Job ID = 9158485 sra ファイルのダウンロード中... Completed: 1996192K bytes transferred in 19 seconds (854863K 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 59637629 spots for /home/okishinya/chipatlas/results/dm3/SRX1361344/SRR2749782.sra Written 59637629 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: 00:00:01 Time loading mirror index: 00:00:00 Multiseed full-index search: 00:34:29 59637629 reads; of these: 59637629 (100.00%) were unpaired; of these: 2782682 (4.67%) aligned 0 times 23096296 (38.73%) aligned exactly 1 time 33758651 (56.61%) aligned >1 times 95.33% overall alignment rate Time searching: 00:34:30 Overall time: 00:34:30 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 24 files... [bam_rmdupse_core] 22919903 / 56854947 = 0.4031 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 17:52:32: # Command line: callpeak -t SRX1361344.bam -f BAM -g dm -n SRX1361344.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX1361344.10 # format = BAM # ChIP-seq file = ['SRX1361344.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, 27 Jun 2017 17:52:32: #1 read tag files... INFO @ Tue, 27 Jun 2017 17:52:32: #1 read treatment tags... INFO @ Tue, 27 Jun 2017 17:52:32: # Command line: callpeak -t SRX1361344.bam -f BAM -g dm -n SRX1361344.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX1361344.20 # format = BAM # ChIP-seq file = ['SRX1361344.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, 27 Jun 2017 17:52:32: #1 read tag files... INFO @ Tue, 27 Jun 2017 17:52:32: #1 read treatment tags... INFO @ Tue, 27 Jun 2017 17:52:32: # Command line: callpeak -t SRX1361344.bam -f BAM -g dm -n SRX1361344.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX1361344.05 # format = BAM # ChIP-seq file = ['SRX1361344.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, 27 Jun 2017 17:52:32: #1 read tag files... INFO @ Tue, 27 Jun 2017 17:52:32: #1 read treatment tags... INFO @ Tue, 27 Jun 2017 17:52:40: 1000000 INFO @ Tue, 27 Jun 2017 17:52:40: 1000000 INFO @ Tue, 27 Jun 2017 17:52:40: 1000000 INFO @ Tue, 27 Jun 2017 17:52:49: 2000000 INFO @ Tue, 27 Jun 2017 17:52:49: 2000000 INFO @ Tue, 27 Jun 2017 17:52:49: 2000000 INFO @ Tue, 27 Jun 2017 17:52:57: 3000000 INFO @ Tue, 27 Jun 2017 17:52:57: 3000000 INFO @ Tue, 27 Jun 2017 17:52:57: 3000000 INFO @ Tue, 27 Jun 2017 17:53:05: 4000000 INFO @ Tue, 27 Jun 2017 17:53:05: 4000000 INFO @ Tue, 27 Jun 2017 17:53:05: 4000000 INFO @ Tue, 27 Jun 2017 17:53:14: 5000000 INFO @ Tue, 27 Jun 2017 17:53:14: 5000000 INFO @ Tue, 27 Jun 2017 17:53:14: 5000000 INFO @ Tue, 27 Jun 2017 17:53:22: 6000000 INFO @ Tue, 27 Jun 2017 17:53:22: 6000000 INFO @ Tue, 27 Jun 2017 17:53:22: 6000000 INFO @ Tue, 27 Jun 2017 17:53:30: 7000000 INFO @ Tue, 27 Jun 2017 17:53:30: 7000000 INFO @ Tue, 27 Jun 2017 17:53:30: 7000000 INFO @ Tue, 27 Jun 2017 17:53:38: 8000000 INFO @ Tue, 27 Jun 2017 17:53:38: 8000000 INFO @ Tue, 27 Jun 2017 17:53:38: 8000000 INFO @ Tue, 27 Jun 2017 17:53:47: 9000000 INFO @ Tue, 27 Jun 2017 17:53:47: 9000000 INFO @ Tue, 27 Jun 2017 17:53:47: 9000000 INFO @ Tue, 27 Jun 2017 17:53:55: 10000000 INFO @ Tue, 27 Jun 2017 17:53:55: 10000000 INFO @ Tue, 27 Jun 