Job ID = 11158506 sra ファイルのダウンロード中... Completed: 1172879K bytes transferred in 27 seconds (349255K 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 33634765 spots for /home/okishinya/chipatlas/results/dm3/SRX4546288/SRR7685803.sra Written 33634765 spots for /home/okishinya/chipatlas/results/dm3/SRX4546288/SRR7685803.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: 01:02:57 33634765 reads; of these: 33634765 (100.00%) were paired; of these: 7726344 (22.97%) aligned concordantly 0 times 15313061 (45.53%) aligned concordantly exactly 1 time 10595360 (31.50%) aligned concordantly >1 times ---- 7726344 pairs aligned concordantly 0 times; of these: 2228894 (28.85%) aligned discordantly 1 time ---- 5497450 pairs aligned 0 times concordantly or discordantly; of these: 10994900 mates make up the pairs; of these: 6946802 (63.18%) aligned 0 times 1032249 (9.39%) aligned exactly 1 time 3015849 (27.43%) aligned >1 times 89.67% overall alignment rate Time searching: 01:02:58 Overall time: 01:02:58 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 28 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] 8794337 / 27750552 = 0.3169 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 10:56:18: # Command line: callpeak -t SRX4546288.bam -f BAM -g dm -n SRX4546288.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX4546288.10 # format = BAM # ChIP-seq file = ['SRX4546288.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 10:56:18: # Command line: callpeak -t SRX4546288.bam -f BAM -g dm -n SRX4546288.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX4546288.05 # format = BAM # ChIP-seq file = ['SRX4546288.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 10:56:18: # Command line: callpeak -t SRX4546288.bam -f BAM -g dm -n SRX4546288.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX4546288.20 # format = BAM # ChIP-seq file = ['SRX4546288.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 10:56:18: #1 read tag files... INFO @ Tue, 04 Sep 2018 10:56:18: #1 read tag files... INFO @ Tue, 04 Sep 2018 10:56:18: #1 read tag files... INFO @ Tue, 04 Sep 2018 10:56:18: #1 read treatment tags... INFO @ Tue, 04 Sep 2018 10:56:18: #1 read treatment tags... INFO @ Tue, 04 Sep 2018 10:56:18: #1 read treatment tags... INFO @ Tue, 04 Sep 2018 10:56:23: 1000000 INFO @ Tue, 04 Sep 2018 10:56:23: 1000000 INFO @ Tue, 04 Sep 2018 10:56:23: 1000000 INFO @ Tue, 04 Sep 2018 10:56:29: 2000000 INFO @ Tue, 04 Sep 2018 10:56:29: 2000000 INFO @ Tue, 04 Sep 2018 10:56:29: 2000000 INFO @ Tue, 04 Sep 2018 10:56:34: 3000000 INFO @ Tue, 04 Sep 2018 10:56:34: 3000000 INFO @ Tue, 04 Sep 2018 10:56:35: 3000000 INFO @ Tue, 04 Sep 2018 10:56:40: 4000000 INFO @ Tue, 04 Sep 2018 10:56:40: 4000000 INFO @ Tue, 04 Sep 2018 10:56:41: 4000000 INFO @ Tue, 04 Sep 2018 10:56:45: 