Job ID = 9157145 sra ファイルのダウンロード中... Completed: 697697K bytes transferred in 8 seconds (673350K 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 33038431 spots for /home/okishinya/chipatlas/results/ce10/SRX2228874/SRR4380330.sra Written 33038431 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: 00:06:27 33038431 reads; of these: 33038431 (100.00%) were unpaired; of these: 12099921 (36.62%) aligned 0 times 17142693 (51.89%) aligned exactly 1 time 3795817 (11.49%) aligned >1 times 63.38% overall alignment rate Time searching: 00:06:27 Overall time: 00:06:27 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] 4439649 / 20938510 = 0.2120 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 10:55:48: # Command line: callpeak -t SRX2228874.bam -f BAM -g ce -n SRX2228874.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX2228874.10 # format = BAM # ChIP-seq file = ['SRX2228874.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 10:55:48: #1 read tag files... INFO @ Tue, 27 Jun 2017 10:55:48: #1 read treatment tags... INFO @ Tue, 27 Jun 2017 10:55:48: # Command line: callpeak -t SRX2228874.bam -f BAM -g ce -n SRX2228874.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX2228874.05 # format = BAM # ChIP-seq file = ['SRX2228874.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 10:55:48: #1 read tag files... INFO @ Tue, 27 Jun 2017 10:55:48: #1 read treatment tags... INFO @ Tue, 27 Jun 2017 10:55:48: # Command line: callpeak -t SRX2228874.bam -f BAM -g ce -n SRX2228874.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX2228874.20 # format = BAM # ChIP-seq file = ['SRX2228874.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 10:55:48: #1 read tag files... INFO @ Tue, 27 Jun 2017 10:55:48: #1 read treatment tags... INFO @ Tue, 27 Jun 2017 10:55:55: 1000000 INFO @ Tue, 27 Jun 2017 10:55:55: 1000000 INFO @ Tue, 27 Jun 2017 10:55:55: 1000000 INFO @ Tue, 27 Jun 2017 10:56:01: 2000000 INFO @ Tue, 27 Jun 2017 10:56:01: 2000000 INFO @ Tue, 27 Jun 2017 10:56:01: 2000000 INFO @ Tue, 27 Jun 2017 10:56:08: 3000000 INFO @ Tue, 27 Jun 2017 10:56:08: 3000000 INFO @ Tue, 27 Jun 2017 10:56:08: 3000000 INFO @ Tue, 27 Jun 2017 10:56:14: 4000000 INFO @ Tue, 27 Jun 2017 10:56:15: 4000000 INFO @ Tue, 27 Jun 2017 10:56:15: 4000000 INFO @ Tue, 27 Jun 2017 10:56:20: 5000000 INFO @ Tue, 27 Jun 2017 10:56:21: 5000000 INFO @ Tue, 27 Jun 2017 10:56:21: 5000000 INFO @ Tue, 27 Jun 2017 10:56:26: 6000000 INFO @ Tue, 27 Jun 2017 10:56:28: 6000000 INFO @ Tue, 27 Jun 2017 10:56:28: 6000000 INFO @ Tue, 27 Jun 2017 10:56:32: 7000000 INFO @ Tue, 27 Jun 2017 10:56:36: 7000000 INFO @ Tue, 27 Jun 2017 10:56:36: 7000000 INFO @ Tue, 27 Jun 2017 10:56:39: 8000000 INFO @ Tue, 27 Jun 2017 10:56:44: 8000000 INFO @ Tue, 27 Jun 2017 10:56:44: 8000000 INFO @ Tue, 27 Jun 2017 10:56:45: 9000000 INFO @ Tue, 27 Jun 2017 10:56:50: 9000000 INFO @ Tue, 27 Jun 2017 10:56:51: 9000000 INFO @ Tue, 27 Jun 2017 10:56:51: 10000000 INFO @ Tue, 27 Jun 2017 10:56:57: 10000000 INFO @ Tue, 27 Jun 2017 10:56:57: 10000000 INFO @ Tue, 27 Jun 2017 10:56:57: 11000000 INFO @ Tue, 27 Jun 2017 10:57:03: 11000000 INFO @ Tue, 27 Jun 2017 10:57:03: 12000000 INFO @ Tue, 27 Jun 2017 10:57:03: 11000000 INFO @ Tue, 27 Jun 2017 10:57:10: 12000000 INFO @ Tue, 27 Jun 2017 10:57:10: 13000000 INFO @ Tue, 27 Jun 2017 10:57:10: 12000000 INFO @ Tue, 27 Jun 2017 10:57:16: 14000000 INFO @ Tue, 27 Jun 2017 10:57:16: 13000000 INFO @ Tue, 27 Jun 2017 10:57:16: 13000000 