Job ID = 11158467 sra ファイルのダウンロード中... Completed: 1877978K bytes transferred in 192 seconds (80000K 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 29580588 spots for /home/okishinya/chipatlas/results/ce10/SRX4029333/SRR7100993.sra Written 29580588 spots for /home/okishinya/chipatlas/results/ce10/SRX4029333/SRR7100993.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: 00:42:54 29580588 reads; of these: 29580588 (100.00%) were paired; of these: 5942550 (20.09%) aligned concordantly 0 times 21496785 (72.67%) aligned concordantly exactly 1 time 2141253 (7.24%) aligned concordantly >1 times ---- 5942550 pairs aligned concordantly 0 times; of these: 1880569 (31.65%) aligned discordantly 1 time ---- 4061981 pairs aligned 0 times concordantly or discordantly; of these: 8123962 mates make up the pairs; of these: 6903095 (84.97%) aligned 0 times 799846 (9.85%) aligned exactly 1 time 421021 (5.18%) aligned >1 times 88.33% overall alignment rate Time searching: 00:42:54 Overall time: 00:42:54 マッピングが完了しました。 samtools でBAM に変換中... [samopen] SAM header is present: 7 sequences. [bam_sort_core] merging from 24 files... [bam_rmdup_core] processing reference chrI... [bam_rmdup_core] processing reference chrII... [bam_rmdup_core] processing reference chrIII... [bam_rmdup_core] processing reference chrIV... [bam_rmdup_core] processing reference chrV... [bam_rmdup_core] processing reference chrX... [bam_rmdup_core] processing reference chrM... [bam_rmdup_core] 3114721 / 25496018 = 0.1222 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 09:40:48: # Command line: callpeak -t SRX4029333.bam -f BAM -g ce -n SRX4029333.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX4029333.10 # format = BAM # ChIP-seq file = ['SRX4029333.bam'] # control file = None # effective genome size = 9.00e+07 # 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 09:40:48: # Command line: callpeak -t SRX4029333.bam -f BAM -g ce -n SRX4029333.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX4029333.05 # format = BAM # ChIP-seq file = ['SRX4029333.bam'] # control file = None # effective genome size = 9.00e+07 # 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 09:40:48: # Command line: callpeak -t SRX4029333.bam -f BAM -g ce -n SRX4029333.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX4029333.20 # format = BAM # ChIP-seq file = ['SRX4029333.bam'] # control file = None # effective genome size = 9.00e+07 # 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 09:40:48: #1 read tag files... INFO @ Tue, 04 Sep 2018 09:40:48: #1 read tag files... INFO @ Tue, 04 Sep 2018 09:40:48: #1 read treatment tags... INFO @ Tue, 04 Sep 2018 09:40:48: #1 read tag files... INFO @ Tue, 04 Sep 2018 09:40:48: #1 read treatment tags... INFO @ Tue, 04 Sep 2018 09:40:48: #1 read treatment tags... INFO @ Tue, 04 Sep 2018 09:40:55: 1000000 INFO @ Tue, 04 Sep 2018 09:40:55: 1000000 INFO @ Tue, 04 Sep 2018 09:40:55: 1000000 