Job ID = 10480687 sra ファイルのダウンロード中... Completed: 394672K bytes transferred in 26 seconds (122632K 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... Written 13264499 spots for /home/okishinya/chipatlas/results/dm3/SRX3068958/SRR5907434.sra Written 13264499 spots total 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: 00:00:01 Time loading mirror index: 00:00:00 Multiseed full-index search: 00:03:58 13264499 reads; of these: 13264499 (100.00%) were unpaired; of these: 1280844 (9.66%) aligned 0 times 10418196 (78.54%) aligned exactly 1 time 1565459 (11.80%) aligned >1 times 90.34% overall alignment rate Time searching: 00:03:59 Overall time: 00:03:59 マッピングが完了しました。 samtools でBAM に変換中... [samopen] SAM header is present: 15 sequences. [bam_sort_core] merging from 8 files... [bam_rmdupse_core] 2821164 / 11983655 = 0.2354 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, 16 Mar 2018 07:43:40: # Command line: callpeak -t SRX3068958.bam -f BAM -g dm -n SRX3068958.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX3068958.05 # format = BAM # ChIP-seq file = ['SRX3068958.bam'] # control file = None # effective genome size = 1.20e+08 # 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, 16 Mar 2018 07:43:40: #1 read tag files... INFO @ Fri, 16 Mar 2018 07:43:40: #1 read treatment tags... INFO @ Fri, 16 Mar 2018 07:43:40: # Command line: callpeak -t SRX3068958.bam -f BAM -g dm -n SRX3068958.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX3068958.10 # format = BAM # ChIP-seq file = ['SRX3068958.bam'] # control file = None # effective genome size = 1.20e+08 # 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, 16 Mar 2018 07:43:40: #1 read tag files... INFO @ Fri, 16 Mar 2018 07:43:40: #1 read treatment tags... INFO @ Fri, 16 Mar 2018 07:43:40: # Command line: callpeak -t SRX3068958.bam -f BAM -g dm -n SRX3068958.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX3068958.20 # format = BAM # ChIP-seq file = ['SRX3068958.bam'] # control file = None # effective genome size = 1.20e+08 # 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, 16 Mar 2018 07:43:40: #1 read tag files... INFO @ Fri, 16 Mar 2018 07:43:40: #1 read treatment tags... INFO @ Fri, 16 Mar 2018 07:43:47: 1000000 INFO @ Fri, 16 Mar 2018 07:43:47: 1000000 INFO @ Fri, 16 Mar 2018 07:43:47: 1000000 INFO @ Fri, 16 Mar 2018 07:43:54: 2000000 INFO @ Fri, 16 Mar 2018 07:43:55: 2000000 INFO @ Fri, 16 Mar 2018 07:43:55: 2000000 INFO @ Fri, 16 Mar 2018 07:44:00: 3000000 INFO @ Fri, 16 Mar 2018 07:44:03: 3000000 INFO @ Fri, 16 Mar 2018 07:44:03: 3000000 INFO @ Fri, 16 Mar 2018 07:44:07: 4000000 INFO @ Fri, 16 Mar 2018 07:44:11: 4000000 INFO @ Fri, 16 Mar 2018 07:44:11: 4000000 INFO @ Fri, 16 Mar 2018 07:44:14: 5000000 INFO @ Fri, 16 Mar 2018 07:44:18: 5000000 INFO @ Fri, 16 Mar 2018 07:44:18: 5000000 INFO @ Fri, 16 Mar 2018 07:44:21: 6000000 INFO @ Fri, 16 Mar 2018 07:44:26: 6000000 INFO @ Fri, 16 Mar 2018 07:44:26: 6000000 INFO @ Fri, 16 Mar 2018 07:44:28: 7000000 INFO @ Fri, 16 Mar 2018 07:44:34: 7000000 INFO @ Fri, 16 Mar 2018 07:44:34: 7000000 INFO @ Fri, 16 Mar 2018 07:44:35: 8000000 INFO @ Fri, 16 Mar 2018 07:44:42: 9000000 INFO @ Fri, 16 Mar 2018 07:44:42: 8000000 INFO @ Fri, 16 Mar 2018 07:44:42: 8000000 INFO @ Fri, 16 Mar 2018 07:44:43: #1 tag size is determined as 51 bps INFO @ Fri, 16 Mar 2018 07:44:43: #1 tag size = 51 INFO @ Fri, 16 Mar 2018 07:44:43: #1 total tags in treatment: 9162491 INFO @ Fri, 16 Mar 2018 07:44:43: #1 user defined the maximum tags... INFO @ Fri, 16 Mar 2018 07:44:43: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 16 Mar 2018 07:44:43: #1 tags after filtering in treatment: 9162491 INFO @ Fri, 16 Mar 2018 07:44:43: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 16 Mar 2018 07:44:43: #1 finished! INFO @ Fri, 16 Mar 2018 07:44:43: #2 Build Peak Model... INFO @ Fri, 16 Mar 2018 07:44:43: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 16 Mar 2018 07:44:44: #2 number of paired peaks: 4199 INFO @ Fri, 16 Mar 2018 07:44:44: start model_add_line... INFO @ Fri, 16 Mar 2018 07:44:44: start X-correlation... INFO @ Fri, 16 Mar 2018 07:44:44: end of X-cor INFO @ Fri, 16 Mar 2018 07:44:44: #2 finished! INFO @ Fri, 16 Mar 2018 07:44:44: #2 predicted fragment length is 151 bps INFO @ Fri, 16 Mar 2018 07:44:44: #2 alternative fragment length(s) may be 151 bps INFO @ Fri, 16 Mar 2018 07:44:44: #2.2 Generate R script for model : SRX3068958.20_model.r