Job ID = 9157395 sra ファイルのダウンロード中... Completed: 675417K bytes transferred in 10 seconds (551976K 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 24704893 spots for /home/okishinya/chipatlas/results/ce10/SRX1936236/SRR3879842.sra Written 24704893 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: 00:06:35 24704893 reads; of these: 24704893 (100.00%) were unpaired; of these: 1155966 (4.68%) aligned 0 times 19675752 (79.64%) aligned exactly 1 time 3873175 (15.68%) aligned >1 times 95.32% overall alignment rate Time searching: 00:06:35 Overall time: 00:06:35 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 12 files... [bam_rmdupse_core] 3589205 / 23548927 = 0.1524 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 11:53:28: # Command line: callpeak -t SRX1936236.bam -f BAM -g ce -n SRX1936236.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX1936236.10 # format = BAM # ChIP-seq file = ['SRX1936236.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 11:53:28: #1 read tag files... INFO @ Tue, 27 Jun 2017 11:53:28: #1 read treatment tags... INFO @ Tue, 27 Jun 2017 11:53:28: # Command line: callpeak -t SRX1936236.bam -f BAM -g ce -n SRX1936236.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX1936236.05 # format = BAM # ChIP-seq file = ['SRX1936236.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 11:53:28: #1 read tag files... INFO @ Tue, 27 Jun 2017 11:53:28: #1 read treatment tags... INFO @ Tue, 27 Jun 2017 11:53:28: # Command line: callpeak -t SRX1936236.bam -f BAM -g ce -n SRX1936236.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX1936236.20 # format = BAM # ChIP-seq file = ['SRX1936236.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 11:53:28: #1 read tag files... INFO @ Tue, 27 Jun 2017 11:53:28: #1 read treatment tags... INFO @ Tue, 27 Jun 2017 11:53:35: 1000000 INFO @ Tue, 27 Jun 2017 11:53:35: 1000000 INFO @ Tue, 27 Jun 2017 11:53:35: 1000000 INFO @ Tue, 27 Jun 2017 11:53:42: 2000000 INFO @ Tue, 27 Jun 2017 11:53:42: 2000000 INFO @ Tue, 27 Jun 2017 11:53:43: 2000000 INFO @ Tue, 27 Jun 2017 11:53:49: 3000000 INFO @ Tue, 27 Jun 2017 11:53:50: 3000000 INFO @ Tue, 27 Jun 2017 11:53:51: 3000000 INFO @ Tue, 27 Jun 2017 11:53:56: 4000000 INFO @ Tue, 27 Jun 2017 11:53:58: 4000000 INFO @ Tue, 27 Jun 2017 11:53:58: 4000000 INFO @ Tue, 27 Jun 2017 11:54:03: 5000000 INFO @ Tue, 27 Jun 2017 11:54:05: 5000000 INFO @ Tue, 27 Jun 2017 11:54:06: 5000000 INFO @ Tue, 27 Jun 2017 11:54:11: 6000000 INFO @ Tue, 27 Jun 2017 11:54:13: 6000000 INFO @ Tue, 27 Jun 2017 11:54:13: 6000000 INFO @ Tue, 27 Jun 2017 11:54:18: 7000000 INFO @ Tue, 27 Jun 2017 11:54:21: 7000000 INFO @ Tue, 27 Jun 2017 11:54:21: 7000000 INFO @ Tue, 27 Jun 2017 11:54:25: 8000000 INFO @ Tue, 27 Jun 2017 11:54:28: 8000000 INFO @ Tue, 27 Jun 2017 11:54:28: 8000000 INFO @ Tue, 27 Jun 2017 11:54:32: 9000000 INFO @ Tue, 27 Jun 2017 11:54:36: 9000000 INFO @ Tue, 27 Jun 2017 11:54:36: 9000000 INFO @ Tue, 27 Jun 2017 11:54:39: 10000000 INFO @ Tue, 27 Jun 2017 11:54:43: 10000000 INFO @ Tue, 27 Jun 2017 11:54:44: 10000000 INFO @ Tue, 27 Jun 2017 11:54:47: 11000000 INFO @ Tue, 27 Jun 2017 11:54:51: 11000000 INFO @ Tue, 27 Jun 2017 11:54:51: 11000000 INFO @ Tue, 27 Jun 2017 11:54:54: 12000000 INFO @ Tue, 27 Jun 2017 11:54:59: 12000000 INFO @ Tue, 27 Jun 2017 11:54:59: 12000000 INFO @ Tue, 27 Jun 2017 11:55:01: 13000000 INFO @ Tue, 27 Jun 2017 11:55:06: 13000000 INFO @ Tue, 27 Jun 2017 11:55:07: 13000000 INFO @ Tue, 27 Jun 2017 11:55:08: 14000000 INFO @ Tue, 27 Jun 2017 11:55:14: 14000000 INFO @ Tue, 27 