Job ID = 10201969 sra ファイルのダウンロード中... Completed: 413854K bytes transferred in 13 seconds (253382K 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 23329304 spots for /home/okishinya/chipatlas/results/ce10/SRX2576638/SRR5272595.sra Written 23329304 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: 00:05:51 23329304 reads; of these: 23329304 (100.00%) were unpaired; of these: 1500994 (6.43%) aligned 0 times 17632032 (75.58%) aligned exactly 1 time 4196278 (17.99%) aligned >1 times 93.57% overall alignment rate Time searching: 00:05:51 Overall time: 00:05:51 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 12 files... [bam_rmdupse_core] 10067360 / 21828310 = 0.4612 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 13:19:24: # Command line: callpeak -t SRX2576638.bam -f BAM -g ce -n SRX2576638.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX2576638.05 # format = BAM # ChIP-seq file = ['SRX2576638.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 13:19:24: # Command line: callpeak -t SRX2576638.bam -f BAM -g ce -n SRX2576638.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX2576638.20 # format = BAM # ChIP-seq file = ['SRX2576638.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 13:19:24: # Command line: callpeak -t SRX2576638.bam -f BAM -g ce -n SRX2576638.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX2576638.10 # format = BAM # ChIP-seq file = ['SRX2576638.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 13:19:24: #1 read tag files... INFO @ Mon, 13 Nov 2017 13:19:24: #1 read tag files... INFO @ Mon, 13 Nov 2017 13:19:24: #1 read tag files... INFO @ Mon, 13 Nov 2017 13:19:24: #1 read treatment tags... INFO @ Mon, 13 Nov 2017 13:19:24: #1 read treatment tags... INFO @ Mon, 13 Nov 2017 13:19:24: #1 read treatment tags... INFO @ Mon, 13 Nov 2017 13:19:31: 1000000 INFO @ Mon, 13 Nov 2017 13:19:31: 1000000 INFO @ Mon, 13 Nov 2017 13:19:31: 1000000 INFO @ Mon, 13 Nov 2017 13:19:37: 2000000 INFO @ Mon, 13 Nov 2017 13:19:38: 2000000 INFO @ Mon, 13 Nov 2017 13:19:38: 2000000 INFO @ Mon, 13 Nov 2017 13:19:44: 3000000 INFO @ Mon, 13 Nov 2017 13:19:44: 3000000 INFO @ Mon, 13 Nov 2017 13:19:44: 3000000 INFO @ Mon, 13 Nov 2017 13:19:51: 4000000 INFO @ Mon, 13 Nov 2017 13:19:51: 4000000 INFO @ Mon, 13 Nov 2017 13:19:51: 4000000 INFO @ Mon, 13 Nov 2017 13:19:57: 5000000 INFO @ Mon, 13 Nov 2017 13:19:58: 5000000 INFO @ Mon, 13 Nov 2017 13:19:58: 5000000 INFO @ Mon, 13 Nov 2017 13:20:04: 6000000 INFO @ Mon, 13 Nov 2017 13:20:04: 6000000 INFO @ Mon, 13 Nov 2017 13:20:04: 6000000 INFO @ Mon, 13 Nov 2017 13:20:10: 7000000 INFO @ Mon, 13 Nov 2017 13:20:11: 7000000 INFO @ Mon, 13 Nov 2017 13:20:11: 7000000 INFO @ Mon, 13 Nov 2017 13:20:17: 8000000 INFO @ Mon, 13 Nov 2017 13:20:18: 8000000 INFO @ Mon, 13 Nov 2017 13:20:18: 8000000 INFO @ Mon, 13 Nov 2017 13:20:24: 9000000 INFO @ Mon, 13 Nov 2017 13:20:24: 9000000 INFO @ Mon, 13 Nov 2017 13:20:25: 9000000 INFO @ Mon, 13 Nov 2017 13:20:30: 10000000 INFO @ Mon, 13 Nov 2017 13:20:31: 10000000 INFO @ Mon, 13 Nov 2017 13:20:31: 10000000 INFO @ Mon, 13 Nov 2017 13:20:37: 11000000 INFO @ Mon, 13 Nov 2017 13:20:38: 11000000 INFO @ Mon, 13 Nov 2017 13:20:38: 11000000 INFO @ Mon, 13 Nov 2017 13:20:42: #1 tag size is determined as 51 bps INFO @ Mon, 13 Nov 2017 13:20:42: #1 tag size = 51 INFO @ Mon, 13 Nov 2017 13:20:42: #1 total tags in treatment: 11760950 INFO @ Mon, 13 Nov 2017 13:20:42: #1 user defined the maximum tags... INFO @ Mon, 13 Nov 2017 13:20:42: #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 13:20:42: #1 tags after filtering in treatment: 11760950 INFO @ Mon, 13 Nov 2017 13:20:42: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 13 Nov 2017 13:20:42: #1 finished! INFO @ Mon, 13 Nov 2017 13:20:42: #2 Build Peak Model... INFO @ Mon, 13 Nov 2017 13:20:42: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 13 Nov 2017 13:20:43: #1 tag size is determined as 51 bps INFO @ Mon, 13 Nov 2017 13:20:43: #1 tag size = 51 INFO @ Mon, 13 Nov 2017 13:20:43: #1 total tags in treatment: 11760950 INFO @ Mon, 13 Nov 2017 13:20:43: #1 user defined the maximum tags... INFO @ Mon, 13 Nov 2017 13:20:43: #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 13:20:43: #1 tags after filtering in treatment: 11760950 INFO @ Mon, 13 Nov 2017 13:20:43: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 