Job ID = 10201975 sra ファイルのダウンロード中... Completed: 632559K bytes transferred in 19 seconds (263263K 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 18608517 spots for /home/okishinya/chipatlas/results/ce10/SRX2576644/SRR5272601.sra Written 18608517 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: 00:11:55 18608517 reads; of these: 18608517 (100.00%) were unpaired; of these: 2089035 (11.23%) aligned 0 times 13639210 (73.30%) aligned exactly 1 time 2880272 (15.48%) aligned >1 times 88.77% overall alignment rate Time searching: 00:11:56 Overall time: 00:11:56 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] 7748441 / 16519482 = 0.4690 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 @ Mon, 13 Nov 2017 13:27:17: # Command line: callpeak -t SRX2576644.bam -f BAM -g ce -n SRX2576644.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX2576644.20 # format = BAM # ChIP-seq file = ['SRX2576644.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 @ Mon, 13 Nov 2017 13:27:17: # Command line: callpeak -t SRX2576644.bam -f BAM -g ce -n SRX2576644.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX2576644.10 # format = BAM # ChIP-seq file = ['SRX2576644.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 @ Mon, 13 Nov 2017 13:27:17: #1 read tag files... INFO @ Mon, 13 Nov 2017 13:27:17: #1 read tag files... INFO @ Mon, 13 Nov 2017 13:27:17: #1 read treatment tags... INFO @ Mon, 13 Nov 2017 13:27:17: #1 read treatment tags... INFO @ Mon, 13 Nov 2017 13:27:17: # Command line: callpeak -t SRX2576644.bam -f BAM -g ce -n SRX2576644.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX2576644.05 # format = BAM # ChIP-seq file = ['SRX2576644.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 @ Mon, 13 Nov 2017 13:27:17: #1 read tag files... INFO @ Mon, 13 Nov 2017 13:27:17: #1 read treatment tags... INFO @ Mon, 13 Nov 2017 13:27:28: 1000000 INFO @ Mon, 13 Nov 2017 13:27:28: 1000000 INFO @ Mon, 13 Nov 2017 13:27:29: 1000000 INFO @ Mon, 13 Nov 2017 13:27:39: 2000000 INFO @ Mon, 13 Nov 2017 13:27:39: 2000000 INFO @ Mon, 13 Nov 2017 13:27:42: 2000000 INFO @ Mon, 13 Nov 2017 13:27:49: 3000000 INFO @ Mon, 13 Nov 2017 13:27:49: 3000000 INFO @ Mon, 13 Nov 2017 13:27:55: 3000000 INFO @ Mon, 13 Nov 2017 13:28:02: 4000000 INFO @ Mon, 13 Nov 2017 13:28:02: 4000000 INFO @ Mon, 13 Nov 2017 13:28:12: 4000000 INFO @ Mon, 13 Nov 2017 13:28:15: 5000000 INFO @ Mon, 13 Nov 2017 13:28:15: 5000000 INFO @ Mon, 13 Nov 2017 13:28:28: 6000000 INFO @ Mon, 13 Nov 2017 13:28:28: 6000000 INFO @ Mon, 13 Nov 2017 13:28:29: 5000000 INFO @ Mon, 13 Nov 2017 13:28:42: 7000000 INFO @ Mon, 13 Nov 2017 13:28:42: 7000000 INFO @ Mon, 13 Nov 2017 13:28:47: 6000000 INFO @ Mon, 13 Nov 2017 13:28:55: 8000000 INFO @ Mon, 13 Nov 2017 13:28:55: 8000000 INFO @ Mon, 13 Nov 2017 13:29:05: #1 tag size is determined as 50 bps INFO @ Mon, 13 Nov 2017 13:29:05: #1 tag size = 50 INFO @ Mon, 13 Nov 2017 13:29:05: #1 total tags in treatment: 8771041 INFO @ Mon, 13 Nov 2017 13:29:05: #1 user defined the maximum tags... INFO @ Mon, 13 Nov 2017 13:29:05: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Mon, 13 Nov 2017 13:29:05: #1 tag size is determined as 50 bps INFO @ Mon, 13 Nov 2017 13:29:05: #1 tag size = 50 INFO @ Mon, 13 Nov 2017 13:29:05: #1 total tags in treatment: 8771041 INFO @ Mon, 13 Nov 2017 13:29:05: #1 user defined the maximum tags... INFO @ Mon, 13 Nov 2017 13:29:05: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Mon, 13 Nov 2017 13:29:05: #1 tags after filtering in treatment: 8771041 INFO @ Mon, 13 Nov 2017 13:29:05: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 13 Nov 2017 13:29:05: #1 finished! INFO @ Mon, 13 Nov 2017 13:29:05: #2 Build Peak Model... INFO @ Mon, 13 Nov 2017 13:29:05: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 13 Nov 2017 13:29:05: #1 tags after filtering in treatment: 8771041 INFO @ Mon, 13 Nov 2017 13:29:05: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 13 Nov 2017 13:29:05: #1 finished! INFO @ Mon, 13 Nov 2017 13:29:05: #2 Build Peak Model... INFO @ Mon, 13 Nov 2017 13:29:05: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 13 Nov 2017 13:29:05: 7000000 INFO @ Mon, 13 Nov 2017 13:29:06: #2 number of paired peaks: 1077 