM # ChIP-seq file = ['SRX2226583.bam'] # control file = None # effective genome size = 2.15e+09 # 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, 15 Sep 2018 09:20:34: #1 read tag files... INFO @ Sat, 15 Sep 2018 09:20:34: #1 read treatment tags... INFO @ Sat, 15 Sep 2018 09:20:34: # Command line: callpeak -t SRX2226583.bam -f BAM -g 2.15e9 -n SRX2226583.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX2226583.05 # format = BAM # ChIP-seq file = ['SRX2226583.bam'] # control file = None # effective genome size = 2.15e+09 # 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, 15 Sep 2018 09:20:34: #1 read tag files... INFO @ Sat, 15 Sep 2018 09:20:34: #1 read treatment tags... INFO @ Sat, 15 Sep 2018 09:20:34: # Command line: callpeak -t SRX2226583.bam -f BAM -g 2.15e9 -n SRX2226583.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX2226583.10 # format = BAM # ChIP-seq file = ['SRX2226583.bam'] # control file = None # effective genome size = 2.15e+09 # 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, 15 Sep 2018 09:20:34: #1 read tag files... INFO @ Sat, 15 Sep 2018 09:20:34: #1 read treatment tags... INFO @ Sat, 15 Sep 2018 09:20:41: 1000000 INFO @ Sat, 15 Sep 2018 09:20:41: 1000000 INFO @ Sat, 15 Sep 2018 09:20:41: 1000000 INFO @ Sat, 15 Sep 2018 09:20:47: 2000000 INFO @ Sat, 15 Sep 2018 09:20:47: 2000000 INFO @ Sat, 15 Sep 2018 09:20:47: 2000000 INFO @ Sat, 15 Sep 2018 09:20:53: 3000000 INFO @ Sat, 15 Sep 2018 09:20:54: 3000000 INFO @ Sat, 15 Sep 2018 09:20:54: 3000000 INFO @ Sat, 15 Sep 2018 09:21:00: 4000000 INFO @ Sat, 15 Sep 2018 09:21:00: 4000000 INFO @ Sat, 15 Sep 2018 09:21:00: 4000000 INFO @ Sat, 15 Sep 2018 09:21:06: 5000000 INFO @ Sat, 15 Sep 2018 09:21:07: 5000000 INFO @ Sat, 15 Sep 2018 09:21:07: 5000000 INFO @ Sat, 15 Sep 2018 09:21:12: 6000000 INFO @ Sat, 15 Sep 2018 09:21:13: 6000000 INFO @ Sat, 15 Sep 2018 09:21:14: 6000000 INFO @ Sat, 15 Sep 2018 09:21:19: 7000000 INFO @ Sat, 15 Sep 2018 09:21:20: 7000000 INFO @ Sat, 15 Sep 2018 09:21:20: 7000000 INFO @ Sat, 15 Sep 2018 09:21:25: 8000000 INFO @ Sat, 15 Sep 2018 09:21:26: 8000000 INFO @ Sat, 15 Sep 2018 09:21:27: 8000000 INFO @ Sat, 15 Sep 2018 09:21:32: 9000000 INFO @ Sat, 15 Sep 2018 09:21:33: 9000000 INFO @ Sat, 15 Sep 2018 09:21:34: 9000000 INFO @ Sat, 15 Sep 2018 09:21:38: 10000000 INFO @ Sat, 15 Sep 2018 09:21:39: 10000000 INFO @ Sat, 15 Sep 2018 09:21:40: 10000000 INFO @ Sat, 15 Sep 2018 09:21:44: 11000000 INFO @ Sat, 15 Sep 2018 09:21:46: 11000000 INFO @ Sat, 15 Sep 2018 09:21:47: 11000000 INFO @ Sat, 15 Sep 2018 09:21:51: 12000000 INFO @ Sat, 15 Sep 2018 09:21:53: 12000000 INFO @ Sat, 15 Sep 2018 09:21:53: 12000000 INFO @ Sat, 15 Sep 2018 09:21:57: 13000000 INFO @ Sat, 15 Sep 2018 09:21:59: 13000000 INFO @ Sat, 15 Sep 2018 09:22:00: 13000000 INFO @ Sat, 15 Sep 2018 09:22:04: 14000000 INFO @ Sat, 15 Sep 2018 09:22:05: #1 tag size is determined as 50 bps INFO @ Sat, 15 Sep 2018 09:22:05: #1 tag size = 50 INFO @ Sat, 15 Sep 2018 09:22:05: #1 total tags in treatment: 14116848 INFO @ Sat, 15 Sep 2018 09:22:05: #1 user defined the maximum tags... INFO @ Sat, 15 Sep 2018 09:22:05: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 15 Sep 2018 09:22:05: #1 tags after filtering in treatment: 14116691 INFO @ Sat, 15 Sep 2018 09:22:05: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 15 Sep 2018 09:22:05: #1 finished! INFO @ Sat, 15 Sep 2018 09:22:05: #2 Build Peak Model... INFO @ Sat, 15 Sep 2018 09:22:05: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Sep 2018 09:22:06: 14000000 INFO @ Sat, 15 Sep 2018 09:22:06: 14000000 INFO @ Sat, 15 Sep 2018 09:22:07: #1 tag size is determined as 50 bps INFO @ Sat, 15 Sep 2018 09:22:07: #1 tag size = 50 INFO @ Sat, 15 Sep 2018 09:22:07: #1 total tags in treatment: 14116848 INFO @ Sat, 15 Sep 2018 09:22:07: #1 user defined the maximum tags... INFO @ Sat, 15 Sep 2018 09:22:07: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 15 Sep 2018 09:22:07: #1 tags after filtering in treatment: 14116691 INFO @ Sat, 15 Sep 2018 09:22:07: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 15 Sep 2018 09:22:07: #1 finished! INFO @ Sat, 15 Sep 2018 09:22:07: #2 Build Peak Model... INFO @ Sat, 15 Sep 2018 09:22:07: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Sep 