5000000 INFO @ Tue, 04 Sep 2018 10:56:46: 5000000 INFO @ Tue, 04 Sep 2018 10:56:47: 5000000 INFO @ Tue, 04 Sep 2018 10:56:51: 6000000 INFO @ Tue, 04 Sep 2018 10:56:51: 6000000 INFO @ Tue, 04 Sep 2018 10:56:53: 6000000 INFO @ Tue, 04 Sep 2018 10:56:56: 7000000 INFO @ Tue, 04 Sep 2018 10:56:57: 7000000 INFO @ Tue, 04 Sep 2018 10:56:59: 7000000 INFO @ Tue, 04 Sep 2018 10:57:02: 8000000 INFO @ Tue, 04 Sep 2018 10:57:03: 8000000 INFO @ Tue, 04 Sep 2018 10:57:05: 8000000 INFO @ Tue, 04 Sep 2018 10:57:07: 9000000 INFO @ Tue, 04 Sep 2018 10:57:09: 9000000 INFO @ Tue, 04 Sep 2018 10:57:11: 9000000 INFO @ Tue, 04 Sep 2018 10:57:13: 10000000 INFO @ Tue, 04 Sep 2018 10:57:14: 10000000 INFO @ Tue, 04 Sep 2018 10:57:17: 10000000 INFO @ Tue, 04 Sep 2018 10:57:18: 11000000 INFO @ Tue, 04 Sep 2018 10:57:20: 11000000 INFO @ Tue, 04 Sep 2018 10:57:23: 11000000 INFO @ Tue, 04 Sep 2018 10:57:23: 12000000 INFO @ Tue, 04 Sep 2018 10:57:26: 12000000 INFO @ Tue, 04 Sep 2018 10:57:29: 12000000 INFO @ Tue, 04 Sep 2018 10:57:29: 13000000 INFO @ Tue, 04 Sep 2018 10:57:31: 13000000 INFO @ Tue, 04 Sep 2018 10:57:34: 14000000 INFO @ Tue, 04 Sep 2018 10:57:35: 13000000 INFO @ Tue, 04 Sep 2018 10:57:37: 14000000 INFO @ Tue, 04 Sep 2018 10:57:40: 15000000 INFO @ Tue, 04 Sep 2018 10:57:41: 14000000 INFO @ Tue, 04 Sep 2018 10:57:43: 15000000 INFO @ Tue, 04 Sep 2018 10:57:45: 16000000 INFO @ Tue, 04 Sep 2018 10:57:47: 15000000 INFO @ Tue, 04 Sep 2018 10:57:48: 16000000 INFO @ Tue, 04 Sep 2018 10:57:51: 17000000 INFO @ Tue, 04 Sep 2018 10:57:53: 16000000 INFO @ Tue, 04 Sep 2018 10:57:54: 17000000 INFO @ Tue, 04 Sep 2018 10:57:56: 18000000 INFO @ Tue, 04 Sep 2018 10:57:59: 17000000 INFO @ Tue, 04 Sep 2018 10:58:00: 18000000 INFO @ Tue, 04 Sep 2018 10:58:02: 19000000 INFO @ Tue, 04 Sep 2018 10:58:05: 18000000 INFO @ Tue, 04 Sep 2018 10:58:05: 19000000 INFO @ Tue, 04 Sep 2018 10:58:07: 20000000 INFO @ Tue, 04 Sep 2018 10:58:11: 19000000 INFO @ Tue, 04 Sep 2018 10:58:11: 20000000 INFO @ Tue, 04 Sep 2018 10:58:12: 21000000 INFO @ Tue, 04 Sep 2018 10:58:17: 20000000 INFO @ Tue, 04 Sep 2018 10:58:17: 21000000 INFO @ Tue, 04 Sep 2018 10:58:18: 22000000 INFO @ Tue, 04 Sep 2018 10:58:22: 22000000 INFO @ Tue, 04 Sep 2018 10:58:22: 21000000 INFO @ Tue, 04 Sep 2018 10:58:23: 23000000 INFO @ Tue, 04 Sep 2018 10:58:28: 23000000 INFO @ Tue, 04 Sep 2018 10:58:28: 22000000 INFO @ Tue, 04 Sep 2018 10:58:29: 24000000 INFO @ Tue, 04 Sep 2018 10:58:34: 24000000 INFO @ Tue, 04 Sep 2018 10:58:34: 25000000 INFO @ Tue, 04 Sep 2018 10:58:34: 23000000 INFO @ Tue, 04 Sep 2018 10:58:39: 25000000 INFO @ Tue, 04 Sep 2018 10:58:40: 26000000 INFO @ Tue, 04 Sep 2018 10:58:40: 24000000 INFO @ Tue, 04 Sep 2018 10:58:45: 26000000 INFO @ Tue, 04 Sep 2018 10:58:45: 27000000 INFO @ Tue, 04 Sep 2018 10:58:46: 25000000 INFO @ Tue, 