Job ID = 10924618 sra ファイルのダウンロード中... Completed: 293695K bytes transferred in 10 seconds (230562K 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... Read 13448762 spots for /home/okishinya/chipatlas/results/dm3/SRX2399658/SRR5081492.sra Written 13448762 spots for /home/okishinya/chipatlas/results/dm3/SRX2399658/SRR5081492.sra 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: 00:00:01 Multiseed full-index search: 00:05:38 13448762 reads; of these: 13448762 (100.00%) were unpaired; of these: 913167 (6.79%) aligned 0 times 8525195 (63.39%) aligned exactly 1 time 4010400 (29.82%) aligned >1 times 93.21% overall alignment rate Time searching: 00:05:39 Overall time: 00:05:39 マッピングが完了しました。 samtools でBAM に変換中... [samopen] SAM header is present: 15 sequences. [bam_sort_core] merging from 8 files... [bam_rmdupse_core] 2873778 / 12535595 = 0.2292 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, 06 Aug 2018 10:35:32: # Command line: callpeak -t SRX2399658.bam -f BAM -g dm -n SRX2399658.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX2399658.05 # format = BAM # ChIP-seq file = ['SRX2399658.bam'] # control file = None # effective genome size = 1.20e+08 # 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, 06 Aug 2018 10:35:32: # Command line: callpeak -t SRX2399658.bam -f BAM -g dm -n SRX2399658.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX2399658.10 # format = BAM # ChIP-seq file = ['SRX2399658.bam'] # control file = None # effective genome size = 1.20e+08 # 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, 06 Aug 2018 10:35:32: #1 read tag files... INFO @ Mon, 06 Aug 2018 10:35:32: #1 read tag files... INFO @ Mon, 06 Aug 2018 10:35:32: #1 read treatment tags... INFO @ Mon, 06 Aug 2018 10:35:32: #1 read treatment tags... INFO @ Mon, 06 Aug 2018 10:35:32: # Command line: callpeak -t SRX2399658.bam -f BAM -g dm -n SRX2399658.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX2399658.20 # format = BAM # ChIP-seq file = ['SRX2399658.bam'] # control file = None # effective genome size = 1.20e+08 # 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, 06 Aug 2018 10:35:32: #1 read tag files... INFO @ Mon, 06 Aug 2018 10:35:32: #1 read treatment tags... INFO @ Mon, 06 Aug 2018 10:35:39: 1000000 INFO @ Mon, 06 Aug 2018 10:35:39: 1000000 INFO @ Mon, 06 Aug 2018 10:35:39: 1000000 INFO @ Mon, 06 Aug 2018 10:35:46: 2000000 INFO @ Mon, 06 Aug 2018 10:35:46: 2000000 INFO @ Mon, 06 Aug 2018 10:35:46: 2000000 INFO @ Mon, 06 Aug 2018 10:35:53: 3000000 INFO @ Mon, 06 Aug 2018 10:35:53: 3000000 INFO @ Mon, 06 Aug 2018 10:35:53: 3000000 INFO @ Mon, 06 Aug 2018 10:36:00: 4000000 INFO @ Mon, 06 Aug 2018 10:36:00: 4000000 INFO @ Mon, 06 Aug 2018 10:36:00: 4000000 INFO @ Mon, 06 Aug 2018 10:36:07: 5000000 INFO @ Mon, 06 Aug 2018 10:36:07: 5000000 INFO @ Mon, 06 Aug 2018 10:36:07: 5000000 INFO @ Mon, 06 Aug 2018 10:36:13: 6000000 INFO @ Mon, 06 Aug 2018 10:36:14: 6000000 INFO @ Mon, 06 Aug 2018 10:36:14: 6000000 INFO @ Mon, 06 Aug 