Job ID = 9025655 sra ファイルのダウンロード中... Completed: 247194K bytes transferred in 6 seconds (325575K bits/sec), in 1 file, 2 directories. % Total % Received % Xferd Average Speed Time Time Time Current Dload Upload Total Spent Left Speed 0 0 0 0 0 0 0 0 --:--:-- 0:00:06 --:--:-- 0 0 0 0 0 0 0 0 0 --:--:-- 0:00:07 --:--:-- 0 100 7663 0 7663 0 0 1003 0 --:--:-- 0:00:07 --:--:-- 6194 100 30318 0 30318 0 0 3512 0 --:--:-- 0:00:08 --:--:-- 13577 100 53434 0 53434 0 0 5852 0 --:--:-- 0:00:09 --:--:-- 19551 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 8842349 spots for /home/okishinya/chipatlas/results/ce10/SRX2144181/SRR4188785.sra Written 8842349 spots total 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: 00:01:38 8842349 reads; of these: 8842349 (100.00%) were unpaired; of these: 3823107 (43.24%) aligned 0 times 4325955 (48.92%) aligned exactly 1 time 693287 (7.84%) aligned >1 times 56.76% overall alignment rate Time searching: 00:01:38 Overall time: 00:01:38 マッピングが完了しました。 samtools でBAM に変換中... [samopen] SAM header is present: 7 sequences. [bam_rmdupse_core] 1279611 / 5019242 = 0.2549 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, 03 Jun 2017 04:51:08: # Command line: callpeak -t SRX2144181.bam -f BAM -g ce -n SRX2144181.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX2144181.10 # format = BAM # ChIP-seq file = ['SRX2144181.bam'] # control file = None # effective genome size = 9.00e+07 # 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 INFO @ Sat, 03 Jun 2017 04:51:08: #1 read tag files... INFO @ Sat, 03 Jun 2017 04:51:08: #1 read treatment tags... INFO @ Sat, 03 Jun 2017 04:51:08: # Command line: callpeak -t SRX2144181.bam -f BAM -g ce -n SRX2144181.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX2144181.05 # format = BAM # ChIP-seq file = ['SRX2144181.bam'] # control file = None # effective genome size = 9.00e+07 # 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 INFO @ Sat, 03 Jun 2017 04:51:08: #1 read tag files... INFO @ Sat, 03 Jun 2017 04:51:08: #1 read treatment tags... INFO @ Sat, 03 Jun 2017 04:51:08: # Command line: callpeak -t SRX2144181.bam -f BAM -g ce -n SRX2144181.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX2144181.20 # format = BAM # ChIP-seq file = ['SRX2144181.bam'] # control file = None # effective genome size = 9.00e+07 # 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 INFO @ Sat, 03 Jun 2017 04:51:08: #1 read tag files... INFO @ Sat, 03 Jun 2017 04:51:08: #1 read treatment tags... INFO @ Sat, 03 Jun 2017 04:51:13: 1000000 INFO @ Sat, 03 Jun 2017 04:51:13: 1000000 INFO @ Sat, 03 Jun 2017 04:51:14: 1000000 INFO @ Sat, 03 Jun 2017 04:51:19: 2000000 INFO @ Sat, 03 Jun 2017 04:51:19: 2000000 INFO @ Sat, 03 Jun 2017 04:51:20: 2000000 INFO @ Sat, 03 Jun 2017 04:51:24: 3000000 INFO @ Sat, 03 Jun 2017 04:51:25: 3000000 INFO @ Sat, 03 Jun 2017 04:51:27: 3000000 INFO @ Sat, 03 Jun 2017 04:51:28: #1 tag size is determined as 50 bps INFO @ Sat, 03 Jun 2017 04:51:28: #1 tag size = 50 INFO @ Sat, 03 Jun 2017 04:51:28: #1 total tags in treatment: 3739631 INFO @ Sat, 03 Jun 2017 04:51:28: #1 user defined the maximum tags... INFO @ Sat, 03 Jun 2017 04:51:28: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 03 Jun 2017 04:51:29: #1 tags after filtering in treatment: 3738573 INFO @ Sat, 03 Jun 2017 04:51:29: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 03 Jun 2017 04:51:29: #1 finished! INFO @ Sat, 03 Jun 2017 04:51:29: #2 Build Peak Model... INFO @ Sat, 03 Jun 2017 04:51:29: #1 tag size is determined as 50 bps INFO @ Sat, 03 Jun 2017 04:51:29: #1 tag size = 50 INFO @ Sat, 03 Jun 2017 04:51:29: #1 total tags in treatment: 3739631 INFO @ Sat, 03 Jun 2017 04:51:29: #1 user defined the maximum tags... INFO @ Sat, 03 Jun 2017 04:51:29: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 03 Jun 2017 04:51:30: #1 tags after filtering in treatment: 3738573 INFO @ Sat, 03 Jun 2017 04:51:30: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 03 Jun 2017 04:51:30: #1 finished! INFO @ Sat, 03 Jun 2017 04:51:30: #2 Build