Job ID = 11158498 sra ファイルのダウンロード中... Completed: 1703406K bytes transferred in 43 seconds (320737K 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 26336895 spots for /home/okishinya/chipatlas/results/dm3/SRX4279684/SRR7408118.sra Written 26336895 spots for /home/okishinya/chipatlas/results/dm3/SRX4279684/SRR7408118.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: 03:02:21 26336895 reads; of these: 26336895 (100.00%) were paired; of these: 3164682 (12.02%) aligned concordantly 0 times 6321524 (24.00%) aligned concordantly exactly 1 time 16850689 (63.98%) aligned concordantly >1 times ---- 3164682 pairs aligned concordantly 0 times; of these: 7608 (0.24%) aligned discordantly 1 time ---- 3157074 pairs aligned 0 times concordantly or discordantly; of these: 6314148 mates make up the pairs; of these: 3723546 (58.97%) aligned 0 times 284690 (4.51%) aligned exactly 1 time 2305912 (36.52%) aligned >1 times 92.93% overall alignment rate Time searching: 03:02:21 Overall time: 03:02:21 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] 933480 / 23127493 = 0.0404 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 13:01:02: # Command line: callpeak -t SRX4279684.bam -f BAM -g dm -n SRX4279684.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX4279684.05 # format = BAM # ChIP-seq file = ['SRX4279684.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 13:01:02: # Command line: callpeak -t SRX4279684.bam -f BAM -g dm -n SRX4279684.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX4279684.20 # format = BAM # ChIP-seq file = ['SRX4279684.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 13:01:02: # Command line: callpeak -t SRX4279684.bam -f BAM -g dm -n SRX4279684.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX4279684.10 # format = BAM # ChIP-seq file = ['SRX4279684.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 13:01:02: #1 read tag files... INFO @ Tue, 04 Sep 2018 13:01:02: #1 read tag files... INFO @ Tue, 04 Sep 2018 13:01:02: #1 read tag files... INFO @ Tue, 04 Sep 2018 13:01:02: #1 read treatment tags... INFO @ Tue, 04 Sep 2018 13:01:02: #1 read treatment tags... INFO @ Tue, 04 Sep 2018 13:01:02: #1 read treatment tags... INFO @ Tue, 04 Sep 2018 13:01:09: 1000000 INFO @ Tue, 04 Sep 2018 13:01:09: 1000000 INFO @ Tue, 04 Sep 2018 13:01:09: 1000000 INFO @ Tue, 04 Sep 2018 13:01:15: 2000000 INFO @ Tue, 04 Sep 2018 13:01:15: 2000000 INFO @ Tue, 04 Sep 2018 13:01:15: 2000000 INFO @ Tue, 04 Sep 2018 13:01:21: 3000000 INFO @ Tue, 04 Sep 2018 13:01:22: 3000000 INFO @ Tue, 04 Sep 2018 13:01:22: 3000000 INFO @ Tue, 04 Sep 2018 13:01:28: 4000000 INFO @ Tue, 04 Sep 2018 13:01:28: 4000000 INFO @ Tue, 04 Sep 2018 13:01:28: 4000000 INFO @ Tue, 04 Sep 2018 13:01:34: 5000000 INFO @ Tue, 04 Sep 2018 13:01:35: 5000000 INFO @ Tue, 04 Sep 2018 13:01:35: 5000000 INFO @ Tue, 04 Sep 2018 13:01:40: 6000000 INFO @ Tue, 04 Sep 2018 13:01:41: 6000000 INFO @ Tue, 04 Sep 