Job ID = 9029602 sra ファイルのダウンロード中... Completed: 1497845K bytes transferred in 18 seconds (670364K 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 22317 0 22317 0 0 2850 0 --:--:-- 0:00:07 --:--:-- 15861 100 43277 0 43277 0 0 4997 0 --:--:-- 0:00:08 --:--:-- 19345 100 108k 0 108k 0 0 11473 0 --:--:-- 0:00:09 --:--:-- 34268 100 158k 0 158k 0 0 15865 0 --:--:-- 0:00:10 --:--:-- 42541 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 47880602 spots for /home/okishinya/chipatlas/results/dm3/SRX1872291/SRR3712752.sra Written 47880602 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: 00:13:41 47880602 reads; of these: 47880602 (100.00%) were unpaired; of these: 21008170 (43.88%) aligned 0 times 20475825 (42.76%) aligned exactly 1 time 6396607 (13.36%) aligned >1 times 56.12% overall alignment rate Time searching: 00:13:41 Overall time: 00:13:41 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] 21101611 / 26872432 = 0.7853 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 14:42:39: # Command line: callpeak -t SRX1872291.bam -f BAM -g dm -n SRX1872291.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX1872291.05 # format = BAM # ChIP-seq file = ['SRX1872291.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 14:42:39: #1 read tag files... INFO @ Sat, 03 Jun 2017 14:42:39: #1 read treatment tags... INFO @ Sat, 03 Jun 2017 14:42:39: # Command line: callpeak -t SRX1872291.bam -f BAM -g dm -n SRX1872291.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX1872291.20 # format = BAM # ChIP-seq file = ['SRX1872291.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 14:42:39: #1 read tag files... INFO @ Sat, 03 Jun 2017 14:42:39: #1 read treatment tags... INFO @ Sat, 03 Jun 2017 14:42:39: # Command line: callpeak -t SRX1872291.bam -f BAM -g dm -n SRX1872291.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX1872291.10 # format = BAM # ChIP-seq file = ['SRX1872291.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 14:42:39: #1 read tag files... INFO @ Sat, 03 Jun 2017 14:42:39: #1 read treatment tags... INFO @ Sat, 03 Jun 2017 14:42:45: 1000000 INFO @ Sat, 03 Jun 2017 14:42:45: 1000000 INFO @ Sat, 03 Jun 2017 14:42:45: 1000000 INFO @ Sat, 03 Jun 2017 14:42:51: 2000000 INFO @ Sat, 03 Jun 2017 14:42:51: 2000000 INFO @ Sat, 03 Jun 2017 14:42:51: 2000000 INFO @ Sat, 03 Jun 2017 14:42:57: 3000000 INFO @ Sat, 03 Jun 2017 14:42:57: 3000000 INFO @ Sat, 03 Jun 2017 14:42:57: 3000000 INFO @ Sat, 03 Jun 2017 14:43:03: 4000000 INFO @ Sat, 03 Jun 2017 14:43:03: 4000000 INFO @ Sat, 03 Jun 2017 14:43:03: 4000000 INFO @ Sat, 03 Jun 2017 14:43:09: 5000000 INFO @ Sat, 03 Jun 2017 14:43:09: 5000000 INFO @ Sat, 03 Jun 2017 14:43:09: 5000000 INFO @ Sat, 03 Jun 2017 14:43:14: #1 tag size is determined as 50 bps INFO @ Sat, 03 Jun 2017 14:43:14: #1 tag size = 50 INFO @ Sat, 03 Jun 2017 14:43:14: #1 total tags in treatment: 5770821 INFO @ Sat, 03 Jun 2017 14:43:14: #1 user defined the maximum tags... INFO @ Sat, 03 Jun 2017 14:43:14: #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 14:43:14: #1 tag size is determined as 50 bps INFO @ Sat, 03 Jun 2017 14:43:14: #1 tag size = 50 INFO @ Sat, 03 Jun 2017 14:43:14: #1 total tags in treatment: 5770821 INFO @ Sat, 03 Jun 2017 14:43:14: #1 user defined the maximum tags... INFO @ Sat, 03 Jun 2017 14:43:14: #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 14:43:14: #1 tag size is determined as 50 bps INFO @ Sat, 03 Jun 2017 14:43:14: #1 tag size = 50 INFO @ Sat, 03 Jun 2017 14:43:14: #1 total tags in treatment: 5770821 INFO @ Sat, 03 Jun 2017 14:43:14: #1 user defined the maximum tags... INFO @ Sat, 03 Jun 2017 14:43:14: #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 14:43:15: #1 tags after filtering in treatment: 5765704 INFO @ Sat, 03 Jun 2017 14:43:15: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 03 Jun 2017 14:43:15: #1 finished! INFO @ Sat, 03 Jun 2017 14:43:15: #2 Build Peak Model... INFO @ Sat, 03 Jun 2017 14:43:15: #1 tags after filtering in treatment: 