Peak Model... INFO @ Sat, 03 Jun 2017 04:51:30: #2 number of paired peaks: 2809 INFO @ Sat, 03 Jun 2017 04:51:30: start model_add_line... INFO @ Sat, 03 Jun 2017 04:51:31: #2 number of paired peaks: 2809 INFO @ Sat, 03 Jun 2017 04:51:31: start model_add_line... INFO @ Sat, 03 Jun 2017 04:51:31: #1 tag size is determined as 50 bps INFO @ Sat, 03 Jun 2017 04:51:31: #1 tag size = 50 INFO @ Sat, 03 Jun 2017 04:51:31: #1 total tags in treatment: 3739631 INFO @ Sat, 03 Jun 2017 04:51:31: #1 user defined the maximum tags... INFO @ Sat, 03 Jun 2017 04:51:31: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 03 Jun 2017 04:51:32: #1 tags after filtering in treatment: 3738573 INFO @ Sat, 03 Jun 2017 04:51:32: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 03 Jun 2017 04:51:32: #1 finished! INFO @ Sat, 03 Jun 2017 04:51:32: #2 Build Peak Model... INFO @ Sat, 03 Jun 2017 04:51:33: #2 number of paired peaks: 2809 INFO @ Sat, 03 Jun 2017 04:51:33: start model_add_line... INFO @ Sat, 03 Jun 2017 04:51:42: start X-correlation... INFO @ Sat, 03 Jun 2017 04:51:42: end of X-cor INFO @ Sat, 03 Jun 2017 04:51:42: #2 finished! INFO @ Sat, 03 Jun 2017 04:51:42: #2 predicted fragment length is 132 bps INFO @ Sat, 03 Jun 2017 04:51:42: #2 alternative fragment length(s) may be 132 bps INFO @ Sat, 03 Jun 2017 04:51:42: #2.2 Generate R script for model : SRX2144181.05_model.r INFO @ Sat, 03 Jun 2017 04:51:42: #3 Call peaks... INFO @ Sat, 03 Jun 2017 04:51:42: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Jun 2017 04:51:42: start X-correlation... INFO @ Sat, 03 Jun 2017 04:51:42: end of X-cor INFO @ Sat, 03 Jun 2017 04:51:42: #2 finished! INFO @ Sat, 03 Jun 2017 04:51:42: #2 predicted fragment length is 132 bps INFO @ Sat, 03 Jun 2017 04:51:42: #2 alternative fragment length(s) may be 132 bps INFO @ Sat, 03 Jun 2017 04:51:42: #2.2 Generate R script for model : SRX2144181.10_model.r INFO @ Sat, 03 Jun 2017 04:51:42: #3 Call peaks... INFO @ Sat, 03 Jun 2017 04:51:42: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Jun 2017 04:51:45: start X-correlation... INFO @ Sat, 03 Jun 2017 04:51:45: end of X-cor INFO @ Sat, 03 Jun 2017 04:51:45: #2 finished! INFO @ Sat, 03 Jun 2017 04:51:45: #2 predicted fragment length is 132 bps INFO @ Sat, 03 Jun 2017 04:51:45: #2 alternative fragment length(s) may be 132 bps INFO @ Sat, 03 Jun 2017 04:51:45: #2.2 Generate R script for model : SRX2144181.20_model.r INFO @ Sat, 03 Jun 2017 04:51:45: #3 Call peaks... INFO @ Sat, 03 Jun 2017 04:51:45: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Jun 2017 04:52:05: #3 Call peaks for each chromosome... INFO @ Sat, 03 Jun 2017 04:52:06: #3 Call peaks for each chromosome... INFO @ Sat, 03 Jun 2017 04:52:08: #3 Call peaks for each chromosome... INFO @ Sat, 03 Jun 2017 04:52:24: #4 Write output xls file... SRX2144181.10_peaks.xls INFO @ Sat, 03 Jun 2017 04:52:24: #4 Write peak in narrowPeak format file... SRX2144181.10_peaks.narrowPeak INFO @ Sat, 03 Jun 2017 04:52:24: #4 Write summits bed file... SRX2144181.10_summits.bed INFO @ Sat, 03 Jun 2017 04:52:24: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (1446 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Sat, 03 Jun 2017 04:52:24: #4 Write output xls file... SRX2144181.05_peaks.xls INFO @ Sat, 03 Jun 2017 04:52:24: #4 Write peak in narrowPeak format file... SRX2144181.05_peaks.narrowPeak INFO @ Sat, 03 Jun 2017 04:52:24: #4 Write summits bed file... SRX2144181.05_summits.bed INFO @ Sat, 03 Jun 2017 04:52:24: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (3074 records, 4 fields): 5 millis CompletedMACS2peakCalling INFO @ Sat, 03 Jun 2017 04:52:25: #4 Write output xls file... SRX2144181.20_peaks.xls INFO @ Sat, 03 Jun 2017 04:52:25: #4 Write peak in narrowPeak format file... SRX2144181.20_peaks.narrowPeak INFO @ Sat, 03 Jun 2017 04:52:25: #4 Write summits bed file... SRX2144181.20_summits.bed INFO @ Sat, 03 Jun 2017 04:52:25: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (477 records, 4 fields): 2 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。