Job ID = 9025620 sra ファイルのダウンロード中... Completed: 191842K bytes transferred in 5 seconds (310813K 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 0 970 0 --:--:-- 0:00:07 --:--:-- 9750 100 30245 0 30245 0 0 3808 0 --:--:-- 0:00:07 --:--:-- 19652 100 46435 0 46435 0 0 5612 0 --:--:-- 0:00:08 --:--:-- 24818 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 6972845 spots for /home/okishinya/chipatlas/results/ce10/SRX208756/SRR628890.sra Written 6972845 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: 00:02:42 6972845 reads; of these: 6972845 (100.00%) were unpaired; of these: 835398 (11.98%) aligned 0 times 5303813 (76.06%) aligned exactly 1 time 833634 (11.96%) aligned >1 times 88.02% overall alignment rate Time searching: 00:02:42 Overall time: 00:02:42 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] 2355122 / 6137447 = 0.3837 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 04:40:01: # Command line: callpeak -t SRX208756.bam -f BAM -g ce -n SRX208756.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX208756.05 # format = BAM # ChIP-seq file = ['SRX208756.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 04:40:01: #1 read tag files... INFO @ Sat, 03 Jun 2017 04:40:01: #1 read treatment tags... INFO @ Sat, 03 Jun 2017 04:40:01: # Command line: callpeak -t SRX208756.bam -f BAM -g ce -n SRX208756.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX208756.20 # format = BAM # ChIP-seq file = ['SRX208756.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 04:40:01: #1 read tag files... INFO @ Sat, 03 Jun 2017 04:40:01: #1 read treatment tags... INFO @ Sat, 03 Jun 2017 04:40:01: # Command line: callpeak -t SRX208756.bam -f BAM -g ce -n SRX208756.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX208756.10 # format = BAM # ChIP-seq file = ['SRX208756.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 04:40:01: #1 read tag files... INFO @ Sat, 03 Jun 2017 04:40:01: #1 read treatment tags... INFO @ Sat, 03 Jun 2017 04:40:07: 1000000 INFO @ Sat, 03 Jun 2017 04:40:07: 1000000 INFO @ Sat, 03 Jun 2017 04:40:07: 1000000 INFO @ Sat, 03 Jun 2017 04:40:13: 2000000 INFO @ Sat, 03 Jun 2017 04:40:13: 2000000 INFO @ Sat, 03 Jun 2017 04:40:14: 2000000 INFO @ Sat, 03 Jun 2017 04:40:20: 3000000 INFO @ Sat, 03 Jun 2017 04:40:20: 3000000 INFO @ Sat, 03 Jun 2017 04:40:21: 3000000 INFO @ Sat, 03 Jun 2017 04:40:25: #1 tag size is determined as 50 bps INFO @ Sat, 03 Jun 2017 04:40:25: #1 tag size = 50 INFO @ Sat, 03 Jun 2017 04:40:25: #1 total tags in treatment: 3782325 INFO @ Sat, 03 Jun 2017 04:40:25: #1 user defined the maximum tags... INFO @ Sat, 03 Jun 2017 04:40:25: #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 04:40:25: #1 tag size is determined as 50 bps INFO @ Sat, 03 Jun 2017 04:40:25: #1 tag size = 50 INFO @ Sat, 03 Jun 2017 04:40:25: #1 total tags in treatment: 3782325 INFO @ Sat, 03 Jun 2017 04:40:25: #1 user defined the maximum tags... INFO @ Sat, 03 Jun 2017 04:40:25: #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 04:40:26: #1 tags after filtering in treatment: 3766047 INFO @ Sat, 03 Jun 2017 04:40:26: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 03 Jun 2017 04:40:26: #1 finished! INFO @ Sat, 03 Jun 2017 04:40:26: #2 Build Peak Model... INFO @ Sat, 03 Jun 2017 04:40:26: #1 tags after filtering in treatment: 3766047 INFO @ Sat, 03 Jun 2017 04:40:26: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 03 Jun 2017 04:40:26: #1 finished! INFO @ Sat, 03 Jun 2017 04:40:26: #2 Build Peak Model... INFO @ Sat, 03 Jun 2017 04:40:26: #1 tag size is determined as 50 bps INFO @ Sat, 03 Jun 2017 04:40:26: #1 tag size = 50 INFO @ Sat, 03 Jun 2017 04:40:26: #1 total tags in treatment: 3782325 INFO @ Sat, 03 Jun 2017 04:40:26: #1 user defined the maximum tags... INFO @ Sat, 03 Jun 2017 04:40:26: #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 04:40:27: #2 number of paired peaks: 3009 INFO @ Sat, 03 Jun 2017 04:40:27: start model_add_line... INFO @ Sat, 03 Jun 2017 04:40:27: #2 number of paired peaks: 3009 INFO @ Sat, 03 Jun 2017 04:40:27: start model_add_line... INFO @ Sat, 03 Jun 2017 04:40:27: #1 tags after filtering in treatment: 3766047 INFO @ Sat, 03 Jun 2017 04:40:27: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 03 Jun 2017 04:40:27: #1 finished! INFO @ Sat, 03 Jun 2017 04:40:27: #2 Build Peak Model... INFO @ Sat, 03 Jun 2017 04:40:28: #2 number of paired peaks: 3009 INFO @ Sat, 03 Jun 2017 04:40:28: start model_add_line... INFO @ Sat, 03 Jun 2017 04:40:37: start X-correlation... INFO @ Sat, 03 Jun 2017 04:40:37: end of X-cor INFO @ Sat, 03 Jun 2017 04:40:37: #2 finished! INFO @ Sat, 03 Jun 2017 04:40:37: #2 predicted fragment length is 292 bps INFO @ Sat, 03 Jun 2017 04:40:37: #2 alternative fragment length(s) may be 292 bps INFO @ Sat, 03 Jun 2017 04:40:37: #2.2 Generate R script for model : SRX208756.05_model.r INFO @ Sat, 03 Jun 2017 04:40:37: #3 Call peaks... INFO @ Sat, 03 Jun 2017 04:40:37: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Jun 2017 04:40:37: start X-correlation... INFO @ Sat, 03 Jun 2017 04:40:37: end of X-cor INFO @ Sat, 03 Jun 2017 04:40:37: #2 finished! INFO @ Sat, 03 Jun 2017 04:40:37: #2 predicted fragment length is 292 bps INFO @ Sat, 03 Jun 2017 04:40:37: #2 alternative fragment length(s) may be 292 bps INFO @ Sat, 03 Jun 2017 04:40:37: #2.2 Generate R script for model : SRX208756.10_model.r INFO @ Sat, 03 Jun 2017 04:40:37: #3 Call peaks... INFO @ Sat, 03 Jun 2017 04:40:37: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Jun 2017 04:40:38: start X-correlation... INFO @ Sat, 03 Jun 2017 04:40:38: end of X-cor INFO @ Sat, 03 Jun 2017 04:40:38: #2 finished! INFO @ Sat, 03 Jun 2017 04:40:38: #2 predicted fragment length is 292 bps INFO @ Sat, 03 Jun 2017 04:40:38: #2 alternative fragment length(s) may be 292 bps INFO @ Sat, 03 Jun 2017 04:40:38: #2.2 Generate R script for model : SRX208756.20_model.r INFO @ Sat, 03 Jun 2017 04:40:38: #3 Call peaks... INFO @ Sat, 03 Jun 2017 04:40:38: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Jun 2017 04:41:01: #3 Call peaks for each chromosome... INFO @ Sat, 03 Jun 2017 04:41:02: #3 Call peaks for each chromosome... INFO @ Sat, 03 Jun 2017 04:41:04: #3 Call peaks for each chromosome... INFO @ Sat, 03 Jun 2017 04:41:21: #4 Write output xls file... SRX208756.20_peaks.xls INFO @ Sat, 03 Jun 2017 04:41:21: #4 Write peak in narrowPeak format file... SRX208756.20_peaks.narrowPeak INFO @ Sat, 03 Jun 2017 04:41:21: #4 Write summits bed file... SRX208756.20_summits.bed INFO @ Sat, 03 Jun 2017 04:41:21: Done! pass1 - making usageList (6 chroms): 9 millis pass2 - checking and writing primary data (456 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Sat, 03 Jun 2017 04:41:21: #4 Write output xls file... SRX208756.10_peaks.xls INFO @ Sat, 03 Jun 2017 04:41:21: #4 Write peak in narrowPeak format file... SRX208756.10_peaks.narrowPeak INFO @ Sat, 03 Jun 2017 04:41:21: #4 Write summits bed file... SRX208756.10_summits.bed INFO @ Sat, 03 Jun 2017 04:41:21: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (1863 records, 4 fields): 4 millis CompletedMACS2peakCalling INFO @ Sat, 03 Jun 2017 04:41:26: #4 Write output xls file... SRX208756.05_peaks.xls INFO @ Sat, 03 Jun 2017 04:41:26: #4 Write peak in narrowPeak format file... SRX208756.05_peaks.narrowPeak INFO @ Sat, 03 Jun 2017 04:41:26: #4 Write summits bed file... SRX208756.05_summits.bed INFO @ Sat, 03 Jun 2017 04:41:26: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (4712 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。