INFO @ Tue, 27 Jun 2017 10:57:22: 15000000 INFO @ Tue, 27 Jun 2017 10:57:23: 14000000 INFO @ Tue, 27 Jun 2017 10:57:23: 14000000 INFO @ Tue, 27 Jun 2017 10:57:28: 16000000 INFO @ Tue, 27 Jun 2017 10:57:29: 15000000 INFO @ Tue, 27 Jun 2017 10:57:30: 15000000 INFO @ Tue, 27 Jun 2017 10:57:32: #1 tag size is determined as 51 bps INFO @ Tue, 27 Jun 2017 10:57:32: #1 tag size = 51 INFO @ Tue, 27 Jun 2017 10:57:32: #1 total tags in treatment: 16498861 INFO @ Tue, 27 Jun 2017 10:57:32: #1 user defined the maximum tags... INFO @ Tue, 27 Jun 2017 10:57:32: #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 10:57:32: #1 tags after filtering in treatment: 16498861 INFO @ Tue, 27 Jun 2017 10:57:32: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 27 Jun 2017 10:57:32: #1 finished! INFO @ Tue, 27 Jun 2017 10:57:32: #2 Build Peak Model... INFO @ Tue, 27 Jun 2017 10:57:32: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 27 Jun 2017 10:57:33: #2 number of paired peaks: 274 WARNING @ Tue, 27 Jun 2017 10:57:33: Fewer paired peaks (274) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 274 pairs to build model! INFO @ Tue, 27 Jun 2017 10:57:33: start model_add_line... INFO @ Tue, 27 Jun 2017 10:57:33: start X-correlation... INFO @ Tue, 27 Jun 2017 10:57:33: end of X-cor INFO @ Tue, 27 Jun 2017 10:57:33: #2 finished! INFO @ Tue, 27 Jun 2017 10:57:33: #2 predicted fragment length is 2 bps INFO @ Tue, 27 Jun 2017 10:57:33: #2 alternative fragment length(s) may be 2,42,501,540,544,573 bps INFO @ Tue, 27 Jun 2017 10:57:33: #2.2 Generate R script for model : SRX2228874.05_model.r WARNING @ Tue, 27 Jun 2017 10:57:33: #2 Since the d (2) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 27 Jun 2017 10:57:33: #2 You may need to consider one of the other alternative d(s): 2,42,501,540,544,573 WARNING @ Tue, 27 Jun 2017 10:57:33: #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 10:57:33: #3 Call peaks... INFO @ Tue, 27 Jun 2017 10:57:33: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 27 Jun 2017 10:57:36: 16000000 INFO @ Tue, 27 Jun 2017 10:57:36: 16000000 INFO @ Tue, 27 Jun 2017 10:57:39: #1 tag size is determined as 51 bps INFO @ Tue, 27 Jun 2017 10:57:39: #1 tag size = 51 INFO @ Tue, 27 Jun 2017 10:57:39: #1 total tags in treatment: 16498861 INFO @ Tue, 27 Jun 2017 10:57:39: #1 user defined the maximum tags... INFO @ Tue, 27 Jun 2017 10:57:39: #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 10:57:39: #1 tags after filtering in treatment: 16498861 INFO @ Tue, 27 Jun 2017 10:57:39: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 27 Jun 2017 10:57:39: #1 finished! INFO @ Tue, 27 Jun 2017 10:57:39: #2 Build Peak Model... INFO @ Tue, 27 Jun 2017 10:57:39: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 27 Jun 2017 10:57:39: #1 tag size is determined as 51 bps INFO @ Tue, 27 Jun 2017 10:57:39: #1 tag size = 51 INFO @ Tue, 27 Jun 2017 10:57:39: #1 total tags in treatment: 16498861 INFO @ Tue, 27 Jun 2017 10:57:39: #1 user defined the maximum tags... INFO @ Tue, 27 Jun 2017 10:57:39: #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 10:57:40: #1 tags after filtering in treatment: 16498861 INFO @ Tue, 27 Jun 2017 10:57:40: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 27 Jun 2017 10:57:40: #1 finished! INFO @ Tue, 27 Jun 2017 10:57:40: #2 Build Peak Model... INFO @ Tue, 27 Jun 2017 10:57:40: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 27 Jun 2017 10:57:41: #2 number of