Job ID = 9025512 sra ファイルのダウンロード中... Completed: 146196K bytes transferred in 4 seconds (259191K 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 --:--:-- 0 100 6903 0 6903 0 0 954 0 --:--:-- 0:00:07 --:--:-- 10769 100 36038 0 36038 0 0 4379 0 --:--:-- 0:00:08 --:--:-- 22014 100 47182 0 47182 0 0 5619 0 --:--:-- 0:00:08 --:--:-- 26154 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 6278884 spots for /home/okishinya/chipatlas/results/ce10/SRX1388761/SRR2832477.sra Written 6278884 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: 00:01:52 6278884 reads; of these: 6278884 (100.00%) were unpaired; of these: 373635 (5.95%) aligned 0 times 5163016 (82.23%) aligned exactly 1 time 742233 (11.82%) aligned >1 times 94.05% overall alignment rate Time searching: 00:01:52 Overall time: 00:01:52 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] 618655 / 5905249 = 0.1048 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 04:14:22: # Command line: callpeak -t SRX1388761.bam -f BAM -g ce -n SRX1388761.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX1388761.10 # format = BAM # ChIP-seq file = ['SRX1388761.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 04:14:22: #1 read tag files... INFO @ Sat, 03 Jun 2017 04:14:22: #1 read treatment tags... INFO @ Sat, 03 Jun 2017 04:14:22: # Command line: callpeak -t SRX1388761.bam -f BAM -g ce -n SRX1388761.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX1388761.05 # format = BAM # ChIP-seq file = ['SRX1388761.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 04:14:22: #1 read tag files... INFO @ Sat, 03 Jun 2017 04:14:22: #1 read treatment tags... INFO @ Sat, 03 Jun 2017 04:14:22: # Command line: callpeak -t SRX1388761.bam -f BAM -g ce -n SRX1388761.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX1388761.20 # format = BAM # ChIP-seq file = ['SRX1388761.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 04:14:22: #1 read tag files... INFO @ Sat, 03 Jun 2017 04:14:22: #1 read treatment tags... INFO @ Sat, 03 Jun 2017 04:14:29: 1000000 INFO @ Sat, 03 Jun 2017 04:14:29: 1000000 INFO @ Sat, 03 Jun 2017 04:14:29: 1000000 INFO @ Sat, 03 Jun 2017 04:14:37: 2000000 INFO @ Sat, 03 Jun 2017 04:14:37: 2000000 INFO @ Sat, 03 Jun 2017 04:14:37: 2000000 INFO @ Sat, 03 Jun 2017 04:14:45: 3000000 INFO @ Sat, 03 Jun 2017 04:14:45: 3000000 INFO @ Sat, 03 Jun 2017 04:14:45: 3000000 INFO @ Sat, 03 Jun 2017 04:14:52: 4000000 INFO @ Sat, 03 Jun 2017 04:14:52: 4000000 INFO @ Sat, 03 Jun 2017 04:14:52: 4000000 INFO @ Sat, 03 Jun 2017 04:15:00: 5000000 INFO @ Sat, 03 Jun 2017 04:15:00: 5000000 INFO @ Sat, 03 Jun 2017 04:15:00: 5000000 INFO @ Sat, 03 Jun 2017 04:15:02: #1 tag size is determined as 50 bps INFO @ Sat, 03 Jun 2017 04:15:02: #1 tag size = 50 INFO @ Sat, 03 Jun 2017 04:15:02: #1 total tags in treatment: 5286594 INFO @ Sat, 03 Jun 2017 04:15:02: #1 user defined the maximum tags... INFO @ Sat, 03 Jun 2017 04:15:02: #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 04:15:02: #1 tag size is determined as 50 bps INFO @ Sat, 03 Jun 2017 04:15:02: #1 tag size = 50 INFO @ Sat, 03 Jun 2017 04:15:02: #1 total tags in treatment: 5286594 INFO @ Sat, 03 Jun 2017 04:15:02: #1 user defined the maximum tags... INFO @ Sat, 03 Jun 2017 04:15:02: #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 04:15:02: #1 tag size is determined as 50 bps INFO @ Sat, 03 Jun 2017 04:15:02: #1 tag size = 50 INFO @ Sat, 03 Jun 2017 04:15:02: #1 total tags in treatment: 5286594 INFO @ Sat, 03 Jun 2017 04:15:02: #1 user defined the maximum tags... INFO @ Sat, 03 Jun 2017 04:15:02: #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 04:15:03: #1 tags after filtering in treatment: 5285357 INFO @ Sat, 03 Jun 2017 04:15:03: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 03 Jun 2017 04:15:03: #1 finished! INFO @ Sat, 03 Jun 2017 04:15:03: #2 Build Peak Model... INFO @ Sat, 03 Jun 2017 04:15:03: #1 tags after filtering in