Job ID = 3001497 sra ファイルのダウンロード中... Completed: 58867K bytes transferred in 5 seconds (94747K 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 --:--:-- --:--:-- --:--:-- 0 108 1082 0 1082 0 0 1959 0 --:--:-- --:--:-- --:--:-- 2988 100 14953 0 14953 0 0 8586 0 --:--:-- 0:00:01 --:--:-- 9640 100 14953 0 14953 0 0 5450 0 --:--:-- 0:00:02 --:--:-- 5857 100 14953 0 14953 0 0 3992 0 --:--:-- 0:00:03 --:--:-- 4206 100 14953 0 14953 0 0 3150 0 --:--:-- 0:00:04 --:--:-- 3282 100 14953 0 14953 0 0 2601 0 --:--:-- 0:00:05 --:--:-- 2669 100 14953 0 14953 0 0 2215 0 --:--:-- 0:00:06 --:--:-- 0 100 14953 0 14953 0 0 1928 0 --:--:-- 0:00:07 --:--:-- 0 100 14953 0 14953 0 0 1708 0 --:--:-- 0:00:08 --:--:-- 0 100 14953 0 14953 0 0 1532 0 --:--:-- 0:00:09 --:--:-- 0 100 14953 0 14953 0 0 1390 0 --:--:-- 0:00:10 --:--:-- 0 100 14953 0 14953 0 0 1271 0 --:--:-- 0:00:11 --:--:-- 0 100 14953 0 14953 0 0 1171 0 --:--:-- 0:00:12 --:--:-- 0 100 14953 0 14953 0 0 1086 0 --:--:-- 0:00:13 --:--:-- 0 100 14953 0 14953 0 0 1012 0 --:--:-- 0:00:14 --:--:-- 0 100 14953 0 14953 0 0 948 0 --:--:-- 0:00:15 --:--:-- 0 100 14953 0 14953 0 0 891 0 --:--:-- 0:00:16 --:--:-- 0 100 14953 0 14953 0 0 841 0 --:--:-- 0:00:17 --:--:-- 0 100 14953 0 14953 0 0 796 0 --:--:-- 0:00:18 --:--:-- 0 100 14953 0 14953 0 0 756 0 --:--:-- 0:00:19 --:--:-- 0 100 14953 0 14953 0 0 719 0 --:--:-- 0:00:20 --:--:-- 0 100 14953 0 14953 0 0 686 0 --:--:-- 0:00:21 --:--:-- 0 100 14953 0 14953 0 0 656 0 --:--:-- 0:00:22 --:--:-- 0 100 14953 0 14953 0 0 628 0 --:--:-- 0:00:23 --:--:-- 0 100 14953 0 14953 0 0 603 0 --:--:-- 0:00:24 --:--:-- 0 100 14953 0 14953 0 0 579 0 --:--:-- 0:00:25 --:--:-- 0 100 14953 0 14953 0 0 558 0 --:--:-- 0:00:26 --:--:-- 0 100 14953 0 14953 0 0 538 0 --:--:-- 0:00:27 --:--:-- 0 100 14953 0 14953 0 0 519 0 --:--:-- 0:00:28 --:--:-- 0 100 14953 0 14953 0 0 501 0 --:--:-- 0:00:29 --:--:-- 0 100 16407 0 16407 0 0 536 0 --:--:-- 0:00:30 --:--:-- 301 100 32853 0 32853 0 0 1067 0 --:--:-- 0:00:30 --:--:-- 4469 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 3482818 spots for /home/okishinya/chipatlas/results/ce10/SRX005631/SRR017600.sra Written 3482818 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: 00:00:26 3482818 reads; of these: 3482818 (100.00%) were unpaired; of these: 1724269 (49.51%) aligned 0 times 1564986 (44.93%) aligned exactly 1 time 193563 (5.56%) aligned >1 times 50.49% overall alignment rate Time searching: 00:00:26 Overall time: 00:00:26 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] 230285 / 1758549 = 0.1310 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 @ Mon, 07 Sep 2015 18:46:09: # Command line: callpeak -t SRX005631.bam -f BAM -g ce -n SRX005631.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX005631.10 # format = BAM # ChIP-seq file = ['SRX005631.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 @ Mon, 07 Sep 2015 18:46:09: # Command line: callpeak -t SRX005631.bam -f BAM -g ce -n SRX005631.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX005631.05 # format = BAM # ChIP-seq file = ['SRX005631.