Job ID = 10320311 sra ファイルのダウンロード中... Completed: 282279K bytes transferred in 39 seconds (58540K 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 7667127 spots for /home/okishinya/chipatlas/results/ce10/SRX3043402/SRR5875886.sra Written 7667127 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: 00:02:36 7667127 reads; of these: 7667127 (100.00%) were unpaired; of these: 225699 (2.94%) aligned 0 times 6603818 (86.13%) aligned exactly 1 time 837610 (10.92%) aligned >1 times 97.06% overall alignment rate Time searching: 00:02:36 Overall time: 00:02:36 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] 662246 / 7441428 = 0.0890 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 02:09:43: # Command line: callpeak -t SRX3043402.bam -f BAM -g ce -n SRX3043402.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX3043402.20 # format = BAM # ChIP-seq file = ['SRX3043402.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 02:09:43: # Command line: callpeak -t SRX3043402.bam -f BAM -g ce -n SRX3043402.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX3043402.05 # format = BAM # ChIP-seq file = ['SRX3043402.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 02:09:43: # Command line: callpeak -t SRX3043402.bam -f BAM -g ce -n SRX3043402.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX3043402.10 # format = BAM # ChIP-seq file = ['SRX3043402.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 02:09:43: #1 read tag files... INFO @ Thu, 11 Jan 2018 02:09:43: #1 read tag files... INFO @ Thu, 11 Jan 2018 02:09:43: #1 read tag files... INFO @ Thu, 11 Jan 2018 02:09:43: #1 read treatment tags... INFO @ Thu, 11 Jan 2018 02:09:43: #1 read treatment tags... INFO @ Thu, 11 Jan 2018 02:09:43: #1 read treatment tags... INFO @ Thu, 11 Jan 2018 02:09:50: 1000000 INFO @ Thu, 11 Jan 2018 02:09:50: 1000000 INFO @ Thu, 11 Jan 2018 02:09:50: 1000000 INFO @ Thu, 11 Jan 2018 02:09:57: 2000000 INFO @ Thu, 11 Jan 2018 02:09:57: 2000000 INFO @ Thu, 11 Jan 2018 02:09:57: 2000000 INFO @ Thu, 11 Jan 2018 02:10:04: 3000000 INFO @ Thu, 11 Jan 2018 02:10:04: 3000000 INFO @ Thu, 11 Jan 2018 02:10:05: 3000000 INFO @ Thu, 11 Jan 2018 02:10:11: 4000000 INFO @ Thu, 11 Jan 2018 02:10:11: 4000000 INFO @ Thu, 11 Jan 2018 02:10:12: 4000000 INFO @ Thu, 11 Jan 2018 02:10:18: 5000000 INFO @ Thu, 11 Jan 2018 02:10:19: 5000000 INFO @ Thu, 11 Jan 2018 02:10:20: 5000000 INFO @ Thu, 11 Jan 2018 02:10:25: 6000000 INFO @ Thu, 11 Jan 2018 02:10:26: 6000000 INFO @ Thu, 11 Jan 2018 02:10:27: 6000000 INFO @ Thu, 11 Jan 2018 02:10:31: #1 tag size is determined as 51 bps INFO @ Thu, 11 Jan 2018 02:10:31: #1 tag size = 51 INFO @ Thu, 11 Jan 2018 02:10:31: #1 total tags in treatment: 6779182 INFO @ Thu, 11 Jan 2018 02:10:31: #1 user defined the maximum tags... INFO @ Thu, 11 Jan 2018 02:10:31: #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 02:10:31: #1 tags after filtering in treatment: 6779182 INFO @ Thu, 11 Jan 2018 02:10:31: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 11 Jan 2018 02:10:31: #1 finished! INFO @ Thu, 11 Jan 2018 02:10:31: #2 Build Peak Model... INFO @ Thu, 11 Jan 2018 02:10:31: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 11 Jan 2018 02:10:31: #2 number of paired peaks: 1198 INFO @ Thu, 11 Jan 2018 02:10:31: start model_add_line... INFO @ Thu, 11 Jan 2018 02:10:31: start X-correlation... INFO @ Thu, 11 Jan 2018 02:10:32: end of X-cor INFO @ Thu, 11 Jan 2018 02:10:32: #2 finished! INFO @ Thu, 11 Jan 2018 02:10:32: #2 predicted fragment length is 143 bps INFO @ Thu, 11 Jan 2018 02:10:32: #2 alternative fragment length(s) may be 143 bps INFO @ Thu, 11 Jan 2018 02:10:32: #2.2 Generate R script for model : SRX3043402.10_model.r INFO @ Thu, 11 Jan 2018 02:10:32: #1 tag size is determined as 51 bps INFO @ Thu, 11 Jan 2018 02:10:32: #1 tag size = 51 INFO @ Thu, 11 Jan 2018 02:10:32: #1 total tags in treatment: 6779182 INFO @ Thu, 11 Jan 2018 02:10:32: #1 user defined the maximum tags... INFO @ Thu, 11 Jan 2018 02:10:32: #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 