Job ID = 9157344 sra ファイルのダウンロード中... Completed: 1052612K bytes transferred in 12 seconds (693854K bits/sec), in 1 file, 2 directories. sra ファイルのダウンロードが完了しました。 Read layout: SINGLE fastq に変換中... Written 46755661 spots for /home/okishinya/chipatlas/results/ce10/SRX059222/SRR190662.sra Written 46755661 spots total 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: 00:08:05 46755661 reads; of these: 46755661 (100.00%) were unpaired; of these: 14945859 (31.97%) aligned 0 times 26131060 (55.89%) aligned exactly 1 time 5678742 (12.15%) aligned >1 times 68.03% overall alignment rate Time searching: 00:08:05 Overall time: 00:08:05 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 8 files... [bam_rmdupse_core] 4505469 / 31809802 = 0.1416 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, 27 Jun 2017 11:42:24: # Command line: callpeak -t SRX059222.bam -f BAM -g ce -n SRX059222.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX059222.05 # format = BAM # ChIP-seq file = ['SRX059222.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, 27 Jun 2017 11:42:24: #1 read tag files... INFO @ Tue, 27 Jun 2017 11:42:24: #1 read treatment tags... INFO @ Tue, 27 Jun 2017 11:42:24: # Command line: callpeak -t SRX059222.bam -f BAM -g ce -n SRX059222.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX059222.10 # format = BAM # ChIP-seq file = ['SRX059222.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, 27 Jun 2017 11:42:24: #1 read tag files... INFO @ Tue, 27 Jun 2017 11:42:24: #1 read treatment tags... INFO @ Tue, 27 Jun 2017 11:42:24: # Command line: callpeak -t SRX059222.bam -f BAM -g ce -n SRX059222.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX059222.20 # format = BAM # ChIP-seq file = ['SRX059222.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, 27 Jun 2017 11:42:24: #1 read tag files... INFO @ Tue, 27 Jun 2017 11:42:24: #1 read treatment tags... INFO @ Tue, 27 Jun 2017 11:42:31: 1000000 INFO @ Tue, 27 Jun 2017 11:42:31: 1000000 INFO @ Tue, 27 Jun 2017 11:42:32: 1000000 INFO @ Tue, 27 Jun 2017 11:42:38: 2000000 INFO @ Tue, 27 Jun 2017 11:42:39: 2000000 INFO @ Tue, 27 Jun 2017 11:42:39: 2000000 INFO @ Tue, 27 Jun 2017 11:42:45: 3000000 INFO @ Tue, 27 Jun 2017 11:42:46: 3000000 INFO @ Tue, 27 Jun 2017 11:42:47: 3000000 INFO @ Tue, 27 Jun 2017 11:42:53: 4000000 INFO @ Tue, 27 Jun 2017 11:42:54: 4000000 INFO @ Tue, 27 Jun 2017 11:42:55: 4000000 INFO @ Tue, 27 Jun 2017 11:43:00: 5000000 INFO @ Tue, 27 Jun 2017 11:43:01: 5000000 INFO @ Tue, 27 Jun 2017 11:43:03: 5000000 INFO @ Tue, 27 Jun 2017 11:43:07: 6000000 INFO @ Tue, 27 Jun 2017 11:43:09: 6000000 INFO @ Tue, 27 Jun 2017 11:43:10: 6000000 INFO @ Tue, 27 Jun 2017 11:43:14: 7000000 INFO @ Tue, 27 Jun 2017 11:43:17: 7000000 INFO @ Tue, 27 Jun 2017 11:43:18: 7000000 INFO @ Tue, 27 Jun 2017 11:43:22: 8000000 INFO @ Tue, 27 Jun 2017 11:43:24: 8000000 INFO @ Tue, 27 Jun 2017 11:43:26: 8000000 INFO @ Tue, 27 Jun 2017 11:43:29: 9000000 INFO @ Tue, 27 Jun 2017 11:43:32: 9000000 