Job ID = 10714419 sra ファイルのダウンロード中... Completed: 417974K bytes transferred in 36 seconds (92774K 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 20054326 spots for /home/okishinya/chipatlas/results/ce10/SRX4082379/SRR7164197.sra Written 20054326 spots for /home/okishinya/chipatlas/results/ce10/SRX4082379/SRR7164197.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: 00:00:00 Time loading mirror index: 00:00:00 Multiseed full-index search: 00:04:52 20054326 reads; of these: 20054326 (100.00%) were unpaired; of these: 3693110 (18.42%) aligned 0 times 12474702 (62.20%) aligned exactly 1 time 3886514 (19.38%) aligned >1 times 81.58% overall alignment rate Time searching: 00:04:52 Overall time: 00:04:52 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] 4784613 / 16361216 = 0.2924 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 @ Sun, 03 Jun 2018 12:39:02: # Command line: callpeak -t SRX4082379.bam -f BAM -g ce -n SRX4082379.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX4082379.05 # format = BAM # ChIP-seq file = ['SRX4082379.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 @ Sun, 03 Jun 2018 12:39:02: #1 read tag files... INFO @ Sun, 03 Jun 2018 12:39:02: #1 read treatment tags... INFO @ Sun, 03 Jun 2018 12:39:02: # Command line: callpeak -t SRX4082379.bam -f BAM -g ce -n SRX4082379.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX4082379.10 # format = BAM # ChIP-seq file = ['SRX4082379.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 @ Sun, 03 Jun 2018 12:39:02: #1 read tag files... INFO @ Sun, 03 Jun 2018 12:39:02: #1 read treatment tags... INFO @ Sun, 03 Jun 2018 12:39:02: # Command line: callpeak -t SRX4082379.bam -f BAM -g ce -n SRX4082379.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX4082379.20 # format = BAM # ChIP-seq file = ['SRX4082379.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 @ Sun, 03 Jun 2018 12:39:02: #1 read tag files... INFO @ Sun, 03 Jun 2018 12:39:02: #1 read treatment tags... INFO @ Sun, 03 Jun 2018 12:39:09: 1000000 INFO @ Sun, 03 Jun 2018 12:39:10: 1000000 INFO @ Sun, 03 Jun 2018 12:39:10: 1000000 INFO @ Sun, 03 Jun 2018 12:39:17: 2000000 INFO @ Sun, 03 Jun 2018 12:39:17: 2000000 INFO @ Sun, 03 Jun 2018 12:39:18: 2000000 INFO @ Sun, 03 Jun 2018 12:39:24: 3000000 INFO @ Sun, 03 Jun 2018 12:39:25: 3000000 INFO @ Sun, 03 Jun 2018 12:39:27: 3000000 INFO @ Sun, 03 Jun 2018 12:39:31: 4000000 INFO @ Sun, 03 Jun 2018 12:39:33: 4000000 INFO @ Sun, 03 Jun 2018 12:39:36: 4000000 INFO @ Sun, 03 Jun 2018 12:39:39: 5000000 INFO @ Sun, 03 Jun 2018 12:39:41: 5000000 INFO @ Sun, 03 Jun 2018 12:39:44: 5000000 INFO @ Sun, 03 Jun 2018 12:39:46: 6000000 INFO @ Sun, 03 Jun 2018 12:39:48: 6000000 INFO @ Sun, 03 Jun 2018 12:39:53: 6000000 INFO @ Sun, 03 Jun 2018 12:39:54: 7000000 INFO @ Sun, 03 Jun 2018 12:39:56: 7000000 INFO @ Sun, 03 Jun 2018 12:40:01: 7000000 INFO @ Sun, 03 Jun 2018 12:40:01: 8000000 INFO @ Sun, 03 Jun 2018 12:40:04: 8000000 INFO @ Sun, 03 Jun 2018 12:40:08: 9000000 INFO @ Sun, 03 Jun 2018 12:40:10: 8000000 INFO @ Sun, 03 Jun 2018 12:40:12: 9000000 INFO @ Sun, 03 Jun 2018 12:40:16: 10000000 INFO @ Sun, 03 Jun 2018 12:40:18: 9000000 INFO @ Sun, 03 Jun 2018 12:40:20: 10000000 INFO @ Sun, 03 Jun 2018 12:40:23: 11000000 INFO @ Sun, 03 Jun 2018 12:40:26: 10000000 INFO @ Sun, 03 Jun 2018 12:40:28: #1 tag size is determined as 51 bps INFO @ Sun, 03 Jun 2018 12:40:28: #1 tag