Job ID = 11170835 sra ファイルのダウンロード中... Completed: 976961K bytes transferred in 116 seconds (68954K 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: SINGLE fastq に変換中... Read 36795442 spots for /home/okishinya/chipatlas/results/ce10/SRX3583335/SRR6493991.sra Written 36795442 spots for /home/okishinya/chipatlas/results/ce10/SRX3583335/SRR6493991.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: 00:00:01 Time loading mirror index: 00:00:00 Multiseed full-index search: 00:12:20 36795442 reads; of these: 36795442 (100.00%) were unpaired; of these: 6314685 (17.16%) aligned 0 times 26168360 (71.12%) aligned exactly 1 time 4312397 (11.72%) aligned >1 times 82.84% overall alignment rate Time searching: 00:12:21 Overall time: 00:12:21 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_rmdupse_core] 7761885 / 30480757 = 0.2546 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 @ Sat, 08 Sep 2018 11:47:52: # Command line: callpeak -t SRX3583335.bam -f BAM -g ce -n SRX3583335.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX3583335.20 # format = BAM # ChIP-seq file = ['SRX3583335.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 @ Sat, 08 Sep 2018 11:47:52: # Command line: callpeak -t SRX3583335.bam -f BAM -g ce -n SRX3583335.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX3583335.10 # format = BAM # ChIP-seq file = ['SRX3583335.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 @ Sat, 08 Sep 2018 11:47:52: #1 read tag files... INFO @ Sat, 08 Sep 2018 11:47:52: #1 read tag files... INFO @ Sat, 08 Sep 2018 11:47:52: #1 read treatment tags... INFO @ Sat, 08 Sep 2018 11:47:52: #1 read treatment tags... INFO @ Sat, 08 Sep 2018 11:47:52: # Command line: callpeak -t SRX3583335.bam -f BAM -g ce -n SRX3583335.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX3583335.05 # format = BAM # ChIP-seq file = ['SRX3583335.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 @ Sat, 08 Sep 2018 11:47:52: #1 read tag files... INFO @ Sat, 08 Sep 2018 11:47:52: #1 read treatment tags... INFO @ Sat, 08 Sep 2018 11:48:00: 1000000 INFO @ Sat, 08 Sep 2018 11:48:00: 1000000 INFO @ Sat, 08 Sep 2018 11:48:00: 1000000 INFO @ Sat, 08 Sep 2018 11:48:08: 2000000 INFO @ Sat, 08 Sep 2018 11:48:08: 2000000 INFO @ Sat, 08 Sep 2018 11:48:08: 2000000 INFO @ Sat, 08 Sep 2018 11:48:16: 3000000 INFO @ Sat, 08 Sep 2018 11:48:16: 3000000 INFO @ Sat, 08 Sep 2018 11:48:16: 3000000 INFO @ Sat, 08 Sep 2018 11:48:23: 4000000 INFO @ Sat, 08 Sep 2018 11:48:23: 4000000 INFO @ Sat, 08 Sep 2018 11:48:23: 4000000 INFO @ Sat, 08 Sep 2018 11:48:31: 5000000 INFO @ Sat, 08 Sep 2018 11:48:31: 5000000 INFO @ Sat, 08 Sep 2018 11:48:31: 5000000 INFO @ Sat, 08 Sep 2018 11:48:38: 6000000 INFO @ Sat, 08 Sep 2018 11:48:39: 6000000 INFO @ Sat, 08 Sep 2018 11:48:39: 6000000 INFO @ Sat, 08 Sep 2018 11:48:46: 7000000 INFO @ Sat, 08 Sep 2018 11:48:46: 7000000 INFO @ Sat, 08 Sep 2018 11:48:46: 7000000 INFO @ Sat, 08 Sep 2018 11:48:54: 8000000 INFO @ Sat, 08 Sep 2018 11:48:54: 8000000 INFO @ Sat, 08 Sep 2018 11:48:54: 8000000 INFO @ Sat, 08 Sep 2018 11:49:01: 9000000 INFO @ Sat, 08 Sep 2018 11:49:01: 9000000 INFO @ Sat, 08 Sep 2018 11:49:02: 9000000 INFO @ Sat, 08 Sep 2018 11:49:09: 10000000 INFO @ Sat, 08 Sep 2018 11:49:09: 10000000 INFO @ Sat, 08 Sep 2018 11:49:09: 10000000 INFO @ Sat, 08 Sep 2018 11:49:16: 11000000 INFO @ Sat, 08 Sep 2018 11:49:17: 11000000 INFO @ Sat, 08 Sep 2018 11:49:17: 11000000 INFO @ Sat, 08 Sep 2018 11:49:24: 12000000 INFO @ Sat, 08 Sep 2018 11:49:25: 12000000 INFO @ Sat, 08 Sep 2018 11:49:25: 12000000 INFO @ Sat, 08 Sep 2018 11:49:31: 13000000 INFO @ Sat, 08 Sep 2018 11:49:33: 13000000 INFO @ Sat, 08 Sep 2018 11:49:34: 13000000 INFO @ Sat, 08 Sep 2018 11:49:39: 14000000 INFO @ Sat, 08 Sep 2018 11:49:41: 14000000 INFO @ Sat, 08 Sep 2018 11:49:42: 14000000 INFO @ Sat, 08 Sep 2018 11:49:46: 15000000 