Job ID = 11171333 sra ファイルのダウンロード中... Completed: 249602K bytes transferred in 8 seconds (229440K 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 6317813 spots for /home/okishinya/chipatlas/results/dm3/SRX3511960/SRR6418945.sra Written 6317813 spots for /home/okishinya/chipatlas/results/dm3/SRX3511960/SRR6418945.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: 00:04:00 6317813 reads; of these: 6317813 (100.00%) were unpaired; of these: 497968 (7.88%) aligned 0 times 4153138 (65.74%) aligned exactly 1 time 1666707 (26.38%) aligned >1 times 92.12% overall alignment rate Time searching: 00:04:00 Overall time: 00:04:00 マッピングが完了しました。 samtools でBAM に変換中... [samopen] SAM header is present: 15 sequences. [bam_rmdupse_core] 579485 / 5819845 = 0.0996 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 13:51:31: # Command line: callpeak -t SRX3511960.bam -f BAM -g dm -n SRX3511960.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX3511960.05 # format = BAM # ChIP-seq file = ['SRX3511960.bam'] # control file = None # effective genome size = 1.20e+08 # 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 13:51:31: # Command line: callpeak -t SRX3511960.bam -f BAM -g dm -n SRX3511960.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX3511960.10 # format = BAM # ChIP-seq file = ['SRX3511960.bam'] # control file = None # effective genome size = 1.20e+08 # 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 13:51:31: # Command line: callpeak -t SRX3511960.bam -f BAM -g dm -n SRX3511960.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX3511960.20 # format = BAM # ChIP-seq file = ['SRX3511960.bam'] # control file = None # effective genome size = 1.20e+08 # 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 13:51:31: #1 read tag files... INFO @ Sat, 08 Sep 2018 13:51:31: #1 read tag files... INFO @ Sat, 08 Sep 2018 13:51:31: #1 read tag files... INFO @ Sat, 08 Sep 2018 13:51:31: #1 read treatment tags... INFO @ Sat, 08 Sep 2018 13:51:31: #1 read treatment tags... INFO @ Sat, 08 Sep 2018 13:51:31: #1 read treatment tags... INFO @ Sat, 08 Sep 2018 13:51:40: 1000000 INFO @ Sat, 08 Sep 2018 13:51:41: 1000000 INFO @ Sat, 08 Sep 2018 13:51:41: 1000000 INFO @ Sat, 08 Sep 2018 13:51:49: 2000000 INFO @ Sat, 08 Sep 2018 13:51:50: 2000000 INFO @ Sat, 08 Sep 2018 13:51:50: 2000000 INFO @ Sat, 08 Sep 2018 13:51:58: 3000000 INFO @ Sat, 08 Sep 2018 13:52:00: 3000000 INFO @ Sat, 08 Sep 2018 13:52:00: 3000000 INFO @ Sat, 08 Sep 2018 13:52:08: 4000000 INFO @ Sat, 08 Sep 2018 13:52:09: 4000000 INFO @ Sat, 08 Sep 2018 13:52:09: 4000000 INFO @ Sat, 08 Sep 2018 13:52:17: 5000000 INFO @ Sat, 08 Sep 2018 13:52:18: 5000000 INFO @ Sat, 08 Sep 2018 13:52:18: 5000000 INFO @ Sat, 08 Sep 2018 13:52:19: #1 tag size is determined as 98 bps INFO @ Sat, 08 Sep 2018 13:52:19: #1 tag size = 98 INFO @ Sat, 08 Sep 2018 13:52:19: #1 total tags in treatment: 5240360 INFO @ Sat, 08 Sep 2018 13:52:19: #1 user defined the maximum tags... INFO @ Sat, 08 Sep 2018 13:52:19: #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 13:52:19: #1 tags after filtering in treatment: 5240360 INFO @ Sat, 08 Sep 2018 13:52:19: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 08 Sep 2018 13:52:19: #1 finished! INFO @ Sat, 08 Sep 2018 13:52:19: #2 Build Peak Model... INFO @ Sat, 08 Sep 2018 13:52:19: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 08 Sep 2018 13:52:19: #2 number of paired peaks: 184 WARNING @ Sat, 08 Sep 2018 13:52:19: Fewer paired peaks (184) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 184 pairs to build model! INFO @ Sat, 08 Sep 2018 13:52:19: start model_add_line... INFO @ Sat, 08 Sep 2018 13:52:19: start X-correlation... INFO @ Sat, 08 Sep 2018 13:52:20: end of X-cor INFO @ Sat, 08 Sep 2018 13:52:20: #2 finished! INFO @ Sat, 08 Sep 2018 13:52:20: #2 predicted fragment length is 146 bps INFO @ Sat, 08 Sep 2018 13:52:20: #2 alternative fragment length(s) may be 75,102,116,146,202,284,391 bps INFO @ Sat, 08 Sep 2018 13:52:20: #2.2 Generate R script for model : SRX3511960.20_model.r WARNING @ Sat, 08 Sep 2018 13:52:20: #2 Since the d (146) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 08 Sep 2018 13:52:20: #2 You may need to consider one of the other alternative d(s): 75,102,116,146,202,284,391 WARNING @ Sat, 08 Sep 2018 13:52:20: #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 13:52:20: #3 Call peaks... INFO @ Sat, 08 Sep 2018 13:52:20: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 08 Sep 2018 13:52:21: #1 tag size is determined as 98 bps INFO @ Sat, 08 Sep 2018 13:52:21: #1 tag size is determined as 98 bps INFO @ Sat, 08 Sep 2018 13:52:21: #1 tag size = 98 INFO @ Sat, 08 Sep 2018 13:52:21: #1 tag size = 98 INFO @ Sat, 08 Sep 2018 13:52:21: #1 total tags in treatment: 5240360 INFO @ Sat, 08 Sep 2018 13:52:21: #1 