2018 13:01:41: 6000000 INFO @ Tue, 04 Sep 2018 13:01:47: 7000000 INFO @ Tue, 04 Sep 2018 13:01:47: 7000000 INFO @ Tue, 04 Sep 2018 13:01:48: 7000000 INFO @ Tue, 04 Sep 2018 13:01:53: 8000000 INFO @ Tue, 04 Sep 2018 13:01:54: 8000000 INFO @ Tue, 04 Sep 2018 13:01:54: 8000000 INFO @ Tue, 04 Sep 2018 13:02:00: 9000000 INFO @ Tue, 04 Sep 2018 13:02:00: 9000000 INFO @ Tue, 04 Sep 2018 13:02:00: 9000000 INFO @ Tue, 04 Sep 2018 13:02:06: 10000000 INFO @ Tue, 04 Sep 2018 13:02:07: 10000000 INFO @ Tue, 04 Sep 2018 13:02:07: 10000000 INFO @ Tue, 04 Sep 2018 13:02:13: 11000000 INFO @ Tue, 04 Sep 2018 13:02:13: 11000000 INFO @ Tue, 04 Sep 2018 13:02:14: 11000000 INFO @ Tue, 04 Sep 2018 13:02:19: 12000000 INFO @ Tue, 04 Sep 2018 13:02:19: 12000000 INFO @ Tue, 04 Sep 2018 13:02:20: 12000000 INFO @ Tue, 04 Sep 2018 13:02:26: 13000000 INFO @ Tue, 04 Sep 2018 13:02:26: 13000000 INFO @ Tue, 04 Sep 2018 13:02:27: 13000000 INFO @ Tue, 04 Sep 2018 13:02:32: 14000000 INFO @ Tue, 04 Sep 2018 13:02:33: 14000000 INFO @ Tue, 04 Sep 2018 13:02:34: 14000000 INFO @ Tue, 04 Sep 2018 13:02:38: 15000000 INFO @ Tue, 04 Sep 2018 13:02:39: 15000000 INFO @ Tue, 04 Sep 2018 13:02:40: 15000000 INFO @ Tue, 04 Sep 2018 13:02:44: 16000000 INFO @ Tue, 04 Sep 2018 13:02:46: 16000000 INFO @ Tue, 04 Sep 2018 13:02:47: 16000000 INFO @ Tue, 04 Sep 2018 13:02:50: 17000000 INFO @ Tue, 04 Sep 2018 13:02:52: 17000000 INFO @ Tue, 04 Sep 2018 13:02:54: 17000000 INFO @ Tue, 04 Sep 2018 13:02:56: 18000000 INFO @ Tue, 04 Sep 2018 13:02:59: 18000000 INFO @ Tue, 04 Sep 2018 13:03:00: 18000000 INFO @ Tue, 04 Sep 2018 13:03:02: 19000000 INFO @ Tue, 04 Sep 2018 13:03:05: 19000000 INFO @ Tue, 04 Sep 2018 13:03:07: 19000000 INFO @ Tue, 04 Sep 2018 13:03:08: 20000000 INFO @ Tue, 04 Sep 2018 13:03:12: 20000000 INFO @ Tue, 04 Sep 2018 13:03:14: 20000000 INFO @ Tue, 04 Sep 2018 13:03:14: 21000000 INFO @ Tue, 04 Sep 2018 13:03:18: 21000000 INFO @ Tue, 04 Sep 2018 13:03:20: 21000000 INFO @ Tue, 04 Sep 2018 13:03:20: 22000000 INFO @ Tue, 04 Sep 2018 13:03:25: 22000000 INFO @ Tue, 04 Sep 2018 13:03:27: 23000000 INFO @ Tue, 04 Sep 2018 13:03:27: 22000000 INFO @ Tue, 04 Sep 2018 13:03:31: 23000000 INFO @ Tue, 04 Sep 2018 13:03:33: 24000000 INFO @ Tue, 04 Sep 2018 13:03:34: 23000000 INFO @ Tue, 04 Sep 2018 13:03:38: 24000000 INFO @ Tue, 04 Sep 2018 13:03:39: 25000000 INFO @ Tue, 04 Sep 2018 13:03:40: 24000000 INFO @ Tue, 04 Sep 2018 13:03:44: 25000000 INFO @ Tue, 04 Sep 2018 13:03:45: 26000000 INFO @ Tue, 04 Sep 2018 13:03:47: 25000000 INFO @ Tue, 04 Sep 2018 13:03:51: 26000000 INFO @ Tue, 04 Sep 2018 13:03:51: 27000000 INFO @ Tue, 04 Sep 2018 13:03:54: 26000000 INFO @ Tue, 04 Sep 2018 13:03:57: 28000000 INFO @ Tue, 04 Sep 2018 13:03:57: 27000000 INFO @ Tue, 04 Sep 2018 13:04:00: 27000000 INFO @ Tue, 04 Sep 2018 13:04:03: 29000000 INFO @ Tue, 04 Sep 2018 13:04:04: 28000000 INFO @ Tue, 04 Sep 2018 13:04:07: 28000000 INFO @ Tue, 04 Sep 2018 13:04:09: 