size = 51 INFO @ Sun, 03 Jun 2018 12:40:28: #1 total tags in treatment: 11576603 INFO @ Sun, 03 Jun 2018 12:40:28: #1 user defined the maximum tags... INFO @ Sun, 03 Jun 2018 12:40:28: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sun, 03 Jun 2018 12:40:28: 11000000 INFO @ Sun, 03 Jun 2018 12:40:28: #1 tags after filtering in treatment: 11576603 INFO @ Sun, 03 Jun 2018 12:40:28: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 03 Jun 2018 12:40:28: #1 finished! INFO @ Sun, 03 Jun 2018 12:40:28: #2 Build Peak Model... INFO @ Sun, 03 Jun 2018 12:40:28: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 03 Jun 2018 12:40:29: #2 number of paired peaks: 504 WARNING @ Sun, 03 Jun 2018 12:40:29: Fewer paired peaks (504) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 504 pairs to build model! INFO @ Sun, 03 Jun 2018 12:40:29: start model_add_line... INFO @ Sun, 03 Jun 2018 12:40:29: start X-correlation... INFO @ Sun, 03 Jun 2018 12:40:29: end of X-cor INFO @ Sun, 03 Jun 2018 12:40:29: #2 finished! INFO @ Sun, 03 Jun 2018 12:40:29: #2 predicted fragment length is 47 bps INFO @ Sun, 03 Jun 2018 12:40:29: #2 alternative fragment length(s) may be 2,47,567,574 bps INFO @ Sun, 03 Jun 2018 12:40:29: #2.2 Generate R script for model : SRX4082379.05_model.r WARNING @ Sun, 03 Jun 2018 12:40:29: #2 Since the d (47) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 03 Jun 2018 12:40:29: #2 You may need to consider one of the other alternative d(s): 2,47,567,574 WARNING @ Sun, 03 Jun 2018 12:40:29: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sun, 03 Jun 2018 12:40:29: #3 Call peaks... INFO @ Sun, 03 Jun 2018 12:40:29: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 03 Jun 2018 12:40:32: #1 tag size is determined as 51 bps INFO @ Sun, 03 Jun 2018 12:40:32: #1 tag size = 51 INFO @ Sun, 03 Jun 2018 12:40:32: #1 total tags in treatment: 11576603 INFO @ Sun, 03 Jun 2018 12:40:32: #1 user defined the maximum tags... INFO @ Sun, 03 Jun 2018 12:40:32: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sun, 03 Jun 2018 12:40:32: #1 tags after filtering in treatment: 11576603 INFO @ Sun, 03 Jun 2018 12:40:32: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 03 Jun 2018 12:40:32: #1 finished! INFO @ Sun, 03 Jun 2018 12:40:32: #2 Build Peak Model... INFO @ Sun, 03 Jun 2018 12:40:32: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 03 Jun 2018 12:40:33: #2 number of paired peaks: 504 WARNING @ Sun, 03 Jun 2018 12:40:33: Fewer paired peaks (504) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 504 pairs to build model! INFO @ Sun, 03 Jun 2018 12:40:33: start model_add_line... INFO @ Sun, 03 Jun 2018 12:40:33: start X-correlation... INFO @ Sun, 03 Jun 2018 12:40:33: end of X-cor INFO @ Sun, 03 Jun 2018 12:40:33: #2 finished! INFO @ Sun, 03 Jun 2018 12:40:33: #2 predicted fragment length is 47 bps INFO @ Sun, 03 Jun 2018 12:40:33: #2 alternative fragment length(s) may be 2,47,567,574 bps INFO @ Sun, 03 Jun 2018 12:40:33: #2.2 Generate R script for model : SRX4082379.10_model.r WARNING @ Sun, 03 Jun 2018 12:40:33: #2 Since the d (47) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 03 Jun 2018 12:40:33: #2 You may need to consider one of the other alternative d(s): 2,47,567,574 WARNING @ Sun, 03 Jun 2018 12:40:33: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sun, 03 Jun 2018 12:40:33: #3 Call peaks... INFO @ Sun, 03 Jun 2018 