Job ID = 10714565 sra ファイルのダウンロード中... Completed: 310323K bytes transferred in 23 seconds (109552K 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 16328647 spots for /home/okishinya/chipatlas/results/dm3/SRX4053299/SRR7132414.sra Written 16328647 spots for /home/okishinya/chipatlas/results/dm3/SRX4053299/SRR7132414.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: 00:00:00 Multiseed full-index search: 00:03:56 16328647 reads; of these: 16328647 (100.00%) were unpaired; of these: 1997079 (12.23%) aligned 0 times 13323936 (81.60%) aligned exactly 1 time 1007632 (6.17%) aligned >1 times 87.77% overall alignment rate Time searching: 00:03:56 Overall time: 00:03:57 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] 6699568 / 14331568 = 0.4675 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 @ Sun, 03 Jun 2018 13:35:51: # Command line: callpeak -t SRX4053299.bam -f BAM -g dm -n SRX4053299.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX4053299.05 # format = BAM # ChIP-seq file = ['SRX4053299.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 @ Sun, 03 Jun 2018 13:35:51: #1 read tag files... INFO @ Sun, 03 Jun 2018 13:35:51: #1 read treatment tags... INFO @ Sun, 03 Jun 2018 13:35:51: # Command line: callpeak -t SRX4053299.bam -f BAM -g dm -n SRX4053299.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX4053299.20 # format = BAM # ChIP-seq file = ['SRX4053299.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 @ Sun, 03 Jun 2018 13:35:51: #1 read tag files... INFO @ Sun, 03 Jun 2018 13:35:51: #1 read treatment tags... INFO @ Sun, 03 Jun 2018 13:35:51: # Command line: callpeak -t SRX4053299.bam -f BAM -g dm -n SRX4053299.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX4053299.10 # format = BAM # ChIP-seq file = ['SRX4053299.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 @ Sun, 03 Jun 2018 13:35:51: #1 read tag files... INFO @ Sun, 03 Jun 2018 13:35:51: #1 read treatment tags... INFO @ Sun, 03 Jun 2018 13:35:58: 1000000 INFO @ Sun, 03 Jun 2018 13:35:58: 1000000 INFO @ Sun, 03 Jun 2018 13:35:58: 1000000 INFO @ Sun, 03 Jun 2018 13:36:04: 2000000 INFO @ Sun, 03 Jun 2018 13:36:05: 2000000 INFO @ Sun, 03 Jun 2018 13:36:05: 2000000 INFO @ Sun, 03 Jun 2018 13:36:11: 3000000 INFO @ Sun, 03 Jun 2018 13:36:11: 3000000 INFO @ Sun, 03 Jun 2018 13:36:11: 3000000 INFO @ Sun, 03 Jun 2018 13:36:17: 4000000 INFO @ Sun, 03 Jun 2018 13:36:18: 4000000 INFO @ Sun, 03 Jun 2018 13:36:18: 4000000 INFO @ Sun, 03 Jun 2018 13:36:24: 5000000 INFO @ Sun, 03 Jun 2018 13:36:25: 5000000 INFO @ Sun, 03 Jun 2018 13:36:25: 5000000 INFO @ Sun, 03 Jun 2018 13:36:30: 6000000 INFO @ Sun, 03 Jun 2018 13:36:31: 6000000 INFO @ Sun, 03 Jun 2018 13:36:32: 6000000 INFO @ Sun, 03 Jun 2018 13:36:37: 7000000 INFO @ Sun, 03 Jun 2018 13:36:38: 7000000 INFO @ Sun, 03 Jun 2018 13:36:38: 7000000 INFO @ Sun, 03 Jun 2018 13:36:41: #1 tag size is determined as 50 bps INFO @ Sun, 03 Jun 2018 13:36:41: #1 tag size = 50 INFO @ Sun, 03 Jun 2018 13:36:41: #1 total tags in treatment: 7632000 INFO @ Sun, 03 Jun 2018 13:36:41: #1 user defined the maximum tags... INFO @ Sun, 03 Jun 2018 13:36:41: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sun, 03 Jun 2018 13:36:41: #1 tags after filtering in treatment: 7632000 INFO @ Sun, 03 Jun 2018 13:36:41: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 03 Jun 2018 13:36:41: #1 finished! INFO @ Sun, 03 Jun 2018 13:36:41: #2 Build Peak Model... INFO @ Sun, 03 Jun 2018 13:36:41: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 03 Jun 2018 13:36:42: #2 number of paired peaks: 10521 INFO @ Sun, 03 Jun 2018 13:36:42: start model_add_line... INFO @ Sun, 03 Jun 2018 13:36:42: #1 tag size is determined as 50 bps INFO @ Sun, 03 Jun 2018 13:36:42: #1 tag size = 50 INFO @ Sun, 03 Jun 2018 13:36:42: #1 total tags in treatment: 7632000 INFO @ Sun, 03 Jun 2018 13:36:42: #1 user defined the maximum tags... INFO @ Sun, 03 Jun 2018 13:36:42: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sun, 03 Jun 2018 13:36:43: #1 tags after filtering in treatment: 7632000 INFO @ Sun, 03 Jun 2018 13:36:43: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 03 Jun 2018 13:36:43: #1 finished! INFO @ Sun, 03 Jun 2018 13:36:43: #2 