Job ID = 9028831 sra ファイルのダウンロード中... Completed: 239044K bytes transferred in 5 seconds (380064K 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 14324 0 14324 0 0 1927 0 --:--:-- 0:00:07 --:--:-- 14858 100 54318 0 54318 0 0 6443 0 --:--:-- 0:00:08 --:--:-- 27713 100 68202 0 68202 0 0 7934 0 --:--:-- 0:00:08 --:--:-- 32095 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 7224626 spots for /home/okishinya/chipatlas/results/ce10/SRX982067/SRR1956543.sra Written 7224626 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: 00:01:47 7224626 reads; of these: 7224626 (100.00%) were unpaired; of these: 1276377 (17.67%) aligned 0 times 5059959 (70.04%) aligned exactly 1 time 888290 (12.30%) aligned >1 times 82.33% overall alignment rate Time searching: 00:01:47 Overall time: 00:01:47 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] 795070 / 5948249 = 0.1337 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 11:58:33: # Command line: callpeak -t SRX982067.bam -f BAM -g ce -n SRX982067.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX982067.05 # format = BAM # ChIP-seq file = ['SRX982067.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 11:58:33: #1 read tag files... INFO @ Sat, 03 Jun 2017 11:58:33: #1 read treatment tags... INFO @ Sat, 03 Jun 2017 11:58:33: # Command line: callpeak -t SRX982067.bam -f BAM -g ce -n SRX982067.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX982067.10 # format = BAM # ChIP-seq file = ['SRX982067.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 11:58:33: #1 read tag files... INFO @ Sat, 03 Jun 2017 11:58:33: #1 read treatment tags... INFO @ Sat, 03 Jun 2017 11:58:33: # Command line: callpeak -t SRX982067.bam -f BAM -g ce -n SRX982067.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX982067.20 # format = BAM # ChIP-seq file = ['SRX982067.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 11:58:33: #1 read tag files... INFO @ Sat, 03 Jun 2017 11:58:33: #1 read treatment tags... INFO @ Sat, 03 Jun 2017 11:58:38: 1000000 INFO @ Sat, 03 Jun 2017 11:58:39: 1000000 INFO @ Sat, 03 Jun 2017 11:58:39: 1000000 INFO @ Sat, 03 Jun 2017 11:58:44: 2000000 INFO @ Sat, 03 Jun 2017 11:58:44: 2000000 INFO @ Sat, 03 Jun 2017 11:58:44: 2000000 INFO @ Sat, 03 Jun 2017 11:58:49: 3000000 INFO @ Sat, 03 Jun 2017 11:58:49: 3000000 INFO @ Sat, 03 Jun 2017 11:58:50: 3000000 INFO @ Sat, 03 Jun 2017 11:58:54: 4000000 INFO @ Sat, 03 Jun 2017 11:58:55: 4000000 INFO @ Sat, 03 Jun 2017 11:58:55: 4000000 INFO @ Sat, 03 Jun 2017 11:58:59: 5000000 INFO @ Sat, 03 Jun 2017 11:59:00: #1 tag size is determined as 51 bps INFO @ Sat, 03 Jun 2017 11:59:00: #1 tag size = 51 INFO @ Sat, 03 Jun 2017 11:59:00: #1 total tags in treatment: 5153179 INFO @ Sat, 03 Jun 2017 11:59:00: #1 user defined the maximum tags... INFO @ Sat, 03 Jun 2017 11:59:00: #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 11:59:01: 5000000 INFO @ Sat, 03 Jun 2017 11:59:01: 5000000 INFO @ Sat, 03 Jun 2017 11:59:01: #1 tags after filtering in treatment: 5152587 INFO @ Sat, 03 Jun 2017 11:59:01: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 03 Jun 2017 11:59:01: #1 finished! INFO @ Sat, 03 Jun 2017 11:59:01: #2 Build Peak Model... INFO @ Sat, 03 Jun 2017 11:59:02: #1 tag size is determined as 51 bps INFO @ Sat, 03 Jun 2017 11:59:02: #1 tag size = 51 INFO @ Sat, 03 Jun 2017 11:59:02: #1 total tags in treatment: 5153179 INFO @ Sat, 03 Jun 2017 11:59:02: #1 user defined the maximum tags... INFO @ Sat, 03 Jun 2017 11:59:02: #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 11:59:02: #1 tag size is determined as 51 bps INFO @ Sat, 03 Jun 2017 11:59:02: #1 tag size = 51 INFO @ Sat, 03 Jun 2017 11:59:02: #1 total tags in treatment: 5153179 INFO @ Sat, 03 Jun 2017 11:59:02: #1 user defined the maximum tags... INFO @ Sat, 03 Jun 2017 11:59:02: #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 11:59:02: #2 number of paired