treatment: 5285357 INFO @ Sat, 03 Jun 2017 04:15:03: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 03 Jun 2017 04:15:03: #1 finished! INFO @ Sat, 03 Jun 2017 04:15:03: #2 Build Peak Model... INFO @ Sat, 03 Jun 2017 04:15:03: #1 tags after filtering in treatment: 5285357 INFO @ Sat, 03 Jun 2017 04:15:03: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 03 Jun 2017 04:15:03: #1 finished! INFO @ Sat, 03 Jun 2017 04:15:03: #2 Build Peak Model... INFO @ Sat, 03 Jun 2017 04:15:04: #2 number of paired peaks: 3061 INFO @ Sat, 03 Jun 2017 04:15:04: start model_add_line... INFO @ Sat, 03 Jun 2017 04:15:04: #2 number of paired peaks: 3061 INFO @ Sat, 03 Jun 2017 04:15:04: start model_add_line... INFO @ Sat, 03 Jun 2017 04:15:05: #2 number of paired peaks: 3061 INFO @ Sat, 03 Jun 2017 04:15:05: start model_add_line... INFO @ Sat, 03 Jun 2017 04:15:21: start X-correlation... INFO @ Sat, 03 Jun 2017 04:15:21: end of X-cor INFO @ Sat, 03 Jun 2017 04:15:21: #2 finished! INFO @ Sat, 03 Jun 2017 04:15:21: #2 predicted fragment length is 172 bps INFO @ Sat, 03 Jun 2017 04:15:21: #2 alternative fragment length(s) may be 172 bps INFO @ Sat, 03 Jun 2017 04:15:21: #2.2 Generate R script for model : SRX1388761.20_model.r INFO @ Sat, 03 Jun 2017 04:15:21: #3 Call peaks... INFO @ Sat, 03 Jun 2017 04:15:21: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Jun 2017 04:15:22: start X-correlation... INFO @ Sat, 03 Jun 2017 04:15:22: end of X-cor INFO @ Sat, 03 Jun 2017 04:15:22: #2 finished! INFO @ Sat, 03 Jun 2017 04:15:22: #2 predicted fragment length is 172 bps INFO @ Sat, 03 Jun 2017 04:15:22: #2 alternative fragment length(s) may be 172 bps INFO @ Sat, 03 Jun 2017 04:15:22: #2.2 Generate R script for model : SRX1388761.10_model.r INFO @ Sat, 03 Jun 2017 04:15:22: #3 Call peaks... INFO @ Sat, 03 Jun 2017 04:15:22: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Jun 2017 04:15:22: start X-correlation... INFO @ Sat, 03 Jun 2017 04:15:22: end of X-cor INFO @ Sat, 03 Jun 2017 04:15:22: #2 finished! INFO @ Sat, 03 Jun 2017 04:15:22: #2 predicted fragment length is 172 bps INFO @ Sat, 03 Jun 2017 04:15:22: #2 alternative fragment length(s) may be 172 bps INFO @ Sat, 03 Jun 2017 04:15:22: #2.2 Generate R script for model : SRX1388761.05_model.r INFO @ Sat, 03 Jun 2017 04:15:22: #3 Call peaks... INFO @ Sat, 03 Jun 2017 04:15:22: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Jun 2017 04:15:53: #3 Call peaks for each chromosome... INFO @ Sat, 03 Jun 2017 04:15:55: #3 Call peaks for each chromosome... INFO @ Sat, 03 Jun 2017 04:15:55: #3 Call peaks for each chromosome... INFO @ Sat, 03 Jun 2017 04:16:18: #4 Write output xls file... SRX1388761.10_peaks.xls INFO @ Sat, 03 Jun 2017 04:16:18: #4 Write peak in narrowPeak format file... SRX1388761.10_peaks.narrowPeak INFO @ Sat, 03 Jun 2017 04:16:18: #4 Write summits bed file... SRX1388761.10_summits.bed INFO @ Sat, 03 Jun 2017 04:16:18: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (2367 records, 4 fields): 4 millis CompletedMACS2peakCalling INFO @ Sat, 03 Jun 2017 04:16:18: #4 Write output xls file... SRX1388761.20_peaks.xls INFO @ Sat, 03 Jun 2017 04:16:18: #4 Write peak in narrowPeak format file... SRX1388761.20_peaks.narrowPeak INFO @ Sat, 03 Jun 2017 04:16:18: #4 Write summits bed file... SRX1388761.20_summits.bed INFO @ Sat, 03 Jun 2017 04:16:18: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (848 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Sat, 03 Jun 2017 04:16:22: #4 Write output xls file... SRX1388761.05_peaks.xls INFO @ Sat, 03 Jun 2017 04:16:22: #4 Write peak in narrowPeak format file... SRX1388761.05_peaks.narrowPeak INFO @ Sat, 03 Jun 2017 04:16:22: #4 Write summits bed file... SRX1388761.05_summits.bed INFO @ Sat, 03 Jun 2017 04:16:22: Done! pass1 - making usageList (6 chroms): 2 millis pass2 - checking and writing primary data (4202 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。