Job ID = 10714469 sra ファイルのダウンロード中... Completed: 1433910K bytes transferred in 24 seconds (482830K 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 23416339 spots for /home/okishinya/chipatlas/results/ce10/SRX4085385/SRR7167414.sra Written 23416339 spots for /home/okishinya/chipatlas/results/ce10/SRX4085385/SRR7167414.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: 00:21:23 23416339 reads; of these: 23416339 (100.00%) were paired; of these: 7189082 (30.70%) aligned concordantly 0 times 13750829 (58.72%) aligned concordantly exactly 1 time 2476428 (10.58%) aligned concordantly >1 times ---- 7189082 pairs aligned concordantly 0 times; of these: 456439 (6.35%) aligned discordantly 1 time ---- 6732643 pairs aligned 0 times concordantly or discordantly; of these: 13465286 mates make up the pairs; of these: 9841485 (73.09%) aligned 0 times 3091236 (22.96%) aligned exactly 1 time 532565 (3.96%) aligned >1 times 78.99% overall alignment rate Time searching: 00:21:23 Overall time: 00:21:23 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 16 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] 1323428 / 16500151 = 0.0802 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 @ Sun, 03 Jun 2018 13:14:55: # Command line: callpeak -t SRX4085385.bam -f BAM -g ce -n SRX4085385.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX4085385.10 # format = BAM # ChIP-seq file = ['SRX4085385.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 @ Sun, 03 Jun 2018 13:14:55: #1 read tag files... INFO @ Sun, 03 Jun 2018 13:14:55: #1 read treatment tags... INFO @ Sun, 03 Jun 2018 13:14:55: # Command line: callpeak -t SRX4085385.bam -f BAM -g ce -n SRX4085385.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX4085385.20 # format = BAM # ChIP-seq file = ['SRX4085385.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 @ Sun, 03 Jun 2018 13:14:55: #1 read tag files... INFO @ Sun, 03 Jun 2018 13:14:55: #1 read treatment tags... INFO @ Sun, 03 Jun 2018 13:14:55: # Command line: callpeak -t SRX4085385.bam -f BAM -g ce -n SRX4085385.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX4085385.05 # format = BAM # ChIP-seq file = ['SRX4085385.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 @ Sun, 03 Jun 2018 13:14:55: #1 read tag files... INFO @ Sun, 03 Jun 2018 13:14:55: #1 read treatment tags... INFO @ Sun, 03 Jun 2018 13:15:02: 1000000 INFO @ Sun, 03 Jun 2018 13:15:02: 1000000 INFO @ Sun, 03 Jun 2018 13:15:02: 1000000 INFO @ Sun, 03 Jun 2018 13:15:09: 2000000 INFO @ Sun, 03 Jun 2018 13:15:09: 2000000 INFO @ Sun, 03 Jun 2018 13:15:09: 2000000 INFO @ Sun, 03 Jun 2018 13:15:16: 3000000 INFO @ Sun, 03 Jun 2018 13:15:16: 3000000 INFO @ Sun, 03 Jun 2018 13:15:16: 3000000 INFO @ Sun, 03 Jun 2018 13:15:23: 4000000 INFO @ Sun, 03 Jun 2018 13:15:23: 4000000 INFO @ Sun, 03 Jun 2018 13:15:23: 4000000 INFO @ Sun, 03 Jun 2018 13:15:30: 5000000 INFO @ Sun, 03 Jun 2018 13:15:30: 5000000 INFO @ Sun, 03 Jun 2018 13:15:30: 5000000 INFO @ Sun, 03 Jun 2018 13:15:37: 6000000 INFO @ Sun, 03 Jun 2018 13:15:38: 6000000 INFO @ Sun, 03 Jun 2018 13:15:38: 6000000 INFO @ Sun, 03 Jun 2018 13:15:44: 7000000 INFO @ Sun, 03 Jun 2018 13:15:45: 7000000 INFO @ Sun, 03 Jun 2018 13:15:45: 7000000 INFO @ Sun, 03 Jun 2018 13:15:51: 8000000 INFO @ Sun, 03 Jun 2018 13:15:52: 8000000 INFO @ Sun, 03 Jun 2018 13:15:52: 8000000 INFO @ Sun, 03 Jun 2018 13:15:58: 9000000 INFO @ Sun, 03 Jun 2018 13:15:59: 9000000 INFO @ Sun, 03 Jun 2018 13:15:59: 9000000 INFO @ Sun, 03 Jun 2018 13:16:05: 10000000 INFO @ Sun, 03 Jun 2018 13:16:06: 10000000 INFO @ Sun, 03 Jun 2018 13:16:06: 10000000 INFO @ Sun, 03 Jun 2018 13:16:12: 11000000 INFO @ Sun, 03 Jun 2018 13:16:13: 11000000 INFO @ Sun, 03 Jun 2018 13:16:13: 11000000 INFO @ Sun, 03 Jun 2018 13:16:19: 12000000 INFO @ Sun, 03 Jun 2018 13:16:20: 12000000 INFO @ Sun, 03 Jun 2018 13:16:20: 12000000 INFO @ Sun, 03 Jun 2018 13:16:26: 13000000 INFO @ Sun, 03 Jun 2018 13:16:27: 13000000 INFO @ Sun, 03 Jun 2018 13:16:27: 13000000 INFO @ Sun, 03 Jun 2018 13:16:33: 14000000 INFO @ Sun, 03 Jun 2018 13:16:34: 14000000 INFO @ Sun, 03 Jun 2018 13:16:34: 14000000 INFO @ Sun, 03 Jun 2018 13:16:40: 15000000 INFO @ Sun, 03 Jun 2018 13:16:41: 15000000 INFO @ Sun, 03 Jun 2018 13:16:41: 15000000 INFO @ Sun, 03 Jun 2018 13:16:47: 16000000 INFO @ Sun, 03 Jun 2018 13:16:49: 16000000 INFO @ Sun, 03 Jun 2018 13:16:49: 16000000 INFO @ Sun, 03 Jun 2018 13:16:53: 17000000 INFO @ Sun, 03 Jun 2018 13:16:56: 17000000 INFO @ Sun, 03 Jun 2018 13:16:56: 17000000 INFO @ Sun, 03 Jun 2018 13:17:00: 18000000 INFO @ Sun, 03 Jun 2018 13:17:03: 18000000 INFO @ Sun, 03 Jun 2018 13:17:03: 18000000 INFO @ Sun, 03 Jun 2018 13:17:07: 19000000 INFO @ Sun, 03 Jun 2018 13:17:10: 19000000 INFO @ Sun, 03 Jun 2018 13:17:10: 19000000 INFO @ Sun, 03 Jun 2018 13:17:14: 20000000 INFO @ Sun, 03 Jun 2018 13:17:18: 20000000 INFO @ Sun, 03 Jun 2018 13:17:18: 20000000 INFO @ Sun, 03 Jun 2018 13:17:20: 21000000 INFO @ Sun, 03 Jun 2018 13:17:25: 21000000 INFO @ Sun, 03 Jun 2018 13:17:25: 21000000 INFO @ Sun, 03 Jun 2018 13:17:27: 22000000 INFO @ Sun, 03 Jun 2018 13:17:32: 22000000 INFO @ Sun, 03 Jun 2018 13:17:32: 22000000 INFO @ Sun, 03 Jun 2018 13:17:34: 23000000 INFO @ Sun, 03 Jun 2018 13:17:40: 23000000 INFO @ Sun, 03 Jun 2018 13:17:40: 23000000 INFO @ Sun, 03 Jun 2018 13:17:41: 24000000 INFO @ Sun, 03 Jun 2018 13:17:47: 24000000 INFO @ Sun, 03 Jun 2018 13:17:47: 24000000 INFO @ Sun, 03 Jun 2018 13:17:48: 25000000 INFO @ Sun, 03 Jun 2018 13:17:54: 25000000 INFO @ Sun, 03 Jun 2018 13:17:54: 25000000 INFO @ Sun, 03 Jun 2018 13:17:55: 26000000 INFO @ Sun, 03 Jun 2018 13:18:01: 26000000 INFO @ Sun, 03 Jun 2018 13:18:01: 26000000 INFO @ Sun, 03 Jun 2018 13:18:02: 27000000 INFO @ Sun, 03 Jun 2018 13:18:09: 27000000 INFO @ Sun, 03 Jun 2018 13:18:09: 27000000 INFO @ Sun, 03 Jun 2018 13:18:09: 28000000 INFO @ Sun, 03 Jun 2018 13:18:16: 29000000 INFO @ Sun, 03 Jun 2018 13:18:16: 28000000 INFO @ Sun, 03 Jun 2018 13:18:16: 28000000 INFO @ Sun, 03 Jun 2018 13:18:23: 30000000 INFO @ Sun, 03 Jun 2018 13:18:23: 29000000 INFO @ Sun, 03 Jun 2018 13:18:23: 29000000 INFO @ Sun, 03 Jun 2018 13:18:29: 31000000 INFO @ Sun, 03 Jun 2018 13:18:30: 30000000 INFO @ Sun, 03 Jun 2018 13:18:30: 30000000 INFO @ Sun, 03 Jun 2018 13:18:36: 32000000 INFO @ Sun, 03 Jun 2018 13:18:37: 31000000 INFO @ Sun, 03 Jun 2018 13:18:37: 31000000 INFO @ Sun, 03 Jun 2018 13:18:44: 33000000 INFO @ Sun, 03 Jun 2018 13:18:44: 32000000 INFO @ Sun, 03 Jun 2018 13:18:44: 32000000 INFO @ Sun, 03 Jun 2018 13:18:50: 34000000 INFO @ Sun, 03 Jun 2018 13:18:52: 33000000 INFO @ Sun, 03 Jun 2018 13:18:52: 33000000 INFO @ Sun, 03 Jun 2018 13:18:52: #1 tag size is determined as 51 bps INFO @ Sun, 03 Jun 2018 