Job ID = 11170877 sra ファイルのダウンロード中... Completed: 487179K bytes transferred in 33 seconds (120174K 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 17425224 spots for /home/okishinya/chipatlas/results/ce10/SRX3942557/SRR7010078.sra Written 17425224 spots for /home/okishinya/chipatlas/results/ce10/SRX3942557/SRR7010078.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: 00:07:10 17425224 reads; of these: 17425224 (100.00%) were unpaired; of these: 1376305 (7.90%) aligned 0 times 12856266 (73.78%) aligned exactly 1 time 3192653 (18.32%) aligned >1 times 92.10% overall alignment rate Time searching: 00:07:10 Overall time: 00:07:10 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] 3621262 / 16048919 = 0.2256 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 11:38:25: # Command line: callpeak -t SRX3942557.bam -f BAM -g ce -n SRX3942557.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX3942557.05 # format = BAM # ChIP-seq file = ['SRX3942557.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 11:38:25: # Command line: callpeak -t SRX3942557.bam -f BAM -g ce -n SRX3942557.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX3942557.10 # format = BAM # ChIP-seq file = ['SRX3942557.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 11:38:25: # Command line: callpeak -t SRX3942557.bam -f BAM -g ce -n SRX3942557.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX3942557.20 # format = BAM # ChIP-seq file = ['SRX3942557.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 11:38:25: #1 read tag files... INFO @ Sat, 08 Sep 2018 11:38:25: #1 read tag files... INFO @ Sat, 08 Sep 2018 11:38:25: #1 read tag files... INFO @ Sat, 08 Sep 2018 11:38:25: #1 read treatment tags... INFO @ Sat, 08 Sep 2018 11:38:25: #1 read treatment tags... INFO @ Sat, 08 Sep 2018 11:38:25: #1 read treatment tags... INFO @ Sat, 08 Sep 2018 11:38:32: 1000000 INFO @ Sat, 08 Sep 2018 11:38:32: 1000000 INFO @ Sat, 08 Sep 2018 11:38:33: 1000000 INFO @ Sat, 08 Sep 2018 11:38:39: 2000000 INFO @ Sat, 08 Sep 2018 11:38:39: 2000000 INFO @ Sat, 08 Sep 2018 11:38:41: 2000000 INFO @ Sat, 08 Sep 2018 11:38:47: 3000000 INFO @ Sat, 08 Sep 2018 11:38:47: 3000000 INFO @ Sat, 08 Sep 2018 11:38:48: 3000000 INFO @ Sat, 08 Sep 2018 11:38:54: 4000000 INFO @ Sat, 08 Sep 2018 11:38:54: 4000000 INFO @ Sat, 08 Sep 2018 11:38:55: 4000000 INFO @ Sat, 08 Sep 2018 11:39:01: 5000000 INFO @ Sat, 08 Sep 2018 11:39:01: 5000000 INFO @ Sat, 08 Sep 2018 11:39:03: 5000000 INFO @ Sat, 08 Sep 2018 11:39:08: 6000000 INFO @ Sat, 08 Sep 2018 11:39:08: 6000000 INFO @ Sat, 08 Sep 2018 11:39:10: 6000000 INFO @ Sat, 08 Sep 2018 11:39:15: 7000000 INFO @ Sat, 08 Sep 2018 11:39:15: 7000000 INFO @ Sat, 08 Sep 2018 11:39:17: 7000000 INFO @ Sat, 08 Sep 2018 11:39:22: 8000000 INFO @ Sat, 08 Sep 2018 11:39:22: 8000000 INFO @ Sat, 08 Sep 2018 11:39:24: 8000000 INFO @ Sat, 08 Sep 2018 11:39:29: 9000000 INFO @ Sat, 08 Sep 2018 11:39:29: 9000000 INFO @ Sat, 08 Sep 2018 11:39:31: 9000000 INFO @ Sat, 08 Sep 2018 11:39:36: 10000000 INFO @ Sat, 08 Sep 2018 11:39:36: 10000000 INFO @ Sat, 08 Sep 2018 11:39:38: 10000000 INFO @ Sat, 08 Sep 2018 11:39:43: 11000000 INFO @ Sat, 08 Sep 2018 11:39:43: 11000000 INFO @ Sat, 08 Sep 2018 11:39:45: 11000000 INFO @ Sat, 08 Sep 2018 11:39:50: 12000000 INFO @ Sat, 08 Sep 2018 11:39:50: 12000000 INFO @ Sat, 08 Sep 2018 11:39:52: 12000000 