02:10:32: #3 Call peaks... INFO @ Thu, 11 Jan 2018 02:10:32: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 11 Jan 2018 02:10:32: #1 tags after filtering in treatment: 6779182 INFO @ Thu, 11 Jan 2018 02:10:32: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 11 Jan 2018 02:10:32: #1 finished! INFO @ Thu, 11 Jan 2018 02:10:32: #2 Build Peak Model... INFO @ Thu, 11 Jan 2018 02:10:32: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 11 Jan 2018 02:10:32: #2 number of paired peaks: 1198 INFO @ Thu, 11 Jan 2018 02:10:32: start model_add_line... INFO @ Thu, 11 Jan 2018 02:10:33: start X-correlation... INFO @ Thu, 11 Jan 2018 02:10:33: end of X-cor INFO @ Thu, 11 Jan 2018 02:10:33: #2 finished! INFO @ Thu, 11 Jan 2018 02:10:33: #2 predicted fragment length is 143 bps INFO @ Thu, 11 Jan 2018 02:10:33: #2 alternative fragment length(s) may be 143 bps INFO @ Thu, 11 Jan 2018 02:10:33: #2.2 Generate R script for model : SRX3043402.05_model.r INFO @ Thu, 11 Jan 2018 02:10:33: #3 Call peaks... INFO @ Thu, 11 Jan 2018 02:10:33: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 11 Jan 2018 02:10:33: #1 tag size is determined as 51 bps INFO @ Thu, 11 Jan 2018 02:10:33: #1 tag size = 51 INFO @ Thu, 11 Jan 2018 02:10:33: #1 total tags in treatment: 6779182 INFO @ Thu, 11 Jan 2018 02:10:33: #1 user defined the maximum tags... INFO @ Thu, 11 Jan 2018 02:10:33: #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 02:10:33: #1 tags after filtering in treatment: 6779182 INFO @ Thu, 11 Jan 2018 02:10:33: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 11 Jan 2018 02:10:33: #1 finished! INFO @ Thu, 11 Jan 2018 02:10:33: #2 Build Peak Model... INFO @ Thu, 11 Jan 2018 02:10:33: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 11 Jan 2018 02:10:34: #2 number of paired peaks: 1198 INFO @ Thu, 11 Jan 2018 02:10:34: start model_add_line... INFO @ Thu, 11 Jan 2018 02:10:34: start X-correlation... INFO @ Thu, 11 Jan 2018 02:10:34: end of X-cor INFO @ Thu, 11 Jan 2018 02:10:34: #2 finished! INFO @ Thu, 11 Jan 2018 02:10:34: #2 predicted fragment length is 143 bps INFO @ Thu, 11 Jan 2018 02:10:34: #2 alternative fragment length(s) may be 143 bps INFO @ Thu, 11 Jan 2018 02:10:34: #2.2 Generate R script for model : SRX3043402.20_model.r INFO @ Thu, 11 Jan 2018 02:10:34: #3 Call peaks... INFO @ Thu, 11 Jan 2018 02:10:34: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 11 Jan 2018 02:10:48: #3 Call peaks for each chromosome... INFO @ Thu, 11 Jan 2018 02:10:49: #3 Call peaks for each chromosome... INFO @ Thu, 11 Jan 2018 02:10:51: #3 Call peaks for each chromosome... INFO @ Thu, 11 Jan 2018 02:10:56: #4 Write output xls file... SRX3043402.10_peaks.xls INFO @ Thu, 11 Jan 2018 02:10:57: #4 Write peak in narrowPeak format file... SRX3043402.10_peaks.narrowPeak INFO @ Thu, 11 Jan 2018 02:10:57: #4 Write summits bed file... SRX3043402.10_summits.bed INFO @ Thu, 11 Jan 2018 02:10:57: Done! pass1 - making usageList (6 chroms): 2 millis pass2 - checking and writing primary data (2970 records, 4 fields): 5 millis CompletedMACS2peakCalling INFO @ Thu, 11 Jan 2018 02:10:57: #4 Write output xls file... SRX3043402.05_peaks.xls INFO @ Thu, 11 Jan 2018 02:10:57: #4 Write peak in narrowPeak format file... SRX3043402.05_peaks.narrowPeak INFO @ Thu, 11 Jan 2018 02:10:58: #4 Write summits bed file... SRX3043402.05_summits.bed INFO @ Thu, 11 Jan 2018 02:10:58: Done! pass1 - making usageList (6 chroms): 2 millis pass2 - checking and writing primary data (4292 records, 4 fields): 6 millis CompletedMACS2peakCalling INFO @ Thu, 11 Jan 2018 02:10:59: #4 Write output xls file... SRX3043402.20_peaks.xls INFO @ Thu, 11 Jan 2018 02:10:59: #4 Write peak in narrowPeak format file... SRX3043402.20_peaks.narrowPeak INFO @ Thu, 11 Jan 2018 02:10:59: #4 Write summits bed file... SRX3043402.20_summits.bed INFO @ Thu, 11 Jan 2018 02:10:59: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (1676 records, 4 fields): 3 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。