2017 17:53:55: 10000000 INFO @ Tue, 27 Jun 2017 17:54:03: 11000000 INFO @ Tue, 27 Jun 2017 17:54:03: 11000000 INFO @ Tue, 27 Jun 2017 17:54:03: 11000000 INFO @ Tue, 27 Jun 2017 17:54:11: 12000000 INFO @ Tue, 27 Jun 2017 17:54:11: 12000000 INFO @ Tue, 27 Jun 2017 17:54:11: 12000000 INFO @ Tue, 27 Jun 2017 17:54:19: 13000000 INFO @ Tue, 27 Jun 2017 17:54:19: 13000000 INFO @ Tue, 27 Jun 2017 17:54:19: 13000000 INFO @ Tue, 27 Jun 2017 17:54:27: 14000000 INFO @ Tue, 27 Jun 2017 17:54:27: 14000000 INFO @ Tue, 27 Jun 2017 17:54:27: 14000000 INFO @ Tue, 27 Jun 2017 17:54:36: 15000000 INFO @ Tue, 27 Jun 2017 17:54:36: 15000000 INFO @ Tue, 27 Jun 2017 17:54:36: 15000000 INFO @ Tue, 27 Jun 2017 17:54:43: 16000000 INFO @ Tue, 27 Jun 2017 17:54:46: 16000000 INFO @ Tue, 27 Jun 2017 17:54:46: 16000000 INFO @ Tue, 27 Jun 2017 17:54:51: 17000000 INFO @ Tue, 27 Jun 2017 17:54:55: 17000000 INFO @ Tue, 27 Jun 2017 17:54:55: 17000000 INFO @ Tue, 27 Jun 2017 17:54:58: 18000000 INFO @ Tue, 27 Jun 2017 17:55:03: 18000000 INFO @ Tue, 27 Jun 2017 17:55:04: 18000000 INFO @ Tue, 27 Jun 2017 17:55:05: 19000000 INFO @ Tue, 27 Jun 2017 17:55:12: 19000000 INFO @ Tue, 27 Jun 2017 17:55:13: 20000000 INFO @ Tue, 27 Jun 2017 17:55:13: 19000000 INFO @ Tue, 27 Jun 2017 17:55:20: 20000000 INFO @ Tue, 27 Jun 2017 17:55:21: 21000000 INFO @ Tue, 27 Jun 2017 17:55:21: 20000000 INFO @ Tue, 27 Jun 2017 17:55:28: 21000000 INFO @ Tue, 27 Jun 2017 17:55:29: 22000000 INFO @ Tue, 27 Jun 2017 17:55:29: 21000000 INFO @ Tue, 27 Jun 2017 17:55:36: 22000000 INFO @ Tue, 27 Jun 2017 17:55:37: 23000000 INFO @ Tue, 27 Jun 2017 17:55:37: 22000000 INFO @ Tue, 27 Jun 2017 17:55:45: 23000000 INFO @ Tue, 27 Jun 2017 17:55:45: 24000000 INFO @ Tue, 27 Jun 2017 17:55:46: 23000000 INFO @ Tue, 27 Jun 2017 17:55:52: 25000000 INFO @ Tue, 27 Jun 2017 17:55:53: 24000000 INFO @ Tue, 27 Jun 2017 17:55:54: 24000000 INFO @ Tue, 27 Jun 2017 17:56:00: 26000000 INFO @ Tue, 27 Jun 2017 17:56:01: 25000000 INFO @ Tue, 27 Jun 2017 17:56:02: 25000000 INFO @ Tue, 27 Jun 2017 17:56:08: 27000000 INFO @ Tue, 27 Jun 2017 17:56:09: 26000000 INFO @ Tue, 27 Jun 2017 17:56:10: 26000000 INFO @ Tue, 27 Jun 2017 17:56:17: 28000000 INFO @ Tue, 27 Jun 2017 17:56:17: 27000000 INFO @ Tue, 27 Jun 2017 17:56:19: 27000000 INFO @ Tue, 27 Jun 2017 17:56:24: 29000000 INFO @ Tue, 27 Jun 2017 17:56:27: 28000000 INFO @ Tue, 27 Jun 2017 17:56:28: 28000000 INFO @ Tue, 27 Jun 2017 17:56:31: 30000000 INFO @ Tue, 27 Jun 2017 17:56:36: 29000000 INFO @ Tue, 27 Jun 2017 17:56:37: 29000000 INFO @ Tue, 27 Jun 2017 17:56:39: 31000000 INFO @ Tue, 27 Jun 2017 17:56:45: 30000000 INFO @ Tue, 27 Jun 2017 17:56:46: 32000000 INFO @ Tue, 27 Jun 2017 17:56:47: 30000000 INFO @ Tue, 27 Jun 2017 17:56:53: 33000000 INFO @ Tue, 27 Jun 2017 17:56:55: 31000000 INFO @ Tue, 27 Jun 2017 17:56:56: 31000000 INFO @ Tue, 27 Jun 2017 17:57:01: #1 tag size is determined as 50 bps INFO @ Tue, 27 Jun 2017 17:57:01: #1 tag size = 50 INFO @ Tue, 27 Jun 2017 17:57:01: #1 total tags in treatment: 33935044 INFO @ Tue, 27 Jun 2017 17:57:01: #1 user defined the maximum tags... INFO @ Tue, 27 Jun 2017 17:57:01: #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 