Job ID = 9157408 sra ファイルのダウンロード中... Completed: 459903K bytes transferred in 6 seconds (615384K bits/sec), in 1 file, 2 directories. 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 13827258 spots for /home/okishinya/chipatlas/results/ce10/SRX208772/SRR628906.sra Written 13827258 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: 00:05:28 13827258 reads; of these: 13827258 (100.00%) were unpaired; of these: 1126085 (8.14%) aligned 0 times 10067373 (72.81%) aligned exactly 1 time 2633800 (19.05%) aligned >1 times 91.86% overall alignment rate Time searching: 00:05:28 Overall time: 00:05:28 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_sort_core] merging from 8 files... [bam_rmdupse_core] 9083581 / 12701173 = 0.7152 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 @ Tue, 27 Jun 2017 11:54:32: # Command line: callpeak -t SRX208772.bam -f BAM -g ce -n SRX208772.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX208772.10 # format = BAM # ChIP-seq file = ['SRX208772.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 # Paired-End mode is off INFO @ Tue, 27 Jun 2017 11:54:32: #1 read tag files... INFO @ Tue, 27 Jun 2017 11:54:32: #1 read treatment tags... INFO @ Tue, 27 Jun 2017 11:54:32: # Command line: callpeak -t SRX208772.bam -f BAM -g ce -n SRX208772.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX208772.20 # format = BAM # ChIP-seq file = ['SRX208772.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 # Paired-End mode is off INFO @ Tue, 27 Jun 2017 11:54:32: #1 read tag files... INFO @ Tue, 27 Jun 2017 11:54:32: # Command line: callpeak -t SRX208772.bam -f BAM -g ce -n SRX208772.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX208772.05 # format = BAM # ChIP-seq file = ['SRX208772.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 # Paired-End mode is off INFO @ Tue, 27 Jun 2017 11:54:32: #1 read treatment tags... INFO @ Tue, 27 Jun 2017 11:54:32: #1 read tag files... INFO @ Tue, 27 Jun 2017 11:54:32: #1 read treatment tags... INFO @ Tue, 27 Jun 2017 11:54:40: 1000000 INFO @ Tue, 27 Jun 2017 11:54:40: 1000000 INFO @ Tue, 27 Jun 2017 11:54:40: 1000000 INFO @ Tue, 27 Jun 2017 11:54:48: 2000000 INFO @ Tue, 27 Jun 2017 11:54:48: 2000000 INFO @ Tue, 27 Jun 2017 11:54:48: 2000000 INFO @ Tue, 27 Jun 2017 11:54:56: 3000000 INFO @ Tue, 27 Jun 2017 11:54:56: 3000000 INFO @ Tue, 27 Jun 2017 11:54:56: 3000000 INFO @ Tue, 27 Jun 2017 11:55:01: #1 tag size is determined as 50 bps INFO @ Tue, 27 Jun 2017 11:55:01: #1 tag size = 50 INFO @ Tue, 27 Jun 2017 11:55:01: #1 total tags in treatment: 3617592 INFO @ Tue, 27 Jun 2017 11:55:01: #1 user defined the maximum tags... INFO @ Tue, 27 Jun 2017 11:55:01: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 27 Jun 2017 11:55:01: #1 tag size is determined as 50 bps INFO @ Tue, 27 Jun 2017 11:55:01: #1 tag size = 50 INFO @ Tue, 27 Jun 2017 11:55:01: #1 total tags in treatment: 3617592 INFO @ Tue, 27 Jun 2017 11:55:01: #1 user defined the maximum tags... INFO @ Tue, 27 Jun 2017 11:55:01: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 27 Jun 2017 11:55:01: #1 tag size is determined as 50 bps INFO @ Tue, 27 Jun 2017 11:55:01: #1 tag size = 50 INFO @ Tue, 27 Jun 2017 11:55:01: #1 total tags in treatment: 3617592 INFO @ Tue, 27 Jun 2017 11:55:01: #1 user defined the maximum tags... INFO @ Tue, 27 Jun 2017 11:55:01: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 27 Jun 2017 11:55:01: #1 tags after filtering in treatment: 3617592 INFO @ Tue, 27 Jun 2017 11:55:01: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 27 Jun 2017 11:55:01: #1 finished! INFO @ Tue, 27 Jun 2017 11:55:01: #2 Build Peak Model... INFO @ Tue, 27 Jun 2017 11:55:01: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 27 Jun 2017 11:55:01: #1 tags after filtering in treatment: 3617592 INFO @ Tue, 27 Jun 2017 11:55:01: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 27 Jun 2017 11:55:01: #1 finished! INFO @ Tue, 27 Jun 