Job ID = 10714378 sra ファイルのダウンロード中... Completed: 322960K bytes transferred in 11 seconds (235862K 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 14310994 spots for /home/okishinya/chipatlas/results/ce10/SRX4082338/SRR7164156.sra Written 14310994 spots for /home/okishinya/chipatlas/results/ce10/SRX4082338/SRR7164156.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: 00:00:01 Multiseed full-index search: 00:03:24 14310994 reads; of these: 14310994 (100.00%) were unpaired; of these: 1563440 (10.92%) aligned 0 times 11725607 (81.93%) aligned exactly 1 time 1021947 (7.14%) aligned >1 times 89.08% overall alignment rate Time searching: 00:03:25 Overall time: 00:03:25 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] 3015921 / 12747554 = 0.2366 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 12:35:14: # Command line: callpeak -t SRX4082338.bam -f BAM -g ce -n SRX4082338.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX4082338.20 # format = BAM # ChIP-seq file = ['SRX4082338.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 12:35:14: # Command line: callpeak -t SRX4082338.bam -f BAM -g ce -n SRX4082338.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX4082338.05 # format = BAM # ChIP-seq file = ['SRX4082338.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 12:35:14: #1 read tag files... INFO @ Sun, 03 Jun 2018 12:35:14: #1 read tag files... INFO @ Sun, 03 Jun 2018 12:35:14: #1 read treatment tags... INFO @ Sun, 03 Jun 2018 12:35:14: #1 read treatment tags... INFO @ Sun, 03 Jun 2018 12:35:14: # Command line: callpeak -t SRX4082338.bam -f BAM -g ce -n SRX4082338.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX4082338.10 # format = BAM # ChIP-seq file = ['SRX4082338.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 12:35:14: #1 read tag files... INFO @ Sun, 03 Jun 2018 12:35:14: #1 read treatment tags... INFO @ Sun, 03 Jun 2018 12:35:22: 1000000 INFO @ Sun, 03 Jun 2018 12:35:22: 1000000 INFO @ Sun, 03 Jun 2018 12:35:22: 1000000 INFO @ Sun, 03 Jun 2018 12:35:30: 2000000 INFO @ Sun, 03 Jun 2018 12:35:30: 2000000 INFO @ Sun, 03 Jun 2018 12:35:30: 2000000 INFO @ Sun, 03 Jun 2018 12:35:37: 3000000 INFO @ Sun, 03 Jun 2018 12:35:38: 3000000 INFO @ Sun, 03 Jun 2018 12:35:38: 3000000 INFO @ Sun, 03 Jun 2018 12:35:45: 4000000 INFO @ Sun, 03 Jun 2018 12:35:46: 4000000 INFO @ Sun, 03 Jun 2018 12:35:46: 4000000 INFO @ Sun, 03 Jun 2018 12:35:52: 5000000 INFO @ Sun, 03 Jun 2018 12:35:54: 5000000 INFO @ Sun, 03 Jun 2018 12:35:54: 5000000 INFO @ Sun, 03 Jun 2018 12:36:00: 6000000 INFO @ Sun, 03 Jun 2018 12:36:02: 6000000 INFO @ Sun, 03 Jun 2018 12:36:02: 6000000 INFO @ Sun, 03 Jun 2018 12:36:07: 7000000 INFO @ Sun, 03 Jun 2018 12:36:10: 7000000 INFO @ Sun, 03 Jun 2018 12:36:10: 7000000 INFO @ Sun, 03 Jun 2018 12:36:14: 8000000 INFO @ Sun, 03 Jun 2018 12:36:18: 8000000 INFO @ Sun, 03 Jun 2018 12:36:18: 8000000 INFO @ Sun, 03 Jun 2018 12:36:22: 9000000 INFO @ Sun, 03 Jun 2018 12:36:26: 9000000 INFO @ Sun, 03 Jun 2018 12:36:26: 9000000 INFO @ Sun, 03 Jun 2018 12:36:27: #1 tag size is determined as 50 bps INFO @ Sun, 03 Jun 2018 12:36:27: #1 tag size = 50 INFO @ Sun, 03 Jun 2018 12:36:27: #1 total tags in treatment: 9731633 INFO @ Sun, 03 Jun 2018 12:36:27: #1 user defined the maximum tags... INFO @ Sun, 03 Jun 2018 12:36:27: #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 12:36:27: #1 tags after filtering in treatment: 9731633 INFO @ Sun, 03 Jun 2018 12:36:27: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 03 Jun 2018 12:36:27: #1 finished! INFO @ Sun, 03 Jun 2018 12:36:27: #2 Build Peak Model... INFO @ Sun, 03 Jun 2018 12:36:27: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 03 Jun 2018 12:36:28: #2 number of paired peaks: 5369 INFO @ Sun, 03 Jun 2018 12:36:28: start model_add_line... INFO @ Sun, 03 Jun 2018 12:36:29: start X-correlation... INFO @ Sun, 03 Jun 2018 12:36:29: end of X-cor INFO @ Sun, 03 Jun 2018 12:36:29: #2 finished! INFO @ Sun, 03 Jun 2018 12:36:29: #2 predicted fragment length is 144 bps INFO @ Sun, 03 Jun 2018 12:36:29: #2 alternative fragment length(s) may be 144 bps INFO @ Sun, 03 Jun 2018 12:36:29: #2.2 Generate R script for model : SRX4082338.10_model.r INFO @ Sun, 03 Jun 2018 12:36:29: #3 Call peaks... INFO @ Sun, 03 Jun 2018 12:36:29: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 03 Jun 2018 12:36:32: #1 tag size is determined as 50 bps INFO @ Sun, 03 Jun 2018 12:36:32: #1 tag size = 50 INFO @ Sun, 03 Jun 2018 12:36:32: #1 total tags in treatment: 9731633 INFO @ Sun, 03 Jun 2018 12:36:32: #1 user defined the maximum tags... INFO @ Sun, 03 Jun 2018 12:36:32: #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 12:36:32: #1 tag size is determined as 50 bps INFO @ Sun, 03 Jun 2018 12:36:32: #1 tag size = 50 INFO @ Sun, 03 Jun 2018 12:36:32: #1 total tags in treatment: 9731633 INFO @ Sun, 03 Jun 2018 12:36:32: #1 user defined the maximum tags... INFO @ Sun, 03 Jun 2018 12:36:32: #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 12:36:32: #1 tags after filtering in treatment: 9731633 INFO @ Sun, 03 Jun 2018 12:36:32: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 03 Jun 2018 12:36:32: #1 finished! INFO @ Sun, 03 Jun 2018 12:36:32: #2 Build Peak Model... INFO @ Sun, 03 Jun 2018 12:36:32: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 03 Jun 2018 12:36:32: #1 tags after filtering in treatment: 9731633 INFO @ Sun, 03 Jun 2018 12:36:32: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 03 Jun 2018 12:36:32: #1 finished! INFO @ Sun, 03 Jun 2018 12:36:32: #2 Build Peak Model... INFO @ Sun, 03 Jun 2018 12:36:32: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 03 Jun 2018 12:36:33: #2 number of paired peaks: 5369 INFO @ Sun, 03 Jun 2018 12:36:33: start model_add_line... INFO @ Sun, 03 Jun 2018 12:36:33: #2 number of paired peaks: 5369 INFO @ Sun, 03 Jun 2018 12:36:33: start model_add_line... INFO @ Sun, 03 Jun 2018 12:36:33: start X-correlation... INFO @ Sun, 03 Jun 2018 12:36:33: start X-correlation... INFO @ Sun, 03 Jun 2018 12:36:33: end of X-cor INFO @ Sun, 03 Jun 2018 12:36:33: end of X-cor INFO @ Sun, 03 Jun 2018 12:36:33: #2 finished! INFO @ Sun, 03 Jun 2018 12:36:33: #2 finished! INFO @ Sun, 03 Jun 2018 12:36:33: #2 predicted fragment length is 144 bps INFO @ Sun, 03 Jun 2018 12:36:33: #2 predicted fragment length is 144 bps INFO @ Sun, 03 Jun 2018 12:36:33: #2 alternative fragment length(s) may be 144 bps INFO @ Sun, 03 Jun 2018 12:36:33: #2 alternative fragment length(s) may be 144 bps INFO @ Sun, 03 Jun 2018 12:36:33: #2.2 Generate R script for model : SRX4082338.20_model.r INFO @ Sun, 03 Jun 2018 12:36:33: #2.2 Generate R script for model : SRX4082338.05_model.r INFO @ Sun, 03 Jun 2018 12:36:33: #3 Call peaks... INFO @ Sun, 03 Jun 2018 12:36:33: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 03 Jun 2018 12:36:33: #3 Call peaks... INFO @ Sun, 03 Jun 2018 12:36:33: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 03 Jun 2018 12:36:56: #3 Call peaks for each chromosome... INFO @ Sun, 03 Jun 2018 12:37:00: #3 Call peaks for each chromosome... INFO @ Sun, 03 Jun 2018 12:37:02: #3 Call peaks for each chromosome... INFO @ Sun, 03 Jun 2018 12:37:09: #4 Write output xls file... SRX4082338.10_peaks.xls INFO @ Sun, 03 Jun 2018 12:37:09: #4 Write peak in narrowPeak format file... SRX4082338.10_peaks.narrowPeak INFO @ Sun, 03 Jun 2018 12:37:09: #4 Write summits bed file... SRX4082338.10_summits.bed INFO @ Sun, 03 Jun 2018 12:37:09: Done! pass1 - making usageList (6 chroms): 2 millis pass2 - checking and writing primary data (5588 records, 4 fields): 8 millis CompletedMACS2peakCalling INFO @ Sun, 03 Jun 2018 12:37:15: #4 Write output xls file... SRX4082338.20_peaks.xls INFO @ Sun, 03 Jun 2018 12:37:15: #4 Write peak in narrowPeak format file... SRX4082338.20_peaks.narrowPeak INFO @ Sun, 03 Jun 2018 12:37:15: #4 Write summits bed file... SRX4082338.20_summits.bed INFO @ Sun, 03 Jun 2018 12:37:15: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (4446 records, 4 fields): 7 millis CompletedMACS2peakCalling INFO @ Sun, 03 Jun 2018 12:37:17: #4 Write output xls file... SRX4082338.05_peaks.xls INFO @ Sun, 03 Jun 2018 12:37:18: #4 Write peak in narrowPeak format file... SRX4082338.05_peaks.narrowPeak INFO @ Sun, 03 Jun 2018 12:37:18: #4 Write summits bed file... SRX4082338.05_summits.bed INFO @ Sun, 03 Jun 2018 12:37:18: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (7201 records, 4 fields): 10 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。