2018 10:36:20: 7000000 INFO @ Mon, 06 Aug 2018 10:36:21: 7000000 INFO @ Mon, 06 Aug 2018 10:36:21: 7000000 INFO @ Mon, 06 Aug 2018 10:36:27: 8000000 INFO @ Mon, 06 Aug 2018 10:36:28: 8000000 INFO @ Mon, 06 Aug 2018 10:36:28: 8000000 INFO @ Mon, 06 Aug 2018 10:36:34: 9000000 INFO @ Mon, 06 Aug 2018 10:36:35: 9000000 INFO @ Mon, 06 Aug 2018 10:36:35: 9000000 INFO @ Mon, 06 Aug 2018 10:36:38: #1 tag size is determined as 51 bps INFO @ Mon, 06 Aug 2018 10:36:38: #1 tag size = 51 INFO @ Mon, 06 Aug 2018 10:36:38: #1 total tags in treatment: 9661817 INFO @ Mon, 06 Aug 2018 10:36:38: #1 user defined the maximum tags... INFO @ Mon, 06 Aug 2018 10:36:38: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Mon, 06 Aug 2018 10:36:38: #1 tags after filtering in treatment: 9661817 INFO @ Mon, 06 Aug 2018 10:36:38: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 06 Aug 2018 10:36:38: #1 finished! INFO @ Mon, 06 Aug 2018 10:36:38: #2 Build Peak Model... INFO @ Mon, 06 Aug 2018 10:36:38: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 06 Aug 2018 10:36:40: #2 number of paired peaks: 8066 INFO @ Mon, 06 Aug 2018 10:36:40: start model_add_line... INFO @ Mon, 06 Aug 2018 10:36:40: #1 tag size is determined as 51 bps INFO @ Mon, 06 Aug 2018 10:36:40: #1 tag size = 51 INFO @ Mon, 06 Aug 2018 10:36:40: #1 total tags in treatment: 9661817 INFO @ Mon, 06 Aug 2018 10:36:40: #1 user defined the maximum tags... INFO @ Mon, 06 Aug 2018 10:36:40: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Mon, 06 Aug 2018 10:36:40: #1 tag size is determined as 51 bps INFO @ Mon, 06 Aug 2018 10:36:40: #1 tag size = 51 INFO @ Mon, 06 Aug 2018 10:36:40: #1 total tags in treatment: 9661817 INFO @ Mon, 06 Aug 2018 10:36:40: #1 user defined the maximum tags... INFO @ Mon, 06 Aug 2018 10:36:40: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Mon, 06 Aug 2018 10:36:40: start X-correlation... INFO @ Mon, 06 Aug 2018 10:36:40: #1 tags after filtering in treatment: 9661817 INFO @ Mon, 06 Aug 2018 10:36:40: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 06 Aug 2018 10:36:40: #1 finished! INFO @ Mon, 06 Aug 2018 10:36:40: #2 Build Peak Model... INFO @ Mon, 06 Aug 2018 10:36:40: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 06 Aug 2018 10:36:40: #1 tags after filtering in treatment: 9661817 INFO @ Mon, 06 Aug 2018 10:36:40: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 06 Aug 2018 10:36:40: #1 finished! INFO @ Mon, 06 Aug 2018 10:36:40: #2 Build Peak Model... INFO @ Mon, 06 Aug 2018 10:36:40: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 06 Aug 2018 10:36:40: end of X-cor INFO @ Mon, 06 Aug 2018 10:36:40: #2 finished! INFO @ Mon, 06 Aug 2018 10:36:40: #2 predicted fragment length is 180 bps INFO @ Mon, 06 Aug 2018 10:36:40: #2 alternative fragment length(s) may be 180 bps INFO @ Mon, 06 Aug 2018 10:36:40: #2.2 Generate R script for model : SRX2399658.10_model.r INFO @ Mon, 06 Aug 2018 10:36:40: #3 Call peaks... INFO @ Mon, 06 Aug 2018 