Job ID = 11597692 sra ファイルのダウンロード中... Completed: 3177283K bytes transferred in 43 seconds (604433K 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 27259598 spots for /home/okishinya/chipatlas/results/ce10/SRX5064640/SRR8246576.sra Written 27259598 spots for /home/okishinya/chipatlas/results/ce10/SRX5064640/SRR8246576.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: 01:36:20 27259598 reads; of these: 27259598 (100.00%) were paired; of these: 1876811 (6.88%) aligned concordantly 0 times 19208103 (70.46%) aligned concordantly exactly 1 time 6174684 (22.65%) aligned concordantly >1 times ---- 1876811 pairs aligned concordantly 0 times; of these: 374690 (19.96%) aligned discordantly 1 time ---- 1502121 pairs aligned 0 times concordantly or discordantly; of these: 3004242 mates make up the pairs; of these: 2350452 (78.24%) aligned 0 times 297890 (9.92%) aligned exactly 1 time 355900 (11.85%) aligned >1 times 95.69% overall alignment rate Time searching: 01:36:20 Overall time: 01:36:20 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 40 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] 7975639 / 25714880 = 0.3102 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 @ Wed, 30 Jan 2019 16:19:31: # Command line: callpeak -t SRX5064640.bam -f BAM -g ce -n SRX5064640.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX5064640.10 # format = BAM # ChIP-seq file = ['SRX5064640.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 @ Wed, 30 Jan 2019 16:19:31: #1 read tag files... INFO @ Wed, 30 Jan 2019 16:19:31: #1 read treatment tags... INFO @ Wed, 30 Jan 2019 16:19:31: # Command line: callpeak -t SRX5064640.bam -f BAM -g ce -n SRX5064640.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX5064640.05 # format = BAM # ChIP-seq file = ['SRX5064640.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 @ Wed, 30 Jan 2019 16:19:31: # Command line: callpeak -t SRX5064640.bam -f BAM -g ce -n SRX5064640.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX5064640.20 # format = BAM # ChIP-seq file = ['SRX5064640.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 @ Wed, 30 Jan 2019 16:19:31: #1 read tag files... INFO @ Wed, 30 Jan 2019 16:19:31: #1 read tag files... INFO @ Wed, 30 Jan 2019 16:19:31: #1 read treatment tags... INFO @ Wed, 30 Jan 2019 16:19:31: #1 read treatment tags... INFO @ Wed, 30 Jan 2019 16:19:41: 1000000 INFO @ Wed, 30 Jan 2019 16:19:41: 1000000 INFO @ Wed, 30 Jan 2019 16:19:41: 1000000 INFO @ Wed, 30 Jan 2019 16:19:50: 2000000 INFO @ Wed, 30 Jan 2019 16:19:50: 2000000 INFO @ Wed, 30 Jan 2019 16:19:50: 2000000 INFO @ Wed, 30 Jan 2019 16:19:59: 3000000 INFO @ Wed, 30 Jan 2019 16:19:59: 3000000 INFO @ Wed, 30 Jan 2019 16:19:59: 3000000 INFO @ Wed, 30 Jan 2019 16:20:08: 4000000 INFO @ Wed, 30 Jan 2019 16:20:09: 4000000 INFO @ Wed, 30 Jan 2019 16:20:09: 4000000 INFO @ Wed, 30 Jan 2019 16:20:18: 5000000 INFO @ Wed, 30 Jan 2019 16:20:18: 5000000 INFO @ Wed, 30 Jan 2019 16:20:19: 5000000 INFO @ Wed, 30 Jan 2019 16:20:27: 6000000 INFO @ Wed, 30 Jan 2019 16:20:27: 6000000 INFO @ Wed, 30 Jan 2019 16:20:29: 6000000 INFO @ Wed, 30 Jan 2019 16:20:36: 7000000 INFO @ Wed, 30 Jan 2019 16:20:37: 7000000 INFO @ Wed, 30 Jan 2019 16:20:38: 7000000 INFO @ Wed, 30 Jan 2019 16:20:46: 8000000 INFO @ Wed, 30 Jan 2019 16:20:48: 8000000 INFO @ Wed, 30 Jan 2019 16:20:49: 8000000 