Job ID = 10201979 sra ファイルのダウンロード中... Completed: 369303K bytes transferred in 13 seconds (221246K 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 20813824 spots for /home/okishinya/chipatlas/results/ce10/SRX2576648/SRR5272605.sra Written 20813824 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: 00:04:52 20813824 reads; of these: 20813824 (100.00%) were unpaired; of these: 5242988 (25.19%) aligned 0 times 12359185 (59.38%) aligned exactly 1 time 3211651 (15.43%) aligned >1 times 74.81% overall alignment rate Time searching: 00:04:52 Overall time: 00:04:52 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] 8823227 / 15570836 = 0.5667 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 13:17:09: # Command line: callpeak -t SRX2576648.bam -f BAM -g ce -n SRX2576648.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX2576648.10 # format = BAM # ChIP-seq file = ['SRX2576648.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 13:17:09: # Command line: callpeak -t SRX2576648.bam -f BAM -g ce -n SRX2576648.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX2576648.05 # format = BAM # ChIP-seq file = ['SRX2576648.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 13:17:09: # Command line: callpeak -t SRX2576648.bam -f BAM -g ce -n SRX2576648.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX2576648.20 # format = BAM # ChIP-seq file = ['SRX2576648.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 13:17:09: #1 read tag files... INFO @ Mon, 13 Nov 2017 13:17:09: #1 read tag files... INFO @ Mon, 13 Nov 2017 13:17:09: #1 read tag files... INFO @ Mon, 13 Nov 2017 13:17:09: #1 read treatment tags... INFO @ Mon, 13 Nov 2017 13:17:09: #1 read treatment tags... INFO @ Mon, 13 Nov 2017 13:17:09: #1 read treatment tags... INFO @ Mon, 13 Nov 2017 13:17:15: 1000000 INFO @ Mon, 13 Nov 2017 13:17:15: 1000000 INFO @ Mon, 13 Nov 2017 13:17:15: 1000000 INFO @ Mon, 13 Nov 2017 13:17:21: 2000000 INFO @ Mon, 13 Nov 2017 13:17:21: 2000000 INFO @ Mon, 13 Nov 2017 13:17:22: 2000000 INFO @ Mon, 13 Nov 2017 13:17:27: 3000000 INFO @ Mon, 13 Nov 2017 13:17:27: 3000000 INFO @ Mon, 13 Nov 2017 13:17:28: 3000000 INFO @ Mon, 13 Nov 2017 13:17:34: 4000000 INFO @ Mon, 13 Nov 2017 13:17:34: 4000000 INFO @ Mon, 13 Nov 2017 13:17:35: 4000000 INFO @ Mon, 13 Nov 2017 13:17:40: 5000000 INFO @ Mon, 13 Nov 2017 13:17:40: 5000000 INFO @ Mon, 13 Nov 2017 13:17:42: 5000000 INFO @ Mon, 13 Nov 2017 13:17:46: 6000000 INFO @ Mon, 13 Nov 2017 13:17:47: 6000000 INFO @ Mon, 13 Nov 2017 13:17:49: 6000000 INFO @ Mon, 13 Nov 2017 13:17:51: #1 tag size is determined as 51 bps INFO @ Mon, 13 Nov 2017 13:17:51: #1 tag size = 51 INFO @ Mon, 13 Nov 2017 13:17:51: #1 total tags in treatment: 6747609 INFO @ Mon, 13 Nov 2017 13:17:51: #1 user defined the maximum tags... INFO @ Mon, 13 Nov 2017 13:17:51: #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 13:17:51: #1 tags after filtering in treatment: 6747609 INFO @ Mon, 13 Nov 2017 13:17:51: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 13 Nov 2017 13:17:51: #1 finished! INFO @ Mon, 13 Nov 2017 13:17:51: #2 Build Peak Model... INFO @ Mon, 13 Nov 2017 13:17:51: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 13 Nov 2017 13:17:51: #1 tag size is determined as 51 bps INFO @ Mon, 13 Nov 2017 13:17:51: #1 tag size = 51 INFO @ Mon, 13 Nov 2017 13:17:51: #1 total tags in treatment: 6747609 INFO @ Mon, 13 Nov 2017 13:17:51: #1 user defined the maximum tags... INFO @ Mon, 13 Nov 2017 13:17:51: #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 13:17:51: #1 tags after filtering in treatment: 6747609 INFO @ Mon, 13 Nov 2017 13:17:51: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 13 Nov 2017 13:17:51: #1 finished! INFO @ Mon, 13 Nov 2017 13:17:51: #2 Build Peak Model... INFO @ Mon, 13 Nov 2017 13:17:51: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 13 Nov 2017 13:17:52: #2 number of paired peaks: 1869 INFO @ Mon, 13 Nov 2017 13:17:52: start model_add_line... INFO @ Mon, 13 Nov 