Job ID = 11171306 sra ファイルのダウンロード中... Completed: 481401K bytes transferred in 20 seconds (195930K 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 10879524 spots for /home/okishinya/chipatlas/results/dm3/SRX3511943/SRR6418928.sra Written 10879524 spots for /home/okishinya/chipatlas/results/dm3/SRX3511943/SRR6418928.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: 00:06:54 10879524 reads; of these: 10879524 (100.00%) were unpaired; of these: 1025244 (9.42%) aligned 0 times 7434883 (68.34%) aligned exactly 1 time 2419397 (22.24%) aligned >1 times 90.58% overall alignment rate Time searching: 00:06:54 Overall time: 00:06:54 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_sort_core] merging from 8 files... [bam_rmdupse_core] 467686 / 9854280 = 0.0475 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 13:46:54: # Command line: callpeak -t SRX3511943.bam -f BAM -g dm -n SRX3511943.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX3511943.10 # format = BAM # ChIP-seq file = ['SRX3511943.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 13:46:54: #1 read tag files... INFO @ Sat, 08 Sep 2018 13:46:54: #1 read treatment tags... INFO @ Sat, 08 Sep 2018 13:46:54: # Command line: callpeak -t SRX3511943.bam -f BAM -g dm -n SRX3511943.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX3511943.05 # format = BAM # ChIP-seq file = ['SRX3511943.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 13:46:54: #1 read tag files... INFO @ Sat, 08 Sep 2018 13:46:54: #1 read treatment tags... INFO @ Sat, 08 Sep 2018 13:46:54: # Command line: callpeak -t SRX3511943.bam -f BAM -g dm -n SRX3511943.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX3511943.20 # format = BAM # ChIP-seq file = ['SRX3511943.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 13:46:54: #1 read tag files... INFO @ Sat, 08 Sep 2018 13:46:54: #1 read treatment tags... INFO @ Sat, 08 Sep 2018 13:47:01: 1000000 INFO @ Sat, 08 Sep 2018 13:47:02: 1000000 INFO @ Sat, 08 Sep 2018 13:47:02: 1000000 INFO @ Sat, 08 Sep 2018 13:47:09: 2000000 INFO @ Sat, 08 Sep 2018 13:47:09: 2000000 INFO @ Sat, 08 Sep 2018 13:47:09: 2000000 INFO @ Sat, 08 Sep 2018 13:47:16: 3000000 INFO @ Sat, 08 Sep 2018 13:47:17: 3000000 INFO @ Sat, 08 Sep 2018 13:47:17: 3000000 INFO @ Sat, 08 Sep 2018 13:47:24: 4000000 INFO @ Sat, 08 Sep 2018 13:47:25: 4000000 INFO @ Sat, 08 Sep 2018 13:47:25: 4000000 INFO @ Sat, 08 Sep 2018 13:47:31: 5000000 INFO @ Sat, 08 Sep 2018 13:47:32: 5000000 INFO @ Sat, 08 Sep 2018 13:47:32: 5000000 INFO @ Sat, 08 Sep 2018 13:47:39: 6000000 INFO @ Sat, 08 Sep 2018 13:47:40: 6000000 INFO @ Sat, 08 Sep 2018 13:47:40: 6000000 INFO @ Sat, 08 Sep 2018 13:47:46: 7000000 INFO @ Sat, 08 Sep 2018 13:47:48: 7000000 INFO @ Sat, 08 Sep 2018 13:47:48: 7000000 INFO @ Sat, 08 Sep 2018 13:47:54: 8000000 INFO @ Sat, 08 Sep 2018 13:47:56: 8000000 INFO @ Sat, 08 Sep 2018 13:47:56: 8000000 INFO @ Sat, 08 Sep 2018 13:48:01: 9000000 INFO @ Sat, 08 Sep 2018 13:48:03: 9000000 INFO @ Sat, 08 Sep 2018 13:48:03: 9000000 INFO @ Sat, 08 Sep 2018 13:48:04: #1 tag size is determined as 100 bps INFO @ Sat, 08 Sep 2018 13:48:04: #1 tag size = 100 INFO @ Sat, 08 Sep 2018 13:48:04: #1 total tags in treatment: 9386594 INFO @ Sat, 08 Sep 2018 13:48:04: #1 user defined