Job ID = 11158491 sra ファイルのダウンロード中... Completed: 1858381K bytes transferred in 24 seconds (632045K 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: PAIRED fastq に変換中... Read 29087789 spots for /home/okishinya/chipatlas/results/dm3/SRX4279662/SRR7408140.sra Written 29087789 spots for /home/okishinya/chipatlas/results/dm3/SRX4279662/SRR7408140.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: 01:08:35 29087789 reads; of these: 29087789 (100.00%) were paired; of these: 7024751 (24.15%) aligned concordantly 0 times 18184116 (62.51%) aligned concordantly exactly 1 time 3878922 (13.34%) aligned concordantly >1 times ---- 7024751 pairs aligned concordantly 0 times; of these: 44582 (0.63%) aligned discordantly 1 time ---- 6980169 pairs aligned 0 times concordantly or discordantly; of these: 13960338 mates make up the pairs; of these: 12422829 (88.99%) aligned 0 times 914170 (6.55%) aligned exactly 1 time 623339 (4.47%) aligned >1 times 78.65% overall alignment rate Time searching: 01:08:35 Overall time: 01:08:36 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 20 files... [bam_rmdup_core] processing reference chr2L... [bam_rmdup_core] processing reference chr2LHet... [bam_rmdup_core] processing reference chr2R... [bam_rmdup_core] processing reference chr2RHet... [bam_rmdup_core] processing reference chr3L... [bam_rmdup_core] processing reference chr3LHet... [bam_rmdup_core] processing reference chr3R... [bam_rmdup_core] processing reference chr3RHet... [bam_rmdup_core] processing reference chr4... [bam_rmdup_core] processing reference chrM... [bam_rmdup_core] processing reference chrU... [bam_rmdup_core] processing reference chrUextra... [bam_rmdup_core] processing reference chrX... [bam_rmdup_core] processing reference chrXHet... [bam_rmdup_core] processing reference chrYHet... [bam_rmdup_core] 17415963 / 22044620 = 0.7900 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 @ Tue, 04 Sep 2018 10:58:35: # Command line: callpeak -t SRX4279662.bam -f BAM -g dm -n SRX4279662.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX4279662.20 # format = BAM # ChIP-seq file = ['SRX4279662.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 @ Tue, 04 Sep 2018 10:58:35: # Command line: callpeak -t SRX4279662.bam -f BAM -g dm -n SRX4279662.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX4279662.05 # format = BAM # ChIP-seq file = ['SRX4279662.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 @ Tue, 04 Sep 2018 10:58:35: # Command line: callpeak -t SRX4279662.bam -f BAM -g dm -n SRX4279662.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX4279662.10 # format = BAM # ChIP-seq file = ['SRX4279662.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 @ Tue, 04 Sep 2018 10:58:35: #1 read tag files... INFO @ Tue, 04 Sep 2018 10:58:35: #1 read tag files... INFO @ Tue, 04 Sep 2018 10:58:35: #1 read tag files... INFO @ Tue, 04 Sep 2018 10:58:35: #1 read treatment tags... INFO @ Tue, 04 Sep 2018 10:58:35: #1 read treatment tags... INFO @ Tue, 04 Sep 2018 10:58:35: #1 read treatment tags... INFO @ Tue, 04 Sep 2018 10:58:43: 1000000 INFO @ Tue, 04 Sep 2018 10:58:43: 1000000 INFO @ Tue, 04 Sep 2018 10:58:43: 1000000 INFO @ Tue, 04 Sep 2018 10:58:50: 2000000 INFO @ Tue, 04 Sep 2018 10:58:51: 2000000 INFO @ Tue, 04 Sep 2018 10:58:51: 2000000 