Job ID = 9029283 sra ファイルのダウンロード中... Completed: 889937K bytes transferred in 9 seconds (777073K 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 --:--:-- 0:00:06 --:--:-- 0 100 14324 0 14324 0 0 1868 0 --:--:-- 0:00:07 --:--:-- 11468 100 46173 0 46173 0 0 5435 0 --:--:-- 0:00:08 --:--:-- 22209 100 103k 0 103k 0 0 11624 0 --:--:-- 0:00:09 --:--:-- 38792 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 25714480 spots for /home/okishinya/chipatlas/results/dm3/SRX1531759/SRR3102817.sra Written 25714480 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: 00:00:01 Time loading mirror index: 00:00:00 Multiseed full-index search: 00:04:55 25714480 reads; of these: 25714480 (100.00%) were unpaired; of these: 19232863 (74.79%) aligned 0 times 4871620 (18.95%) aligned exactly 1 time 1609997 (6.26%) aligned >1 times 25.21% overall alignment rate Time searching: 00:04:56 Overall time: 00:04:56 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_rmdupse_core] 2585928 / 6481617 = 0.3990 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 13:07:44: # Command line: callpeak -t SRX1531759.bam -f BAM -g dm -n SRX1531759.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX1531759.20 # format = BAM # ChIP-seq file = ['SRX1531759.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 INFO @ Sat, 03 Jun 2017 13:07:44: #1 read tag files... INFO @ Sat, 03 Jun 2017 13:07:44: #1 read treatment tags... INFO @ Sat, 03 Jun 2017 13:07:44: # Command line: callpeak -t SRX1531759.bam -f BAM -g dm -n SRX1531759.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX1531759.05 # format = BAM # ChIP-seq file = ['SRX1531759.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 INFO @ Sat, 03 Jun 2017 13:07:44: #1 read tag files... INFO @ Sat, 03 Jun 2017 13:07:44: #1 read treatment tags... INFO @ Sat, 03 Jun 2017 13:07:44: # Command line: callpeak -t SRX1531759.bam -f BAM -g dm -n SRX1531759.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX1531759.10 # format = BAM # ChIP-seq file = ['SRX1531759.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 INFO @ Sat, 03 Jun 2017 13:07:44: #1 read tag files... INFO @ Sat, 03 Jun 2017 13:07:44: #1 read treatment tags... INFO @ Sat, 03 Jun 2017 13:07:51: 1000000 INFO @ Sat, 03 Jun 2017 13:07:51: 1000000 INFO @ Sat, 03 Jun 2017 13:07:51: 1000000 INFO @ Sat, 03 Jun 2017 13:07:58: 2000000 INFO @ Sat, 03 Jun 2017 13:07:58: 2000000 INFO @ Sat, 03 Jun 2017 13:07:58: 2000000 INFO @ Sat, 03 Jun 2017 13:08:04: 3000000 INFO @ Sat, 03 Jun 2017 13:08:04: 3000000 INFO @ Sat, 03 Jun 2017 13:08:04: 3000000 INFO @ Sat, 03 Jun 2017 13:08:10: #1 tag size is determined as 51 bps INFO @ Sat, 03 Jun 2017 13:08:10: #1 tag size = 51 INFO @ Sat, 03 Jun 2017 13:08:10: #1 total tags in treatment: 3895689 INFO @ Sat, 03 Jun 2017 13:08:10: #1 user defined the maximum tags... INFO @ Sat, 03 Jun 2017 13:08:10: #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 13:08:10: #1 tag size is determined as 51 bps INFO @ Sat, 03 Jun 2017 13:08:10: #1 tag size = 51 INFO @ Sat, 03 Jun 2017 13:08:10: #1 total tags in treatment: 3895689 INFO @ Sat, 03 Jun 2017 13:08:10: #1 user defined the maximum tags... INFO @ Sat, 03 Jun 2017 13:08:10: #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 13:08:10: #1 tag size is determined as 51 bps INFO @ Sat, 03 Jun 2017 13:08:10: #1 tag size = 51 INFO @ Sat, 03 Jun 2017 13:08:10: #1 total tags in treatment: 3895689 INFO @ Sat, 03 Jun 2017 13:08:10: #1 user defined the maximum tags... INFO @ Sat, 03 Jun 2017 13:08:10: #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 13:08:11: #1 tags after filtering in treatment: 3892631 INFO @ Sat, 03 Jun 2017 13:08:11: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 03 Jun 2017 13:08:11: #1 finished! INFO @ Sat, 03 Jun 2017 13:08:11: #2 Build Peak Model... INFO @ Sat, 03 Jun 2017 13:08:11: #1 tags after filtering in treatment: 3892631 INFO @ Sat, 03 Jun 2017 