INFO @ Tue, 04 Sep 2018 09:41:02: 2000000 INFO @ Tue, 04 Sep 2018 09:41:03: 2000000 INFO @ Tue, 04 Sep 2018 09:41:03: 2000000 INFO @ Tue, 04 Sep 2018 09:41:10: 3000000 INFO @ Tue, 04 Sep 2018 09:41:11: 3000000 INFO @ Tue, 04 Sep 2018 09:41:11: 3000000 INFO @ Tue, 04 Sep 2018 09:41:17: 4000000 INFO @ Tue, 04 Sep 2018 09:41:19: 4000000 INFO @ Tue, 04 Sep 2018 09:41:19: 4000000 INFO @ Tue, 04 Sep 2018 09:41:24: 5000000 INFO @ Tue, 04 Sep 2018 09:41:26: 5000000 INFO @ Tue, 04 Sep 2018 09:41:26: 5000000 INFO @ Tue, 04 Sep 2018 09:41:31: 6000000 INFO @ Tue, 04 Sep 2018 09:41:34: 6000000 INFO @ Tue, 04 Sep 2018 09:41:34: 6000000 INFO @ Tue, 04 Sep 2018 09:41:38: 7000000 INFO @ Tue, 04 Sep 2018 09:41:42: 7000000 INFO @ Tue, 04 Sep 2018 09:41:42: 7000000 INFO @ Tue, 04 Sep 2018 09:41:46: 8000000 INFO @ Tue, 04 Sep 2018 09:41:49: 8000000 INFO @ Tue, 04 Sep 2018 09:41:49: 8000000 INFO @ Tue, 04 Sep 2018 09:41:53: 9000000 INFO @ Tue, 04 Sep 2018 09:41:57: 9000000 INFO @ Tue, 04 Sep 2018 09:41:57: 9000000 INFO @ Tue, 04 Sep 2018 09:42:00: 10000000 INFO @ Tue, 04 Sep 2018 09:42:04: 10000000 INFO @ Tue, 04 Sep 2018 09:42:04: 10000000 INFO @ Tue, 04 Sep 2018 09:42:07: 11000000 INFO @ Tue, 04 Sep 2018 09:42:12: 11000000 INFO @ Tue, 04 Sep 2018 09:42:12: 11000000 INFO @ Tue, 04 Sep 2018 09:42:15: 12000000 INFO @ Tue, 04 Sep 2018 09:42:20: 12000000 INFO @ Tue, 04 Sep 2018 09:42:20: 12000000 INFO @ Tue, 04 Sep 2018 09:42:22: 13000000 INFO @ Tue, 04 Sep 2018 09:42:27: 13000000 INFO @ Tue, 04 Sep 2018 09:42:27: 13000000 INFO @ Tue, 04 Sep 2018 09:42:29: 14000000 INFO @ Tue, 04 Sep 2018 09:42:35: 14000000 INFO @ Tue, 04 Sep 2018 09:42:35: 14000000 INFO @ Tue, 04 Sep 2018 09:42:36: 15000000 INFO @ Tue, 04 Sep 2018 09:42:42: 15000000 INFO @ Tue, 04 Sep 2018 09:42:42: 15000000 INFO @ Tue, 04 Sep 2018 09:42:43: 16000000 INFO @ Tue, 04 Sep 2018 09:42:50: 16000000 INFO @ Tue, 04 Sep 2018 09:42:50: 16000000 INFO @ Tue, 04 Sep 2018 09:42:50: 17000000 INFO @ Tue, 04 Sep 2018 09:42:58: 18000000 INFO @ Tue, 04 Sep 2018 09:42:58: 17000000 INFO @ Tue, 04 Sep 2018 09:42:58: 17000000 INFO @ Tue, 04 Sep 2018 09:43:05: 19000000 INFO @ Tue, 04 Sep 2018 09:43:06: 18000000 INFO @ Tue, 04 Sep 2018 09:43:06: 18000000 INFO @ Tue, 04 Sep 2018 09:43:12: 20000000 INFO @ Tue, 04 Sep 2018 09:43:13: 19000000 INFO @ Tue, 04 Sep 2018 09:43:13: 19000000 INFO @ Tue, 04 Sep 2018 09:43:20: 21000000 INFO @ Tue, 04 Sep 2018 09:43:21: 20000000 INFO @ Tue, 04 Sep 2018 09:43:21: 20000000 INFO @ Tue, 04 Sep 2018 09:43:27: 22000000 INFO @ Tue, 04 Sep 2018 09:43:29: 21000000 INFO @ Tue, 04 Sep 2018 09:43:29: 21000000 INFO @ Tue, 04 Sep 2018 09:43:34: 23000000 INFO @ Tue, 04 Sep 2018 09:43:36: 22000000 INFO @ Tue, 04 Sep 2018 09:43:36: 22000000 INFO @ Tue, 04 Sep 2018 09:43:41: 24000000 INFO @ Tue, 04 Sep 2018 09:43:44: 23000000 INFO @ Tue, 04 Sep 2018 09:43:44: 23000000 INFO @ Tue, 04 Sep 2018 09:43:49: 25000000 INFO @ Tue, 04 Sep 2018 09:43:52: 