INFO @ Tue, 27 Jun 2017 11:43:34: 9000000 INFO @ Tue, 27 Jun 2017 11:43:36: 10000000 INFO @ Tue, 27 Jun 2017 11:43:39: 10000000 INFO @ Tue, 27 Jun 2017 11:43:41: 10000000 INFO @ Tue, 27 Jun 2017 11:43:43: 11000000 INFO @ Tue, 27 Jun 2017 11:43:47: 11000000 INFO @ Tue, 27 Jun 2017 11:43:49: 11000000 INFO @ Tue, 27 Jun 2017 11:43:51: 12000000 INFO @ Tue, 27 Jun 2017 11:43:54: 12000000 INFO @ Tue, 27 Jun 2017 11:43:57: 12000000 INFO @ Tue, 27 Jun 2017 11:43:58: 13000000 INFO @ Tue, 27 Jun 2017 11:44:02: 13000000 INFO @ Tue, 27 Jun 2017 11:44:04: 13000000 INFO @ Tue, 27 Jun 2017 11:44:05: 14000000 INFO @ Tue, 27 Jun 2017 11:44:10: 14000000 INFO @ Tue, 27 Jun 2017 11:44:12: 14000000 INFO @ Tue, 27 Jun 2017 11:44:12: 15000000 INFO @ Tue, 27 Jun 2017 11:44:17: 15000000 INFO @ Tue, 27 Jun 2017 11:44:19: 15000000 INFO @ Tue, 27 Jun 2017 11:44:20: 16000000 INFO @ Tue, 27 Jun 2017 11:44:25: 16000000 INFO @ Tue, 27 Jun 2017 11:44:27: 16000000 INFO @ Tue, 27 Jun 2017 11:44:27: 17000000 INFO @ Tue, 27 Jun 2017 11:44:33: 17000000 INFO @ Tue, 27 Jun 2017 11:44:34: 17000000 INFO @ Tue, 27 Jun 2017 11:44:35: 18000000 INFO @ Tue, 27 Jun 2017 11:44:40: 18000000 INFO @ Tue, 27 Jun 2017 11:44:42: 18000000 INFO @ Tue, 27 Jun 2017 11:44:42: 19000000 INFO @ Tue, 27 Jun 2017 11:44:48: 19000000 INFO @ Tue, 27 Jun 2017 11:44:49: 20000000 INFO @ Tue, 27 Jun 2017 11:44:49: 19000000 INFO @ Tue, 27 Jun 2017 11:44:55: 20000000 INFO @ Tue, 27 Jun 2017 11:44:56: 21000000 INFO @ Tue, 27 Jun 2017 11:44:57: 20000000 INFO @ Tue, 27 Jun 2017 11:45:03: 21000000 INFO @ Tue, 27 Jun 2017 11:45:03: 22000000 INFO @ Tue, 27 Jun 2017 11:45:05: 21000000 INFO @ Tue, 27 Jun 2017 11:45:10: 22000000 INFO @ Tue, 27 Jun 2017 11:45:10: 23000000 INFO @ Tue, 27 Jun 2017 11:45:13: 22000000 INFO @ Tue, 27 Jun 2017 11:45:17: 24000000 INFO @ Tue, 27 Jun 2017 11:45:17: 23000000 INFO @ Tue, 27 Jun 2017 11:45:20: 23000000 INFO @ Tue, 27 Jun 2017 11:45:24: 25000000 INFO @ Tue, 27 Jun 2017 11:45:25: 24000000 INFO @ Tue, 27 Jun 2017 11:45:28: 24000000 INFO @ Tue, 27 Jun 2017 11:45:31: 26000000 INFO @ Tue, 27 Jun 2017 11:45:32: 25000000 INFO @ Tue, 27 Jun 2017 11:45:36: 25000000 INFO @ Tue, 27 Jun 2017 11:45:38: 27000000 INFO @ Tue, 27 Jun 2017 11:45:39: 26000000 INFO @ Tue, 27 Jun 2017 11:45:40: #1 tag size is determined as 37 bps INFO @ Tue, 27 Jun 2017 11:45:40: #1 tag size = 37 INFO @ Tue, 27 Jun 2017 11:45:40: #1 total tags in treatment: 27304333 INFO @ Tue, 27 Jun 2017 11:45:40: #1 user defined the maximum tags... INFO @ Tue, 27 Jun 2017 11:45:40: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 27 Jun 2017 11:45:41: #1 tags after filtering in treatment: 27304333 INFO @ Tue, 27 Jun 2017 11:45:41: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 27 Jun 2017 11:45:41: #1 finished! INFO @ Tue, 27 Jun 2017 11:45:41: #2 Build Peak Model... INFO @ Tue, 27 Jun 2017 11:45:41: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 27 Jun 2017 11:45:43: #2 number of paired peaks: 122 WARNING @ Tue, 27 