13:08:11: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 03 Jun 2017 13:08:11: #1 finished! INFO @ Sat, 03 Jun 2017 13:08:11: #2 Build Peak Model... INFO @ Sat, 03 Jun 2017 13:08:11: #1 tags after filtering in treatment: 3892631 INFO @ Sat, 03 Jun 2017 13:08:11: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 03 Jun 2017 13:08:11: #1 finished! INFO @ Sat, 03 Jun 2017 13:08:11: #2 Build Peak Model... INFO @ Sat, 03 Jun 2017 13:08:12: #2 number of paired peaks: 1222 INFO @ Sat, 03 Jun 2017 13:08:12: start model_add_line... INFO @ Sat, 03 Jun 2017 13:08:12: #2 number of paired peaks: 1222 INFO @ Sat, 03 Jun 2017 13:08:12: start model_add_line... INFO @ Sat, 03 Jun 2017 13:08:12: #2 number of paired peaks: 1222 INFO @ Sat, 03 Jun 2017 13:08:12: start model_add_line... INFO @ Sat, 03 Jun 2017 13:08:15: start X-correlation... INFO @ Sat, 03 Jun 2017 13:08:15: end of X-cor INFO @ Sat, 03 Jun 2017 13:08:15: #2 finished! INFO @ Sat, 03 Jun 2017 13:08:15: #2 predicted fragment length is 121 bps INFO @ Sat, 03 Jun 2017 13:08:15: #2 alternative fragment length(s) may be 121 bps INFO @ Sat, 03 Jun 2017 13:08:15: #2.2 Generate R script for model : SRX1531759.20_model.r INFO @ Sat, 03 Jun 2017 13:08:15: #3 Call peaks... INFO @ Sat, 03 Jun 2017 13:08:15: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Jun 2017 13:08:15: start X-correlation... INFO @ Sat, 03 Jun 2017 13:08:15: end of X-cor INFO @ Sat, 03 Jun 2017 13:08:15: #2 finished! INFO @ Sat, 03 Jun 2017 13:08:15: #2 predicted fragment length is 121 bps INFO @ Sat, 03 Jun 2017 13:08:15: #2 alternative fragment length(s) may be 121 bps INFO @ Sat, 03 Jun 2017 13:08:15: #2.2 Generate R script for model : SRX1531759.10_model.r INFO @ Sat, 03 Jun 2017 13:08:15: #3 Call peaks... INFO @ Sat, 03 Jun 2017 13:08:15: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Jun 2017 13:08:16: start X-correlation... INFO @ Sat, 03 Jun 2017 13:08:16: end of X-cor INFO @ Sat, 03 Jun 2017 13:08:16: #2 finished! INFO @ Sat, 03 Jun 2017 13:08:16: #2 predicted fragment length is 121 bps INFO @ Sat, 03 Jun 2017 13:08:16: #2 alternative fragment length(s) may be 121 bps INFO @ Sat, 03 Jun 2017 13:08:16: #2.2 Generate R script for model : SRX1531759.05_model.r INFO @ Sat, 03 Jun 2017 13:08:16: #3 Call peaks... INFO @ Sat, 03 Jun 2017 13:08:16: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Jun 2017 13:08:38: #3 Call peaks for each chromosome... INFO @ Sat, 03 Jun 2017 13:08:40: #3 Call peaks for each chromosome... INFO @ Sat, 03 Jun 2017 13:08:40: #3 Call peaks for each chromosome... INFO @ Sat, 03 Jun 2017 13:08:57: #4 Write output xls file... SRX1531759.20_peaks.xls INFO @ Sat, 03 Jun 2017 13:08:57: #4 Write peak in narrowPeak format file... SRX1531759.20_peaks.narrowPeak INFO @ Sat, 03 Jun 2017 13:08:57: #4 Write summits bed file... SRX1531759.20_summits.bed INFO @ Sat, 03 Jun 2017 13:08:57: Done! pass1 - making usageList (12 chroms): 1 millis pass2 - checking and writing primary data (1234 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Sat, 03 Jun 2017 13:08:57: #4 Write output xls file... SRX1531759.05_peaks.xls INFO @ Sat, 03 Jun 2017 13:08:57: #4 Write peak in narrowPeak format file... SRX1531759.05_peaks.narrowPeak INFO @ Sat, 03 Jun 2017 13:08:57: #4 Write summits bed file... SRX1531759.05_summits.bed INFO @ Sat, 03 Jun 2017 13:08:57: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (2884 records, 4 fields): 5 millis CompletedMACS2peakCalling INFO @ Sat, 03 Jun 2017 13:08:59: #4 Write output xls file... SRX1531759.10_peaks.xls INFO @ Sat, 03 Jun 2017 13:08:59: #4 Write peak in narrowPeak format file... SRX1531759.10_peaks.narrowPeak INFO @ Sat, 03 Jun 2017 13:08:59: #4 Write summits bed file... SRX1531759.10_summits.bed INFO @ Sat, 03 Jun 2017 13:08:59: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (1971 records, 4 fields): 4 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。