Job ID = 10609061 sra ファイルのダウンロード中... Completed: 272397K bytes transferred in 27 seconds (82538K bits/sec), in 1 file. 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... Read 24890077 spots for /home/okishinya/chipatlas/results/ce10/SRX2202788/SRR4319294.sra Written 24890077 spots for /home/okishinya/chipatlas/results/ce10/SRX2202788/SRR4319294.sra rm: cannot remove `[DSE]RX*': そのようなファイルやディレクトリはありません 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: 00:06:45 24890077 reads; of these: 24890077 (100.00%) were unpaired; of these: 3597573 (14.45%) aligned 0 times 10585814 (42.53%) aligned exactly 1 time 10706690 (43.02%) aligned >1 times 85.55% overall alignment rate Time searching: 00:06:45 Overall time: 00:06:45 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 12 files... [bam_rmdupse_core] 10124305 / 21292504 = 0.4755 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 @ Fri, 04 May 2018 07:14:16: # Command line: callpeak -t SRX2202788.bam -f BAM -g ce -n SRX2202788.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX2202788.10 # format = BAM # ChIP-seq file = ['SRX2202788.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 @ Fri, 04 May 2018 07:14:16: #1 read tag files... INFO @ Fri, 04 May 2018 07:14:16: #1 read treatment tags... INFO @ Fri, 04 May 2018 07:14:16: # Command line: callpeak -t SRX2202788.bam -f BAM -g ce -n SRX2202788.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX2202788.20 # format = BAM # ChIP-seq file = ['SRX2202788.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 @ Fri, 04 May 2018 07:14:16: #1 read tag files... INFO @ Fri, 04 May 2018 07:14:16: #1 read treatment tags... INFO @ Fri, 04 May 2018 07:14:16: # Command line: callpeak -t SRX2202788.bam -f BAM -g ce -n SRX2202788.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX2202788.05 # format = BAM # ChIP-seq file = ['SRX2202788.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 @ Fri, 04 May 2018 07:14:16: #1 read tag files... INFO @ Fri, 04 May 2018 07:14:16: #1 read treatment tags... INFO @ Fri, 04 May 2018 07:14:22: 1000000 INFO @ Fri, 04 May 2018 07:14:23: 1000000 INFO @ Fri, 04 May 2018 07:14:23: 1000000 INFO @ Fri, 04 May 2018 07:14:29: 2000000 INFO @ Fri, 04 May 2018 07:14:29: 2000000 INFO @ Fri, 04 May 2018 07:14:29: 2000000 INFO @ Fri, 04 May 2018 07:14:35: 3000000 INFO @ Fri, 04 May 2018 07:14:36: 3000000 INFO @ Fri, 04 May 2018 07:14:36: 3000000 INFO @ Fri, 04 May 2018 07:14:41: 4000000 INFO @ Fri, 04 May 2018 07:14:43: 4000000 INFO @ Fri, 04 May 2018 07:14:43: 4000000 INFO @ Fri, 04 May 2018 07:14:48: 5000000 INFO @ Fri, 04 May 2018 07:14:50: 5000000 INFO @ Fri, 04 May 2018 07:14:50: 5000000 INFO @ Fri, 04 May 2018 07:14:54: 6000000 INFO @ Fri, 04 May 2018 07:14:57: 6000000 INFO @ Fri, 04 May 2018 07:14:57: 6000000 INFO @ Fri, 04 May 2018 07:15:01: 7000000 INFO @ Fri, 04 May 2018 07:15:03: 7000000 INFO @ Fri, 04 May 2018 07:15:03: 7000000 INFO @ Fri, 04 May 2018 07:15:07: 8000000 INFO @ Fri, 04 May 2018 07:15:10: 8000000 INFO @ Fri, 04 May 2018 07:15:10: 8000000 INFO @ Fri, 04 May 2018 07:15:14: 9000000 INFO @ Fri, 04 May 2018 07:15:17: 9000000 INFO @ Fri, 04 May 2018 07:15:17: 9000000 INFO @ Fri, 04 May 2018 07:15:20: 10000000 INFO @ Fri, 04 May 2018 07:15:24: 10000000 INFO @ Fri, 04 May 2018 07:15:24: 10000000 INFO @ Fri, 04 May 2018 07:15:27: 11000000 INFO @ Fri, 04 May 2018 07:15:28: #1 tag size is determined as 51 bps INFO @ Fri, 04 May 2018 07:15:28: #1 tag size = 51 INFO @ Fri, 04 May 2018 07:15:28: #1 total tags in treatment: 11168199 INFO @ Fri, 04 May 2018 07:15:28: #1 user defined the maximum tags... INFO @ Fri, 04 May 2018 07:15:28: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 04 May 2018 07:15:28: #1 tags after filtering in treatment: 11168199 INFO @ Fri, 04 May 2018 07:15:28: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 04 May 2018 07:15:28: #1 finished! INFO @ Fri, 04 May 2018 07:15:28: #2 Build Peak Model... INFO @ Fri, 04 May 2018 07:15:28: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 04 May 2018 07:15:29: #2 number of paired peaks: 1969 INFO @ Fri, 04 May 2018 07:15:29: start model_add_line... INFO @ Fri, 04 May 2018 07:15:29: start X-correlation... INFO @ Fri, 04 May 2018 07:15:29: end of X-cor INFO @ Fri, 04 May 2018 07:15:29: #2 finished! INFO @ Fri, 04 May 2018 07:15:29: #2 predicted fragment length is 141 bps INFO @ Fri, 04 May 2018 07:15:29: #2 alternative fragment length(s) may be 141 bps INFO @ Fri, 04 May 2018 07:15:29: #2.2 Generate R script for model : SRX2202788.05_model.r INFO @ Fri, 04 May 2018 07:15:29: #3 Call peaks... INFO @ Fri, 04 May 2018 07:15:29: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 04 May 2018 07:15:30: 11000000 INFO @ Fri, 04 May 2018 07:15:30: 11000000 INFO @ Fri, 04 May 2018 07:15:31: #1 tag size is determined as 51 bps INFO @ Fri, 04 May 2018 07:15:31: #1 tag size = 51 INFO @ Fri, 04 May 2018 07:15:31: #1 total tags in treatment: 11168199 INFO @ Fri, 04 May 2018 07:15:31: #1 user defined the maximum tags... INFO @ Fri, 04 May 2018 07:15:31: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 04 May 2018 07:15:31: #1 tag size is determined as 51 bps INFO @ Fri, 04 May 2018 07:15:31: #1 tag size = 51 INFO @ Fri, 04 May 2018 07:15:31: #1 total tags in treatment: 11168199 INFO @ Fri, 04 May 2018 07:15:31: #1 user defined the maximum tags... INFO @ Fri, 04 May 2018 07:15:31: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 04 May 2018 07:15:31: #1 tags after filtering in treatment: 11168199 INFO @ Fri, 04 May 2018 07:15:31: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 04 May 2018 07:15:31: #1 finished! INFO @ Fri, 04 May 2018 07:15:31: #2 Build Peak Model... INFO @ Fri, 04 May 2018 07:15:31: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 04 May 2018 07:15:31: #1 tags after filtering in treatment: 11168199 INFO @ Fri, 04 May 2018 07:15:31: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 04 May 2018 07:15:31: #1 finished! INFO @ Fri, 04 May 2018 07:15:31: #2 Build Peak Model... INFO @ Fri, 04 May 2018 07:15:31: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 04 May 2018 07:15:32: #2 number of paired peaks: 1969 INFO @ Fri, 04 May 2018 07:15:32: start model_add_line... INFO @ Fri, 04 May 2018 07:15:33: start X-correlation... INFO @ Fri, 04 May 2018 07:15:33: end of X-cor INFO @ Fri, 04 May 2018 07:15:33: #2 finished! INFO @ Fri, 04 May 2018 07:15:33: #2 predicted fragment length is 141 bps INFO @ Fri, 04 May 2018 07:15:33: #2 alternative fragment length(s) may be 141 bps INFO @ Fri, 04 May 2018 07:15:33: #2.2 Generate R script for model : SRX2202788.20_model.r INFO @ Fri, 04 May 2018 07:15:33: #3 Call peaks... INFO @ Fri, 04 May 2018 07:15:33: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 04 May 2018 07:15:33: #2 number of paired peaks: 1969 INFO @ Fri, 04 May 2018 07:15:33: start model_add_line... INFO @ Fri, 04 May 2018 07:15:33: start X-correlation... INFO @ Fri, 04 May 2018 07:15:33: end of X-cor INFO @ Fri, 04 May 2018 07:15:33: #2 finished! INFO @ Fri, 04 May 2018 07:15:33: #2 predicted fragment length is 141 bps INFO @ Fri, 04 May 2018 07:15:33: #2 alternative fragment length(s) may be 141 bps INFO @ Fri, 04 May 2018 07:15:33: #2.2 Generate R script for model : SRX2202788.10_model.r INFO @ Fri, 04 May 2018 07:15:33: #3 Call peaks... INFO @ Fri, 04 May 2018 07:15:33: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 04 May 2018 07:16:00: #3 Call peaks for each chromosome... INFO @ Fri, 04 May 2018 07:16:03: #3 Call peaks for each chromosome... INFO @ Fri, 04 May 2018 07:16:05: #3 Call peaks for each chromosome... INFO @ Fri, 04 May 2018 07:16:14: #4 Write output xls file... SRX2202788.05_peaks.xls INFO @ Fri, 04 May 2018 07:16:14: #4 Write peak in narrowPeak format file... SRX2202788.05_peaks.narrowPeak INFO @ Fri, 04 May 2018 07:16:14: #4 Write summits bed file... SRX2202788.05_summits.bed INFO @ Fri, 04 May 2018 07:16:14: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (7630 records, 4 fields): 12 millis CompletedMACS2peakCalling INFO @ Fri, 04 May 2018 07:16:19: #4 Write output xls file... SRX2202788.20_peaks.xls INFO @ Fri, 04 May 2018 07:16:19: #4 Write peak in narrowPeak format file... SRX2202788.20_peaks.narrowPeak INFO @ Fri, 04 May 2018 07:16:19: #4 Write summits bed file... SRX2202788.20_summits.bed INFO @ Fri, 04 May 2018 07:16:19: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (2986 records, 4 fields): 5 millis CompletedMACS2peakCalling INFO @ Fri, 04 May 2018 07:16:20: #4 Write output xls file... SRX2202788.10_peaks.xls INFO @ Fri, 04 May 2018 07:16:20: #4 Write peak in narrowPeak format file... SRX2202788.10_peaks.narrowPeak INFO @ Fri, 04 May 2018 07:16:20: #4 Write summits bed file... SRX2202788.10_summits.bed INFO @ Fri, 04 May 2018 07:16:20: Done! pass1 - making usageList (7 chroms): 2 millis pass2 - checking and writing primary data (5004 records, 4 fields): 7 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。