13:18:52: #1 tag size = 51 INFO @ Sun, 03 Jun 2018 13:18:52: #1 total tags in treatment: 14922872 INFO @ Sun, 03 Jun 2018 13:18:52: #1 user defined the maximum tags... INFO @ Sun, 03 Jun 2018 13:18:52: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sun, 03 Jun 2018 13:18:53: #1 tags after filtering in treatment: 12646134 INFO @ Sun, 03 Jun 2018 13:18:53: #1 Redundant rate of treatment: 0.15 INFO @ Sun, 03 Jun 2018 13:18:53: #1 finished! INFO @ Sun, 03 Jun 2018 13:18:53: #2 Build Peak Model... INFO @ Sun, 03 Jun 2018 13:18:53: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 03 Jun 2018 13:18:54: #2 number of paired peaks: 248 WARNING @ Sun, 03 Jun 2018 13:18:54: Fewer paired peaks (248) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 248 pairs to build model! INFO @ Sun, 03 Jun 2018 13:18:54: start model_add_line... INFO @ Sun, 03 Jun 2018 13:18:54: start X-correlation... INFO @ Sun, 03 Jun 2018 13:18:54: end of X-cor INFO @ Sun, 03 Jun 2018 13:18:54: #2 finished! INFO @ Sun, 03 Jun 2018 13:18:54: #2 predicted fragment length is 98 bps INFO @ Sun, 03 Jun 2018 13:18:54: #2 alternative fragment length(s) may be 3,98 bps INFO @ Sun, 03 Jun 2018 13:18:54: #2.2 Generate R script for model : SRX4085385.10_model.r WARNING @ Sun, 03 Jun 2018 13:18:54: #2 Since the d (98) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 03 Jun 2018 13:18:54: #2 You may need to consider one of the other alternative d(s): 3,98 WARNING @ Sun, 03 Jun 2018 13:18:54: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sun, 03 Jun 2018 13:18:54: #3 Call peaks... INFO @ Sun, 03 Jun 2018 13:18:54: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 03 Jun 2018 13:18:58: 34000000 INFO @ Sun, 03 Jun 2018 13:18:58: 34000000 INFO @ Sun, 03 Jun 2018 13:19:01: #1 tag size is determined as 51 bps INFO @ Sun, 03 Jun 2018 13:19:01: #1 tag size = 51 INFO @ Sun, 03 Jun 2018 13:19:01: #1 total tags in treatment: 14922872 INFO @ Sun, 03 Jun 2018 13:19:01: #1 user defined the maximum tags... INFO @ Sun, 03 Jun 2018 13:19:01: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sun, 03 Jun 2018 13:19:01: #1 tag size is determined as 51 bps INFO @ Sun, 03 Jun 2018 13:19:01: #1 tag size = 51 INFO @ Sun, 03 Jun 2018 13:19:01: #1 total tags in treatment: 14922872 INFO @ Sun, 03 Jun 2018 13:19:01: #1 user defined the maximum tags... INFO @ Sun, 03 Jun 2018 13:19:01: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sun, 03 Jun 2018 13:19:01: #1 tags after filtering in treatment: 12646134 INFO @ Sun, 03 Jun 2018 13:19:01: #1 Redundant rate of treatment: 0.15 INFO @ Sun, 03 Jun 2018 13:19:01: #1 finished! INFO @ Sun, 03 Jun 2018 13:19:01: #2 Build Peak Model... INFO @ Sun, 03 Jun 2018 13:19:01: #1 tags after filtering in treatment: 12646134 INFO @ Sun, 03 Jun 2018 13:19:01: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 03 Jun 2018 13:19:01: #1 Redundant rate of treatment: 0.15 INFO @ Sun, 03 Jun 2018 13:19:01: #1 finished! INFO @ Sun, 03 Jun 2018 13:19:01: #2 Build Peak Model... INFO @ Sun, 03 Jun 2018 13:19:01: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 03 Jun 2018 13:19:02: #2 number of paired peaks: 248 WARNING @ Sun, 03 Jun 2018 13:19:02: Fewer paired peaks (248) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 248 pairs to build model! INFO @ Sun, 03 Jun 2018 13:19:02: start model_add_line... INFO @ Sun, 03 Jun 2018 13:19:02: #2 number of paired peaks: 248 WARNING @ Sun, 03 Jun 2018 13:19:02: Fewer paired peaks (248) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 248 pairs to build model! INFO @ Sun, 03 Jun 2018 13:19:02: start model_add_line... INFO @ Sun, 03 Jun 2018 13:19:02: start X-correlation... INFO @ Sun, 03 Jun 2018 13:19:02: end of X-cor INFO @ Sun, 03 Jun 2018 13:19:02: #2 finished! INFO @ Sun, 03 Jun 2018 13:19:02: #2 predicted fragment length is 98 bps INFO @ Sun, 03 Jun 2018 13:19:02: #2 alternative fragment length(s) may be 3,98 bps INFO @ Sun, 03 Jun 2018 13:19:02: #2.2 Generate R script for model : SRX4085385.05_model.r WARNING @ Sun, 03 Jun 2018 13:19:02: #2 Since the d (98) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 03 Jun 2018 13:19:02: #2 You may need to consider one of the other alternative d(s): 3,98 WARNING @ Sun, 03 Jun 2018 13:19:02: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sun, 03 Jun 2018 13:19:02: #3 Call peaks... INFO @ Sun, 03 Jun 2018 13:19:02: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 03 Jun 2018 13:19:02: start X-correlation... INFO @ Sun, 03 Jun 2018 13:19:02: end of X-cor INFO @ Sun, 03 Jun 2018 13:19:02: #2 finished! INFO @ Sun, 03 Jun 2018 13:19:02: #2 predicted fragment length is 98 bps INFO @ Sun, 03 Jun 2018 13:19:02: #2 alternative fragment length(s) may be 3,98 bps INFO @ Sun, 03 Jun 2018 13:19:02: #2.2 Generate R script for model : SRX4085385.20_model.r WARNING @ Sun, 03 Jun 2018 13:19:02: #2 Since the d (98) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 03 Jun 2018 13:19:02: #2 You may need to consider one of the other alternative d(s): 3,98 WARNING @ Sun, 03 Jun 2018 13:19:02: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sun, 03 Jun 2018 13:19:02: #3 Call peaks... INFO @ Sun, 03 Jun 2018 13:19:02: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 03 Jun 2018 13:19:21: #3 Call peaks for each chromosome... INFO @ Sun, 03 Jun 2018 13:19:30: #3 Call peaks for each chromosome... INFO @ Sun, 03 Jun 2018 13:19:30: #3 Call peaks for each chromosome... INFO @ Sun, 03 Jun 2018 13:19:36: #4 Write output xls file... SRX4085385.10_peaks.xls INFO @ Sun, 03 Jun 2018 13:19:36: #4 Write peak in narrowPeak format file... SRX4085385.10_peaks.narrowPeak INFO @ Sun, 03 Jun 2018 13:19:36: #4 Write summits bed file... SRX4085385.10_summits.bed INFO @ Sun, 03 Jun 2018 13:19:36: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (987 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Sun, 03 Jun 2018 13:19:43: #4 Write output xls file... SRX4085385.20_peaks.xls INFO @ Sun, 03 Jun 2018 13:19:43: #4 Write peak in narrowPeak format file... SRX4085385.20_peaks.narrowPeak INFO @ Sun, 03 Jun 2018 13:19:43: #4 Write summits bed file... SRX4085385.20_summits.bed INFO @ Sun, 03 Jun 2018 13:19:43: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (349 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Sun, 03 Jun 2018 13:19:44: #4 Write output xls file... SRX4085385.05_peaks.xls INFO @ Sun, 03 Jun 2018 13:19:44: #4 Write peak in narrowPeak format file... SRX4085385.05_peaks.narrowPeak INFO @ Sun, 03 Jun 2018 13:19:44: #4 Write summits bed file... SRX4085385.05_summits.bed INFO @ Sun, 03 Jun 2018 13:19:44: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (1823 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。