peaks: 1640 INFO @ Sat, 03 Jun 2017 11:59:02: start model_add_line... INFO @ Sat, 03 Jun 2017 11:59:02: #1 tags after filtering in treatment: 5152587 INFO @ Sat, 03 Jun 2017 11:59:02: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 03 Jun 2017 11:59:02: #1 finished! INFO @ Sat, 03 Jun 2017 11:59:02: #2 Build Peak Model... INFO @ Sat, 03 Jun 2017 11:59:03: #1 tags after filtering in treatment: 5152587 INFO @ Sat, 03 Jun 2017 11:59:03: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 03 Jun 2017 11:59:03: #1 finished! INFO @ Sat, 03 Jun 2017 11:59:03: #2 Build Peak Model... INFO @ Sat, 03 Jun 2017 11:59:04: #2 number of paired peaks: 1640 INFO @ Sat, 03 Jun 2017 11:59:04: start model_add_line... INFO @ Sat, 03 Jun 2017 11:59:04: #2 number of paired peaks: 1640 INFO @ Sat, 03 Jun 2017 11:59:04: start model_add_line... INFO @ Sat, 03 Jun 2017 11:59:12: start X-correlation... INFO @ Sat, 03 Jun 2017 11:59:12: end of X-cor INFO @ Sat, 03 Jun 2017 11:59:12: #2 finished! INFO @ Sat, 03 Jun 2017 11:59:12: #2 predicted fragment length is 170 bps INFO @ Sat, 03 Jun 2017 11:59:12: #2 alternative fragment length(s) may be 170 bps INFO @ Sat, 03 Jun 2017 11:59:12: #2.2 Generate R script for model : SRX982067.05_model.r INFO @ Sat, 03 Jun 2017 11:59:12: #3 Call peaks... INFO @ Sat, 03 Jun 2017 11:59:12: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Jun 2017 11:59:13: start X-correlation... INFO @ Sat, 03 Jun 2017 11:59:13: end of X-cor INFO @ Sat, 03 Jun 2017 11:59:13: #2 finished! INFO @ Sat, 03 Jun 2017 11:59:13: #2 predicted fragment length is 170 bps INFO @ Sat, 03 Jun 2017 11:59:13: #2 alternative fragment length(s) may be 170 bps INFO @ Sat, 03 Jun 2017 11:59:13: #2.2 Generate R script for model : SRX982067.20_model.r INFO @ Sat, 03 Jun 2017 11:59:13: #3 Call peaks... INFO @ Sat, 03 Jun 2017 11:59:13: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Jun 2017 11:59:14: start X-correlation... INFO @ Sat, 03 Jun 2017 11:59:14: end of X-cor INFO @ Sat, 03 Jun 2017 11:59:14: #2 finished! INFO @ Sat, 03 Jun 2017 11:59:14: #2 predicted fragment length is 170 bps INFO @ Sat, 03 Jun 2017 11:59:14: #2 alternative fragment length(s) may be 170 bps INFO @ Sat, 03 Jun 2017 11:59:14: #2.2 Generate R script for model : SRX982067.10_model.r INFO @ Sat, 03 Jun 2017 11:59:14: #3 Call peaks... INFO @ Sat, 03 Jun 2017 11:59:14: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Jun 2017 11:59:43: #3 Call peaks for each chromosome... INFO @ Sat, 03 Jun 2017 11:59:44: #3 Call peaks for each chromosome... INFO @ Sat, 03 Jun 2017 11:59:49: #3 Call peaks for each chromosome... INFO @ Sat, 03 Jun 2017 12:00:05: #4 Write output xls file... SRX982067.20_peaks.xls INFO @ Sat, 03 Jun 2017 12:00:05: #4 Write peak in narrowPeak format file... SRX982067.20_peaks.narrowPeak INFO @ Sat, 03 Jun 2017 12:00:05: #4 Write summits bed file... SRX982067.20_summits.bed INFO @ Sat, 03 Jun 2017 12:00:05: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (501 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Sat, 03 Jun 2017 12:00:07: #4 Write output xls file... SRX982067.05_peaks.xls INFO @ Sat, 03 Jun 2017 12:00:07: #4 Write peak in narrowPeak format file... SRX982067.05_peaks.narrowPeak INFO @ Sat, 03 Jun 2017 12:00:07: #4 Write summits bed file... SRX982067.05_summits.bed INFO @ Sat, 03 Jun 2017 12:00:07: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (1734 records, 4 fields): 4 millis CompletedMACS2peakCalling INFO @ Sat, 03 Jun 2017 12:00:12: #4 Write output xls file... SRX982067.10_peaks.xls INFO @ Sat, 03 Jun 2017 12:00:12: #4 Write peak in narrowPeak format file... SRX982067.10_peaks.narrowPeak INFO @ Sat, 03 Jun 2017 12:00:12: #4 Write summits bed file... SRX982067.10_summits.bed INFO @ Sat, 03 Jun 2017 12:00:12: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (1109 records, 4 fields): 3 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。