INFO @ Fri, 16 Mar 2018 07:44:44: #3 Call peaks... INFO @ Fri, 16 Mar 2018 07:44:44: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 16 Mar 2018 07:44:49: 9000000 INFO @ Fri, 16 Mar 2018 07:44:49: 9000000 INFO @ Fri, 16 Mar 2018 07:44:51: #1 tag size is determined as 51 bps INFO @ Fri, 16 Mar 2018 07:44:51: #1 tag size = 51 INFO @ Fri, 16 Mar 2018 07:44:51: #1 total tags in treatment: 9162491 INFO @ Fri, 16 Mar 2018 07:44:51: #1 user defined the maximum tags... INFO @ Fri, 16 Mar 2018 07:44:51: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 16 Mar 2018 07:44:51: #1 tag size is determined as 51 bps INFO @ Fri, 16 Mar 2018 07:44:51: #1 tag size = 51 INFO @ Fri, 16 Mar 2018 07:44:51: #1 total tags in treatment: 9162491 INFO @ Fri, 16 Mar 2018 07:44:51: #1 user defined the maximum tags... INFO @ Fri, 16 Mar 2018 07:44:51: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 16 Mar 2018 07:44:51: #1 tags after filtering in treatment: 9162491 INFO @ Fri, 16 Mar 2018 07:44:51: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 16 Mar 2018 07:44:51: #1 finished! INFO @ Fri, 16 Mar 2018 07:44:51: #2 Build Peak Model... INFO @ Fri, 16 Mar 2018 07:44:51: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 16 Mar 2018 07:44:51: #1 tags after filtering in treatment: 9162491 INFO @ Fri, 16 Mar 2018 07:44:51: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 16 Mar 2018 07:44:51: #1 finished! INFO @ Fri, 16 Mar 2018 07:44:51: #2 Build Peak Model... INFO @ Fri, 16 Mar 2018 07:44:51: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 16 Mar 2018 07:44:52: #2 number of paired peaks: 4199 INFO @ Fri, 16 Mar 2018 07:44:52: start model_add_line... INFO @ Fri, 16 Mar 2018 07:44:52: #2 number of paired peaks: 4199 INFO @ Fri, 16 Mar 2018 07:44:52: start model_add_line... INFO @ Fri, 16 Mar 2018 07:44:52: start X-correlation... INFO @ Fri, 16 Mar 2018 07:44:52: end of X-cor INFO @ Fri, 16 Mar 2018 07:44:52: #2 finished! INFO @ Fri, 16 Mar 2018 07:44:52: #2 predicted fragment length is 151 bps INFO @ Fri, 16 Mar 2018 07:44:52: #2 alternative fragment length(s) may be 151 bps INFO @ Fri, 16 Mar 2018 07:44:52: #2.2 Generate R script for model : SRX3068958.10_model.r INFO @ Fri, 16 Mar 2018 07:44:52: #3 Call peaks... INFO @ Fri, 16 Mar 2018 07:44:52: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 16 Mar 2018 07:44:52: start X-correlation... INFO @ Fri, 16 Mar 2018 07:44:52: end of X-cor INFO @ Fri, 16 Mar 2018 07:44:52: #2 finished! INFO @ Fri, 16 Mar 2018 07:44:52: #2 predicted fragment length is 151 bps INFO @ Fri, 16 Mar 2018 07:44:52: #2 alternative fragment length(s) may be 151 bps INFO @ Fri, 16 Mar 2018 07:44:52: #2.2 Generate R script for model : SRX3068958.05_model.r INFO @ Fri, 16 Mar 2018 07:44:52: #3 Call peaks... INFO @ Fri, 16 Mar 2018 07:44:52: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 16 Mar 2018 07:45:10: #3 Call peaks for each chromosome... INFO @ Fri, 16 Mar 2018 07:45:17: #3 Call peaks for each chromosome... INFO @ Fri, 16 Mar 2018 07:45:18: #3 Call peaks for each chromosome... INFO @ Fri, 16 Mar 2018 07:45:24: #4 Write output xls file... SRX3068958.20_peaks.xls INFO @ Fri, 16 Mar 2018 07:45:25: #4 Write peak in narrowPeak format file... SRX3068958.20_peaks.narrowPeak INFO @ Fri, 16 Mar 2018 07:45:25: #4 Write summits bed file... SRX3068958.20_summits.bed INFO @ Fri, 16 Mar 2018 07:45:25: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (4995 records, 4 fields): 8 millis CompletedMACS2peakCalling INFO @ Fri, 16 Mar 2018 07:45:30: #4 Write output xls file... SRX3068958.05_peaks.xls INFO @ Fri, 16 Mar 2018 07:45:31: #4 Write peak in narrowPeak format file... SRX3068958.05_peaks.narrowPeak INFO @ Fri, 16 Mar 2018 07:45:31: #4 Write summits bed file... SRX3068958.05_summits.bed INFO @ Fri, 16 Mar 2018 07:45:31: Done! INFO @ Fri, 16 Mar 2018 07:45:31: #4 Write output xls file... SRX3068958.10_peaks.xls pass1 - making usageList (14 chroms): 3 millis pass2 - checking and writing primary data (10615 records, 4 fields): 14 millis CompletedMACS2peakCalling INFO @ Fri, 16 Mar 2018 07:45:31: #4 Write peak in narrowPeak format file... SRX3068958.10_peaks.narrowPeak INFO @ Fri, 16 Mar 2018 07:45:31: #4 Write summits bed file... SRX3068958.10_summits.bed INFO @ Fri, 16 Mar 2018 07:45:31: Done! pass1 - making usageList (14 chroms): 2 millis pass2 - checking and writing primary data (7682 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。