INFO @ Sat, 08 Sep 2018 11:49:49: 15000000 INFO @ Sat, 08 Sep 2018 11:49:50: 15000000 INFO @ Sat, 08 Sep 2018 11:49:53: 16000000 INFO @ Sat, 08 Sep 2018 11:49:57: 16000000 INFO @ Sat, 08 Sep 2018 11:49:58: 16000000 INFO @ Sat, 08 Sep 2018 11:50:01: 17000000 INFO @ Sat, 08 Sep 2018 11:50:05: 17000000 INFO @ Sat, 08 Sep 2018 11:50:06: 17000000 INFO @ Sat, 08 Sep 2018 11:50:08: 18000000 INFO @ Sat, 08 Sep 2018 11:50:12: 18000000 INFO @ Sat, 08 Sep 2018 11:50:14: 18000000 INFO @ Sat, 08 Sep 2018 11:50:16: 19000000 INFO @ Sat, 08 Sep 2018 11:50:20: 19000000 INFO @ Sat, 08 Sep 2018 11:50:21: 19000000 INFO @ Sat, 08 Sep 2018 11:50:24: 20000000 INFO @ Sat, 08 Sep 2018 11:50:27: 20000000 INFO @ Sat, 08 Sep 2018 11:50:29: 20000000 INFO @ Sat, 08 Sep 2018 11:50:32: 21000000 INFO @ Sat, 08 Sep 2018 11:50:35: 21000000 INFO @ Sat, 08 Sep 2018 11:50:37: 21000000 INFO @ Sat, 08 Sep 2018 11:50:39: 22000000 INFO @ Sat, 08 Sep 2018 11:50:42: 22000000 INFO @ Sat, 08 Sep 2018 11:50:45: 22000000 INFO @ Sat, 08 Sep 2018 11:50:45: #1 tag size is determined as 76 bps INFO @ Sat, 08 Sep 2018 11:50:45: #1 tag size = 76 INFO @ Sat, 08 Sep 2018 11:50:45: #1 total tags in treatment: 22718872 INFO @ Sat, 08 Sep 2018 11:50:45: #1 user defined the maximum tags... INFO @ Sat, 08 Sep 2018 11:50:45: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 08 Sep 2018 11:50:45: #1 tags after filtering in treatment: 22718872 INFO @ Sat, 08 Sep 2018 11:50:45: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 08 Sep 2018 11:50:45: #1 finished! INFO @ Sat, 08 Sep 2018 11:50:45: #2 Build Peak Model... INFO @ Sat, 08 Sep 2018 11:50:45: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 08 Sep 2018 11:50:47: #2 number of paired peaks: 128 WARNING @ Sat, 08 Sep 2018 11:50:47: Fewer paired peaks (128) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 128 pairs to build model! INFO @ Sat, 08 Sep 2018 11:50:47: start model_add_line... INFO @ Sat, 08 Sep 2018 11:50:47: start X-correlation... INFO @ Sat, 08 Sep 2018 11:50:47: end of X-cor INFO @ Sat, 08 Sep 2018 11:50:47: #2 finished! INFO @ Sat, 08 Sep 2018 11:50:47: #2 predicted fragment length is 2 bps INFO @ Sat, 08 Sep 2018 11:50:47: #2 alternative fragment length(s) may be 2,18,36,40,43,52,54,568 bps INFO @ Sat, 08 Sep 2018 11:50:47: #2.2 Generate R script for model : SRX3583335.05_model.r WARNING @ Sat, 08 Sep 2018 11:50:47: #2 Since the d (2) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 08 Sep 2018 11:50:47: #2 You may need to consider one of the other alternative d(s): 2,18,36,40,43,52,54,568 WARNING @ Sat, 08 Sep 2018 11:50:47: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sat, 08 Sep 2018 11:50:47: #3 Call peaks... INFO @ Sat, 08 Sep 2018 11:50:47: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 08 Sep 2018 11:50:48: #1 tag size is determined as 76 bps INFO @ Sat, 08 Sep 2018 11:50:48: #1 tag size = 76 INFO @ Sat, 08 Sep 2018 11:50:48: #1 total tags in treatment: 22718872 INFO @ Sat, 08 Sep 2018 11:50:48: #1 user defined the maximum tags... INFO @ Sat, 08 Sep 2018 11:50:48: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 08 Sep 2018 11:50:48: #1 tags after filtering in treatment: 22718872 INFO @ Sat, 08 Sep 2018 11:50:48: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 08 Sep 2018 11:50:48: #1 finished! INFO @ Sat, 08 Sep 2018 11:50:48: #2 Build Peak Model... INFO @ Sat, 08 Sep 2018 11:50:48: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 08 Sep 2018 11:50:50: #2 number of paired peaks: 128 WARNING @ Sat, 08 Sep 2018 11:50:50: Fewer paired peaks (128) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 128 pairs to build model! INFO @ Sat, 08 Sep 2018 11:50:50: start model_add_line... INFO @ Sat, 08 Sep 2018 11:50:50: #1 tag size is determined as 76 bps INFO @ Sat, 08 Sep 2018 11:50:50: #1 tag size = 76 INFO @ Sat, 08 Sep 2018 