04 Sep 2018 10:58:50: 27000000 INFO @ Tue, 04 Sep 2018 10:58:50: 28000000 INFO @ Tue, 04 Sep 2018 10:58:52: 26000000 INFO @ Tue, 04 Sep 2018 10:58:56: 29000000 INFO @ Tue, 04 Sep 2018 10:58:56: 28000000 INFO @ Tue, 04 Sep 2018 10:58:58: 27000000 INFO @ Tue, 04 Sep 2018 10:59:01: 30000000 INFO @ Tue, 04 Sep 2018 10:59:02: 29000000 INFO @ Tue, 04 Sep 2018 10:59:04: 28000000 INFO @ Tue, 04 Sep 2018 10:59:06: 31000000 INFO @ Tue, 04 Sep 2018 10:59:07: 30000000 INFO @ Tue, 04 Sep 2018 10:59:10: 29000000 INFO @ Tue, 04 Sep 2018 10:59:12: 32000000 INFO @ Tue, 04 Sep 2018 10:59:13: 31000000 INFO @ Tue, 04 Sep 2018 10:59:16: 30000000 INFO @ Tue, 04 Sep 2018 10:59:17: 33000000 INFO @ Tue, 04 Sep 2018 10:59:18: 32000000 INFO @ Tue, 04 Sep 2018 10:59:21: 31000000 INFO @ Tue, 04 Sep 2018 10:59:22: 34000000 INFO @ Tue, 04 Sep 2018 10:59:24: 33000000 INFO @ Tue, 04 Sep 2018 10:59:27: 32000000 INFO @ Tue, 04 Sep 2018 10:59:28: 35000000 INFO @ Tue, 04 Sep 2018 10:59:30: 34000000 INFO @ Tue, 04 Sep 2018 10:59:33: 33000000 INFO @ Tue, 04 Sep 2018 10:59:33: 36000000 INFO @ Tue, 04 Sep 2018 10:59:35: 35000000 INFO @ Tue, 04 Sep 2018 10:59:39: 37000000 INFO @ Tue, 04 Sep 2018 10:59:39: 34000000 INFO @ Tue, 04 Sep 2018 10:59:41: 36000000 INFO @ Tue, 04 Sep 2018 10:59:44: 38000000 INFO @ Tue, 04 Sep 2018 10:59:45: 35000000 INFO @ Tue, 04 Sep 2018 10:59:47: 37000000 INFO @ Tue, 04 Sep 2018 10:59:49: 39000000 INFO @ Tue, 04 Sep 2018 10:59:51: 36000000 INFO @ Tue, 04 Sep 2018 10:59:52: 38000000 INFO @ Tue, 04 Sep 2018 10:59:55: 40000000 INFO @ Tue, 04 Sep 2018 10:59:57: 37000000 INFO @ Tue, 04 Sep 2018 10:59:58: 39000000 INFO @ Tue, 04 Sep 2018 11:00:00: 41000000 INFO @ Tue, 04 Sep 2018 11:00:03: 38000000 INFO @ Tue, 04 Sep 2018 11:00:03: 40000000 INFO @ Tue, 04 Sep 2018 11:00:06: 42000000 INFO @ Tue, 04 Sep 2018 11:00:09: 39000000 INFO @ Tue, 04 Sep 2018 11:00:09: 41000000 INFO @ Tue, 04 Sep 2018 11:00:10: #1 tag size is determined as 51 bps INFO @ Tue, 04 Sep 2018 11:00:10: #1 tag size = 51 INFO @ Tue, 04 Sep 2018 11:00:10: #1 total tags in treatment: 17508719 INFO @ Tue, 04 Sep 2018 11:00:10: #1 user defined the maximum tags... INFO @ Tue, 04 Sep 2018 11:00:10: #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 11:00:10: #1 tags after filtering in treatment: 10703066 INFO @ Tue, 04 Sep 2018 11:00:10: #1 Redundant rate of treatment: 0.39 INFO @ Tue, 04 Sep 2018 11:00:10: #1 finished! INFO @ Tue, 04 Sep 2018 11:00:10: #2 Build Peak Model... INFO @ Tue, 04 Sep 2018 11:00:10: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 04 Sep 2018 11:00:11: #2 number of paired peaks: 2963 INFO @ Tue, 04 Sep 2018 11:00:11: start model_add_line... INFO @ Tue, 04 Sep 2018 11:00:11: start X-correlation... INFO @ Tue, 04 Sep 2018 11:00:12: end of X-cor INFO @ Tue, 04 Sep 2018 11:00:12: #2 finished! INFO @ Tue, 04 Sep 2018 11:00:12: #2 predicted fragment length is 98 bps INFO @ Tue, 04 Sep 2018 11:00:12: #2 alternative fragment length(s) may be 98 bps INFO @ Tue, 04 Sep 2018 11:00:12: #2.2 Generate R script for model : SRX4546288.10_model.r WARNING @ Tue, 04 Sep 2018 11:00:12: #2 Since the d (98) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 04 Sep 2018 11:00:12: #2 You may need to consider one of the other alternative d(s): 98 WARNING @ Tue, 04 Sep 2018 11:00:12: #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 11:00:12: #3 Call peaks... INFO @ Tue, 04 Sep 2018 11:00:12: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 04 Sep 2018 11:00:15: 40000000 INFO @ Tue, 04 Sep 2018 11:00:15: 42000000 INFO @ Tue, 04 Sep 2018 11:00:19: #1 tag size is determined as 51 bps INFO @ Tue, 04 Sep 2018 11:00:19: #1 tag size = 51 INFO @ Tue, 04 Sep 2018 11:00:19: #1 total tags in treatment: 17508719 INFO @ Tue, 04 Sep 2018 11:00:19: #1 user defined the maximum tags... INFO @ Tue, 04 Sep 2018 11:00:19: #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 11:00:19: #1 tags after filtering in treatment: 10703066 INFO @ Tue, 04 Sep 2018 11:00:19: #1 Redundant rate of treatment: 0.39 INFO @ Tue, 04 Sep 2018 11:00:19: #1 finished! INFO @ Tue, 04 Sep 2018 11:00:19: #2 Build Peak Model... INFO @ Tue, 04 Sep 2018 11:00:19: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 04 Sep 2018 11:00:20: #2 number of paired peaks: 2963 INFO @ Tue, 04 Sep 2018 11:00:20: start model_add_line... INFO @ Tue, 04 Sep 2018 11:00:21: 41000000 INFO @ Tue, 04 Sep 2018 11:00:21: start X-correlation... INFO @ Tue, 04 Sep 2018 11:00:21: end of X-cor INFO @ Tue, 04 Sep 2018 11:00:21: #2 finished! INFO @ Tue, 04 Sep 2018 11:00:21: #2 predicted fragment length is 98 bps INFO @ Tue, 04 Sep 2018 11:00:21: #2 alternative fragment length(s) may be 98 bps INFO @ Tue, 04 Sep 2018 11:00:21: #2.2 Generate R script for model : SRX4546288.05_model.r WARNING @ Tue, 04 Sep 2018 11:00:21: #2 Since the d (98) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 04 Sep 2018 11:00:21: #2 You may need to consider one of the other alternative d(s): 98 WARNING @ Tue, 04 Sep 2018 11:00:21: #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 11:00:21: #3 Call peaks... INFO @ Tue, 04 Sep 2018 11:00:21: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 04 Sep 2018 11:00:26: 42000000 INFO @ Tue, 04 Sep 2018 11:00:30: #1 tag size is determined as 51 bps INFO @ Tue, 04 Sep 2018 11:00:30: #1 tag size = 51 INFO @ Tue, 04 Sep 2018 11:00:30: #1 total tags in treatment: 17508719 INFO @ Tue, 04 Sep 2018 11:00:30: #1 user defined the maximum tags... INFO @ Tue, 04 Sep 2018 11:00:30: #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 11:00:31: #1 tags after filtering in treatment: 10703066 