the maximum tags... INFO @ Sat, 08 Sep 2018 13:48:04: #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 13:48:05: #1 tags after filtering in treatment: 9386594 INFO @ Sat, 08 Sep 2018 13:48:05: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 08 Sep 2018 13:48:05: #1 finished! INFO @ Sat, 08 Sep 2018 13:48:05: #2 Build Peak Model... INFO @ Sat, 08 Sep 2018 13:48:05: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 08 Sep 2018 13:48:05: #2 number of paired peaks: 110 WARNING @ Sat, 08 Sep 2018 13:48:05: Fewer paired peaks (110) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 110 pairs to build model! INFO @ Sat, 08 Sep 2018 13:48:05: start model_add_line... INFO @ Sat, 08 Sep 2018 13:48:05: start X-correlation... INFO @ Sat, 08 Sep 2018 13:48:05: end of X-cor INFO @ Sat, 08 Sep 2018 13:48:05: #2 finished! INFO @ Sat, 08 Sep 2018 13:48:05: #2 predicted fragment length is 112 bps INFO @ Sat, 08 Sep 2018 13:48:05: #2 alternative fragment length(s) may be 112 bps INFO @ Sat, 08 Sep 2018 13:48:05: #2.2 Generate R script for model : SRX3511943.10_model.r WARNING @ Sat, 08 Sep 2018 13:48:05: #2 Since the d (112) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 08 Sep 2018 13:48:05: #2 You may need to consider one of the other alternative d(s): 112 WARNING @ Sat, 08 Sep 2018 13:48:05: #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 13:48:05: #3 Call peaks... INFO @ Sat, 08 Sep 2018 13:48:05: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 08 Sep 2018 13:48:06: #1 tag size is determined as 100 bps INFO @ Sat, 08 Sep 2018 13:48:06: #1 tag size is determined as 100 bps INFO @ Sat, 08 Sep 2018 13:48:06: #1 tag size = 100 INFO @ Sat, 08 Sep 2018 13:48:06: #1 tag size = 100 INFO @ Sat, 08 Sep 2018 13:48:06: #1 total tags in treatment: 9386594 INFO @ Sat, 08 Sep 2018 13:48:06: #1 total tags in treatment: 9386594 INFO @ Sat, 08 Sep 2018 13:48:06: #1 user defined the maximum tags... INFO @ Sat, 08 Sep 2018 13:48:06: #1 user defined the maximum tags... INFO @ Sat, 08 Sep 2018 13:48:06: #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 13:48:06: #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 13:48:06: #1 tags after filtering in treatment: 9386594 INFO @ Sat, 08 Sep 2018 13:48:06: #1 tags after filtering in treatment: 9386594 INFO @ Sat, 08 Sep 2018 13:48:06: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 08 Sep 2018 13:48:06: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 08 Sep 2018 13:48:06: #1 finished! INFO @ Sat, 08 Sep 2018 13:48:06: #1 finished! INFO @ Sat, 08 Sep 2018 13:48:06: #2 Build Peak Model... INFO @ Sat, 08 Sep 2018 13:48:06: #2 Build Peak Model... INFO @ Sat, 08 Sep 2018 13:48:06: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 08 Sep 2018 13:48:06: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 08 Sep 2018 13:48:07: #2 number of paired peaks: 110 WARNING @ Sat, 08 Sep 2018 13:48:07: Fewer paired peaks (110) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 110 pairs to build model! INFO @ Sat, 08 Sep 2018 13:48:07: start model_add_line... INFO @ Sat, 08 Sep 2018 13:48:07: start X-correlation... INFO @ Sat, 08 Sep 2018 13:48:07: end of X-cor INFO @ Sat, 08 Sep 2018 13:48:07: #2 finished! INFO @ Sat, 08 Sep 2018 13:48:07: #2 predicted