10:36:40: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 06 Aug 2018 10:36:41: #2 number of paired peaks: 8066 INFO @ Mon, 06 Aug 2018 10:36:41: start model_add_line... INFO @ Mon, 06 Aug 2018 10:36:42: #2 number of paired peaks: 8066 INFO @ Mon, 06 Aug 2018 10:36:42: start model_add_line... INFO @ Mon, 06 Aug 2018 10:36:42: start X-correlation... INFO @ Mon, 06 Aug 2018 10:36:42: end of X-cor INFO @ Mon, 06 Aug 2018 10:36:42: #2 finished! INFO @ Mon, 06 Aug 2018 10:36:42: #2 predicted fragment length is 180 bps INFO @ Mon, 06 Aug 2018 10:36:42: #2 alternative fragment length(s) may be 180 bps INFO @ Mon, 06 Aug 2018 10:36:42: #2.2 Generate R script for model : SRX2399658.20_model.r INFO @ Mon, 06 Aug 2018 10:36:42: #3 Call peaks... INFO @ Mon, 06 Aug 2018 10:36:42: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 06 Aug 2018 10:36:42: start X-correlation... INFO @ Mon, 06 Aug 2018 10:36:42: end of X-cor INFO @ Mon, 06 Aug 2018 10:36:42: #2 finished! INFO @ Mon, 06 Aug 2018 10:36:42: #2 predicted fragment length is 180 bps INFO @ Mon, 06 Aug 2018 10:36:42: #2 alternative fragment length(s) may be 180 bps INFO @ Mon, 06 Aug 2018 10:36:42: #2.2 Generate R script for model : SRX2399658.05_model.r INFO @ Mon, 06 Aug 2018 10:36:42: #3 Call peaks... INFO @ Mon, 06 Aug 2018 10:36:42: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 06 Aug 2018 10:37:08: #3 Call peaks for each chromosome... INFO @ Mon, 06 Aug 2018 10:37:10: #3 Call peaks for each chromosome... INFO @ Mon, 06 Aug 2018 10:37:11: #3 Call peaks for each chromosome... INFO @ Mon, 06 Aug 2018 10:37:22: #4 Write output xls file... SRX2399658.10_peaks.xls INFO @ Mon, 06 Aug 2018 10:37:22: #4 Write peak in narrowPeak format file... SRX2399658.10_peaks.narrowPeak INFO @ Mon, 06 Aug 2018 10:37:22: #4 Write summits bed file... SRX2399658.10_summits.bed INFO @ Mon, 06 Aug 2018 10:37:22: Done! pass1 - making usageList (14 chroms): 3 millis pass2 - checking and writing primary data (8419 records, 4 fields): 12 millis CompletedMACS2peakCalling INFO @ Mon, 06 Aug 2018 10:37:24: #4 Write output xls file... SRX2399658.05_peaks.xls INFO @ Mon, 06 Aug 2018 10:37:24: #4 Write peak in narrowPeak format file... SRX2399658.05_peaks.narrowPeak INFO @ Mon, 06 Aug 2018 10:37:24: #4 Write summits bed file... SRX2399658.05_summits.bed INFO @ Mon, 06 Aug 2018 10:37:24: Done! pass1 - making usageList (14 chroms): 2 millis pass2 - checking and writing primary data (9818 records, 4 fields): 14 millis CompletedMACS2peakCalling INFO @ Mon, 06 Aug 2018 10:37:27: #4 Write output xls file... SRX2399658.20_peaks.xls INFO @ Mon, 06 Aug 2018 10:37:27: #4 Write peak in narrowPeak format file... SRX2399658.20_peaks.narrowPeak INFO @ Mon, 06 Aug 2018 10:37:27: #4 Write summits bed file... SRX2399658.20_summits.bed INFO @ Mon, 06 Aug 2018 10:37:27: Done! pass1 - making usageList (14 chroms): 2 millis pass2 - checking and writing primary data (7074 records, 4 fields): 11 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。