5765704 INFO @ Sat, 03 Jun 2017 14:43:15: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 03 Jun 2017 14:43:15: #1 finished! INFO @ Sat, 03 Jun 2017 14:43:15: #2 Build Peak Model... INFO @ Sat, 03 Jun 2017 14:43:15: #1 tags after filtering in treatment: 5765704 INFO @ Sat, 03 Jun 2017 14:43:15: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 03 Jun 2017 14:43:15: #1 finished! INFO @ Sat, 03 Jun 2017 14:43:15: #2 Build Peak Model... INFO @ Sat, 03 Jun 2017 14:43:16: #2 number of paired peaks: 1591 INFO @ Sat, 03 Jun 2017 14:43:16: start model_add_line... INFO @ Sat, 03 Jun 2017 14:43:16: #2 number of paired peaks: 1591 INFO @ Sat, 03 Jun 2017 14:43:16: start model_add_line... INFO @ Sat, 03 Jun 2017 14:43:17: #2 number of paired peaks: 1591 INFO @ Sat, 03 Jun 2017 14:43:17: start model_add_line... INFO @ Sat, 03 Jun 2017 14:43:25: start X-correlation... INFO @ Sat, 03 Jun 2017 14:43:25: end of X-cor INFO @ Sat, 03 Jun 2017 14:43:25: #2 finished! INFO @ Sat, 03 Jun 2017 14:43:25: #2 predicted fragment length is 145 bps INFO @ Sat, 03 Jun 2017 14:43:25: #2 alternative fragment length(s) may be 145 bps INFO @ Sat, 03 Jun 2017 14:43:25: #2.2 Generate R script for model : SRX1872291.10_model.r INFO @ Sat, 03 Jun 2017 14:43:25: #3 Call peaks... INFO @ Sat, 03 Jun 2017 14:43:25: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Jun 2017 14:43:25: start X-correlation... INFO @ Sat, 03 Jun 2017 14:43:25: end of X-cor INFO @ Sat, 03 Jun 2017 14:43:25: #2 finished! INFO @ Sat, 03 Jun 2017 14:43:25: #2 predicted fragment length is 145 bps INFO @ Sat, 03 Jun 2017 14:43:25: #2 alternative fragment length(s) may be 145 bps INFO @ Sat, 03 Jun 2017 14:43:25: #2.2 Generate R script for model : SRX1872291.05_model.r INFO @ Sat, 03 Jun 2017 14:43:25: #3 Call peaks... INFO @ Sat, 03 Jun 2017 14:43:25: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Jun 2017 14:43:25: start X-correlation... INFO @ Sat, 03 Jun 2017 14:43:25: end of X-cor INFO @ Sat, 03 Jun 2017 14:43:25: #2 finished! INFO @ Sat, 03 Jun 2017 14:43:25: #2 predicted fragment length is 145 bps INFO @ Sat, 03 Jun 2017 14:43:25: #2 alternative fragment length(s) may be 145 bps INFO @ Sat, 03 Jun 2017 14:43:25: #2.2 Generate R script for model : SRX1872291.20_model.r INFO @ Sat, 03 Jun 2017 14:43:26: #3 Call peaks... INFO @ Sat, 03 Jun 2017 14:43:26: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Jun 2017 14:44:00: #3 Call peaks for each chromosome... INFO @ Sat, 03 Jun 2017 14:44:00: #3 Call peaks for each chromosome... INFO @ Sat, 03 Jun 2017 14:44:01: #3 Call peaks for each chromosome... INFO @ Sat, 03 Jun 2017 14:44:27: #4 Write output xls file... SRX1872291.10_peaks.xls INFO @ Sat, 03 Jun 2017 14:44:27: #4 Write peak in narrowPeak format file... SRX1872291.10_peaks.narrowPeak INFO @ Sat, 03 Jun 2017 14:44:27: #4 Write summits bed file... SRX1872291.10_summits.bed INFO @ Sat, 03 Jun 2017 14:44:27: Done! pass1 - making usageList (13 chroms): 0 millis pass2 - checking and writing primary data (2254 records, 4 fields): 5 millis CompletedMACS2peakCalling INFO @ Sat, 03 Jun 2017 14:44:28: #4 Write output xls file... SRX1872291.20_peaks.xls INFO @ Sat, 03 Jun 2017 14:44:28: #4 Write peak in narrowPeak format file... SRX1872291.20_peaks.narrowPeak INFO @ Sat, 03 Jun 2017 14:44:28: #4 Write summits bed file... SRX1872291.20_summits.bed INFO @ Sat, 03 Jun 2017 14:44:28: Done! pass1 - making usageList (13 chroms): 1 millis pass2 - checking and writing primary data (1557 records, 4 fields): 4 millis CompletedMACS2peakCalling INFO @ Sat, 03 Jun 2017 14:44:30: #4 Write output xls file... SRX1872291.05_peaks.xls INFO @ Sat, 03 Jun 2017 14:44:30: #4 Write peak in narrowPeak format file... SRX1872291.05_peaks.narrowPeak INFO @ Sat, 03 Jun 2017 14:44:30: #4 Write summits bed file... SRX1872291.05_summits.bed INFO @ Sat, 03 Jun 2017 14:44:30: Done! pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (3329 records, 4 fields): 6 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。