Job ID = 11158493 sra ファイルのダウンロード中... Completed: 1297991K bytes transferred in 21 seconds (494778K 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 19960698 spots for /home/okishinya/chipatlas/results/dm3/SRX4279671/SRR7408131.sra Written 19960698 spots for /home/okishinya/chipatlas/results/dm3/SRX4279671/SRR7408131.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: 01:10:56 19960698 reads; of these: 19960698 (100.00%) were paired; of these: 8760896 (43.89%) aligned concordantly 0 times 9009835 (45.14%) aligned concordantly exactly 1 time 2189967 (10.97%) aligned concordantly >1 times ---- 8760896 pairs aligned concordantly 0 times; of these: 1525979 (17.42%) aligned discordantly 1 time ---- 7234917 pairs aligned 0 times concordantly or discordantly; of these: 14469834 mates make up the pairs; of these: 7533601 (52.06%) aligned 0 times 3424999 (23.67%) aligned exactly 1 time 3511234 (24.27%) aligned >1 times 81.13% overall alignment rate Time searching: 01:10:56 Overall time: 01:10:56 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 16 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] 1741559 / 11472982 = 0.1518 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 11:01:49: # Command line: callpeak -t SRX4279671.bam -f BAM -g dm -n SRX4279671.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX4279671.05 # format = BAM # ChIP-seq file = ['SRX4279671.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 11:01:49: # Command line: callpeak -t SRX4279671.bam -f BAM -g dm -n SRX4279671.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX4279671.20 # format = BAM # ChIP-seq file = ['SRX4279671.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 11:01:49: # Command line: callpeak -t SRX4279671.bam -f BAM -g dm -n SRX4279671.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX4279671.10 # format = BAM # ChIP-seq file = ['SRX4279671.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 11:01:49: #1 read tag files... INFO @ Tue, 04 Sep 2018 11:01:49: #1 read tag files... INFO @ Tue, 04 Sep 2018 11:01:49: #1 read tag files... INFO @ Tue, 04 Sep 2018 11:01:49: #1 read treatment tags... INFO @ Tue, 04 Sep 2018 11:01:49: #1 read treatment tags... INFO @ Tue, 04 Sep 2018 11:01:49: #1 read treatment tags... INFO @ Tue, 04 Sep 2018 11:01:57: 1000000 INFO @ Tue, 04 Sep 2018 11:01:57: 1000000 INFO @ Tue, 04 Sep 2018 11:01:57: 1000000 INFO @ Tue, 04 Sep 2018 11:02:04: 2000000 INFO @ Tue, 04 Sep 2018 11:02:04: 2000000 INFO @ Tue, 04 Sep 2018 11:02:04: 2000000 INFO @ Tue, 04 Sep 2018 11:02:11: 3000000 INFO @ Tue, 04 Sep 2018 11:02:12: 3000000 INFO @ Tue, 04 Sep 2018 11:02:12: 3000000 INFO @ Tue, 04 Sep 2018 11:02:19: 4000000 INFO @ Tue, 04 Sep 2018 11:02:19: 4000000 INFO @ Tue, 04 Sep 2018 11:02:19: 4000000 INFO @ Tue, 04 Sep 2018 11:02:26: 5000000 INFO @ Tue, 04 Sep 2018 11:02:26: 5000000 INFO @ Tue, 04 Sep 2018 11:02:27: 5000000 INFO @ Tue, 04 Sep 2018 11:02:34: 6000000 INFO @ Tue, 04 Sep 2018 11:02:34: 6000000 INFO @ Tue, 04 Sep 2018 11:02:34: 6000000 INFO @ Tue, 04 Sep 2018 11:02:41: 7000000 INFO @ Tue, 04 Sep 2018 11:02:41: 7000000 INFO @ Tue, 04 Sep 2018 11:02:42: 7000000 INFO @ Tue, 04 Sep 2018 11:02:48: 8000000 INFO @ Tue, 04 Sep 2018 11:02:49: 8000000 INFO @ Tue, 04 Sep 2018 11:02:50: 8000000 INFO @ Tue, 04 Sep 2018 11:02:55: 9000000 INFO @ Tue, 04 Sep 2018 11:02:57: 9000000 INFO @ Tue, 04 Sep 2018 11:02:57: 9000000 INFO @ Tue, 04 Sep 2018 11:03:02: 10000000 INFO @ Tue, 04 Sep 2018 11:03:05: 10000000 INFO @ Tue, 04 Sep 2018 11:03:05: 10000000 INFO @ Tue, 04 Sep 2018 11:03:09: 11000000 INFO @ Tue, 04 Sep 2018 11:03:12: 11000000 INFO @ Tue, 04 Sep 2018 11:03:13: 11000000 INFO @ Tue, 04 Sep 2018 11:03:16: 12000000 INFO @ Tue, 04 Sep 2018 11:03:20: 12000000 INFO @ Tue, 04 Sep 2018 11:03:21: 12000000 INFO @ Tue, 04 Sep 2018 11:03:23: 13000000 INFO @ Tue, 04 Sep 2018 11:03:28: 13000000 INFO @ Tue, 04 Sep 2018 11:03:28: 13000000 INFO @ Tue, 04 Sep 2018 11:03:30: 14000000 INFO @ Tue, 04 Sep 2018 11:03:36: 14000000 INFO @ Tue, 04 Sep 2018 11:03:36: 14000000 INFO @ Tue, 04 Sep 2018 11:03:37: 15000000 INFO @ Tue, 04 Sep 2018 11:03:43: 15000000 INFO @ Tue, 04 Sep 2018 11:03:44: 16000000 INFO @ Tue, 04 Sep 2018 11:03:44: 15000000 INFO @ Tue, 04 Sep 2018 11:03:51: 17000000 INFO @ Tue, 04 Sep 2018 11:03:51: 16000000 INFO @ Tue, 04 Sep 2018 11:03:52: 16000000 INFO @ Tue, 04 Sep 2018 11:03:57: 18000000 INFO @ Tue, 04 Sep 2018 11:03:59: 17000000 INFO @ Tue, 04 Sep 2018 11:04:00: 17000000 INFO @ Tue, 04 Sep 2018 11:04:04: 19000000 INFO @ Tue, 04 Sep 2018 11:04:07: 18000000 INFO @ Tue, 04 Sep 2018 11:04:07: 18000000 INFO @ Tue, 04 Sep 2018 11:04:11: 20000000 INFO @ Tue, 04 Sep 2018 11:04:14: 19000000 INFO @ Tue, 04 Sep 2018 11:04:15: 19000000 INFO @ Tue, 04 Sep 2018 11:04:18: 21000000 INFO @ Tue, 04 Sep 2018 11:04:22: 20000000 INFO @ Tue, 04 Sep 2018 11:04:23: 20000000 INFO @ Tue, 04 Sep 2018 11:04:25: 22000000 INFO @ Tue, 04 Sep 2018 11:04:30: 21000000 INFO @ Tue, 04 Sep 2018 11:04:31: 21000000 INFO @ Tue, 04 Sep 2018 11:04:32: 23000000 INFO @ Tue, 04 Sep 2018 11:04:38: 22000000 INFO @ Tue, 04 Sep 2018 11:04:38: 22000000 INFO @ Tue, 04 Sep 2018 11:04:39: 24000000 INFO @ Tue, 04 Sep 2018 11:04:45: 23000000 INFO @ Tue, 04 Sep 2018 11:04:46: 23000000 INFO @ Tue, 04 Sep 2018 11:04:46: 25000000 INFO @ Tue, 04 Sep 2018 11:04:53: 24000000 INFO @ Tue, 04 Sep 2018 11:04:53: 26000000 INFO @ Tue, 04 Sep 2018 11:04:54: 24000000 INFO @ Tue, 04 Sep 2018 11:05:00: 27000000 INFO @ Tue, 04 Sep 2018 11:05:01: 25000000 INFO @ Tue, 04 Sep 2018 11:05:01: 25000000 INFO @ Tue, 04 Sep 2018 11:05:07: 28000000 INFO @ Tue, 04 Sep 2018 11:05:08: 26000000 INFO @ Tue, 04 Sep 2018 11:05:09: 26000000 INFO @ Tue, 04 Sep 2018 11:05:13: #1 