2017 13:17:52: start X-correlation... INFO @ Mon, 13 Nov 2017 13:17:52: end of X-cor INFO @ Mon, 13 Nov 2017 13:17:52: #2 finished! INFO @ Mon, 13 Nov 2017 13:17:52: #2 predicted fragment length is 206 bps INFO @ Mon, 13 Nov 2017 13:17:52: #2 alternative fragment length(s) may be 206 bps INFO @ Mon, 13 Nov 2017 13:17:52: #2.2 Generate R script for model : SRX2576648.05_model.r INFO @ Mon, 13 Nov 2017 13:17:52: #3 Call peaks... INFO @ Mon, 13 Nov 2017 13:17:52: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 13 Nov 2017 13:17:52: #2 number of paired peaks: 1869 INFO @ Mon, 13 Nov 2017 13:17:52: start model_add_line... INFO @ Mon, 13 Nov 2017 13:17:52: start X-correlation... INFO @ Mon, 13 Nov 2017 13:17:52: end of X-cor INFO @ Mon, 13 Nov 2017 13:17:52: #2 finished! INFO @ Mon, 13 Nov 2017 13:17:52: #2 predicted fragment length is 206 bps INFO @ Mon, 13 Nov 2017 13:17:52: #2 alternative fragment length(s) may be 206 bps INFO @ Mon, 13 Nov 2017 13:17:52: #2.2 Generate R script for model : SRX2576648.20_model.r INFO @ Mon, 13 Nov 2017 13:17:52: #3 Call peaks... INFO @ Mon, 13 Nov 2017 13:17:52: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 13 Nov 2017 13:17:53: #1 tag size is determined as 51 bps INFO @ Mon, 13 Nov 2017 13:17:53: #1 tag size = 51 INFO @ Mon, 13 Nov 2017 13:17:53: #1 total tags in treatment: 6747609 INFO @ Mon, 13 Nov 2017 13:17:53: #1 user defined the maximum tags... INFO @ Mon, 13 Nov 2017 13:17:53: #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 13:17:53: #1 tags after filtering in treatment: 6747609 INFO @ Mon, 13 Nov 2017 13:17:53: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 13 Nov 2017 13:17:53: #1 finished! INFO @ Mon, 13 Nov 2017 13:17:53: #2 Build Peak Model... INFO @ Mon, 13 Nov 2017 13:17:53: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 13 Nov 2017 13:17:54: #2 number of paired peaks: 1869 INFO @ Mon, 13 Nov 2017 13:17:54: start model_add_line... INFO @ Mon, 13 Nov 2017 13:17:54: start X-correlation... INFO @ Mon, 13 Nov 2017 13:17:54: end of X-cor INFO @ Mon, 13 Nov 2017 13:17:54: #2 finished! INFO @ Mon, 13 Nov 2017 13:17:54: #2 predicted fragment length is 206 bps INFO @ Mon, 13 Nov 2017 13:17:54: #2 alternative fragment length(s) may be 206 bps INFO @ Mon, 13 Nov 2017 13:17:54: #2.2 Generate R script for model : SRX2576648.10_model.r INFO @ Mon, 13 Nov 2017 13:17:54: #3 Call peaks... INFO @ Mon, 13 Nov 2017 13:17:54: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 13 Nov 2017 13:18:11: #3 Call peaks for each chromosome... INFO @ Mon, 13 Nov 2017 13:18:12: #3 Call peaks for each chromosome... INFO @ Mon, 13 Nov 2017 13:18:15: #3 Call peaks for each chromosome... INFO @ Mon, 13 Nov 2017 13:18:20: #4 Write output xls file... SRX2576648.05_peaks.xls INFO @ Mon, 13 Nov 2017 13:18:20: #4 Write peak in narrowPeak format file... SRX2576648.05_peaks.narrowPeak INFO @ Mon, 13 Nov 2017 13:18:20: #4 Write summits bed file... SRX2576648.05_summits.bed INFO @ Mon, 13 Nov 2017 13:18:20: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (3309 records, 4 fields): 36 millis CompletedMACS2peakCalling INFO @ Mon, 13 Nov 2017 13:18:21: #4 Write output xls file... SRX2576648.20_peaks.xls INFO @ Mon, 13 Nov 2017 13:18:21: #4 Write peak in narrowPeak format file... SRX2576648.20_peaks.narrowPeak INFO @ Mon, 13 Nov 2017 13:18:21: #4 Write summits bed file... SRX2576648.20_summits.bed INFO @ Mon, 13 Nov 2017 13:18:21: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (1880 records, 4 fields): 38 millis CompletedMACS2peakCalling INFO @ Mon, 13 Nov 2017 13:18:23: #4 Write output xls file... SRX2576648.10_peaks.xls INFO @ Mon, 13 Nov 2017 13:18:23: #4 Write peak in narrowPeak format file... SRX2576648.10_peaks.narrowPeak INFO @ Mon, 13 Nov 2017 13:18:23: #4 Write summits bed file... SRX2576648.10_summits.bed INFO @ Mon, 13 Nov 2017 13:18:23: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (2542 records, 4 fields): 4 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。