12:40:33: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 03 Jun 2018 12:40:35: 11000000 INFO @ Sun, 03 Jun 2018 12:40:40: #1 tag size is determined as 51 bps INFO @ Sun, 03 Jun 2018 12:40:40: #1 tag size = 51 INFO @ Sun, 03 Jun 2018 12:40:40: #1 total tags in treatment: 11576603 INFO @ Sun, 03 Jun 2018 12:40:40: #1 user defined the maximum tags... INFO @ Sun, 03 Jun 2018 12:40:40: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sun, 03 Jun 2018 12:40:40: #1 tags after filtering in treatment: 11576603 INFO @ Sun, 03 Jun 2018 12:40:40: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 03 Jun 2018 12:40:40: #1 finished! INFO @ Sun, 03 Jun 2018 12:40:40: #2 Build Peak Model... INFO @ Sun, 03 Jun 2018 12:40:40: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 03 Jun 2018 12:40:41: #2 number of paired peaks: 504 WARNING @ Sun, 03 Jun 2018 12:40:41: Fewer paired peaks (504) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 504 pairs to build model! INFO @ Sun, 03 Jun 2018 12:40:41: start model_add_line... INFO @ Sun, 03 Jun 2018 12:40:41: start X-correlation... INFO @ Sun, 03 Jun 2018 12:40:41: end of X-cor INFO @ Sun, 03 Jun 2018 12:40:41: #2 finished! INFO @ Sun, 03 Jun 2018 12:40:41: #2 predicted fragment length is 47 bps INFO @ Sun, 03 Jun 2018 12:40:41: #2 alternative fragment length(s) may be 2,47,567,574 bps INFO @ Sun, 03 Jun 2018 12:40:41: #2.2 Generate R script for model : SRX4082379.20_model.r WARNING @ Sun, 03 Jun 2018 12:40:41: #2 Since the d (47) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 03 Jun 2018 12:40:41: #2 You may need to consider one of the other alternative d(s): 2,47,567,574 WARNING @ Sun, 03 Jun 2018 12:40:41: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sun, 03 Jun 2018 12:40:41: #3 Call peaks... INFO @ Sun, 03 Jun 2018 12:40:41: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 03 Jun 2018 12:40:53: #3 Call peaks for each chromosome... INFO @ Sun, 03 Jun 2018 12:40:57: #3 Call peaks for each chromosome... INFO @ Sun, 03 Jun 2018 12:41:05: #3 Call peaks for each chromosome... INFO @ Sun, 03 Jun 2018 12:41:06: #4 Write output xls file... SRX4082379.05_peaks.xls INFO @ Sun, 03 Jun 2018 12:41:06: #4 Write peak in narrowPeak format file... SRX4082379.05_peaks.narrowPeak INFO @ Sun, 03 Jun 2018 12:41:06: #4 Write summits bed file... SRX4082379.05_summits.bed INFO @ Sun, 03 Jun 2018 12:41:06: Done! pass1 - making usageList (6 chroms): 2 millis pass2 - checking and writing primary data (984 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Sun, 03 Jun 2018 12:41:11: #4 Write output xls file... SRX4082379.10_peaks.xls INFO @ Sun, 03 Jun 2018 12:41:11: #4 Write peak in narrowPeak format file... SRX4082379.10_peaks.narrowPeak INFO @ Sun, 03 Jun 2018 12:41:11: #4 Write summits bed file... SRX4082379.10_summits.bed INFO @ Sun, 03 Jun 2018 12:41:11: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (494 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Sun, 03 Jun 2018 12:41:19: #4 Write output xls file... SRX4082379.20_peaks.xls INFO @ Sun, 03 Jun 2018 12:41:19: #4 Write peak in narrowPeak format file... SRX4082379.20_peaks.narrowPeak INFO @ Sun, 03 Jun 2018 12:41:19: #4 Write summits bed file... SRX4082379.20_summits.bed INFO @ Sun, 03 Jun 2018 12:41:19: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (211 records, 4 fields): 2 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。