Jun 2017 11:45:43: Fewer paired peaks (122) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 122 pairs to build model! INFO @ Tue, 27 Jun 2017 11:45:43: start model_add_line... INFO @ Tue, 27 Jun 2017 11:45:43: start X-correlation... INFO @ Tue, 27 Jun 2017 11:45:43: end of X-cor INFO @ Tue, 27 Jun 2017 11:45:43: #2 finished! INFO @ Tue, 27 Jun 2017 11:45:43: #2 predicted fragment length is 1 bps INFO @ Tue, 27 Jun 2017 11:45:43: #2 alternative fragment length(s) may be 1,30,480,547,597 bps INFO @ Tue, 27 Jun 2017 11:45:43: #2.2 Generate R script for model : SRX059222.05_model.r WARNING @ Tue, 27 Jun 2017 11:45:43: #2 Since the d (1) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 27 Jun 2017 11:45:43: #2 You may need to consider one of the other alternative d(s): 1,30,480,547,597 WARNING @ Tue, 27 Jun 2017 11:45:43: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 27 Jun 2017 11:45:43: #3 Call peaks... INFO @ Tue, 27 Jun 2017 11:45:43: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 27 Jun 2017 11:45:43: 26000000 INFO @ Tue, 27 Jun 2017 11:45:46: 27000000 INFO @ Tue, 27 Jun 2017 11:45:48: #1 tag size is determined as 37 bps INFO @ Tue, 27 Jun 2017 11:45:48: #1 tag size = 37 INFO @ Tue, 27 Jun 2017 11:45:48: #1 total tags in treatment: 27304333 INFO @ Tue, 27 Jun 2017 11:45:48: #1 user defined the maximum tags... INFO @ Tue, 27 Jun 2017 11:45:48: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 27 Jun 2017 11:45:49: #1 tags after filtering in treatment: 27304333 INFO @ Tue, 27 Jun 2017 11:45:49: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 27 Jun 2017 11:45:49: #1 finished! INFO @ Tue, 27 Jun 2017 11:45:49: #2 Build Peak Model... INFO @ Tue, 27 Jun 2017 11:45:49: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 27 Jun 2017 11:45:51: #2 number of paired peaks: 122 WARNING @ Tue, 27 Jun 2017 11:45:51: Fewer paired peaks (122) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 122 pairs to build model! INFO @ Tue, 27 Jun 2017 11:45:51: start model_add_line... INFO @ Tue, 27 Jun 2017 11:45:51: start X-correlation... INFO @ Tue, 27 Jun 2017 11:45:51: end of X-cor INFO @ Tue, 27 Jun 2017 11:45:51: #2 finished! INFO @ Tue, 27 Jun 2017 11:45:51: #2 predicted fragment length is 1 bps INFO @ Tue, 27 Jun 2017 11:45:51: #2 alternative fragment length(s) may be 1,30,480,547,597 bps INFO @ Tue, 27 Jun 2017 11:45:51: #2.2 Generate R script for model : SRX059222.20_model.r WARNING @ Tue, 27 Jun 2017 11:45:51: #2 Since the d (1) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 27 Jun 2017 11:45:51: #2 You may need to consider one of the other alternative d(s): 1,30,480,547,597 WARNING @ Tue, 27 Jun 2017 11:45:51: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 27 Jun 2017 11:45:51: #3 Call peaks... INFO @ Tue, 27 Jun 2017 11:45:51: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 27 Jun 2017 11:45:51: 27000000 INFO @ Tue, 27 Jun 2017 11:45:54: #1 tag size is determined as 37 bps INFO @ Tue, 27 Jun 2017 