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 @ Mon, 07 Sep 2015 18:46:09: # Command line: callpeak -t SRX005631.bam -f BAM -g ce -n SRX005631.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX005631.20 # format = BAM # ChIP-seq file = ['SRX005631.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 @ Mon, 07 Sep 2015 18:46:09: #1 read tag files... INFO @ Mon, 07 Sep 2015 18:46:09: #1 read tag files... INFO @ Mon, 07 Sep 2015 18:46:09: #1 read tag files... INFO @ Mon, 07 Sep 2015 18:46:09: #1 read treatment tags... INFO @ Mon, 07 Sep 2015 18:46:09: #1 read treatment tags... INFO @ Mon, 07 Sep 2015 18:46:09: #1 read treatment tags... INFO @ Mon, 07 Sep 2015 18:46:14: 1000000 INFO @ Mon, 07 Sep 2015 18:46:14: 1000000 INFO @ Mon, 07 Sep 2015 18:46:14: 1000000 INFO @ Mon, 07 Sep 2015 18:46:16: #1 tag size is determined as 27 bps INFO @ Mon, 07 Sep 2015 18:46:16: #1 tag size = 27 INFO @ Mon, 07 Sep 2015 18:46:16: #1 total tags in treatment: 1528264 INFO @ Mon, 07 Sep 2015 18:46:16: #1 user defined the maximum tags... INFO @ Mon, 07 Sep 2015 18:46:16: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Mon, 07 Sep 2015 18:46:16: #1 tag size is determined as 27 bps INFO @ Mon, 07 Sep 2015 18:46:16: #1 tag size = 27 INFO @ Mon, 07 Sep 2015 18:46:16: #1 total tags in treatment: 1528264 INFO @ Mon, 07 Sep 2015 18:46:16: #1 user defined the maximum tags... INFO @ Mon, 07 Sep 2015 18:46:16: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Mon, 07 Sep 2015 18:46:16: #1 tag size is determined as 27 bps INFO @ Mon, 07 Sep 2015 18:46:16: #1 tag size = 27 INFO @ Mon, 07 Sep 2015 18:46:16: #1 total tags in treatment: 1528264 INFO @ Mon, 07 Sep 2015 18:46:16: #1 user defined the maximum tags... INFO @ Mon, 07 Sep 2015 18:46:16: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Mon, 07 Sep 2015 18:46:17: #1 tags after filtering in treatment: 1528260 INFO @ Mon, 07 Sep 2015 18:46:17: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 07 Sep 2015 18:46:17: #1 finished! INFO @ Mon, 07 Sep 2015 18:46:17: #2 Build Peak Model... INFO @ Mon, 07 Sep 2015 18:46:17: #1 tags after filtering in treatment: 1528260 INFO @ Mon, 07 Sep 2015 18:46:17: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 07 Sep 2015 18:46:17: #1 finished! INFO @ Mon, 07 Sep 2015 18:46:17: #2 Build Peak Model... INFO @ Mon, 07 Sep 2015 18:46:17: #1 tags after filtering in treatment: 1528260 INFO @ Mon, 07 Sep 2015 18:46:17: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 07 Sep 2015 18:46:17: #1 finished! INFO @ Mon, 07 Sep 2015 18:46:17: #2 Build Peak Model... INFO @ Mon, 07 Sep 2015 18:46:17: #2 number of paired peaks: 2472 INFO @ Mon, 07 Sep 2015 18:46:17: start model_add_line... INFO @ Mon, 07 Sep 2015 18:46:17: #2 number of paired peaks: 2472 INFO @ Mon, 07 Sep 2015 18:46:17: start model_add_line... INFO @ Mon, 07 Sep 2015 18:46:17: #2 number of paired peaks: 2472 INFO @ Mon, 07 Sep 2015 18:46:17: start model_add_line... INFO @ Mon, 07 Sep 2015 18:46:20: start X-correlation... INFO @ Mon, 07 Sep 2015 18:46:20: start X-correlation... INFO @ Mon, 07 Sep 2015 18:46:20: end of X-cor INFO @ Mon, 07 Sep 2015 18:46:20: #2 finished! INFO @ Mon, 07 Sep 2015 18:46:20: end of X-cor INFO @ Mon, 07 Sep 2015 18:46:20: #2 finished! INFO @ Mon, 07 Sep 2015 18:46:20: #2 predicted fragment length is 143 bps INFO @ Mon, 07 Sep 2015 18:46:20: #2 predicted fragment length is 143 bps INFO @ Mon, 07 Sep 2015 18:46:20: #2 alternative fragment length(s) may be 143 bps INFO @ Mon, 07 Sep 2015 18:46:20: #2 alternative fragment length(s) may be 143 bps INFO @ Mon, 07 Sep 2015 18:46:20: #2.2 Generate R script for model : SRX005631.05_model.r INFO @ Mon, 07 Sep 2015 18:46:20: #2.2 Generate R script for model : SRX005631.10_model.r INFO @ Mon, 07 Sep 2015 18:46:20: #3 Call peaks... INFO @ Mon, 07 Sep 2015 18:46:20: #3 Call peaks... INFO @ Mon, 07 Sep 2015 18:46:20: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 07 Sep 2015 18:46:20: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 07 Sep 2015 18:46:20: start X-correlation... INFO @ Mon, 07 Sep 2015 18:46:20: end of X-cor INFO @ Mon, 07 Sep 2015 18:46:20: #2 finished! INFO @ Mon, 07 Sep 2015 18:46:20: #2 predicted fragment length is 143 bps INFO @ Mon, 07 Sep 2015 18:46:20: #2 alternative fragment length(s) may be 143 bps INFO @ Mon, 07 Sep 2015 18:46:20: #2.2 Generate R script for model : SRX005631.20_model.r INFO @ Mon, 07 Sep 2015 18:46:20: #3 Call peaks... INFO @ Mon, 07 Sep 2015 18:46:20: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 07 Sep 2015 18:46:29: #3 Call peaks for each chromosome... INFO @ Mon, 07 Sep 2015 18:46:30: #3 Call peaks for each chromosome... INFO @ Mon, 07 Sep 2015 18:46:30: #3 Call peaks for each chromosome... INFO @ Mon, 07 Sep 2015 18:46:37: #4 Write output xls file... SRX005631.20_peaks.xls INFO @ Mon, 07 Sep 2015 18:46:37: #4 Write peak in narrowPeak format file... SRX005631.20_peaks.narrowPeak INFO @ Mon, 07 Sep 2015 18:46:37: #4 Write summits bed file... SRX005631.20_summits.bed INFO @ Mon, 07 Sep 2015 18:46:37: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (253 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Mon, 07 Sep 2015 18:46:37: #4 Write output xls file... SRX005631.10_peaks.xls INFO @ Mon, 07 Sep 2015 18:46:37: #4 Write peak in narrowPeak format file... SRX005631.10_peaks.narrowPeak INFO @ Mon, 07 Sep 2015 18:46:37: #4 Write summits bed file... SRX005631.10_summits.bed INFO @ Mon, 07 Sep 2015 18:46:37: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (1709 records, 4 fields): 5 millis CompletedMACS2peakCalling INFO @ Mon, 07 Sep 2015 18:46:39: #4 Write output xls file... SRX005631.05_peaks.xls INFO @ Mon, 07 Sep 2015 18:46:39: #4 Write peak in narrowPeak format file... SRX005631.05_peaks.narrowPeak INFO @ Mon, 07 Sep 2015 18:46:39: #4 Write summits bed file... SRX005631.05_summits.bed INFO @ Mon, 07 Sep 2015 18:46:39: Done! pass1 - making usageList (7 chroms): 2 millis pass2 - checking and writing primary data (4578 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。