2017 11:55:01: #2 Build Peak Model... INFO @ Tue, 27 Jun 2017 11:55:01: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 27 Jun 2017 11:55:01: #1 tags after filtering in treatment: 3617592 INFO @ Tue, 27 Jun 2017 11:55:01: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 27 Jun 2017 11:55:01: #1 finished! INFO @ Tue, 27 Jun 2017 11:55:01: #2 Build Peak Model... INFO @ Tue, 27 Jun 2017 11:55:01: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 27 Jun 2017 11:55:01: #2 number of paired peaks: 1754 INFO @ Tue, 27 Jun 2017 11:55:01: start model_add_line... INFO @ Tue, 27 Jun 2017 11:55:01: #2 number of paired peaks: 1754 INFO @ Tue, 27 Jun 2017 11:55:01: start model_add_line... INFO @ Tue, 27 Jun 2017 11:55:01: #2 number of paired peaks: 1754 INFO @ Tue, 27 Jun 2017 11:55:01: start model_add_line... INFO @ Tue, 27 Jun 2017 11:55:01: start X-correlation... INFO @ Tue, 27 Jun 2017 11:55:01: start X-correlation... INFO @ Tue, 27 Jun 2017 11:55:01: end of X-cor INFO @ Tue, 27 Jun 2017 11:55:01: end of X-cor INFO @ Tue, 27 Jun 2017 11:55:01: #2 finished! INFO @ Tue, 27 Jun 2017 11:55:01: #2 finished! INFO @ Tue, 27 Jun 2017 11:55:01: #2 predicted fragment length is 318 bps INFO @ Tue, 27 Jun 2017 11:55:01: #2 predicted fragment length is 318 bps INFO @ Tue, 27 Jun 2017 11:55:01: #2 alternative fragment length(s) may be 318 bps INFO @ Tue, 27 Jun 2017 11:55:01: #2 alternative fragment length(s) may be 318 bps INFO @ Tue, 27 Jun 2017 11:55:01: #2.2 Generate R script for model : SRX208772.05_model.r INFO @ Tue, 27 Jun 2017 11:55:01: #2.2 Generate R script for model : SRX208772.10_model.r INFO @ Tue, 27 Jun 2017 11:55:02: start X-correlation... INFO @ Tue, 27 Jun 2017 11:55:02: #3 Call peaks... INFO @ Tue, 27 Jun 2017 11:55:02: #3 Call peaks... INFO @ Tue, 27 Jun 2017 11:55:02: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 27 Jun 2017 11:55:02: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 27 Jun 2017 11:55:02: end of X-cor INFO @ Tue, 27 Jun 2017 11:55:02: #2 finished! INFO @ Tue, 27 Jun 2017 11:55:02: #2 predicted fragment length is 318 bps INFO @ Tue, 27 Jun 2017 11:55:02: #2 alternative fragment length(s) may be 318 bps INFO @ Tue, 27 Jun 2017 11:55:02: #2.2 Generate R script for model : SRX208772.20_model.r INFO @ Tue, 27 Jun 2017 11:55:02: #3 Call peaks... INFO @ Tue, 27 Jun 2017 11:55:02: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 27 Jun 2017 11:55:12: #3 Call peaks for each chromosome... INFO @ Tue, 27 Jun 2017 11:55:13: #3 Call peaks for each chromosome... INFO @ Tue, 27 Jun 2017 11:55:13: #3 Call peaks for each chromosome... INFO @ Tue, 27 Jun 2017 11:55:18: #4 Write output xls file... SRX208772.10_peaks.xls INFO @ Tue, 27 Jun 2017 11:55:18: #4 Write peak in narrowPeak format file... SRX208772.10_peaks.narrowPeak INFO @ Tue, 27 Jun 2017 11:55:18: #4 Write summits bed file... SRX208772.10_summits.bed INFO @ Tue, 27 Jun 2017 11:55:18: Done! pass1 - making usageList (7 chroms): 0 millis pass2 - checking and writing primary data (1411 records, 4 fields): 4 millis CompletedMACS2peakCalling INFO @ Tue, 27 Jun 2017 11:55:18: #4 Write output xls file... SRX208772.05_peaks.xls INFO @ Tue, 27 Jun 2017 11:55:18: #4 Write peak in narrowPeak format file... SRX208772.05_peaks.narrowPeak INFO @ Tue, 27 Jun 2017 11:55:18: #4 Write summits bed file... SRX208772.05_summits.bed INFO @ Tue, 27 Jun 2017 11:55:18: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (1776 records, 4 fields): 4 millis CompletedMACS2peakCalling INFO @ Tue, 27 Jun 2017 11:55:18: #4 Write output xls file... SRX208772.20_peaks.xls INFO @ Tue, 27 Jun 2017 11:55:18: #4 Write peak in narrowPeak format file... SRX208772.20_peaks.narrowPeak INFO @ Tue, 27 Jun 2017 11:55:18: #4 Write summits bed file... SRX208772.20_summits.bed INFO @ Tue, 27 Jun 2017 11:55:18: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (1104 records, 4 fields): 2 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。