Jun 2017 11:55:14: 14000000 INFO @ Tue, 27 Jun 2017 11:55:15: 15000000 INFO @ Tue, 27 Jun 2017 11:55:21: 15000000 INFO @ Tue, 27 Jun 2017 11:55:22: 15000000 INFO @ Tue, 27 Jun 2017 11:55:23: 16000000 INFO @ Tue, 27 Jun 2017 11:55:29: 16000000 INFO @ Tue, 27 Jun 2017 11:55:30: 16000000 INFO @ Tue, 27 Jun 2017 11:55:30: 17000000 INFO @ Tue, 27 Jun 2017 11:55:36: 17000000 INFO @ Tue, 27 Jun 2017 11:55:37: 18000000 INFO @ Tue, 27 Jun 2017 11:55:37: 17000000 INFO @ Tue, 27 Jun 2017 11:55:44: 18000000 INFO @ Tue, 27 Jun 2017 11:55:44: 19000000 INFO @ Tue, 27 Jun 2017 11:55:45: 18000000 INFO @ Tue, 27 Jun 2017 11:55:51: #1 tag size is determined as 52 bps INFO @ Tue, 27 Jun 2017 11:55:51: #1 tag size = 52 INFO @ Tue, 27 Jun 2017 11:55:51: #1 total tags in treatment: 19959722 INFO @ Tue, 27 Jun 2017 11:55:51: #1 user defined the maximum tags... INFO @ Tue, 27 Jun 2017 11:55:51: #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 11:55:52: 19000000 INFO @ Tue, 27 Jun 2017 11:55:52: #1 tags after filtering in treatment: 19959722 INFO @ Tue, 27 Jun 2017 11:55:52: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 27 Jun 2017 11:55:52: #1 finished! INFO @ Tue, 27 Jun 2017 11:55:52: #2 Build Peak Model... INFO @ Tue, 27 Jun 2017 11:55:52: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 27 Jun 2017 11:55:52: 19000000 INFO @ Tue, 27 Jun 2017 11:55:53: #2 number of paired peaks: 202 WARNING @ Tue, 27 Jun 2017 11:55:53: Fewer paired peaks (202) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 202 pairs to build model! INFO @ Tue, 27 Jun 2017 11:55:53: start model_add_line... INFO @ Tue, 27 Jun 2017 11:55:53: start X-correlation... INFO @ Tue, 27 Jun 2017 11:55:53: end of X-cor INFO @ Tue, 27 Jun 2017 11:55:53: #2 finished! INFO @ Tue, 27 Jun 2017 11:55:53: #2 predicted fragment length is 1 bps INFO @ Tue, 27 Jun 2017 11:55:53: #2 alternative fragment length(s) may be 1,38,575 bps INFO @ Tue, 27 Jun 2017 11:55:53: #2.2 Generate R script for model : SRX1936236.10_model.r WARNING @ Tue, 27 Jun 2017 11:55:53: #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 11:55:53: #2 You may need to consider one of the other alternative d(s): 1,38,575 WARNING @ Tue, 27 Jun 2017 11:55:53: #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 11:55:53: #3 Call peaks... INFO @ Tue, 27 Jun 2017 11:55:53: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 27 Jun 2017 11:55:59: #1 tag size is determined as 52 bps INFO @ Tue, 27 Jun 2017 11:55:59: #1 tag size = 52 INFO @ Tue, 27 Jun 2017 11:55:59: #1 total tags in treatment: 19959722 INFO @ Tue, 27 Jun 2017 11:55:59: #1 user defined the maximum tags... INFO @ Tue, 27 Jun 2017 11:55:59: #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 11:55:59: #1 tag size is determined as 52 bps INFO @ Tue, 27 Jun 2017 11:55:59: #1 tag size = 52 INFO @ Tue, 27 Jun 2017 11:55:59: #1 total tags in treatment: 19959722 INFO @ Tue, 27 Jun 2017 11:55:59: #1 user defined the maximum tags... INFO @ Tue, 27 Jun 2017 11:55:59: #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 11:55:59: #1 tags after filtering in treatment: 19959722 INFO @ Tue, 27 Jun 2017 11:55:59: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 27 Jun 2017 11:55:59: #1 finished! INFO @ Tue, 27 Jun 2017 11:55:59: #2 Build Peak Model... INFO @ Tue, 27 Jun 2017 11:55:59: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 27 Jun 2017 11:56:00: #1 tags after filtering in treatment: 19959722 INFO @ Tue, 27 Jun 2017 11:56:00: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 27 Jun 2017 11:56:00: #1 finished! INFO @ Tue, 27 Jun 2017 11:56:00: #2 Build Peak Model... INFO @ Tue, 27 Jun 2017 11:56:00: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 27 Jun 2017 11:56:01: #2 number of paired peaks: 202 WARNING @ Tue, 27 Jun 2017 11:56:01: Fewer paired peaks (202) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 202 pairs to build model! INFO @ Tue, 27 Jun 2017 11:56:01: start model_add_line... INFO @ Tue, 27 Jun 2017 11:56:01: #2 number of paired peaks: 202 WARNING @ Tue, 27 Jun 2017 11:56:01: Fewer paired peaks (202) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 202 pairs to build model! INFO @ Tue, 27 Jun 2017 11:56:01: start model_add_line... INFO @ Tue, 27 Jun 2017 11:56:01: start X-correlation... INFO @ Tue, 27 Jun 2017 11:56:01: end of X-cor INFO @ Tue, 27 Jun 2017 11:56:01: #2 finished! INFO @ Tue, 27 Jun 2017 11:56:01: #2 predicted fragment length is 1 bps INFO @ Tue, 27 Jun 2017 11:56:01: #2 alternative fragment length(s) may be 1,38,575 bps INFO @ Tue, 27 Jun 2017 11:56:01: #2.2 Generate R script for model : SRX1936236.20_model.r WARNING @ Tue, 27 Jun 2017 11:56:01: #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 11:56:01: #2 You may need to consider one of the other alternative d(s): 1,38,575 WARNING @ Tue, 27 Jun 2017 11:56:01: #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 11:56:01: #3 Call peaks... INFO @ Tue, 27 Jun 2017 11:56:01: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 27 Jun 2017 11:56:01: start X-correlation... INFO @ Tue, 27 Jun 2017 11:56:01: end of X-cor INFO @ Tue, 27 Jun 2017 11:56:01: #2 finished! INFO @ Tue, 27 Jun 2017 11:56:01: #2 predicted fragment length is 1 bps INFO @ Tue, 27 Jun 2017 11:56:01: #2 alternative fragment length(s) may be 1,38,575 bps INFO @ Tue, 27 Jun 2017 11:56:01: #2.2 Generate R script for model : SRX1936236.05_model.r WARNING @ Tue, 27 Jun 2017 11:56:01: #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 11:56:01: #2 You may need to consider one of the other alternative d(s): 1,38,575 WARNING @ Tue, 27 Jun 2017 11:56:01: #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 11:56:01: #3 Call peaks... INFO @ Tue, 27 Jun 2017 11:56:01: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 27 Jun 2017 11:56:27: #3 Call peaks for each chromosome... INFO @ Tue, 27 Jun 2017 11:56:34: #3 Call peaks for each chromosome... INFO @ Tue, 27 Jun 2017 11:56:37: #3 Call peaks for each chromosome... INFO @ Tue, 27 Jun 2017 11:56:44: #4 Write output xls file... SRX1936236.10_peaks.xls INFO @ Tue, 27 Jun 2017 11:56:44: #4 Write peak in narrowPeak format file... SRX1936236.10_peaks.narrowPeak INFO @ Tue, 27 Jun 2017 11:56:44: #4 Write summits bed file... SRX1936236.10_summits.bed INFO @ Tue, 27 Jun 2017 11:56:44: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling INFO @ Tue, 27 Jun 2017 11:56:52: #4 Write output xls file... SRX1936236.05_peaks.xls INFO @ Tue, 27 Jun 2017 11:56:52: #4 Write peak in narrowPeak format file... SRX1936236.05_peaks.narrowPeak INFO @ Tue, 27 Jun 2017 11:56:52: #4 Write summits bed file... SRX1936236.05_summits.bed INFO @ Tue, 27 Jun 2017 11:56:52: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling INFO @ Tue, 27 Jun 2017 11:56:54: #4 Write output xls file... SRX1936236.20_peaks.xls INFO @ Tue, 27 Jun 2017 11:56:54: #4 Write peak in narrowPeak format file... SRX1936236.20_peaks.narrowPeak INFO @ Tue, 27 Jun 2017 11:56:54: #4 Write summits bed file... SRX1936236.20_summits.bed INFO @ Tue, 27 Jun 2017 11:56:54: 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。