INFO @ Wed, 30 Jan 2019 16:20:57: 9000000 INFO @ Wed, 30 Jan 2019 16:20:59: 9000000 INFO @ Wed, 30 Jan 2019 16:21:00: 9000000 INFO @ Wed, 30 Jan 2019 16:21:07: 10000000 INFO @ Wed, 30 Jan 2019 16:21:10: 10000000 INFO @ Wed, 30 Jan 2019 16:21:11: 10000000 INFO @ Wed, 30 Jan 2019 16:21:18: 11000000 INFO @ Wed, 30 Jan 2019 16:21:20: 11000000 INFO @ Wed, 30 Jan 2019 16:21:21: 11000000 INFO @ Wed, 30 Jan 2019 16:21:27: 12000000 INFO @ Wed, 30 Jan 2019 16:21:30: 12000000 INFO @ Wed, 30 Jan 2019 16:21:31: 12000000 INFO @ Wed, 30 Jan 2019 16:21:37: 13000000 INFO @ Wed, 30 Jan 2019 16:21:39: 13000000 INFO @ Wed, 30 Jan 2019 16:21:40: 13000000 INFO @ Wed, 30 Jan 2019 16:21:46: 14000000 INFO @ Wed, 30 Jan 2019 16:21:49: 14000000 INFO @ Wed, 30 Jan 2019 16:21:50: 14000000 INFO @ Wed, 30 Jan 2019 16:21:56: 15000000 INFO @ Wed, 30 Jan 2019 16:21:58: 15000000 INFO @ Wed, 30 Jan 2019 16:21:59: 15000000 INFO @ Wed, 30 Jan 2019 16:22:04: 16000000 INFO @ Wed, 30 Jan 2019 16:22:07: 16000000 INFO @ Wed, 30 Jan 2019 16:22:09: 16000000 INFO @ Wed, 30 Jan 2019 16:22:14: 17000000 INFO @ Wed, 30 Jan 2019 16:22:16: 17000000 INFO @ Wed, 30 Jan 2019 16:22:18: 17000000 INFO @ Wed, 30 Jan 2019 16:22:24: 18000000 INFO @ Wed, 30 Jan 2019 16:22:26: 18000000 INFO @ Wed, 30 Jan 2019 16:22:28: 18000000 INFO @ Wed, 30 Jan 2019 16:22:35: 19000000 INFO @ Wed, 30 Jan 2019 16:22:37: 19000000 INFO @ Wed, 30 Jan 2019 16:22:38: 19000000 INFO @ Wed, 30 Jan 2019 16:22:45: 20000000 INFO @ Wed, 30 Jan 2019 16:22:46: 20000000 INFO @ Wed, 30 Jan 2019 16:22:47: 20000000 INFO @ Wed, 30 Jan 2019 16:22:54: 21000000 INFO @ Wed, 30 Jan 2019 16:22:57: 21000000 INFO @ Wed, 30 Jan 2019 16:22:58: 21000000 INFO @ Wed, 30 Jan 2019 16:23:02: 22000000 INFO @ Wed, 30 Jan 2019 16:23:09: 22000000 INFO @ Wed, 30 Jan 2019 16:23:10: 22000000 INFO @ Wed, 30 Jan 2019 16:23:11: 23000000 INFO @ Wed, 30 Jan 2019 16:23:19: 24000000 INFO @ Wed, 30 Jan 2019 16:23:20: 23000000 INFO @ Wed, 30 Jan 2019 16:23:22: 23000000 INFO @ Wed, 30 Jan 2019 16:23:31: 25000000 INFO @ Wed, 30 Jan 2019 16:23:33: 24000000 INFO @ Wed, 30 Jan 2019 16:23:35: 24000000 INFO @ Wed, 30 Jan 2019 16:23:44: 26000000 INFO @ Wed, 30 Jan 2019 16:23:45: 25000000 INFO @ Wed, 30 Jan 2019 16:23:45: 25000000 INFO @ Wed, 30 Jan 2019 16:23:54: 26000000 INFO @ Wed, 30 Jan 2019 16:23:55: 27000000 INFO @ Wed, 30 Jan 2019 16:23:57: 26000000 INFO @ Wed, 30 Jan 2019 16:24:02: 27000000 INFO @ Wed, 30 Jan 2019 16:24:06: 28000000 INFO @ Wed, 30 Jan 2019 16:24:08: 27000000 INFO @ Wed, 30 Jan 2019 16:24:10: 28000000 INFO @ Wed, 30 Jan 2019 16:24:18: 29000000 INFO @ Wed, 30 Jan 2019 16:24:19: 29000000 INFO @ Wed, 30 Jan 2019 16:24:20: 28000000 INFO @ Wed, 30 Jan 2019 16:24:27: 30000000 INFO @ Wed, 30 Jan 2019 16:24:29: 30000000 INFO @ Wed, 30 Jan 2019 16:24:31: 29000000 INFO @ Wed, 30 Jan 2019 16:24:38: 31000000 INFO @ Wed, 30 Jan 2019 16:24:40: 31000000 INFO @ Wed, 30 Jan 2019 16:24:44: 30000000 INFO @ Wed, 30 Jan 2019 16:24:52: 32000000 INFO @ Wed, 30 Jan 2019 16:24:53: 32000000 INFO @ Wed, 30 Jan 2019 16:24:58: 31000000 INFO @ Wed, 30 Jan 2019 16:25:05: 33000000 INFO @ Wed, 30 Jan 2019 16:25:07: 33000000 INFO @ Wed, 30 Jan 2019 16:25:11: 32000000 INFO @ Wed, 30 Jan 2019 16:25:19: 34000000 INFO @ Wed, 30 Jan 2019 16:25:21: 34000000 INFO @ Wed, 30 Jan 2019 16:25:25: 33000000 INFO @ Wed, 30 Jan 2019 16:25:33: 