24000000 INFO @ Tue, 04 Sep 2018 09:43:52: 24000000 INFO @ Tue, 04 Sep 2018 09:43:56: 26000000 INFO @ Tue, 04 Sep 2018 09:43:59: 25000000 INFO @ Tue, 04 Sep 2018 09:43:59: 25000000 INFO @ Tue, 04 Sep 2018 09:44:03: 27000000 INFO @ Tue, 04 Sep 2018 09:44:07: 26000000 INFO @ Tue, 04 Sep 2018 09:44:07: 26000000 INFO @ Tue, 04 Sep 2018 09:44:10: 28000000 INFO @ Tue, 04 Sep 2018 09:44:14: 27000000 INFO @ Tue, 04 Sep 2018 09:44:14: 27000000 INFO @ Tue, 04 Sep 2018 09:44:17: 29000000 INFO @ Tue, 04 Sep 2018 09:44:22: 28000000 INFO @ Tue, 04 Sep 2018 09:44:22: 28000000 INFO @ Tue, 04 Sep 2018 09:44:25: 30000000 INFO @ Tue, 04 Sep 2018 09:44:30: 29000000 INFO @ Tue, 04 Sep 2018 09:44:30: 29000000 INFO @ Tue, 04 Sep 2018 09:44:32: 31000000 INFO @ Tue, 04 Sep 2018 09:44:37: 30000000 INFO @ Tue, 04 Sep 2018 09:44:37: 30000000 INFO @ Tue, 04 Sep 2018 09:44:39: 32000000 INFO @ Tue, 04 Sep 2018 09:44:45: 31000000 INFO @ Tue, 04 Sep 2018 09:44:45: 31000000 INFO @ Tue, 04 Sep 2018 09:44:46: 33000000 INFO @ Tue, 04 Sep 2018 09:44:52: 32000000 INFO @ Tue, 04 Sep 2018 09:44:52: 32000000 INFO @ Tue, 04 Sep 2018 09:44:53: 34000000 INFO @ Tue, 04 Sep 2018 09:45:00: 33000000 INFO @ Tue, 04 Sep 2018 09:45:00: 33000000 INFO @ Tue, 04 Sep 2018 09:45:00: 35000000 INFO @ Tue, 04 Sep 2018 09:45:08: 34000000 INFO @ Tue, 04 Sep 2018 09:45:08: 34000000 INFO @ Tue, 04 Sep 2018 09:45:08: 36000000 INFO @ Tue, 04 Sep 2018 09:45:15: 37000000 INFO @ Tue, 04 Sep 2018 09:45:15: 35000000 INFO @ Tue, 04 Sep 2018 09:45:15: 35000000 INFO @ Tue, 04 Sep 2018 09:45:22: 38000000 INFO @ Tue, 04 Sep 2018 09:45:23: 36000000 INFO @ Tue, 04 Sep 2018 09:45:23: 36000000 INFO @ Tue, 04 Sep 2018 09:45:29: 39000000 INFO @ Tue, 04 Sep 2018 09:45:30: 37000000 INFO @ Tue, 04 Sep 2018 09:45:30: 37000000 INFO @ Tue, 04 Sep 2018 09:45:36: 40000000 INFO @ Tue, 04 Sep 2018 09:45:38: 38000000 INFO @ Tue, 04 Sep 2018 09:45:38: 38000000 INFO @ Tue, 04 Sep 2018 09:45:43: 41000000 INFO @ Tue, 04 Sep 2018 09:45:45: 39000000 INFO @ Tue, 04 Sep 2018 09:45:45: 39000000 INFO @ Tue, 04 Sep 2018 09:45:50: 42000000 INFO @ Tue, 04 Sep 2018 09:45:53: 40000000 INFO @ Tue, 04 Sep 2018 09:45:53: 40000000 INFO @ Tue, 04 Sep 2018 09:45:57: 43000000 INFO @ Tue, 04 Sep 2018 09:46:00: 41000000 INFO @ Tue, 04 Sep 2018 09:46:00: 41000000 INFO @ Tue, 04 Sep 2018 09:46:04: 44000000 INFO @ Tue, 04 Sep 2018 09:46:08: 42000000 INFO @ Tue, 04 Sep 2018 09:46:08: 42000000 INFO @ Tue, 04 Sep 2018 09:46:11: 45000000 INFO @ Tue, 04 Sep 2018 09:46:16: 43000000 INFO @ Tue, 04 Sep 2018 09:46:16: 43000000 INFO @ Tue, 04 Sep 2018 09:46:18: 46000000 INFO @ Tue, 04 Sep 2018 09:46:18: #1 tag size is determined as 76 bps INFO @ Tue, 04 Sep 2018 09:46:18: #1 tag size = 76 INFO @ Tue, 04 Sep 2018 09:46:18: #1 total tags in treatment: 20620963 INFO @ Tue, 04 Sep 2018 09:46:18: #1 user defined the maximum tags... INFO @ Tue, 04 Sep 2018 09:46:18: #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 