INFO @ Mon, 13 Nov 2017 13:29:06: start model_add_line... INFO @ Mon, 13 Nov 2017 13:29:06: #2 number of paired peaks: 1077 INFO @ Mon, 13 Nov 2017 13:29:06: start model_add_line... INFO @ Mon, 13 Nov 2017 13:29:06: start X-correlation... INFO @ Mon, 13 Nov 2017 13:29:06: end of X-cor INFO @ Mon, 13 Nov 2017 13:29:06: #2 finished! INFO @ Mon, 13 Nov 2017 13:29:06: #2 predicted fragment length is 170 bps INFO @ Mon, 13 Nov 2017 13:29:06: #2 alternative fragment length(s) may be 170 bps INFO @ Mon, 13 Nov 2017 13:29:06: #2.2 Generate R script for model : SRX2576644.10_model.r INFO @ Mon, 13 Nov 2017 13:29:06: start X-correlation... INFO @ Mon, 13 Nov 2017 13:29:06: #3 Call peaks... INFO @ Mon, 13 Nov 2017 13:29:06: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 13 Nov 2017 13:29:06: end of X-cor INFO @ Mon, 13 Nov 2017 13:29:06: #2 finished! INFO @ Mon, 13 Nov 2017 13:29:06: #2 predicted fragment length is 170 bps INFO @ Mon, 13 Nov 2017 13:29:06: #2 alternative fragment length(s) may be 170 bps INFO @ Mon, 13 Nov 2017 13:29:06: #2.2 Generate R script for model : SRX2576644.20_model.r INFO @ Mon, 13 Nov 2017 13:29:06: #3 Call peaks... INFO @ Mon, 13 Nov 2017 13:29:06: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 13 Nov 2017 13:29:21: 8000000 INFO @ Mon, 13 Nov 2017 13:29:32: #1 tag size is determined as 50 bps INFO @ Mon, 13 Nov 2017 13:29:32: #1 tag size = 50 INFO @ Mon, 13 Nov 2017 13:29:32: #1 total tags in treatment: 8771041 INFO @ Mon, 13 Nov 2017 13:29:32: #1 user defined the maximum tags... INFO @ Mon, 13 Nov 2017 13:29:32: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Mon, 13 Nov 2017 13:29:32: #1 tags after filtering in treatment: 8771041 INFO @ Mon, 13 Nov 2017 13:29:32: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 13 Nov 2017 13:29:32: #1 finished! INFO @ Mon, 13 Nov 2017 13:29:32: #2 Build Peak Model... INFO @ Mon, 13 Nov 2017 13:29:32: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 13 Nov 2017 13:29:33: #2 number of paired peaks: 1077 INFO @ Mon, 13 Nov 2017 13:29:33: start model_add_line... INFO @ Mon, 13 Nov 2017 13:29:33: start X-correlation... INFO @ Mon, 13 Nov 2017 13:29:33: end of X-cor INFO @ Mon, 13 Nov 2017 13:29:33: #2 finished! INFO @ Mon, 13 Nov 2017 13:29:33: #2 predicted fragment length is 170 bps INFO @ Mon, 13 Nov 2017 13:29:33: #2 alternative fragment length(s) may be 170 bps INFO @ Mon, 13 Nov 2017 13:29:33: #2.2 Generate R script for model : SRX2576644.05_model.r INFO @ Mon, 13 Nov 2017 13:29:33: #3 Call peaks... INFO @ Mon, 13 Nov 2017 13:29:33: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 13 Nov 2017 13:29:37: #3 Call peaks for each chromosome... INFO @ Mon, 13 Nov 2017 13:29:37: #3 Call peaks for each chromosome... INFO @ Mon, 13 Nov 2017 13:29:54: #4 Write output xls file... SRX2576644.20_peaks.xls INFO @ Mon, 13 Nov 2017 13:29:54: #4 Write peak in narrowPeak format file... SRX2576644.20_peaks.narrowPeak INFO @ Mon, 13 Nov 2017 13:29:54: #4 Write summits bed file... SRX2576644.20_summits.bed INFO @ Mon, 13 Nov 2017 13:29:54: Done! pass1 - making usageList (6 chroms): 2 millis pass2 - checking and writing primary data (1537 records, 4 fields): 6 millis CompletedMACS2peakCalling INFO @ Mon, 13 Nov 2017 13:29:55: #4 Write output xls file... SRX2576644.10_peaks.xls INFO @ Mon, 13 Nov 2017 13:29:55: #4 Write peak in narrowPeak format file... SRX2576644.10_peaks.narrowPeak INFO @ Mon, 13 Nov 2017 13:29:55: #4 Write summits bed file... SRX2576644.10_summits.bed INFO @ Mon, 13 Nov 2017 13:29:55: Done! pass1 - making usageList (7 chroms): 2 millis pass2 - checking and writing primary data (2343 records, 4 fields): 7 millis CompletedMACS2peakCalling INFO @ Mon, 13 Nov 2017 13:30:04: #3 Call peaks for each chromosome... INFO @ Mon, 13 Nov 2017 13:30:20: #4 Write output xls file... SRX2576644.05_peaks.xls INFO @ Mon, 13 Nov 2017 13:30:20: #4 Write peak in narrowPeak format file... SRX2576644.05_peaks.narrowPeak INFO @ Mon, 13 Nov 2017 13:30:20: #4 Write summits bed file... SRX2576644.05_summits.bed INFO @ Mon, 13 Nov 2017 13:30:20: Done! pass1 - making usageList (7 chroms): 3 millis pass2 - checking and writing primary data (3179 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。