35000000 INFO @ Wed, 30 Jan 2019 16:25:34: 35000000 INFO @ Wed, 30 Jan 2019 16:25:39: 34000000 INFO @ Wed, 30 Jan 2019 16:25:47: 36000000 INFO @ Wed, 30 Jan 2019 16:25:48: 36000000 INFO @ Wed, 30 Jan 2019 16:25:50: #1 tag size is determined as 150 bps INFO @ Wed, 30 Jan 2019 16:25:50: #1 tag size = 150 INFO @ Wed, 30 Jan 2019 16:25:50: #1 total tags in treatment: 17472325 INFO @ Wed, 30 Jan 2019 16:25:50: #1 user defined the maximum tags... INFO @ Wed, 30 Jan 2019 16:25:50: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Wed, 30 Jan 2019 16:25:51: #1 tags after filtering in treatment: 13420656 INFO @ Wed, 30 Jan 2019 16:25:51: #1 Redundant rate of treatment: 0.23 INFO @ Wed, 30 Jan 2019 16:25:51: #1 finished! INFO @ Wed, 30 Jan 2019 16:25:51: #2 Build Peak Model... INFO @ Wed, 30 Jan 2019 16:25:51: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 30 Jan 2019 16:25:51: #1 tag size is determined as 150 bps INFO @ Wed, 30 Jan 2019 16:25:51: #1 tag size = 150 INFO @ Wed, 30 Jan 2019 16:25:51: #1 total tags in treatment: 17472325 INFO @ Wed, 30 Jan 2019 16:25:51: #1 user defined the maximum tags... INFO @ Wed, 30 Jan 2019 16:25:51: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Wed, 30 Jan 2019 16:25:52: #1 tags after filtering in treatment: 13420656 INFO @ Wed, 30 Jan 2019 16:25:52: #1 Redundant rate of treatment: 0.23 INFO @ Wed, 30 Jan 2019 16:25:52: #1 finished! INFO @ Wed, 30 Jan 2019 16:25:52: #2 Build Peak Model... INFO @ Wed, 30 Jan 2019 16:25:52: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 30 Jan 2019 16:25:52: #2 number of paired peaks: 2253 INFO @ Wed, 30 Jan 2019 16:25:52: start model_add_line... INFO @ Wed, 30 Jan 2019 16:25:52: start X-correlation... INFO @ Wed, 30 Jan 2019 16:25:52: end of X-cor INFO @ Wed, 30 Jan 2019 16:25:52: #2 finished! INFO @ Wed, 30 Jan 2019 16:25:52: #2 predicted fragment length is 226 bps INFO @ Wed, 30 Jan 2019 16:25:52: #2 alternative fragment length(s) may be 1,226,242,261 bps INFO @ Wed, 30 Jan 2019 16:25:52: #2.2 Generate R script for model : SRX5064640.10_model.r INFO @ Wed, 30 Jan 2019 16:25:52: 35000000 WARNING @ Wed, 30 Jan 2019 16:25:52: #2 Since the d (226) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Wed, 30 Jan 2019 16:25:52: #2 You may need to consider one of the other alternative d(s): 1,226,242,261 WARNING @ Wed, 30 Jan 2019 16:25:52: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Wed, 30 Jan 2019 16:25:52: #3 Call peaks... INFO @ Wed, 30 Jan 2019 16:25:52: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 30 Jan 2019 16:25:53: #2 number of paired peaks: 2253 INFO @ Wed, 30 Jan 2019 16:25:53: start model_add_line... INFO @ Wed, 30 Jan 2019 16:25:53: start X-correlation... INFO @ Wed, 30 Jan 2019 16:25:53: end of X-cor INFO @ Wed, 30 Jan 2019 16:25:53: #2 finished! INFO @ Wed, 30 Jan 2019 16:25:53: #2 predicted fragment length is 226 bps INFO @ Wed, 30 Jan 2019 16:25:53: #2 alternative fragment length(s) may be 1,226,242,261 bps INFO @ Wed, 30 Jan 2019 16:25:53: #2.2 Generate R script for model : SRX5064640.05_model.r WARNING @ Wed, 30 Jan 2019 16:25:53: #2 Since the d (226) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Wed, 30 Jan 2019 16:25:53: #2 You may need to consider one of the other alternative d(s): 1,226,242,261 WARNING @ Wed, 30 Jan 2019 16:25:53: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Wed, 