total tags in treatment: 5240360 INFO @ Sat, 08 Sep 2018 13:52:21: #1 user defined the maximum tags... INFO @ Sat, 08 Sep 2018 13:52:21: #1 user defined the maximum tags... INFO @ Sat, 08 Sep 2018 13:52:21: #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 13:52:21: #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 13:52:21: #1 tags after filtering in treatment: 5240360 INFO @ Sat, 08 Sep 2018 13:52:21: #1 tags after filtering in treatment: 5240360 INFO @ Sat, 08 Sep 2018 13:52:21: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 08 Sep 2018 13:52:21: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 08 Sep 2018 13:52:21: #1 finished! INFO @ Sat, 08 Sep 2018 13:52:21: #1 finished! INFO @ Sat, 08 Sep 2018 13:52:21: #2 Build Peak Model... INFO @ Sat, 08 Sep 2018 13:52:21: #2 Build Peak Model... INFO @ Sat, 08 Sep 2018 13:52:21: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 08 Sep 2018 13:52:21: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 08 Sep 2018 13:52:21: #2 number of paired peaks: 184 WARNING @ Sat, 08 Sep 2018 13:52:21: Fewer paired peaks (184) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 184 pairs to build model! INFO @ Sat, 08 Sep 2018 13:52:21: start model_add_line... INFO @ Sat, 08 Sep 2018 13:52:21: #2 number of paired peaks: 184 WARNING @ Sat, 08 Sep 2018 13:52:21: Fewer paired peaks (184) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 184 pairs to build model! INFO @ Sat, 08 Sep 2018 13:52:21: start model_add_line... INFO @ Sat, 08 Sep 2018 13:52:21: start X-correlation... INFO @ Sat, 08 Sep 2018 13:52:21: end of X-cor INFO @ Sat, 08 Sep 2018 13:52:21: #2 finished! INFO @ Sat, 08 Sep 2018 13:52:21: #2 predicted fragment length is 146 bps INFO @ Sat, 08 Sep 2018 13:52:21: #2 alternative fragment length(s) may be 75,102,116,146,202,284,391 bps INFO @ Sat, 08 Sep 2018 13:52:21: #2.2 Generate R script for model : SRX3511960.10_model.r WARNING @ Sat, 08 Sep 2018 13:52:21: #2 Since the d (146) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 08 Sep 2018 13:52:21: #2 You may need to consider one of the other alternative d(s): 75,102,116,146,202,284,391 WARNING @ Sat, 08 Sep 2018 13:52:21: #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 13:52:21: #3 Call peaks... INFO @ Sat, 08 Sep 2018 13:52:21: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 08 Sep 2018 13:52:21: start X-correlation... INFO @ Sat, 08 Sep 2018 13:52:21: end of X-cor INFO @ Sat, 08 Sep 2018 13:52:21: #2 finished! INFO @ Sat, 08 Sep 2018 13:52:21: #2 predicted fragment length is 146 bps INFO @ Sat, 08 Sep 2018 13:52:21: #2 alternative fragment length(s) may be 75,102,116,146,202,284,391 bps INFO @ Sat, 08 Sep 2018 13:52:21: #2.2 Generate R script for model : SRX3511960.05_model.r WARNING @ Sat, 08 Sep 2018 13:52:21: #2 Since the d (146) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 08 Sep 2018 13:52:21: #2 You may need to consider one of the other alternative d(s): 75,102,116,146,202,284,391 WARNING @ Sat, 08 Sep 2018 13:52:21: #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 13:52:21: #3 Call peaks... INFO @ Sat, 08 Sep 2018 13:52:21: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 08 Sep 2018 13:52:32: #3 Call peaks for each chromosome... INFO @ Sat, 08 Sep 2018 13:52:34: #3 Call peaks for each chromosome... INFO @ Sat, 08 Sep 2018 13:52:34: #3 Call peaks for each chromosome... INFO @ Sat, 08 Sep 2018 13:52:39: #4 Write output xls file... SRX3511960.20_peaks.xls INFO @ Sat, 08 Sep 2018 13:52:39: #4 Write peak in narrowPeak format file... SRX3511960.20_peaks.narrowPeak INFO @ Sat, 08 Sep 2018 13:52:40: #4 Write summits bed file... SRX3511960.20_summits.bed INFO @ Sat, 08 Sep 2018 13:52:40: Done! pass1 - making usageList (3 chroms): 1 millis pass2 - checking and writing primary data (26 records, 4 fields): 5 millis CompletedMACS2peakCalling INFO @ Sat, 08 Sep 2018 13:52:40: #4 Write output xls file... SRX3511960.10_peaks.xls INFO @ Sat, 08 Sep 2018 13:52:40: #4 Write peak in narrowPeak format file... SRX3511960.10_peaks.narrowPeak INFO @ Sat, 08 Sep 2018 13:52:40: #4 Write summits bed file... SRX3511960.10_summits.bed INFO @ Sat, 08 Sep 2018 13:52:40: Done! pass1 - making usageList (8 chroms): 1 millis pass2 - checking and writing primary data (108 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Sat, 08 Sep 2018 13:52:41: #4 Write output xls file... SRX3511960.05_peaks.xls INFO @ Sat, 08 Sep 2018 13:52:41: #4 Write peak in narrowPeak format file... SRX3511960.05_peaks.narrowPeak INFO @ Sat, 08 Sep 2018 13:52:41: #4 Write summits bed file... SRX3511960.05_summits.bed INFO @ Sat, 08 Sep 2018 13:52:41: Done! pass1 - making usageList (12 chroms): 1 millis pass2 - checking and writing primary data (438 records, 4 fields): 3 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。