Job ID = 10714375 sra ファイルのダウンロード中... Completed: 386856K bytes transferred in 28 seconds (111251K 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 19108035 spots for /home/okishinya/chipatlas/results/ce10/SRX4082335/SRR7164153.sra Written 19108035 spots for /home/okishinya/chipatlas/results/ce10/SRX4082335/SRR7164153.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: 00:04:40 19108035 reads; of these: 19108035 (100.00%) were unpaired; of these: 558344 (2.92%) aligned 0 times 16712858 (87.47%) aligned exactly 1 time 1836833 (9.61%) aligned >1 times 97.08% overall alignment rate Time searching: 00:04:40 Overall time: 00:04:40 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] 9040696 / 18549691 = 0.4874 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 @ Sun, 03 Jun 2018 12:37:23: # Command line: callpeak -t SRX4082335.bam -f BAM -g ce -n SRX4082335.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX4082335.05 # format = BAM # ChIP-seq file = ['SRX4082335.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 @ Sun, 03 Jun 2018 12:37:23: #1 read tag files... INFO @ Sun, 03 Jun 2018 12:37:23: #1 read treatment tags... INFO @ Sun, 03 Jun 2018 12:37:23: # Command line: callpeak -t SRX4082335.bam -f BAM -g ce -n SRX4082335.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX4082335.20 # format = BAM # ChIP-seq file = ['SRX4082335.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 @ Sun, 03 Jun 2018 12:37:23: #1 read tag files... INFO @ Sun, 03 Jun 2018 12:37:23: #1 read treatment tags... INFO @ Sun, 03 Jun 2018 12:37:23: # Command line: callpeak -t SRX4082335.bam -f BAM -g ce -n SRX4082335.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX4082335.10 # format = BAM # ChIP-seq file = ['SRX4082335.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 @ Sun, 03 Jun 2018 12:37:23: #1 read tag files... INFO @ Sun, 03 Jun 2018 12:37:23: #1 read treatment tags... INFO @ Sun, 03 Jun 2018 12:37:30: 1000000 INFO @ Sun, 03 Jun 2018 12:37:30: 1000000 INFO @ Sun, 03 Jun 2018 12:37:30: 1000000 INFO @ Sun, 03 Jun 2018 12:37:36: 2000000 INFO @ Sun, 03 Jun 2018 12:37:37: 2000000 INFO @ Sun, 03 Jun 2018 12:37:37: 2000000 INFO @ Sun, 03 Jun 2018 12:37:43: 3000000 INFO @ Sun, 03 Jun 2018 12:37:43: 3000000 INFO @ Sun, 03 Jun 2018 12:37:43: 3000000 INFO @ Sun, 03 Jun 2018 12:37:50: 4000000 INFO @ Sun, 03 Jun 2018 12:37:50: 4000000 INFO @ Sun, 03 Jun 2018 12:37:50: 4000000 INFO @ Sun, 03 Jun 2018 12:37:57: 5000000 INFO @ Sun, 03 Jun 2018 12:37:57: 5000000 INFO @ Sun, 03 Jun 2018 12:37:57: 5000000 INFO @ Sun, 03 Jun 2018 12:38:03: 6000000 INFO @ Sun, 03 Jun 2018 12:38:04: 6000000 INFO @ Sun, 03 Jun 2018 12:38:04: 6000000 INFO @ Sun, 03 Jun 2018 12:38:10: 7000000 INFO @ Sun, 03 Jun 2018 12:38:11: 7000000 INFO @ Sun, 03 Jun 2018 12:38:11: 7000000 INFO @ Sun, 03 Jun 2018 12:38:17: 8000000 INFO @ Sun, 03 Jun 2018 12:38:18: 8000000 INFO @ Sun, 03 Jun 2018 12:38:18: 8000000 INFO @ Sun, 03 Jun 2018 12:38:23: 9000000 INFO @ Sun, 03 Jun 2018 12:38:24: 9000000 INFO @ Sun, 03 Jun 2018 12:38:24: 9000000 INFO @ Sun, 03 Jun 2018 12:38:27: #1 tag size is determined as 50 bps INFO @ Sun, 03 Jun 2018 12:38:27: #1 tag size = 50 INFO @ Sun, 03 Jun 2018 12:38:27: #1 total tags in treatment: 9508995 INFO @ Sun, 03 Jun 2018 12:38:27: #1 user defined the maximum tags... INFO @ Sun, 03 Jun 2018 12:38:27: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sun, 03 Jun 2018 12:38:27: #1 tags after filtering in treatment: 9508995 INFO @ Sun, 03 Jun 2018 12:38:27: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 03 Jun 2018 12:38:27: #1 finished! INFO @ Sun, 03 Jun 2018 12:38:27: #2 Build Peak Model... INFO @ Sun, 03 Jun 2018 12:38:27: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 03 Jun 2018 12:38:28: #1 tag size is determined as 50 bps INFO @ Sun, 03 Jun 2018 12:38:28: #1 tag size = 50 INFO @ Sun, 03 Jun 2018 12:38:28: #1 total tags in treatment: 9508995 INFO @ Sun, 03 Jun 2018 12:38:28: #1 user defined the maximum tags... INFO @ Sun, 03 Jun 2018 12:38:28: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sun, 03 Jun 2018 12:38:28: #1 tag size is determined as 50 bps INFO @ Sun, 03 Jun 2018 12:38:28: #1 tag size = 50 INFO @ Sun, 03 Jun 2018 12:38:28: #1 total tags in treatment: 9508995 INFO @ Sun, 03 Jun 2018 12:38:28: #1 user defined the maximum