09:46:19: #1 tags after filtering in treatment: 17493199 INFO @ Tue, 04 Sep 2018 09:46:19: #1 Redundant rate of treatment: 0.15 INFO @ Tue, 04 Sep 2018 09:46:19: #1 finished! INFO @ Tue, 04 Sep 2018 09:46:19: #2 Build Peak Model... INFO @ Tue, 04 Sep 2018 09:46:19: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 04 Sep 2018 09:46:20: #2 number of paired peaks: 242 WARNING @ Tue, 04 Sep 2018 09:46:20: Fewer paired peaks (242) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 242 pairs to build model! INFO @ Tue, 04 Sep 2018 09:46:20: start model_add_line... INFO @ Tue, 04 Sep 2018 09:46:20: start X-correlation... INFO @ Tue, 04 Sep 2018 09:46:20: end of X-cor INFO @ Tue, 04 Sep 2018 09:46:20: #2 finished! INFO @ Tue, 04 Sep 2018 09:46:20: #2 predicted fragment length is 155 bps INFO @ Tue, 04 Sep 2018 09:46:20: #2 alternative fragment length(s) may be 4,155 bps INFO @ Tue, 04 Sep 2018 09:46:20: #2.2 Generate R script for model : SRX4029333.20_model.r INFO @ Tue, 04 Sep 2018 09:46:20: #3 Call peaks... INFO @ Tue, 04 Sep 2018 09:46:21: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 04 Sep 2018 09:46:23: 44000000 INFO @ Tue, 04 Sep 2018 09:46:23: 44000000 INFO @ Tue, 04 Sep 2018 09:46:30: 45000000 INFO @ Tue, 04 Sep 2018 09:46:30: 45000000 INFO @ Tue, 04 Sep 2018 09:46:37: 46000000 INFO @ Tue, 04 Sep 2018 09:46:37: 46000000 INFO @ Tue, 04 Sep 2018 09:46:38: #1 tag size is determined as 76 bps INFO @ Tue, 04 Sep 2018 09:46:38: #1 tag size = 76 INFO @ Tue, 04 Sep 2018 09:46:38: #1 total tags in treatment: 20620963 INFO @ Tue, 04 Sep 2018 09:46:38: #1 user defined the maximum tags... INFO @ Tue, 04 Sep 2018 09:46:38: #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 09:46:38: #1 tag size is determined as 76 bps INFO @ Tue, 04 Sep 2018 09:46:38: #1 tag size = 76 INFO @ Tue, 04 Sep 2018 09:46:38: #1 total tags in treatment: 20620963 INFO @ Tue, 04 Sep 2018 09:46:38: #1 user defined the maximum tags... INFO @ Tue, 04 Sep 2018 09:46:38: #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 09:46:38: #1 tags after filtering in treatment: 17493199 INFO @ Tue, 04 Sep 2018 09:46:38: #1 Redundant rate of treatment: 0.15 INFO @ Tue, 04 Sep 2018 09:46:38: #1 finished! INFO @ Tue, 04 Sep 2018 09:46:38: #2 Build Peak Model... INFO @ Tue, 04 Sep 2018 09:46:38: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 04 Sep 2018 09:46:38: #1 tags after filtering in treatment: 17493199 INFO @ Tue, 04 Sep 2018 09:46:38: #1 Redundant rate of treatment: 0.15 INFO @ Tue, 04 Sep 2018 09:46:38: #1 finished! INFO @ Tue, 04 Sep 2018 09:46:38: #2 Build Peak Model... INFO @ Tue, 04 Sep 2018 09:46:38: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 04 Sep 2018 09:46:39: #2 number of paired peaks: 242 WARNING @ Tue, 04 Sep 2018 09:46:39: Fewer paired peaks (242) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 242 pairs to build model! INFO @ Tue, 04 Sep 2018 09:46:39: start