17:57:01: #1 tags after filtering in treatment: 33935044 INFO @ Tue, 27 Jun 2017 17:57:01: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 27 Jun 2017 17:57:01: #1 finished! INFO @ Tue, 27 Jun 2017 17:57:01: #2 Build Peak Model... INFO @ Tue, 27 Jun 2017 17:57:01: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 27 Jun 2017 17:57:03: #2 number of paired peaks: 236 WARNING @ Tue, 27 Jun 2017 17:57:03: Fewer paired peaks (236) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 236 pairs to build model! INFO @ Tue, 27 Jun 2017 17:57:03: start model_add_line... INFO @ Tue, 27 Jun 2017 17:57:04: start X-correlation... INFO @ Tue, 27 Jun 2017 17:57:04: end of X-cor INFO @ Tue, 27 Jun 2017 17:57:04: #2 finished! INFO @ Tue, 27 Jun 2017 17:57:04: #2 predicted fragment length is 1 bps INFO @ Tue, 27 Jun 2017 17:57:04: #2 alternative fragment length(s) may be 1,11,28 bps INFO @ Tue, 27 Jun 2017 17:57:04: #2.2 Generate R script for model : SRX1361344.05_model.r WARNING @ Tue, 27 Jun 2017 17:57:04: #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 17:57:04: #2 You may need to consider one of the other alternative d(s): 1,11,28 WARNING @ Tue, 27 Jun 2017 17:57:04: #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 17:57:04: #3 Call peaks... INFO @ Tue, 27 Jun 2017 17:57:04: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 27 Jun 2017 17:57:04: 32000000 INFO @ Tue, 27 Jun 2017 17:57:05: 32000000 INFO @ Tue, 27 Jun 2017 17:57:13: 33000000 INFO @ Tue, 27 Jun 2017 17:57:15: 33000000 INFO @ Tue, 27 Jun 2017 17:57:22: #1 tag size is determined as 50 bps INFO @ Tue, 27 Jun 2017 17:57:22: #1 tag size = 50 INFO @ Tue, 27 Jun 2017 17:57:22: #1 total tags in treatment: 33935044 INFO @ Tue, 27 Jun 2017 17:57:22: #1 user defined the maximum tags... INFO @ Tue, 27 Jun 2017 17:57:22: #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 17:57:23: #1 tags after filtering in treatment: 33935044 INFO @ Tue, 27 Jun 2017 17:57:23: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 27 Jun 2017 17:57:23: #1 finished! INFO @ Tue, 27 Jun 2017 17:57:23: #2 Build Peak Model... INFO @ Tue, 27 Jun 2017 17:57:23: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 27 Jun 2017 17:57:23: #1 tag size is determined as 50 bps INFO @ Tue, 27 Jun 2017 17:57:23: #1 tag size = 50 INFO @ Tue, 27 Jun 2017 17:57:23: #1 total tags in treatment: 33935044 INFO @ Tue, 27 Jun 2017 17:57:23: #1 user defined the maximum tags... INFO @ Tue, 27 Jun 2017 17:57:23: #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 17:57:24: #1 tags after filtering in treatment: 33935044 INFO @ Tue, 27 Jun 2017 17:57:24: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 27 Jun 2017 17:57:24: #1 finished! INFO @ Tue, 27 Jun 2017 17:57:24: #2 Build Peak Model... INFO @ Tue, 27 Jun 2017 17:57:24: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 27 Jun 2017 17:57:25: #2 number of paired peaks: 236 WARNING @ Tue, 27 Jun 2017 17:57:25: Fewer paired peaks (236) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 236 pairs to build model! INFO @ Tue, 27 Jun 2017 17:57:25: start model_add_line... INFO @ Tue, 27 Jun 2017 