Build Peak Model... INFO @ Sun, 03 Jun 2018 13:36:43: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 03 Jun 2018 13:36:43: start X-correlation... INFO @ Sun, 03 Jun 2018 13:36:43: end of X-cor INFO @ Sun, 03 Jun 2018 13:36:43: #2 finished! INFO @ Sun, 03 Jun 2018 13:36:43: #2 predicted fragment length is 173 bps INFO @ Sun, 03 Jun 2018 13:36:43: #2 alternative fragment length(s) may be 173 bps INFO @ Sun, 03 Jun 2018 13:36:43: #2.2 Generate R script for model : SRX4053299.10_model.r INFO @ Sun, 03 Jun 2018 13:36:43: #3 Call peaks... INFO @ Sun, 03 Jun 2018 13:36:43: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 03 Jun 2018 13:36:43: #1 tag size is determined as 50 bps INFO @ Sun, 03 Jun 2018 13:36:43: #1 tag size = 50 INFO @ Sun, 03 Jun 2018 13:36:43: #1 total tags in treatment: 7632000 INFO @ Sun, 03 Jun 2018 13:36:43: #1 user defined the maximum tags... INFO @ Sun, 03 Jun 2018 13:36:43: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sun, 03 Jun 2018 13:36:43: #1 tags after filtering in treatment: 7632000 INFO @ Sun, 03 Jun 2018 13:36:43: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 03 Jun 2018 13:36:43: #1 finished! INFO @ Sun, 03 Jun 2018 13:36:43: #2 Build Peak Model... INFO @ Sun, 03 Jun 2018 13:36:43: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 03 Jun 2018 13:36:44: #2 number of paired peaks: 10521 INFO @ Sun, 03 Jun 2018 13:36:44: start model_add_line... INFO @ Sun, 03 Jun 2018 13:36:44: start X-correlation... INFO @ Sun, 03 Jun 2018 13:36:44: end of X-cor INFO @ Sun, 03 Jun 2018 13:36:44: #2 finished! INFO @ Sun, 03 Jun 2018 13:36:44: #2 predicted fragment length is 173 bps INFO @ Sun, 03 Jun 2018 13:36:44: #2 alternative fragment length(s) may be 173 bps INFO @ Sun, 03 Jun 2018 13:36:44: #2.2 Generate R script for model : SRX4053299.05_model.r INFO @ Sun, 03 Jun 2018 13:36:44: #3 Call peaks... INFO @ Sun, 03 Jun 2018 13:36:44: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 03 Jun 2018 13:36:44: #2 number of paired peaks: 10521 INFO @ Sun, 03 Jun 2018 13:36:44: start model_add_line... INFO @ Sun, 03 Jun 2018 13:36:45: start X-correlation... INFO @ Sun, 03 Jun 2018 13:36:45: end of X-cor INFO @ Sun, 03 Jun 2018 13:36:45: #2 finished! INFO @ Sun, 03 Jun 2018 13:36:45: #2 predicted fragment length is 173 bps INFO @ Sun, 03 Jun 2018 13:36:45: #2 alternative fragment length(s) may be 173 bps INFO @ Sun, 03 Jun 2018 13:36:45: #2.2 Generate R script for model : SRX4053299.20_model.r INFO @ Sun, 03 Jun 2018 13:36:45: #3 Call peaks... INFO @ Sun, 03 Jun 2018 13:36:45: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 03 Jun 2018 13:37:06: #3 Call peaks for each chromosome... INFO @ Sun, 03 Jun 2018 13:37:09: #3 Call peaks for each chromosome... INFO @ Sun, 03 Jun 2018 13:37:09: #3 Call peaks for each chromosome... INFO @ Sun, 03 Jun 2018 13:37:18: #4 Write output xls file... SRX4053299.10_peaks.xls INFO @ Sun, 03 Jun 2018 13:37:18: #4 Write peak in narrowPeak format file... SRX4053299.10_peaks.narrowPeak INFO @ Sun, 03 Jun 2018 13:37:18: #4 Write summits bed file... SRX4053299.10_summits.bed INFO @ Sun, 03 Jun 2018 13:37:18: Done! pass1 - making usageList (15 chroms): 2 millis pass2 - checking and writing primary data (6185 records, 4 fields): 9 millis CompletedMACS2peakCalling INFO @ Sun, 03 Jun 2018 13:37:20: #4 Write output xls file... SRX4053299.05_peaks.xls INFO @ Sun, 03 Jun 2018 13:37:20: #4 Write peak in narrowPeak format file... SRX4053299.05_peaks.narrowPeak INFO @ Sun, 03 Jun 2018 13:37:20: #4 Write summits bed file... SRX4053299.05_summits.bed INFO @ Sun, 03 Jun 2018 13:37:20: Done! pass1 - making usageList (15 chroms): 2 millis pass2 - checking and writing primary data (6545 records, 4 fields): 10 millis CompletedMACS2peakCalling INFO @ Sun, 03 Jun 2018 13:37:21: #4 Write output xls file... SRX4053299.20_peaks.xls INFO @ Sun, 03 Jun 2018 13:37:21: #4 Write peak in narrowPeak format file... SRX4053299.20_peaks.narrowPeak INFO @ Sun, 03 Jun 2018 13:37:21: #4 Write summits bed file... SRX4053299.20_summits.bed INFO @ Sun, 03 Jun 2018 13:37:21: Done! pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (5705 records, 4 fields): 9 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。