model_add_line... INFO @ Tue, 04 Sep 2018 09:46:39: #2 number of paired peaks: 242 WARNING @ Tue, 04 Sep 2018 09:46:39: Fewer paired peaks (242) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 242 pairs to build model! INFO @ Tue, 04 Sep 2018 09:46:39: start model_add_line... INFO @ Tue, 04 Sep 2018 09:46:40: start X-correlation... INFO @ Tue, 04 Sep 2018 09:46:40: end of X-cor INFO @ Tue, 04 Sep 2018 09:46:40: #2 finished! INFO @ Tue, 04 Sep 2018 09:46:40: #2 predicted fragment length is 155 bps INFO @ Tue, 04 Sep 2018 09:46:40: #2 alternative fragment length(s) may be 4,155 bps INFO @ Tue, 04 Sep 2018 09:46:40: #2.2 Generate R script for model : SRX4029333.05_model.r INFO @ Tue, 04 Sep 2018 09:46:40: start X-correlation... INFO @ Tue, 04 Sep 2018 09:46:40: end of X-cor INFO @ Tue, 04 Sep 2018 09:46:40: #2 finished! INFO @ Tue, 04 Sep 2018 09:46:40: #2 predicted fragment length is 155 bps INFO @ Tue, 04 Sep 2018 09:46:40: #3 Call peaks... INFO @ Tue, 04 Sep 2018 09:46:40: #2 alternative fragment length(s) may be 4,155 bps INFO @ Tue, 04 Sep 2018 09:46:40: #2.2 Generate R script for model : SRX4029333.10_model.r INFO @ Tue, 04 Sep 2018 09:46:40: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 04 Sep 2018 09:46:40: #3 Call peaks... INFO @ Tue, 04 Sep 2018 09:46:40: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 04 Sep 2018 09:46:57: #3 Call peaks for each chromosome... INFO @ Tue, 04 Sep 2018 09:47:15: #4 Write output xls file... SRX4029333.20_peaks.xls INFO @ Tue, 04 Sep 2018 09:47:15: #4 Write peak in narrowPeak format file... SRX4029333.20_peaks.narrowPeak INFO @ Tue, 04 Sep 2018 09:47:15: #4 Write summits bed file... SRX4029333.20_summits.bed INFO @ Tue, 04 Sep 2018 09:47:15: Done! INFO @ Tue, 04 Sep 2018 09:47:15: #3 Call peaks for each chromosome... pass1 - making usageList (7 chroms): 16 millis pass2 - checking and writing primary data (218 records, 4 fields): 12 millis CompletedMACS2peakCalling INFO @ Tue, 04 Sep 2018 09:47:17: #3 Call peaks for each chromosome... INFO @ Tue, 04 Sep 2018 09:47:34: #4 Write output xls file... SRX4029333.10_peaks.xls INFO @ Tue, 04 Sep 2018 09:47:34: #4 Write peak in narrowPeak format file... SRX4029333.10_peaks.narrowPeak INFO @ Tue, 04 Sep 2018 09:47:34: #4 Write summits bed file... SRX4029333.10_summits.bed INFO @ Tue, 04 Sep 2018 09:47:34: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (325 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Tue, 04 Sep 2018 09:47:37: #4 Write output xls file... SRX4029333.05_peaks.xls INFO @ Tue, 04 Sep 2018 09:47:37: #4 Write peak in narrowPeak format file... SRX4029333.05_peaks.narrowPeak INFO @ Tue, 04 Sep 2018 09:47:37: #4 Write summits bed file... SRX4029333.05_summits.bed INFO @ Tue, 04 Sep 2018 09:47:37: Done! pass1 - making usageList (7 chroms): 0 millis pass2 - checking and writing primary data (423 records, 4 fields): 3 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。