tag size is determined as 78 bps INFO @ Tue, 04 Sep 2018 11:05:13: #1 tag size = 78 INFO @ Tue, 04 Sep 2018 11:05:13: #1 total tags in treatment: 9487088 INFO @ Tue, 04 Sep 2018 11:05:13: #1 user defined the maximum tags... INFO @ Tue, 04 Sep 2018 11:05:13: #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 11:05:13: #1 tags after filtering in treatment: 8251246 INFO @ Tue, 04 Sep 2018 11:05:13: #1 Redundant rate of treatment: 0.13 INFO @ Tue, 04 Sep 2018 11:05:13: #1 finished! INFO @ Tue, 04 Sep 2018 11:05:13: #2 Build Peak Model... INFO @ Tue, 04 Sep 2018 11:05:13: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 04 Sep 2018 11:05:14: #2 number of paired peaks: 2965 INFO @ Tue, 04 Sep 2018 11:05:14: start model_add_line... INFO @ Tue, 04 Sep 2018 11:05:14: start X-correlation... INFO @ Tue, 04 Sep 2018 11:05:15: end of X-cor INFO @ Tue, 04 Sep 2018 11:05:15: #2 finished! INFO @ Tue, 04 Sep 2018 11:05:15: #2 predicted fragment length is 181 bps INFO @ Tue, 04 Sep 2018 11:05:15: #2 alternative fragment length(s) may be 181 bps INFO @ Tue, 04 Sep 2018 11:05:15: #2.2 Generate R script for model : SRX4279671.05_model.r INFO @ Tue, 04 Sep 2018 11:05:15: #3 Call peaks... INFO @ Tue, 04 Sep 2018 11:05:15: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 04 Sep 2018 11:05:16: 27000000 INFO @ Tue, 04 Sep 2018 11:05:17: 27000000 INFO @ Tue, 04 Sep 2018 11:05:24: 28000000 INFO @ Tue, 04 Sep 2018 11:05:25: 28000000 INFO @ Tue, 04 Sep 2018 11:05:31: #1 tag size is determined as 78 bps INFO @ Tue, 04 Sep 2018 11:05:31: #1 tag size = 78 INFO @ Tue, 04 Sep 2018 11:05:31: #1 total tags in treatment: 9487088 INFO @ Tue, 04 Sep 2018 11:05:31: #1 user defined the maximum tags... INFO @ Tue, 04 Sep 2018 11:05:31: #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 11:05:31: #1 tags after filtering in treatment: 8251246 INFO @ Tue, 04 Sep 2018 11:05:31: #1 Redundant rate of treatment: 0.13 INFO @ Tue, 04 Sep 2018 11:05:31: #1 finished! INFO @ Tue, 04 Sep 2018 11:05:31: #2 Build Peak Model... INFO @ Tue, 04 Sep 2018 11:05:31: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 04 Sep 2018 11:05:32: #1 tag size is determined as 78 bps INFO @ Tue, 04 Sep 2018 11:05:32: #1 tag size = 78 INFO @ Tue, 04 Sep 2018 11:05:32: #1 total tags in treatment: 9487088 INFO @ Tue, 04 Sep 2018 11:05:32: #1 user defined the maximum tags... INFO @ Tue, 04 Sep 2018 11:05:32: #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 11:05:32: #1 tags after filtering in treatment: 8251246 INFO @ Tue, 04 Sep 2018 11:05:32: #1 Redundant rate of treatment: 0.13 INFO @ Tue, 04 Sep 2018 11:05:32: #1 finished! INFO @ Tue, 04 Sep 2018 11:05:32: #2 Build Peak Model... INFO @ Tue, 04 Sep 2018 11:05:32: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 04 Sep 2018 11:05:32: #2 number of paired peaks: 2965 INFO @ Tue, 04 Sep 2018 11:05:32: start model_add_line... INFO @ Tue, 04 Sep 2018 11:05:32: start X-correlation... INFO @ Tue, 04 Sep 2018 11:05:32: end of X-cor INFO @ Tue, 04 Sep 2018 11:05:32: #2 finished! INFO @ Tue, 04 Sep 2018 11:05:32: #2 predicted fragment length is 181 bps INFO @ Tue, 04 Sep 2018 11:05:32: #2 alternative fragment length(s) may be 181 bps INFO @ Tue, 04 Sep 2018 11:05:32: #2.2 Generate R script for model : SRX4279671.10_model.r INFO @ Tue, 04 Sep 2018 11:05:32: #3 Call peaks... INFO @ Tue, 04 Sep 2018 11:05:32: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 04 Sep 2018 11:05:33: #2 number of paired peaks: 2965 INFO @ Tue, 04 Sep 2018 11:05:33: start model_add_line... INFO @ Tue, 04 Sep 2018 11:05:33: start X-correlation... INFO @ Tue, 04 Sep 2018 11:05:33: end of X-cor INFO @ Tue, 04 Sep 2018 11:05:33: #2 finished! INFO @ Tue, 04 Sep 2018 11:05:33: #2 predicted fragment length is 181 bps INFO @ Tue, 04 Sep 2018 11:05:33: #2 alternative fragment length(s) may be 181 bps INFO @ Tue, 04 Sep 2018 11:05:33: #2.2 Generate R script for model : SRX4279671.20_model.r INFO @ Tue, 04 Sep 2018 11:05:33: #3 Call peaks... INFO @ Tue, 04 Sep 2018 11:05:33: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 04 Sep 2018 11:05:37: #3 Call peaks for each chromosome... INFO @ Tue, 04 Sep 2018 11:05:51: #4 Write output xls file... SRX4279671.05_peaks.xls INFO @ Tue, 04 Sep 2018 11:05:51: #4 Write peak in narrowPeak format file... SRX4279671.05_peaks.narrowPeak INFO @ Tue, 04 Sep 2018 11:05:51: #4 Write summits bed file... SRX4279671.05_summits.bed INFO @ Tue, 04 Sep 2018 11:05:51: Done! pass1 - making usageList (15 chroms): 5 millis pass2 - checking and writing primary data (20086 records, 4 fields): 25 millis CompletedMACS2peakCalling INFO @ Tue, 04 Sep 2018 11:05:54: #3 Call peaks for each chromosome... INFO @ Tue, 04 Sep 2018 11:05:55: #3 Call peaks for each chromosome... INFO @ Tue, 04 Sep 2018 11:06:07: #4 Write output xls file... SRX4279671.20_peaks.xls INFO @ Tue, 04 Sep 2018 11:06:07: #4 Write peak in narrowPeak format file... SRX4279671.20_peaks.narrowPeak INFO @ Tue, 04 Sep 2018 11:06:07: #4 Write summits bed file... SRX4279671.20_summits.bed INFO @ Tue, 04 Sep 2018 11:06:07: Done! pass1 - making usageList (14 chroms): 3 millis pass2 - checking and writing primary data (7328 records, 4 fields): 11 millis CompletedMACS2peakCalling INFO @ Tue, 04 Sep 2018 11:06:08: #4 Write output xls file... SRX4279671.10_peaks.xls INFO @ Tue, 04 Sep 2018 11:06:08: #4 Write peak in narrowPeak format file... SRX4279671.10_peaks.narrowPeak INFO @ Tue, 04 Sep 2018 11:06:08: #4 Write summits bed file... SRX4279671.10_summits.bed INFO @ Tue, 04 Sep 2018 11:06:08: Done! pass1 - making usageList (15 chroms): 4 millis pass2 - checking and writing primary data (13728 records, 4 fields): 18 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。