INFO @ Tue, 04 Sep 2018 10:58:58: 3000000 INFO @ Tue, 04 Sep 2018 10:58:58: 3000000 INFO @ Tue, 04 Sep 2018 10:58:58: 3000000 INFO @ Tue, 04 Sep 2018 10:59:05: 4000000 INFO @ Tue, 04 Sep 2018 10:59:06: 4000000 INFO @ Tue, 04 Sep 2018 10:59:06: 4000000 INFO @ Tue, 04 Sep 2018 10:59:13: 5000000 INFO @ Tue, 04 Sep 2018 10:59:13: 5000000 INFO @ Tue, 04 Sep 2018 10:59:13: 5000000 INFO @ Tue, 04 Sep 2018 10:59:20: 6000000 INFO @ Tue, 04 Sep 2018 10:59:21: 6000000 INFO @ Tue, 04 Sep 2018 10:59:21: 6000000 INFO @ Tue, 04 Sep 2018 10:59:28: 7000000 INFO @ Tue, 04 Sep 2018 10:59:28: 7000000 INFO @ Tue, 04 Sep 2018 10:59:28: 7000000 INFO @ Tue, 04 Sep 2018 10:59:35: 8000000 INFO @ Tue, 04 Sep 2018 10:59:36: 8000000 INFO @ Tue, 04 Sep 2018 10:59:36: 8000000 INFO @ Tue, 04 Sep 2018 10:59:43: 9000000 INFO @ Tue, 04 Sep 2018 10:59:44: 9000000 INFO @ Tue, 04 Sep 2018 10:59:44: 9000000 INFO @ Tue, 04 Sep 2018 10:59:50: 10000000 INFO @ Tue, 04 Sep 2018 10:59:51: 10000000 INFO @ Tue, 04 Sep 2018 10:59:51: 10000000 INFO @ Tue, 04 Sep 2018 10:59:57: #1 tag size is determined as 78 bps INFO @ Tue, 04 Sep 2018 10:59:57: #1 tag size = 78 INFO @ Tue, 04 Sep 2018 10:59:57: #1 total tags in treatment: 4658624 INFO @ Tue, 04 Sep 2018 10:59:57: #1 user defined the maximum tags... INFO @ Tue, 04 Sep 2018 10:59:57: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 04 Sep 2018 10:59:57: #1 tags after filtering in treatment: 4481738 INFO @ Tue, 04 Sep 2018 10:59:57: #1 Redundant rate of treatment: 0.04 INFO @ Tue, 04 Sep 2018 10:59:57: #1 finished! INFO @ Tue, 04 Sep 2018 10:59:57: #2 Build Peak Model... INFO @ Tue, 04 Sep 2018 10:59:57: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 04 Sep 2018 10:59:57: #2 number of paired peaks: 1362 INFO @ Tue, 04 Sep 2018 10:59:57: start model_add_line... INFO @ Tue, 04 Sep 2018 10:59:57: start X-correlation... INFO @ Tue, 04 Sep 2018 10:59:58: end of X-cor INFO @ Tue, 04 Sep 2018 10:59:58: #2 finished! INFO @ Tue, 04 Sep 2018 10:59:58: #2 predicted fragment length is 189 bps INFO @ Tue, 04 Sep 2018 10:59:58: #2 alternative fragment length(s) may be 189 bps INFO @ Tue, 04 Sep 2018 10:59:58: #2.2 Generate R script for model : SRX4279662.10_model.r INFO @ Tue, 04 Sep 2018 10:59:58: #3 Call peaks... INFO @ Tue, 04 Sep 2018 10:59:58: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 04 Sep 2018 10:59:58: #1 tag size is determined as 78 bps INFO @ Tue, 04 Sep 2018 10:59:58: #1 tag size = 78 INFO @ Tue, 04 Sep 2018 10:59:58: #1 total tags in treatment: 4658624 INFO @ Tue, 04 Sep 2018 10:59:58: #1 user defined the maximum tags... INFO @ Tue, 04 Sep 2018 10:59:58: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 04 Sep 2018 10:59:58: #1 tag size is determined as 78 bps INFO @ Tue, 04 Sep 2018 10:59:58: #1 tag size = 78 INFO @ Tue, 04 Sep 2018 10:59:58: #1 total tags in treatment: 4658624 INFO @ Tue, 04 Sep 2018 10:59:58: #1 user defined the maximum tags... INFO @ Tue, 04 Sep 2018 10:59:58: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 04 Sep 2018 10:59:58: #1 tags after filtering in treatment: 4481738 INFO @ Tue, 04 Sep 2018 10:59:58: #1 Redundant rate of treatment: 0.04 INFO @ Tue, 04 Sep 2018 10:59:58: #1 finished! INFO @ Tue, 04 Sep 2018 10:59:58: #2 Build Peak Model... INFO @ Tue, 04 Sep 2018 