INFO @ Tue, 04 Sep 2018 11:00:31: #1 Redundant rate of treatment: 0.39 INFO @ Tue, 04 Sep 2018 11:00:31: #1 finished! INFO @ Tue, 04 Sep 2018 11:00:31: #2 Build Peak Model... INFO @ Tue, 04 Sep 2018 11:00:31: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 04 Sep 2018 11:00:32: #2 number of paired peaks: 2963 INFO @ Tue, 04 Sep 2018 11:00:32: start model_add_line... INFO @ Tue, 04 Sep 2018 11:00:32: start X-correlation... INFO @ Tue, 04 Sep 2018 11:00:32: end of X-cor INFO @ Tue, 04 Sep 2018 11:00:32: #2 finished! INFO @ Tue, 04 Sep 2018 11:00:32: #2 predicted fragment length is 98 bps INFO @ Tue, 04 Sep 2018 11:00:32: #2 alternative fragment length(s) may be 98 bps INFO @ Tue, 04 Sep 2018 11:00:32: #2.2 Generate R script for model : SRX4546288.20_model.r WARNING @ Tue, 04 Sep 2018 11:00:32: #2 Since the d (98) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 04 Sep 2018 11:00:32: #2 You may need to consider one of the other alternative d(s): 98 WARNING @ Tue, 04 Sep 2018 11:00:32: #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 11:00:32: #3 Call peaks... INFO @ Tue, 04 Sep 2018 11:00:32: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 04 Sep 2018 11:00:36: #3 Call peaks for each chromosome... INFO @ Tue, 04 Sep 2018 11:00:47: #3 Call peaks for each chromosome... INFO @ Tue, 04 Sep 2018 11:00:51: #4 Write output xls file... SRX4546288.10_peaks.xls INFO @ Tue, 04 Sep 2018 11:00:51: #4 Write peak in narrowPeak format file... SRX4546288.10_peaks.narrowPeak INFO @ Tue, 04 Sep 2018 11:00:51: #4 Write summits bed file... SRX4546288.10_summits.bed INFO @ Tue, 04 Sep 2018 11:00:51: Done! pass1 - making usageList (15 chroms): 3 millis pass2 - checking and writing primary data (11856 records, 4 fields): 15 millis CompletedMACS2peakCalling INFO @ Tue, 04 Sep 2018 11:00:57: #3 Call peaks for each chromosome... INFO @ Tue, 04 Sep 2018 11:01:02: #4 Write output xls file... SRX4546288.05_peaks.xls INFO @ Tue, 04 Sep 2018 11:01:02: #4 Write peak in narrowPeak format file... SRX4546288.05_peaks.narrowPeak INFO @ Tue, 04 Sep 2018 11:01:02: #4 Write summits bed file... SRX4546288.05_summits.bed INFO @ Tue, 04 Sep 2018 11:01:02: Done! pass1 - making usageList (15 chroms): 4 millis pass2 - checking and writing primary data (17970 records, 4 fields): 21 millis CompletedMACS2peakCalling INFO @ Tue, 04 Sep 2018 11:01:10: #4 Write output xls file... SRX4546288.20_peaks.xls INFO @ Tue, 04 Sep 2018 11:01:10: #4 Write peak in narrowPeak format file... SRX4546288.20_peaks.narrowPeak INFO @ Tue, 04 Sep 2018 11:01:10: #4 Write summits bed file... SRX4546288.20_summits.bed INFO @ Tue, 04 Sep 2018 11:01:10: Done! pass1 - making usageList (13 chroms): 2 millis pass2 - checking and writing primary data (5645 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。