17:57:26: start X-correlation... INFO @ Tue, 27 Jun 2017 17:57:26: end of X-cor INFO @ Tue, 27 Jun 2017 17:57:26: #2 finished! INFO @ Tue, 27 Jun 2017 17:57:26: #2 predicted fragment length is 1 bps INFO @ Tue, 27 Jun 2017 17:57:26: #2 alternative fragment length(s) may be 1,11,28 bps INFO @ Tue, 27 Jun 2017 17:57:26: #2.2 Generate R script for model : SRX1361344.10_model.r WARNING @ Tue, 27 Jun 2017 17:57:26: #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 17:57:26: #2 You may need to consider one of the other alternative d(s): 1,11,28 WARNING @ Tue, 27 Jun 2017 17:57:26: #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 17:57:26: #3 Call peaks... INFO @ Tue, 27 Jun 2017 17:57:26: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 27 Jun 2017 17:57:26: #2 number of paired peaks: 236 WARNING @ Tue, 27 Jun 2017 17:57:26: Fewer paired peaks (236) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 236 pairs to build model! INFO @ Tue, 27 Jun 2017 17:57:26: start model_add_line... INFO @ Tue, 27 Jun 2017 17:57:27: start X-correlation... INFO @ Tue, 27 Jun 2017 17:57:27: end of X-cor INFO @ Tue, 27 Jun 2017 17:57:27: #2 finished! INFO @ Tue, 27 Jun 2017 17:57:27: #2 predicted fragment length is 1 bps INFO @ Tue, 27 Jun 2017 17:57:27: #2 alternative fragment length(s) may be 1,11,28 bps INFO @ Tue, 27 Jun 2017 17:57:27: #2.2 Generate R script for model : SRX1361344.20_model.r WARNING @ Tue, 27 Jun 2017 17:57:27: #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 17:57:27: #2 You may need to consider one of the other alternative d(s): 1,11,28 WARNING @ Tue, 27 Jun 2017 17:57:27: #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 17:57:27: #3 Call peaks... INFO @ Tue, 27 Jun 2017 17:57:27: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 27 Jun 2017 17:57:55: #3 Call peaks for each chromosome... INFO @ Tue, 27 Jun 2017 17:58:19: #3 Call peaks for each chromosome... INFO @ Tue, 27 Jun 2017 17:58:19: #3 Call peaks for each chromosome... INFO @ Tue, 27 Jun 2017 17:58:20: #4 Write output xls file... SRX1361344.05_peaks.xls INFO @ Tue, 27 Jun 2017 17:58:20: #4 Write peak in narrowPeak format file... SRX1361344.05_peaks.narrowPeak INFO @ Tue, 27 Jun 2017 17:58:20: #4 Write summits bed file... SRX1361344.05_summits.bed INFO @ Tue, 27 Jun 2017 17:58:20: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling INFO @ Tue, 27 Jun 2017 17:58:43: #4 Write output xls file... SRX1361344.10_peaks.xls INFO @ Tue, 27 Jun 2017 17:58:43: #4 Write peak in narrowPeak format file... SRX1361344.10_peaks.narrowPeak INFO @ Tue, 27 Jun 2017 17:58:43: #4 Write summits bed file... SRX1361344.10_summits.bed INFO @ Tue, 27 Jun 2017 17:58:43: Done! pass1 - making usageList (0 chroms): 0 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling INFO @ Tue, 27 Jun 2017 17:58:45: #4 Write output xls file... SRX1361344.20_peaks.xls INFO @ Tue, 27 Jun 2017 17:58:45: #4 Write peak in narrowPeak format file... SRX1361344.20_peaks.narrowPeak INFO @ Tue, 27 Jun 2017 17:58:45: #4 Write summits bed file... SRX1361344.20_summits.bed INFO @ Tue, 27 Jun 2017 17:58:45: 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。