13 Nov 2017 13:20:43: #1 finished! INFO @ Mon, 13 Nov 2017 13:20:43: #2 Build Peak Model... INFO @ Mon, 13 Nov 2017 13:20:43: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 13 Nov 2017 13:20:43: #1 tag size is determined as 51 bps INFO @ Mon, 13 Nov 2017 13:20:43: #1 tag size = 51 INFO @ Mon, 13 Nov 2017 13:20:43: #1 total tags in treatment: 11760950 INFO @ Mon, 13 Nov 2017 13:20:43: #1 user defined the maximum tags... INFO @ Mon, 13 Nov 2017 13:20:43: #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 13:20:43: #2 number of paired peaks: 1478 INFO @ Mon, 13 Nov 2017 13:20:43: start model_add_line... INFO @ Mon, 13 Nov 2017 13:20:43: #1 tags after filtering in treatment: 11760950 INFO @ Mon, 13 Nov 2017 13:20:43: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 13 Nov 2017 13:20:43: #1 finished! INFO @ Mon, 13 Nov 2017 13:20:43: #2 Build Peak Model... INFO @ Mon, 13 Nov 2017 13:20:43: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 13 Nov 2017 13:20:43: start X-correlation... INFO @ Mon, 13 Nov 2017 13:20:44: end of X-cor INFO @ Mon, 13 Nov 2017 13:20:44: #2 finished! INFO @ Mon, 13 Nov 2017 13:20:44: #2 predicted fragment length is 211 bps INFO @ Mon, 13 Nov 2017 13:20:44: #2 alternative fragment length(s) may be 211 bps INFO @ Mon, 13 Nov 2017 13:20:44: #2.2 Generate R script for model : SRX2576638.10_model.r INFO @ Mon, 13 Nov 2017 13:20:44: #3 Call peaks... INFO @ Mon, 13 Nov 2017 13:20:44: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 13 Nov 2017 13:20:44: #2 number of paired peaks: 1478 INFO @ Mon, 13 Nov 2017 13:20:44: start model_add_line... INFO @ Mon, 13 Nov 2017 13:20:44: start X-correlation... INFO @ Mon, 13 Nov 2017 13:20:44: end of X-cor INFO @ Mon, 13 Nov 2017 13:20:44: #2 finished! INFO @ Mon, 13 Nov 2017 13:20:44: #2 predicted fragment length is 211 bps INFO @ Mon, 13 Nov 2017 13:20:44: #2 alternative fragment length(s) may be 211 bps INFO @ Mon, 13 Nov 2017 13:20:44: #2.2 Generate R script for model : SRX2576638.20_model.r INFO @ Mon, 13 Nov 2017 13:20:44: #3 Call peaks... INFO @ Mon, 13 Nov 2017 13:20:44: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 13 Nov 2017 13:20:44: #2 number of paired peaks: 1478 INFO @ Mon, 13 Nov 2017 13:20:44: start model_add_line... INFO @ Mon, 13 Nov 2017 13:20:45: start X-correlation... INFO @ Mon, 13 Nov 2017 13:20:45: end of X-cor INFO @ Mon, 13 Nov 2017 13:20:45: #2 finished! INFO @ Mon, 13 Nov 2017 13:20:45: #2 predicted fragment length is 211 bps INFO @ Mon, 13 Nov 2017 13:20:45: #2 alternative fragment length(s) may be 211 bps INFO @ Mon, 13 Nov 2017 13:20:45: #2.2 Generate R script for model : SRX2576638.05_model.r INFO @ Mon, 13 Nov 2017 13:20:45: #3 Call peaks... INFO @ Mon, 13 Nov 2017 13:20:45: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 13 Nov 2017 13:21:17: #3 Call peaks for each chromosome... INFO @ Mon, 13 Nov 2017 13:21:17: #3 Call peaks for each chromosome... INFO @ Mon, 13 Nov 2017 13:21:17: #3 Call peaks for each chromosome... INFO @ Mon, 13 Nov 2017 13:21:30: #4 Write output xls file... SRX2576638.10_peaks.xls INFO @ Mon, 13 Nov 2017 13:21:30: #4 Write peak in narrowPeak format file... SRX2576638.10_peaks.narrowPeak INFO @ Mon, 13 Nov 2017 13:21:30: #4 Write summits bed file... SRX2576638.10_summits.bed INFO @ Mon, 13 Nov 2017 13:21:30: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (2576 records, 4 fields): 5 millis CompletedMACS2peakCalling INFO @ Mon, 13 Nov 2017 13:21:31: #4 Write output xls file... SRX2576638.20_peaks.xls INFO @ Mon, 13 Nov 2017 13:21:31: #4 Write peak in narrowPeak format file... SRX2576638.20_peaks.narrowPeak INFO @ Mon, 13 Nov 2017 13:21:31: #4 Write summits bed file... SRX2576638.20_summits.bed INFO @ Mon, 13 Nov 2017 13:21:31: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (1898 records, 4 fields): 4 millis CompletedMACS2peakCalling INFO @ Mon, 13 Nov 2017 13:21:31: #4 Write output xls file... SRX2576638.05_peaks.xls INFO @ Mon, 13 Nov 2017 13:21:31: #4 Write peak in narrowPeak format file... SRX2576638.05_peaks.narrowPeak INFO @ Mon, 13 Nov 2017 13:21:31: #4 Write summits bed file... SRX2576638.05_summits.bed INFO @ Mon, 13 Nov 2017 13:21:31: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (3348 records, 4 fields): 6 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。