30000000 INFO @ Tue, 04 Sep 2018 13:04:10: 29000000 INFO @ Tue, 04 Sep 2018 13:04:13: 29000000 INFO @ Tue, 04 Sep 2018 13:04:15: 31000000 INFO @ Tue, 04 Sep 2018 13:04:17: 30000000 INFO @ Tue, 04 Sep 2018 13:04:20: 30000000 INFO @ Tue, 04 Sep 2018 13:04:21: 32000000 INFO @ Tue, 04 Sep 2018 13:04:23: 31000000 INFO @ Tue, 04 Sep 2018 13:04:27: 31000000 INFO @ Tue, 04 Sep 2018 13:04:27: 33000000 INFO @ Tue, 04 Sep 2018 13:04:29: 32000000 INFO @ Tue, 04 Sep 2018 13:04:33: 32000000 INFO @ Tue, 04 Sep 2018 13:04:33: 34000000 INFO @ Tue, 04 Sep 2018 13:04:36: 33000000 INFO @ Tue, 04 Sep 2018 13:04:39: 35000000 INFO @ Tue, 04 Sep 2018 13:04:40: 33000000 INFO @ Tue, 04 Sep 2018 13:04:42: 34000000 INFO @ Tue, 04 Sep 2018 13:04:45: 36000000 INFO @ Tue, 04 Sep 2018 13:04:47: 34000000 INFO @ Tue, 04 Sep 2018 13:04:49: 35000000 INFO @ Tue, 04 Sep 2018 13:04:51: 37000000 INFO @ Tue, 04 Sep 2018 13:04:53: 35000000 INFO @ Tue, 04 Sep 2018 13:04:55: 36000000 INFO @ Tue, 04 Sep 2018 13:04:58: 38000000 INFO @ Tue, 04 Sep 2018 13:05:00: 36000000 INFO @ Tue, 04 Sep 2018 13:05:02: 37000000 INFO @ Tue, 04 Sep 2018 13:05:04: 39000000 INFO @ Tue, 04 Sep 2018 13:05:06: 37000000 INFO @ Tue, 04 Sep 2018 13:05:08: 38000000 INFO @ Tue, 04 Sep 2018 13:05:10: 40000000 INFO @ Tue, 04 Sep 2018 13:05:13: 38000000 INFO @ Tue, 04 Sep 2018 13:05:15: 39000000 INFO @ Tue, 04 Sep 2018 13:05:16: 41000000 INFO @ Tue, 04 Sep 2018 13:05:20: 39000000 INFO @ Tue, 04 Sep 2018 13:05:21: 40000000 INFO @ Tue, 04 Sep 2018 13:05:22: 42000000 INFO @ Tue, 04 Sep 2018 13:05:26: 40000000 INFO @ Tue, 04 Sep 2018 13:05:28: 41000000 INFO @ Tue, 04 Sep 2018 13:05:28: 43000000 INFO @ Tue, 04 Sep 2018 13:05:33: 41000000 INFO @ Tue, 04 Sep 2018 13:05:34: 44000000 INFO @ Tue, 04 Sep 2018 13:05:34: 42000000 INFO @ Tue, 04 Sep 2018 13:05:39: 42000000 INFO @ Tue, 04 Sep 2018 13:05:40: 45000000 INFO @ Tue, 04 Sep 2018 13:05:40: 43000000 INFO @ Tue, 04 Sep 2018 13:05:46: 46000000 INFO @ Tue, 04 Sep 2018 13:05:46: 43000000 INFO @ Tue, 04 Sep 2018 13:05:47: 44000000 INFO @ Tue, 04 Sep 2018 13:05:52: 47000000 INFO @ Tue, 04 Sep 2018 13:05:52: 44000000 INFO @ Tue, 04 Sep 2018 13:05:53: #1 tag size is determined as 78 bps INFO @ Tue, 04 Sep 2018 13:05:53: #1 tag size = 78 INFO @ Tue, 04 Sep 2018 13:05:53: #1 total tags in treatment: 22238835 INFO @ Tue, 04 Sep 2018 13:05:53: #1 user defined the maximum tags... INFO @ Tue, 04 Sep 2018 13:05:53: #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 13:05:53: #1 tags after filtering in treatment: 17503679 INFO @ Tue, 04 Sep 2018 13:05:53: #1 Redundant rate of treatment: 0.21 INFO @ Tue, 04 Sep 2018 13:05:53: #1 finished! INFO @ Tue, 04 Sep 2018 13:05:53: #2 Build Peak Model... INFO @ Tue, 04 Sep 2018 13:05:53: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 04 Sep 2018 13:05:53: 45000000 INFO @ Tue, 04 Sep 2018 13:05:55: #2 number of paired peaks: 6224 INFO @ Tue, 04 Sep 2018 13:05:55: start