fragment length is 112 bps INFO @ Sat, 08 Sep 2018 13:48:07: #2 alternative fragment length(s) may be 112 bps INFO @ Sat, 08 Sep 2018 13:48:07: #2.2 Generate R script for model : SRX3511943.05_model.r INFO @ Sat, 08 Sep 2018 13:48:07: #2 number of paired peaks: 110 WARNING @ Sat, 08 Sep 2018 13:48:07: Fewer paired peaks (110) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 110 pairs to build model! INFO @ Sat, 08 Sep 2018 13:48:07: start model_add_line... WARNING @ Sat, 08 Sep 2018 13:48:07: #2 Since the d (112) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 08 Sep 2018 13:48:07: #2 You may need to consider one of the other alternative d(s): 112 WARNING @ Sat, 08 Sep 2018 13:48:07: #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 13:48:07: #3 Call peaks... INFO @ Sat, 08 Sep 2018 13:48:07: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 08 Sep 2018 13:48:07: start X-correlation... INFO @ Sat, 08 Sep 2018 13:48:07: end of X-cor INFO @ Sat, 08 Sep 2018 13:48:07: #2 finished! INFO @ Sat, 08 Sep 2018 13:48:07: #2 predicted fragment length is 112 bps INFO @ Sat, 08 Sep 2018 13:48:07: #2 alternative fragment length(s) may be 112 bps INFO @ Sat, 08 Sep 2018 13:48:07: #2.2 Generate R script for model : SRX3511943.20_model.r WARNING @ Sat, 08 Sep 2018 13:48:07: #2 Since the d (112) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 08 Sep 2018 13:48:07: #2 You may need to consider one of the other alternative d(s): 112 WARNING @ Sat, 08 Sep 2018 13:48:07: #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 13:48:07: #3 Call peaks... INFO @ Sat, 08 Sep 2018 13:48:07: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 08 Sep 2018 13:48:27: #3 Call peaks for each chromosome... INFO @ Sat, 08 Sep 2018 13:48:27: #3 Call peaks for each chromosome... INFO @ Sat, 08 Sep 2018 13:48:29: #3 Call peaks for each chromosome... INFO @ Sat, 08 Sep 2018 13:48:38: #4 Write output xls file... SRX3511943.20_peaks.xls INFO @ Sat, 08 Sep 2018 13:48:38: #4 Write peak in narrowPeak format file... SRX3511943.20_peaks.narrowPeak INFO @ Sat, 08 Sep 2018 13:48:38: #4 Write summits bed file... SRX3511943.20_summits.bed INFO @ Sat, 08 Sep 2018 13:48:38: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (220 records, 4 fields): 1 millis CompletedMACS2peakCalling INFO @ Sat, 08 Sep 2018 13:48:39: #4 Write output xls file... SRX3511943.05_peaks.xls INFO @ Sat, 08 Sep 2018 13:48:39: #4 Write peak in narrowPeak format file... SRX3511943.05_peaks.narrowPeak INFO @ Sat, 08 Sep 2018 13:48:39: #4 Write summits bed file... SRX3511943.05_summits.bed INFO @ Sat, 08 Sep 2018 13:48:39: #4 Write output xls file... SRX3511943.10_peaks.xls INFO @ Sat, 08 Sep 2018 13:48:39: #4 Write peak in narrowPeak format file... SRX3511943.10_peaks.narrowPeak INFO @ Sat, 08 Sep 2018 13:48:39: Done! INFO @ Sat, 08 Sep 2018 13:48:39: #4 Write summits bed file... SRX3511943.10_summits.bed INFO @ Sat, 08 Sep 2018 13:48:39: Done! pass1 - making usageList (8 chroms): 1 millis pass1 - making usageList (13 chroms): 1 millis pass2 - checking and writing primary data (409 records, 4 fields): 2 millis pass2 - checking and writing primary data (663 records, 4 fields): 3 millis CompletedMACS2peakCalling CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。