11:50:50: #1 total tags in treatment: 22718872 INFO @ Sat, 08 Sep 2018 11:50:50: #1 user defined the maximum tags... INFO @ Sat, 08 Sep 2018 11:50:50: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 08 Sep 2018 11:50:50: start X-correlation... INFO @ Sat, 08 Sep 2018 11:50:50: end of X-cor INFO @ Sat, 08 Sep 2018 11:50:50: #2 finished! INFO @ Sat, 08 Sep 2018 11:50:50: #2 predicted fragment length is 2 bps INFO @ Sat, 08 Sep 2018 11:50:50: #2 alternative fragment length(s) may be 2,18,36,40,43,52,54,568 bps INFO @ Sat, 08 Sep 2018 11:50:50: #2.2 Generate R script for model : SRX3583335.10_model.r WARNING @ Sat, 08 Sep 2018 11:50:50: #2 Since the d (2) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 08 Sep 2018 11:50:50: #2 You may need to consider one of the other alternative d(s): 2,18,36,40,43,52,54,568 WARNING @ Sat, 08 Sep 2018 11:50:50: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sat, 08 Sep 2018 11:50:50: #3 Call peaks... INFO @ Sat, 08 Sep 2018 11:50:50: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 08 Sep 2018 11:50:50: #1 tags after filtering in treatment: 22718872 INFO @ Sat, 08 Sep 2018 11:50:50: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 08 Sep 2018 11:50:50: #1 finished! INFO @ Sat, 08 Sep 2018 11:50:50: #2 Build Peak Model... INFO @ Sat, 08 Sep 2018 11:50:50: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 08 Sep 2018 11:50:52: #2 number of paired peaks: 128 WARNING @ Sat, 08 Sep 2018 11:50:52: Fewer paired peaks (128) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 128 pairs to build model! INFO @ Sat, 08 Sep 2018 11:50:52: start model_add_line... INFO @ Sat, 08 Sep 2018 11:50:52: start X-correlation... INFO @ Sat, 08 Sep 2018 11:50:52: end of X-cor INFO @ Sat, 08 Sep 2018 11:50:52: #2 finished! INFO @ Sat, 08 Sep 2018 11:50:52: #2 predicted fragment length is 2 bps INFO @ Sat, 08 Sep 2018 11:50:52: #2 alternative fragment length(s) may be 2,18,36,40,43,52,54,568 bps INFO @ Sat, 08 Sep 2018 11:50:52: #2.2 Generate R script for model : SRX3583335.20_model.r WARNING @ Sat, 08 Sep 2018 11:50:52: #2 Since the d (2) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 08 Sep 2018 11:50:52: #2 You may need to consider one of the other alternative d(s): 2,18,36,40,43,52,54,568 WARNING @ Sat, 08 Sep 2018 11:50:52: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sat, 08 Sep 2018 11:50:52: #3 Call peaks... INFO @ Sat, 08 Sep 2018 11:50:52: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 08 Sep 2018 11:51:24: #3 Call peaks for each chromosome... INFO @ Sat, 08 Sep 2018 11:51:25: #3 Call peaks for each chromosome... INFO @ Sat, 08 Sep 2018 11:51:29: #3 Call peaks for each chromosome... INFO @ Sat, 08 Sep 2018 11:51:43: #4 Write output xls file... SRX3583335.05_peaks.xls INFO @ Sat, 08 Sep 2018 11:51:43: #4 Write peak in narrowPeak format file... SRX3583335.05_peaks.narrowPeak INFO @ Sat, 08 Sep 2018 11:51:43: #4 Write summits bed file... SRX3583335.05_summits.bed INFO @ Sat, 08 Sep 2018 11:51:43: Done! pass1 - making usageList (0 chroms): 2 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling INFO @ Sat, 08 Sep 2018 11:51:43: #4 Write output xls file... SRX3583335.10_peaks.xls INFO @ Sat, 08 Sep 2018 11:51:43: #4 Write peak in narrowPeak format file... SRX3583335.10_peaks.narrowPeak INFO @ Sat, 08 Sep 2018 11:51:43: #4 Write summits bed file... SRX3583335.10_summits.bed INFO @ Sat, 08 Sep 2018 11:51:43: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling INFO @ Sat, 08 Sep 2018 11:51:47: #4 Write output xls file... SRX3583335.20_peaks.xls INFO @ Sat, 08 Sep 2018 11:51:47: #4 Write peak in narrowPeak format file... SRX3583335.20_peaks.narrowPeak INFO @ Sat, 08 Sep 2018 11:51:47: #4 Write summits bed file... SRX3583335.20_summits.bed INFO @ Sat, 08 Sep 2018 11:51:47: 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。