11:45:54: #1 tag size = 37 INFO @ Tue, 27 Jun 2017 11:45:54: #1 total tags in treatment: 27304333 INFO @ Tue, 27 Jun 2017 11:45:54: #1 user defined the maximum tags... INFO @ Tue, 27 Jun 2017 11:45:54: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 27 Jun 2017 11:45:54: #1 tags after filtering in treatment: 27304333 INFO @ Tue, 27 Jun 2017 11:45:54: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 27 Jun 2017 11:45:54: #1 finished! INFO @ Tue, 27 Jun 2017 11:45:54: #2 Build Peak Model... INFO @ Tue, 27 Jun 2017 11:45:54: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 27 Jun 2017 11:45:56: #2 number of paired peaks: 122 WARNING @ Tue, 27 Jun 2017 11:45:56: Fewer paired peaks (122) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 122 pairs to build model! INFO @ Tue, 27 Jun 2017 11:45:56: start model_add_line... INFO @ Tue, 27 Jun 2017 11:45:56: start X-correlation... INFO @ Tue, 27 Jun 2017 11:45:56: end of X-cor INFO @ Tue, 27 Jun 2017 11:45:56: #2 finished! INFO @ Tue, 27 Jun 2017 11:45:56: #2 predicted fragment length is 1 bps INFO @ Tue, 27 Jun 2017 11:45:56: #2 alternative fragment length(s) may be 1,30,480,547,597 bps INFO @ Tue, 27 Jun 2017 11:45:56: #2.2 Generate R script for model : SRX059222.10_model.r WARNING @ Tue, 27 Jun 2017 11:45:56: #2 Since the d (1) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 27 Jun 2017 11:45:56: #2 You may need to consider one of the other alternative d(s): 1,30,480,547,597 WARNING @ Tue, 27 Jun 2017 11:45:56: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 27 Jun 2017 11:45:56: #3 Call peaks... INFO @ Tue, 27 Jun 2017 11:45:56: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 27 Jun 2017 11:46:24: #3 Call peaks for each chromosome... INFO @ Tue, 27 Jun 2017 11:46:34: #3 Call peaks for each chromosome... INFO @ Tue, 27 Jun 2017 11:46:39: #3 Call peaks for each chromosome... INFO @ Tue, 27 Jun 2017 11:46:46: #4 Write output xls file... SRX059222.05_peaks.xls INFO @ Tue, 27 Jun 2017 11:46:46: #4 Write peak in narrowPeak format file... SRX059222.05_peaks.narrowPeak INFO @ Tue, 27 Jun 2017 11:46:46: #4 Write summits bed file... SRX059222.05_summits.bed INFO @ Tue, 27 Jun 2017 11:46:46: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling INFO @ Tue, 27 Jun 2017 11:46:55: #4 Write output xls file... SRX059222.20_peaks.xls INFO @ Tue, 27 Jun 2017 11:46:55: #4 Write peak in narrowPeak format file... SRX059222.20_peaks.narrowPeak INFO @ Tue, 27 Jun 2017 11:46:55: #4 Write summits bed file... SRX059222.20_summits.bed INFO @ Tue, 27 Jun 2017 11:46:55: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling INFO @ Tue, 27 Jun 2017 11:47:00: #4 Write output xls file... SRX059222.10_peaks.xls INFO @ Tue, 27 Jun 2017 11:47:00: #4 Write peak in narrowPeak format file... SRX059222.10_peaks.narrowPeak INFO @ Tue, 27 Jun 2017 11:47:00: #4 Write summits bed file... SRX059222.10_summits.bed INFO @ Tue, 27 Jun 2017 11:47:00: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。