INFO @ Sat, 08 Sep 2018 11:39:53: #1 tag size is determined as 75 bps INFO @ Sat, 08 Sep 2018 11:39:53: #1 tag size = 75 INFO @ Sat, 08 Sep 2018 11:39:53: #1 total tags in treatment: 12427657 INFO @ Sat, 08 Sep 2018 11:39:53: #1 user defined the maximum tags... INFO @ Sat, 08 Sep 2018 11:39:53: #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 11:39:53: #1 tag size is determined as 75 bps INFO @ Sat, 08 Sep 2018 11:39:53: #1 tag size = 75 INFO @ Sat, 08 Sep 2018 11:39:53: #1 total tags in treatment: 12427657 INFO @ Sat, 08 Sep 2018 11:39:53: #1 user defined the maximum tags... INFO @ Sat, 08 Sep 2018 11:39:53: #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 11:39:53: #1 tags after filtering in treatment: 12427657 INFO @ Sat, 08 Sep 2018 11:39:53: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 08 Sep 2018 11:39:53: #1 finished! INFO @ Sat, 08 Sep 2018 11:39:53: #2 Build Peak Model... INFO @ Sat, 08 Sep 2018 11:39:53: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 08 Sep 2018 11:39:53: #1 tags after filtering in treatment: 12427657 INFO @ Sat, 08 Sep 2018 11:39:53: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 08 Sep 2018 11:39:53: #1 finished! INFO @ Sat, 08 Sep 2018 11:39:53: #2 Build Peak Model... INFO @ Sat, 08 Sep 2018 11:39:53: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 08 Sep 2018 11:39:54: #2 number of paired peaks: 438 WARNING @ Sat, 08 Sep 2018 11:39:54: Fewer paired peaks (438) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 438 pairs to build model! INFO @ Sat, 08 Sep 2018 11:39:54: start model_add_line... INFO @ Sat, 08 Sep 2018 11:39:54: #2 number of paired peaks: 438 WARNING @ Sat, 08 Sep 2018 11:39:54: Fewer paired peaks (438) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 438 pairs to build model! INFO @ Sat, 08 Sep 2018 11:39:54: start model_add_line... INFO @ Sat, 08 Sep 2018 11:39:54: start X-correlation... INFO @ Sat, 08 Sep 2018 11:39:54: start X-correlation... INFO @ Sat, 08 Sep 2018 11:39:54: end of X-cor INFO @ Sat, 08 Sep 2018 11:39:54: end of X-cor INFO @ Sat, 08 Sep 2018 11:39:54: #2 finished! INFO @ Sat, 08 Sep 2018 11:39:54: #2 finished! INFO @ Sat, 08 Sep 2018 11:39:54: #2 predicted fragment length is 66 bps INFO @ Sat, 08 Sep 2018 11:39:54: #2 predicted fragment length is 66 bps INFO @ Sat, 08 Sep 2018 11:39:54: #2 alternative fragment length(s) may be 2,66,562 bps INFO @ Sat, 08 Sep 2018 11:39:54: #2 alternative fragment length(s) may be 2,66,562 bps INFO @ Sat, 08 Sep 2018 11:39:54: #2.2 Generate R script for model : SRX3942557.20_model.r INFO @ Sat, 08 Sep 2018 11:39:54: #2.2 Generate R script for model : SRX3942557.10_model.r WARNING @ Sat, 08 Sep 2018 11:39:54: #2 Since the d (66) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 08 Sep 2018 11:39:54: #2 You may need to consider one of the other alternative d(s): 2,66,562 WARNING @ Sat, 08 Sep 2018 11:39:54: #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 11:39:54: #3 Call peaks... WARNING @ Sat, 08 Sep 2018 11:39:54: #2 Since the d (66) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 08 Sep 2018 11:39:54: #2 You may need to consider one of the other alternative d(s): 2,66,562 WARNING @ Sat, 08 Sep 2018 11:39:54: #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 11:39:54: #3 Call peaks... INFO @ Sat, 08 Sep 2018 