tags... INFO @ Sun, 03 Jun 2018 12:38:28: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sun, 03 Jun 2018 12:38:28: #1 tags after filtering in treatment: 9508995 INFO @ Sun, 03 Jun 2018 12:38:28: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 03 Jun 2018 12:38:28: #1 finished! INFO @ Sun, 03 Jun 2018 12:38:28: #2 Build Peak Model... INFO @ Sun, 03 Jun 2018 12:38:28: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 03 Jun 2018 12:38:28: #1 tags after filtering in treatment: 9508995 INFO @ Sun, 03 Jun 2018 12:38:28: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 03 Jun 2018 12:38:28: #1 finished! INFO @ Sun, 03 Jun 2018 12:38:28: #2 Build Peak Model... INFO @ Sun, 03 Jun 2018 12:38:28: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 03 Jun 2018 12:38:28: #2 number of paired peaks: 5536 INFO @ Sun, 03 Jun 2018 12:38:28: start model_add_line... INFO @ Sun, 03 Jun 2018 12:38:28: start X-correlation... INFO @ Sun, 03 Jun 2018 12:38:28: end of X-cor INFO @ Sun, 03 Jun 2018 12:38:28: #2 finished! INFO @ Sun, 03 Jun 2018 12:38:28: #2 predicted fragment length is 123 bps INFO @ Sun, 03 Jun 2018 12:38:28: #2 alternative fragment length(s) may be 123 bps INFO @ Sun, 03 Jun 2018 12:38:28: #2.2 Generate R script for model : SRX4082335.20_model.r INFO @ Sun, 03 Jun 2018 12:38:28: #3 Call peaks... INFO @ Sun, 03 Jun 2018 12:38:28: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 03 Jun 2018 12:38:29: #2 number of paired peaks: 5536 INFO @ Sun, 03 Jun 2018 12:38:29: start model_add_line... INFO @ Sun, 03 Jun 2018 12:38:29: #2 number of paired peaks: 5536 INFO @ Sun, 03 Jun 2018 12:38:29: start model_add_line... INFO @ Sun, 03 Jun 2018 12:38:29: start X-correlation... INFO @ Sun, 03 Jun 2018 12:38:29: end of X-cor INFO @ Sun, 03 Jun 2018 12:38:29: #2 finished! INFO @ Sun, 03 Jun 2018 12:38:29: #2 predicted fragment length is 123 bps INFO @ Sun, 03 Jun 2018 12:38:29: #2 alternative fragment length(s) may be 123 bps INFO @ Sun, 03 Jun 2018 12:38:29: #2.2 Generate R script for model : SRX4082335.05_model.r INFO @ Sun, 03 Jun 2018 12:38:29: start X-correlation... INFO @ Sun, 03 Jun 2018 12:38:29: end of X-cor INFO @ Sun, 03 Jun 2018 12:38:29: #2 finished! INFO @ Sun, 03 Jun 2018 12:38:29: #2 predicted fragment length is 123 bps INFO @ Sun, 03 Jun 2018 12:38:29: #2 alternative fragment length(s) may be 123 bps INFO @ Sun, 03 Jun 2018 12:38:29: #2.2 Generate R script for model : SRX4082335.10_model.r INFO @ Sun, 03 Jun 2018 12:38:29: #3 Call peaks... INFO @ Sun, 03 Jun 2018 12:38:29: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 03 Jun 2018 12:38:29: #3 Call peaks... INFO @ Sun, 03 Jun 2018 12:38:29: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 03 Jun 2018 12:38:53: #3 Call peaks for each chromosome... INFO @ Sun, 03 Jun 2018 12:38:53: #3 Call peaks for each chromosome... INFO @ Sun, 03 Jun 2018 12:38:54: #3 Call peaks for each chromosome... INFO @ Sun, 03 Jun 2018 12:39:05: #4 Write output xls file... SRX4082335.20_peaks.xls INFO @ Sun, 03 Jun 2018 12:39:05: #4 Write peak in narrowPeak format file... SRX4082335.20_peaks.narrowPeak INFO @ Sun, 03 Jun 2018 12:39:05: #4 Write summits bed file... SRX4082335.20_summits.bed INFO @ Sun, 03 Jun 2018 12:39:05: Done! pass1 - making usageList (7 chroms): 2 millis pass2 - checking and writing primary data (4701 records, 4 fields): 7 millis CompletedMACS2peakCalling INFO @ Sun, 03 Jun 2018 12:39:06: #4 Write output xls file... SRX4082335.05_peaks.xls INFO @ Sun, 03 Jun 2018 12:39:06: #4 Write peak in narrowPeak format file... SRX4082335.05_peaks.narrowPeak INFO @ Sun, 03 Jun 2018 12:39:06: #4 Write summits bed file... SRX4082335.05_summits.bed INFO @ Sun, 03 Jun 2018 12:39:06: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (7039 records, 4 fields): 10 millis CompletedMACS2peakCalling INFO @ Sun, 03 Jun 2018 12:39:07: #4 Write output xls file... SRX4082335.10_peaks.xls INFO @ Sun, 03 Jun 2018 12:39:07: #4 Write peak in narrowPeak format file... SRX4082335.10_peaks.narrowPeak INFO @ Sun, 03 Jun 2018 12:39:07: #4 Write summits bed file... SRX4082335.10_summits.bed INFO @ Sun, 03 Jun 2018 12:39:07: Done! pass1 - making usageList (7 chroms): 2 millis pass2 - checking and writing primary data (5672 records, 4 fields): 8 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。