Job ID = 10320309 sra ファイルのダウンロード中... Completed: 245456K bytes transferred in 38 seconds (52155K 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 8650033 spots for /home/okishinya/chipatlas/results/ce10/SRX3043400/SRR5875884.sra Written 8650033 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: 00:00:00 Time loading mirror index: 00:00:00 Multiseed full-index search: 00:02:46 8650033 reads; of these: 8650033 (100.00%) were unpaired; of these: 107372 (1.24%) aligned 0 times 7664623 (88.61%) aligned exactly 1 time 878038 (10.15%) aligned >1 times 98.76% overall alignment rate Time searching: 00:02:46 Overall time: 00:02:46 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_rmdupse_core] 1324273 / 8542661 = 0.1550 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 @ Thu, 11 Jan 2018 02:09:54: # Command line: callpeak -t SRX3043400.bam -f BAM -g ce -n SRX3043400.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX3043400.20 # format = BAM # ChIP-seq file = ['SRX3043400.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 @ Thu, 11 Jan 2018 02:09:54: # Command line: callpeak -t SRX3043400.bam -f BAM -g ce -n SRX3043400.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX3043400.10 # format = BAM # ChIP-seq file = ['SRX3043400.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 @ Thu, 11 Jan 2018 02:09:54: #1 read tag files... INFO @ Thu, 11 Jan 2018 02:09:54: #1 read tag files... INFO @ Thu, 11 Jan 2018 02:09:54: #1 read treatment tags... INFO @ Thu, 11 Jan 2018 02:09:54: #1 read treatment tags... INFO @ Thu, 11 Jan 2018 02:09:54: # Command line: callpeak -t SRX3043400.bam -f BAM -g ce -n SRX3043400.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX3043400.05 # format = BAM # ChIP-seq file = ['SRX3043400.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 @ Thu, 11 Jan 2018 02:09:54: #1 read tag files... INFO @ Thu, 11 Jan 2018 02:09:54: #1 read treatment tags... INFO @ Thu, 11 Jan 2018 02:10:01: 1000000 INFO @ Thu, 11 Jan 2018 02:10:01: 1000000 INFO @ Thu, 11 Jan 2018 02:10:01: 1000000 INFO @ Thu, 11 Jan 2018 02:10:07: 2000000 INFO @ Thu, 11 Jan 2018 02:10:07: 2000000 INFO @ Thu, 11 Jan 2018 02:10:07: 2000000 INFO @ Thu, 11 Jan 2018 02:10:14: 3000000 INFO @ Thu, 11 Jan 2018 02:10:14: 3000000 INFO @ Thu, 11 Jan 2018 02:10:14: 3000000 INFO @ Thu, 11 Jan 2018 02:10:20: 4000000 INFO @ Thu, 11 Jan 2018 02:10:20: 4000000 INFO @ Thu, 11 Jan 2018 02:10:21: 4000000 INFO @ Thu, 11 Jan 2018 02:10:26: 5000000 INFO @ Thu, 11 Jan 2018 02:10:27: 5000000 INFO @ Thu, 11 Jan 2018 02:10:28: 5000000 INFO @ Thu, 11 Jan 2018 02:10:33: 6000000 INFO @ Thu, 11 Jan 2018 02:10:33: 6000000 INFO @ Thu, 11 Jan 2018 02:10:35: 6000000 INFO @ Thu, 11 Jan 2018 02:10:39: 7000000 INFO @ Thu, 11 Jan 2018 02:10:40: 7000000 INFO @ Thu, 11 Jan 2018 02:10:40: #1 tag size is determined as 50 bps INFO @ Thu, 11 Jan 2018 02:10:40: #1 tag size = 50 INFO @ Thu, 11 Jan 2018 02:10:40: #1 total tags in treatment: 7218388 INFO @ Thu, 11 Jan 2018 02:10:40: #1 user defined the maximum tags... INFO @ Thu, 11 Jan 2018 02:10:40: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Thu, 11 Jan 2018 02:10:40: #1 tags after filtering in treatment: 7218388 INFO @ Thu, 11 Jan 2018 02:10:40: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 11 Jan 2018 02:10:40: #1 finished! INFO @ Thu, 11 Jan 2018 02:10:40: #2 Build Peak Model... INFO @ Thu, 11 Jan 2018 02:10:40: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 11 Jan 2018 02:10:41: #2 number of paired peaks: 2491 INFO @ Thu, 11 Jan 2018 02:10:41: start model_add_line... INFO @ Thu, 11 Jan 2018 02:10:41: start X-correlation... INFO @ Thu, 11 Jan 2018 02:10:41: #1 tag size is determined as 50 bps INFO @ Thu, 11 Jan 2018 02:10:41: #1 tag size = 50 INFO @ Thu, 11 Jan 2018 02:10:41: #1 total tags in treatment: 7218388 INFO @ Thu, 11 Jan 2018 02:10:41: #1 user defined the maximum tags... INFO @ Thu, 11 Jan 2018 02:10:41: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Thu, 11 Jan 2018 02:10:41: #1 tags after filtering in treatment: 7218388 INFO @ Thu, 11 Jan 2018 02:10:41: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 11 Jan 2018 02:10:41: #1 finished! INFO @ Thu, 11 Jan 2018 02:10:41: #2 Build Peak Model... INFO @ Thu, 11 Jan 2018 02:10:41: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 11 Jan 2018 02:10:42: end of X-cor INFO @ Thu, 11 Jan 2018 02:10:42: #2 finished! INFO @ Thu, 11 Jan 2018 02:10:42: #2 predicted fragment length is 170 bps INFO @ Thu, 11 Jan 2018 02:10:42: #2 alternative fragment length(s) may be 170 bps INFO @ Thu, 11 Jan 2018 02:10:42: #2.2 Generate R script for model : SRX3043400.10_model.r INFO @ Thu, 11 Jan 2018 02:10:42: #3 Call peaks... INFO @ Thu, 11 Jan 2018 02:10:42: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 11 Jan 2018 02:10:42: 7000000 INFO @ Thu, 11 Jan 2018 02:10:42: #2 number of paired peaks: 2491 INFO @ Thu, 11 Jan 2018 02:10:42: start model_add_line... INFO @ Thu, 11 Jan 2018 02:10:42: start X-correlation... INFO @ Thu, 11 Jan 2018 02:10:42: end of X-cor INFO @ Thu, 11 Jan 2018 02:10:42: #2 finished! INFO @ Thu, 11 Jan 2018 02:10:42: #2 predicted fragment length is 170 bps INFO @ Thu, 11 Jan 2018 02:10:42: #2 alternative fragment length(s) may be 170 bps INFO @ Thu, 11 Jan 2018 02:10:42: #2.2 Generate R script for model : SRX3043400.20_model.r INFO @ Thu, 11 Jan 2018 02:10:42: #3 Call peaks... INFO @ Thu, 11 Jan 2018 02:10:42: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 11 Jan 2018 02:10:43: #1 tag size is determined as 50 bps INFO @ Thu, 11 Jan 2018 02:10:43: #1 tag size = 50 INFO @ Thu, 11 Jan 2018 02:10:43: #1 total tags in treatment: 7218388 INFO @ Thu, 11 Jan 2018 02:10:43: #1 user defined the maximum tags... INFO @ Thu, 11 Jan 2018 02:10:43: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Thu, 11 Jan 2018 02:10:43: #1 tags after filtering in treatment: 7218388 INFO @ Thu, 11 Jan 2018 02:10:43: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 11 Jan 2018 02:10:43: #1 finished! INFO @ Thu, 11 Jan 2018 02:10:43: #2 Build Peak Model... INFO @ Thu, 11 Jan 2018 02:10:43: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 11 Jan 2018 02:10:44: #2 number of paired peaks: 2491 INFO @ Thu, 11 Jan 2018 02:10:44: start model_add_line... INFO @ Thu, 11 Jan 2018 02:10:44: start X-correlation... INFO @ Thu, 11 Jan 2018 02:10:44: end of X-cor INFO @ Thu, 11 Jan 2018 02:10:44: #2 finished! INFO @ Thu, 11 Jan 2018 02:10:44: #2 predicted fragment length is 170 bps INFO @ Thu, 11 Jan 2018 02:10:44: #2 alternative fragment length(s) may be 170 bps INFO @ Thu, 11 Jan 2018 02:10:44: #2.2 Generate R script for model : SRX3043400.05_model.r INFO @ Thu, 11 Jan 2018 02:10:44: #3 Call peaks... INFO @ Thu, 11 Jan 2018 02:10:44: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 11 Jan 2018 02:11:00: #3 Call peaks for each chromosome... INFO @ Thu, 11 Jan 2018 02:11:01: #3 Call peaks for each chromosome... INFO @ Thu, 11 Jan 2018 02:11:02: #3 Call peaks for each chromosome... INFO @ Thu, 11 Jan 2018 02:11:11: #4 Write output xls file... SRX3043400.20_peaks.xls INFO @ Thu, 11 Jan 2018 02:11:11: #4 Write peak in narrowPeak format file... SRX3043400.20_peaks.narrowPeak INFO @ Thu, 11 Jan 2018 02:11:11: #4 Write summits bed file... SRX3043400.20_summits.bed INFO @ Thu, 11 Jan 2018 02:11:11: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (2647 records, 4 fields): 5 millis CompletedMACS2peakCalling INFO @ Thu, 11 Jan 2018 02:11:11: #4 Write output xls file... SRX3043400.10_peaks.xls INFO @ Thu, 11 Jan 2018 02:11:11: #4 Write peak in narrowPeak format file... SRX3043400.10_peaks.narrowPeak INFO @ Thu, 11 Jan 2018 02:11:11: #4 Write summits bed file... SRX3043400.10_summits.bed INFO @ Thu, 11 Jan 2018 02:11:11: Done! pass1 - making usageList (6 chroms): 2 millis pass2 - checking and writing primary data (4163 records, 4 fields): 7 millis CompletedMACS2peakCalling INFO @ Thu, 11 Jan 2018 02:11:12: #4 Write output xls file... SRX3043400.05_peaks.xls INFO @ Thu, 11 Jan 2018 02:11:12: #4 Write peak in narrowPeak format file... SRX3043400.05_peaks.narrowPeak INFO @ Thu, 11 Jan 2018 02:11:12: #4 Write summits bed file... SRX3043400.05_summits.bed INFO @ Thu, 11 Jan 2018 02:11:12: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (5855 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。