10:59:58: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 04 Sep 2018 10:59:58: #1 tags after filtering in treatment: 4481738 INFO @ Tue, 04 Sep 2018 10:59:58: #1 Redundant rate of treatment: 0.04 INFO @ Tue, 04 Sep 2018 10:59:58: #1 finished! INFO @ Tue, 04 Sep 2018 10:59:58: #2 Build Peak Model... INFO @ Tue, 04 Sep 2018 10:59:58: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 04 Sep 2018 10:59:58: #2 number of paired peaks: 1362 INFO @ Tue, 04 Sep 2018 10:59:58: start model_add_line... INFO @ Tue, 04 Sep 2018 10:59:58: #2 number of paired peaks: 1362 INFO @ Tue, 04 Sep 2018 10:59:58: start model_add_line... INFO @ Tue, 04 Sep 2018 10:59:58: start X-correlation... INFO @ Tue, 04 Sep 2018 10:59:59: end of X-cor INFO @ Tue, 04 Sep 2018 10:59:59: #2 finished! INFO @ Tue, 04 Sep 2018 10:59:59: #2 predicted fragment length is 189 bps INFO @ Tue, 04 Sep 2018 10:59:59: #2 alternative fragment length(s) may be 189 bps INFO @ Tue, 04 Sep 2018 10:59:59: #2.2 Generate R script for model : SRX4279662.05_model.r INFO @ Tue, 04 Sep 2018 10:59:59: #3 Call peaks... INFO @ Tue, 04 Sep 2018 10:59:59: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 04 Sep 2018 10:59:59: start X-correlation... INFO @ Tue, 04 Sep 2018 10:59:59: end of X-cor INFO @ Tue, 04 Sep 2018 10:59:59: #2 finished! INFO @ Tue, 04 Sep 2018 10:59:59: #2 predicted fragment length is 189 bps INFO @ Tue, 04 Sep 2018 10:59:59: #2 alternative fragment length(s) may be 189 bps INFO @ Tue, 04 Sep 2018 10:59:59: #2.2 Generate R script for model : SRX4279662.20_model.r INFO @ Tue, 04 Sep 2018 10:59:59: #3 Call peaks... INFO @ Tue, 04 Sep 2018 10:59:59: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 04 Sep 2018 11:00:08: #3 Call peaks for each chromosome... INFO @ Tue, 04 Sep 2018 11:00:09: #3 Call peaks for each chromosome... INFO @ Tue, 04 Sep 2018 11:00:10: #3 Call peaks for each chromosome... INFO @ Tue, 04 Sep 2018 11:00:15: #4 Write output xls file... SRX4279662.10_peaks.xls INFO @ Tue, 04 Sep 2018 11:00:15: #4 Write peak in narrowPeak format file... SRX4279662.10_peaks.narrowPeak INFO @ Tue, 04 Sep 2018 11:00:15: #4 Write summits bed file... SRX4279662.10_summits.bed INFO @ Tue, 04 Sep 2018 11:00:15: Done! pass1 - making usageList (12 chroms): 1 millis pass2 - checking and writing primary data (2044 records, 4 fields): 6 millis CompletedMACS2peakCalling INFO @ Tue, 04 Sep 2018 11:00:15: #4 Write output xls file... SRX4279662.05_peaks.xls INFO @ Tue, 04 Sep 2018 11:00:15: #4 Write peak in narrowPeak format file... SRX4279662.05_peaks.narrowPeak INFO @ Tue, 04 Sep 2018 11:00:15: #4 Write summits bed file... SRX4279662.05_summits.bed INFO @ Tue, 04 Sep 2018 11:00:15: Done! INFO @ Tue, 04 Sep 2018 11:00:15: #4 Write output xls file... SRX4279662.20_peaks.xls INFO @ Tue, 04 Sep 2018 11:00:15: #4 Write peak in narrowPeak format file... SRX4279662.20_peaks.narrowPeak INFO @ Tue, 04 Sep 2018 11:00:15: #4 Write summits bed file... SRX4279662.20_summits.bed INFO @ Tue, 04 Sep 2018 11:00:15: Done! pass1 - making usageList (11 chroms): 1 millis pass2 - checking and writing primary data (473 records, 4 fields): 2 millis CompletedMACS2peakCalling pass1 - making usageList (15 chroms): 2 millis pass2 - checking and writing primary data (4851 records, 4 fields): 7 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。