2018 09:22:07: #1 tag size is determined as 50 bps INFO @ Sat, 15 Sep 2018 09:22:07: #1 tag size = 50 INFO @ Sat, 15 Sep 2018 09:22:07: #1 total tags in treatment: 14116848 INFO @ Sat, 15 Sep 2018 09:22:07: #1 user defined the maximum tags... INFO @ Sat, 15 Sep 2018 09:22:07: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 15 Sep 2018 09:22:07: #2 number of paired peaks: 20944 INFO @ Sat, 15 Sep 2018 09:22:07: start model_add_line... INFO @ Sat, 15 Sep 2018 09:22:08: start X-correlation... INFO @ Sat, 15 Sep 2018 09:22:08: end of X-cor INFO @ Sat, 15 Sep 2018 09:22:08: #2 finished! INFO @ Sat, 15 Sep 2018 09:22:08: #2 predicted fragment length is 220 bps INFO @ Sat, 15 Sep 2018 09:22:08: #2 alternative fragment length(s) may be 220 bps INFO @ Sat, 15 Sep 2018 09:22:08: #2.2 Generate R script for model : SRX2226583.10_model.r INFO @ Sat, 15 Sep 2018 09:22:08: #3 Call peaks... INFO @ Sat, 15 Sep 2018 09:22:08: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 15 Sep 2018 09:22:08: #1 tags after filtering in treatment: 14116691 INFO @ Sat, 15 Sep 2018 09:22:08: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 15 Sep 2018 09:22:08: #1 finished! INFO @ Sat, 15 Sep 2018 09:22:08: #2 Build Peak Model... INFO @ Sat, 15 Sep 2018 09:22:08: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Sep 2018 09:22:09: #2 number of paired peaks: 20944 INFO @ Sat, 15 Sep 2018 09:22:09: start model_add_line... INFO @ Sat, 15 Sep 2018 09:22:09: start X-correlation... INFO @ Sat, 15 Sep 2018 09:22:09: end of X-cor INFO @ Sat, 15 Sep 2018 09:22:09: #2 finished! INFO @ Sat, 15 Sep 2018 09:22:09: #2 predicted fragment length is 220 bps INFO @ Sat, 15 Sep 2018 09:22:09: #2 alternative fragment length(s) may be 220 bps INFO @ Sat, 15 Sep 2018 09:22:09: #2.2 Generate R script for model : SRX2226583.20_model.r INFO @ Sat, 15 Sep 2018 09:22:09: #3 Call peaks... INFO @ Sat, 15 Sep 2018 09:22:09: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 15 Sep 2018 09:22:10: #2 number of paired peaks: 20944 INFO @ Sat, 15 Sep 2018 09:22:10: start model_add_line... INFO @ Sat, 15 Sep 2018 09:22:10: start X-correlation... INFO @ Sat, 15 Sep 2018 09:22:10: end of X-cor INFO @ Sat, 15 Sep 2018 09:22:10: #2 finished! INFO @ Sat, 15 Sep 2018 09:22:10: #2 predicted fragment length is 220 bps INFO @ Sat, 15 Sep 2018 09:22:10: #2 alternative fragment length(s) may be 220 bps INFO @ Sat, 15 Sep 2018 09:22:10: #2.2 Generate R script for model : SRX2226583.05_model.r INFO @ Sat, 15 Sep 2018 09:22:10: #3 Call peaks... INFO @ Sat, 15 Sep 2018 09:22:10: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 15 Sep 2018 09:22:44: #3 Call peaks for each chromosome... INFO @ Sat, 15 Sep 2018 09:22:46: #3 Call peaks for each chromosome... INFO @ Sat, 15 Sep 2018 09:22:47: #3 Call peaks for each chromosome... INFO @ Sat, 15 Sep 2018 09:23:04: #4 Write output xls file... SRX2226583.05_peaks.xls INFO @ Sat, 15 Sep 2018 09:23:04: #4 Write peak in narrowPeak format file... SRX2226583.05_peaks.narrowPeak INFO @ Sat, 15 Sep 2018 09:23:04: #4 Write summits bed file... SRX2226583.05_summits.bed INFO @ Sat, 15 Sep 2018 09:23:05: Done! pass1 - making usageList (55 chroms): 10 millis pass2 - checking and writing primary data (3536 records, 4 fields): 17 millis CompletedMACS2peakCalling INFO @ Sat, 15 Sep 2018 09:23:06: #4 Write output xls file... SRX2226583.10_peaks.xls INFO @ Sat, 15 Sep 2018 09:23:06: #4 Write peak in narrowPeak format file... SRX2226583.10_peaks.narrowPeak INFO @ Sat, 15 Sep 2018 09:23:06: #4 Write summits bed file... SRX2226583.10_summits.bed INFO @ Sat, 15 Sep 2018 09:23:06: Done! pass1 - making usageList (40 chroms): 1 millis pass2 - checking and writing primary data (1596 records, 4 fields): 5 millis CompletedMACS2peakCalling INFO @ Sat, 15 Sep 2018 09:23:06: #4 Write output xls file... SRX2226583.20_peaks.xls INFO @ Sat, 15 Sep 2018 09:23:06: #4 Write peak in narrowPeak format file... SRX2226583.20_peaks.narrowPeak INFO @ Sat, 15 Sep 2018 09:23:06: #4 Write summits bed file... SRX2226583.20_summits.bed INFO @ Sat, 15 Sep 2018 09:23:06: Done! pass1 - making usageList (33 chroms): 2 millis pass2 - checking and writing primary data (653 records, 4 fields): 7 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。