11:39:54: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 08 Sep 2018 11:39:54: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 08 Sep 2018 11:39:55: #1 tag size is determined as 75 bps INFO @ Sat, 08 Sep 2018 11:39:55: #1 tag size = 75 INFO @ Sat, 08 Sep 2018 11:39:55: #1 total tags in treatment: 12427657 INFO @ Sat, 08 Sep 2018 11:39:55: #1 user defined the maximum tags... INFO @ Sat, 08 Sep 2018 11:39:55: #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 11:39:55: #1 tags after filtering in treatment: 12427657 INFO @ Sat, 08 Sep 2018 11:39:55: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 08 Sep 2018 11:39:55: #1 finished! INFO @ Sat, 08 Sep 2018 11:39:55: #2 Build Peak Model... INFO @ Sat, 08 Sep 2018 11:39:55: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 08 Sep 2018 11:39:56: #2 number of paired peaks: 438 WARNING @ Sat, 08 Sep 2018 11:39:56: Fewer paired peaks (438) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 438 pairs to build model! INFO @ Sat, 08 Sep 2018 11:39:56: start model_add_line... INFO @ Sat, 08 Sep 2018 11:39:56: start X-correlation... INFO @ Sat, 08 Sep 2018 11:39:56: end of X-cor INFO @ Sat, 08 Sep 2018 11:39:56: #2 finished! INFO @ Sat, 08 Sep 2018 11:39:56: #2 predicted fragment length is 66 bps INFO @ Sat, 08 Sep 2018 11:39:56: #2 alternative fragment length(s) may be 2,66,562 bps INFO @ Sat, 08 Sep 2018 11:39:56: #2.2 Generate R script for model : SRX3942557.05_model.r WARNING @ Sat, 08 Sep 2018 11:39:56: #2 Since the d (66) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 08 Sep 2018 11:39:56: #2 You may need to consider one of the other alternative d(s): 2,66,562 WARNING @ Sat, 08 Sep 2018 11:39:56: #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 11:39:56: #3 Call peaks... INFO @ Sat, 08 Sep 2018 11:39:56: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 08 Sep 2018 11:40:20: #3 Call peaks for each chromosome... INFO @ Sat, 08 Sep 2018 11:40:21: #3 Call peaks for each chromosome... INFO @ Sat, 08 Sep 2018 11:40:22: #3 Call peaks for each chromosome... INFO @ Sat, 08 Sep 2018 11:40:33: #4 Write output xls file... SRX3942557.10_peaks.xls INFO @ Sat, 08 Sep 2018 11:40:33: #4 Write peak in narrowPeak format file... SRX3942557.10_peaks.narrowPeak INFO @ Sat, 08 Sep 2018 11:40:33: #4 Write summits bed file... SRX3942557.10_summits.bed INFO @ Sat, 08 Sep 2018 11:40:33: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (792 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Sat, 08 Sep 2018 11:40:36: #4 Write output xls file... SRX3942557.05_peaks.xls INFO @ Sat, 08 Sep 2018 11:40:36: #4 Write peak in narrowPeak format file... SRX3942557.05_peaks.narrowPeak INFO @ Sat, 08 Sep 2018 11:40:36: #4 Write summits bed file... SRX3942557.05_summits.bed INFO @ Sat, 08 Sep 2018 11:40:36: Done! pass1 - making usageList (6 chroms): 2 millis pass2 - checking and writing primary data (3440 records, 4 fields): 6 millis CompletedMACS2peakCalling INFO @ Sat, 08 Sep 2018 11:40:38: #4 Write output xls file... SRX3942557.20_peaks.xls INFO @ Sat, 08 Sep 2018 11:40:38: #4 Write peak in narrowPeak format file... SRX3942557.20_peaks.narrowPeak INFO @ Sat, 08 Sep 2018 11:40:38: #4 Write summits bed file... SRX3942557.20_summits.bed INFO @ Sat, 08 Sep 2018 11:40:38: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (206 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。