paired peaks: 274 WARNING @ Tue, 27 Jun 2017 10:57:41: Fewer paired peaks (274) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 274 pairs to build model! INFO @ Tue, 27 Jun 2017 10:57:41: start model_add_line... INFO @ Tue, 27 Jun 2017 10:57:41: start X-correlation... INFO @ Tue, 27 Jun 2017 10:57:41: end of X-cor INFO @ Tue, 27 Jun 2017 10:57:41: #2 finished! INFO @ Tue, 27 Jun 2017 10:57:41: #2 predicted fragment length is 2 bps INFO @ Tue, 27 Jun 2017 10:57:41: #2 alternative fragment length(s) may be 2,42,501,540,544,573 bps INFO @ Tue, 27 Jun 2017 10:57:41: #2.2 Generate R script for model : SRX2228874.20_model.r WARNING @ Tue, 27 Jun 2017 10:57:41: #2 Since the d (2) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 27 Jun 2017 10:57:41: #2 You may need to consider one of the other alternative d(s): 2,42,501,540,544,573 WARNING @ Tue, 27 Jun 2017 10:57:41: #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 10:57:41: #3 Call peaks... INFO @ Tue, 27 Jun 2017 10:57:41: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 27 Jun 2017 10:57:41: #2 number of paired peaks: 274 WARNING @ Tue, 27 Jun 2017 10:57:41: Fewer paired peaks (274) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 274 pairs to build model! INFO @ Tue, 27 Jun 2017 10:57:41: start model_add_line... INFO @ Tue, 27 Jun 2017 10:57:41: start X-correlation... INFO @ Tue, 27 Jun 2017 10:57:41: end of X-cor INFO @ Tue, 27 Jun 2017 10:57:41: #2 finished! INFO @ Tue, 27 Jun 2017 10:57:41: #2 predicted fragment length is 2 bps INFO @ Tue, 27 Jun 2017 10:57:41: #2 alternative fragment length(s) may be 2,42,501,540,544,573 bps INFO @ Tue, 27 Jun 2017 10:57:41: #2.2 Generate R script for model : SRX2228874.10_model.r WARNING @ Tue, 27 Jun 2017 10:57:41: #2 Since the d (2) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 27 Jun 2017 10:57:41: #2 You may need to consider one of the other alternative d(s): 2,42,501,540,544,573 WARNING @ Tue, 27 Jun 2017 10:57:41: #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 10:57:41: #3 Call peaks... INFO @ Tue, 27 Jun 2017 10:57:41: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 27 Jun 2017 10:58:04: #3 Call peaks for each chromosome... INFO @ Tue, 27 Jun 2017 10:58:09: #3 Call peaks for each chromosome... INFO @ Tue, 27 Jun 2017 10:58:10: #3 Call peaks for each chromosome... INFO @ Tue, 27 Jun 2017 10:58:21: #4 Write output xls file... SRX2228874.05_peaks.xls INFO @ Tue, 27 Jun 2017 10:58:21: #4 Write peak in narrowPeak format file... SRX2228874.05_peaks.narrowPeak INFO @ Tue, 27 Jun 2017 10:58:21: #4 Write summits bed file... SRX2228874.05_summits.bed INFO @ Tue, 27 Jun 2017 10:58:21: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling INFO @ Tue, 27 Jun 2017 10:58:25: #4 Write output xls file... SRX2228874.20_peaks.xls INFO @ Tue, 27 Jun 2017 10:58:25: #4 Write peak in narrowPeak format file... SRX2228874.20_peaks.narrowPeak INFO @ Tue, 27 Jun 2017 10:58:25: #4 Write summits bed file... SRX2228874.20_summits.bed INFO @ Tue, 27 Jun 2017 10:58:25: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling INFO @ Tue, 27 Jun 2017 10:58:26: #4 Write output xls file... SRX2228874.10_peaks.xls INFO @ Tue, 27 Jun 2017 10:58:26: #4 Write peak in narrowPeak format file... SRX2228874.10_peaks.narrowPeak INFO @ Tue, 27 Jun 2017 10:58:26: #4 Write summits bed file... SRX2228874.10_summits.bed INFO @ Tue, 27 Jun 2017 10:58:26: 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。