30 Jan 2019 16:25:53: #3 Call peaks... INFO @ Wed, 30 Jan 2019 16:25:53: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 30 Jan 2019 16:26:01: 36000000 INFO @ Wed, 30 Jan 2019 16:26:04: #1 tag size is determined as 150 bps INFO @ Wed, 30 Jan 2019 16:26:04: #1 tag size = 150 INFO @ Wed, 30 Jan 2019 16:26:04: #1 total tags in treatment: 17472325 INFO @ Wed, 30 Jan 2019 16:26:04: #1 user defined the maximum tags... INFO @ Wed, 30 Jan 2019 16:26:04: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Wed, 30 Jan 2019 16:26:04: #1 tags after filtering in treatment: 13420656 INFO @ Wed, 30 Jan 2019 16:26:04: #1 Redundant rate of treatment: 0.23 INFO @ Wed, 30 Jan 2019 16:26:04: #1 finished! INFO @ Wed, 30 Jan 2019 16:26:04: #2 Build Peak Model... INFO @ Wed, 30 Jan 2019 16:26:04: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 30 Jan 2019 16:26:05: #2 number of paired peaks: 2253 INFO @ Wed, 30 Jan 2019 16:26:05: start model_add_line... INFO @ Wed, 30 Jan 2019 16:26:05: start X-correlation... INFO @ Wed, 30 Jan 2019 16:26:05: end of X-cor INFO @ Wed, 30 Jan 2019 16:26:05: #2 finished! INFO @ Wed, 30 Jan 2019 16:26:05: #2 predicted fragment length is 226 bps INFO @ Wed, 30 Jan 2019 16:26:05: #2 alternative fragment length(s) may be 1,226,242,261 bps INFO @ Wed, 30 Jan 2019 16:26:05: #2.2 Generate R script for model : SRX5064640.20_model.r WARNING @ Wed, 30 Jan 2019 16:26:05: #2 Since the d (226) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Wed, 30 Jan 2019 16:26:05: #2 You may need to consider one of the other alternative d(s): 1,226,242,261 WARNING @ Wed, 30 Jan 2019 16:26:05: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Wed, 30 Jan 2019 16:26:05: #3 Call peaks... INFO @ Wed, 30 Jan 2019 16:26:05: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 30 Jan 2019 16:26:34: #3 Call peaks for each chromosome... INFO @ Wed, 30 Jan 2019 16:26:36: #3 Call peaks for each chromosome... INFO @ Wed, 30 Jan 2019 16:26:48: #3 Call peaks for each chromosome... INFO @ Wed, 30 Jan 2019 16:26:51: #4 Write output xls file... SRX5064640.05_peaks.xls INFO @ Wed, 30 Jan 2019 16:26:51: #4 Write peak in narrowPeak format file... SRX5064640.05_peaks.narrowPeak INFO @ Wed, 30 Jan 2019 16:26:51: #4 Write summits bed file... SRX5064640.05_summits.bed INFO @ Wed, 30 Jan 2019 16:26:51: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (824 records, 4 fields): 5 millis CompletedMACS2peakCalling INFO @ Wed, 30 Jan 2019 16:26:53: #4 Write output xls file... SRX5064640.10_peaks.xls INFO @ Wed, 30 Jan 2019 16:26:53: #4 Write peak in narrowPeak format file... SRX5064640.10_peaks.narrowPeak INFO @ Wed, 30 Jan 2019 16:26:53: #4 Write summits bed file... SRX5064640.10_summits.bed INFO @ Wed, 30 Jan 2019 16:26:53: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (486 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Wed, 30 Jan 2019 16:27:04: #4 Write output xls file... SRX5064640.20_peaks.xls INFO @ Wed, 30 Jan 2019 16:27:04: #4 Write peak in narrowPeak format file... SRX5064640.20_peaks.narrowPeak INFO @ Wed, 30 Jan 2019 16:27:04: #4 Write summits bed file... SRX5064640.20_summits.bed INFO @ Wed, 30 Jan 2019 16:27:04: Done! pass1 - making usageList (7 chroms): 3 millis pass2 - checking and writing primary data (287 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。