model_add_line... INFO @ Tue, 04 Sep 2018 13:05:55: start X-correlation... INFO @ Tue, 04 Sep 2018 13:05:56: end of X-cor INFO @ Tue, 04 Sep 2018 13:05:56: #2 finished! INFO @ Tue, 04 Sep 2018 13:05:56: #2 predicted fragment length is 151 bps INFO @ Tue, 04 Sep 2018 13:05:56: #2 alternative fragment length(s) may be 151 bps INFO @ Tue, 04 Sep 2018 13:05:56: #2.2 Generate R script for model : SRX4279684.10_model.r WARNING @ Tue, 04 Sep 2018 13:05:56: #2 Since the d (151) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 04 Sep 2018 13:05:56: #2 You may need to consider one of the other alternative d(s): 151 WARNING @ Tue, 04 Sep 2018 13:05:56: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 04 Sep 2018 13:05:56: #3 Call peaks... INFO @ Tue, 04 Sep 2018 13:05:56: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 04 Sep 2018 13:05:59: 45000000 INFO @ Tue, 04 Sep 2018 13:06:00: 46000000 INFO @ Tue, 04 Sep 2018 13:06:05: 46000000 INFO @ Tue, 04 Sep 2018 13:06:06: 47000000 INFO @ Tue, 04 Sep 2018 13:06:07: #1 tag size is determined as 78 bps INFO @ Tue, 04 Sep 2018 13:06:07: #1 tag size = 78 INFO @ Tue, 04 Sep 2018 13:06:07: #1 total tags in treatment: 22238835 INFO @ Tue, 04 Sep 2018 13:06:07: #1 user defined the maximum tags... INFO @ Tue, 04 Sep 2018 13:06:07: #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 13:06:07: #1 tags after filtering in treatment: 17503679 INFO @ Tue, 04 Sep 2018 13:06:07: #1 Redundant rate of treatment: 0.21 INFO @ Tue, 04 Sep 2018 13:06:07: #1 finished! INFO @ Tue, 04 Sep 2018 13:06:07: #2 Build Peak Model... INFO @ Tue, 04 Sep 2018 13:06:07: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 04 Sep 2018 13:06:10: #2 number of paired peaks: 6224 INFO @ Tue, 04 Sep 2018 13:06:10: start model_add_line... INFO @ Tue, 04 Sep 2018 13:06:10: start X-correlation... INFO @ Tue, 04 Sep 2018 13:06:10: end of X-cor INFO @ Tue, 04 Sep 2018 13:06:10: #2 finished! INFO @ Tue, 04 Sep 2018 13:06:10: #2 predicted fragment length is 151 bps INFO @ Tue, 04 Sep 2018 13:06:10: #2 alternative fragment length(s) may be 151 bps INFO @ Tue, 04 Sep 2018 13:06:10: #2.2 Generate R script for model : SRX4279684.20_model.r WARNING @ Tue, 04 Sep 2018 13:06:10: #2 Since the d (151) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 04 Sep 2018 13:06:10: #2 You may need to consider one of the other alternative d(s): 151 WARNING @ Tue, 04 Sep 2018 13:06:10: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 04 Sep 2018 13:06:10: #3 Call peaks... INFO @ Tue, 04 Sep 2018 13:06:10: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 04 Sep 2018 13:06:12: 47000000 INFO @ Tue, 04 Sep 2018 13:06:12: #1 tag size is determined as 78 bps INFO @ Tue, 04 Sep 2018 13:06:12: #1 tag size = 78 INFO @ Tue, 04 Sep 2018 13:06:12: #1 total tags in treatment: 22238835 INFO @ Tue, 04 Sep 2018 13:06:12: #1 user defined the maximum tags... INFO @ Tue, 04 Sep 2018 13:06:12: #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 13:06:13: #1 tags after filtering in treatment: 17503679 INFO @ Tue, 04 Sep 2018 13:06:13: #1 Redundant rate of treatment: 0.21 INFO @ Tue, 04 Sep 2018 13:06:13: #1 finished! INFO @ Tue, 04 Sep 2018 13:06:13: #2 Build Peak Model... INFO @ Tue, 04 Sep 2018 13:06:13: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 04 Sep 2018 13:06:15: #2 number of paired peaks: 6224 INFO @ Tue, 04 Sep 2018 13:06:15: start model_add_line... INFO @ Tue, 04 Sep 2018 13:06:15: start X-correlation... INFO @ Tue, 04 Sep 2018 13:06:15: end of X-cor INFO @ Tue, 04 Sep 2018 13:06:15: #2 finished! INFO @ Tue, 04 Sep 2018 13:06:15: #2 predicted fragment length is 151 bps INFO @ Tue, 04 Sep 2018 13:06:15: #2 alternative fragment length(s) may be 151 bps INFO @ Tue, 04 Sep 2018 13:06:15: #2.2 Generate R script for model : SRX4279684.05_model.r WARNING @ Tue, 04 Sep 2018 13:06:15: #2 Since the d (151) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 04 Sep 2018 13:06:15: #2 You may need to consider one of the other alternative d(s): 151 WARNING @ Tue, 04 Sep 2018 13:06:15: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 04 Sep 2018 13:06:15: #3 Call peaks... INFO @ Tue, 04 Sep 2018 13:06:15: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 04 Sep 2018 13:06:44: #3 Call peaks for each chromosome... INFO @ Tue, 04 Sep 2018 13:07:00: #3 Call peaks for each chromosome... INFO @ Tue, 04 Sep 2018 13:07:04: #3 Call peaks for each chromosome... INFO @ Tue, 04 Sep 2018 13:07:06: #4 Write output xls file... SRX4279684.10_peaks.xls INFO @ Tue, 04 Sep 2018 13:07:06: #4 Write peak in narrowPeak format file... SRX4279684.10_peaks.narrowPeak INFO @ Tue, 04 Sep 2018 13:07:06: #4 Write summits bed file... SRX4279684.10_summits.bed INFO @ Tue, 04 Sep 2018 13:07:06: Done! pass1 - making usageList (14 chroms): 5 millis pass2 - checking and writing primary data (12741 records, 4 fields): 17 millis CompletedMACS2peakCalling INFO @ Tue, 04 Sep 2018 13:07:20: #4 Write output xls file... SRX4279684.20_peaks.xls INFO @ Tue, 04 Sep 2018 13:07:20: #4 Write peak in narrowPeak format file... SRX4279684.20_peaks.narrowPeak INFO @ Tue, 04 Sep 2018 13:07:20: #4 Write summits bed file... SRX4279684.20_summits.bed INFO @ Tue, 04 Sep 2018 13:07:20: Done! pass1 - making usageList (14 chroms): 2 millis pass2 - checking and writing primary data (7160 records, 4 fields): 11 millis CompletedMACS2peakCalling INFO @ Tue, 04 Sep 2018 13:07:27: #4 Write output xls file... SRX4279684.05_peaks.xls INFO @ Tue, 04 Sep 2018 13:07:28: #4 Write peak in narrowPeak format file... SRX4279684.05_peaks.narrowPeak INFO @ Tue, 04 Sep 2018 13:07:28: #4 Write summits bed file... SRX4279684.05_summits.bed INFO @ Tue, 04 Sep 2018 13:07:28: Done! pass1 - making usageList (14 chroms): 4 millis pass2 - checking and writing primary data (18250 records, 4 fields): 23 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。