Job ID = 11240713 sra ファイルのダウンロード中... Completed: 526074K bytes transferred in 8 seconds (479840K 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 25364669 spots for /home/okishinya/chipatlas/results/dm3/SRX3630322/SRR6652844.sra Written 25364669 spots for /home/okishinya/chipatlas/results/dm3/SRX3630322/SRR6652844.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: 00:16:23 25364669 reads; of these: 25364669 (100.00%) were unpaired; of these: 2815491 (11.10%) aligned 0 times 6459031 (25.46%) aligned exactly 1 time 16090147 (63.44%) aligned >1 times 88.90% overall alignment rate Time searching: 00:16:23 Overall time: 00:16:24 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 12 files... [bam_rmdupse_core] 6892377 / 22549178 = 0.3057 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, 07 Oct 2018 20:51:43: # Command line: callpeak -t SRX3630322.bam -f BAM -g dm -n SRX3630322.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX3630322.05 # format = BAM # ChIP-seq file = ['SRX3630322.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 @ Sun, 07 Oct 2018 20:51:43: # Command line: callpeak -t SRX3630322.bam -f BAM -g dm -n SRX3630322.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX3630322.20 # format = BAM # ChIP-seq file = ['SRX3630322.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 @ Sun, 07 Oct 2018 20:51:43: # Command line: callpeak -t SRX3630322.bam -f BAM -g dm -n SRX3630322.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX3630322.10 # format = BAM # ChIP-seq file = ['SRX3630322.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 @ Sun, 07 Oct 2018 20:51:43: #1 read tag files... INFO @ Sun, 07 Oct 2018 20:51:43: #1 read tag files... INFO @ Sun, 07 Oct 2018 20:51:43: #1 read tag files... INFO @ Sun, 07 Oct 2018 20:51:43: #1 read treatment tags... INFO @ Sun, 07 Oct 2018 20:51:43: #1 read treatment tags... INFO @ Sun, 07 Oct 2018 20:51:43: #1 read treatment tags... INFO @ Sun, 07 Oct 2018 20:51:51: 1000000 INFO @ Sun, 07 Oct 2018 20:51:51: 1000000 INFO @ Sun, 07 Oct 2018 20:51:52: 1000000 INFO @ Sun, 07 Oct 2018 20:51:59: 2000000 INFO @ Sun, 07 Oct 2018 20:51:59: 2000000 INFO @ Sun, 07 Oct 2018 20:52:00: 2000000 INFO @ Sun, 07 Oct 2018 20:52:07: 3000000 INFO @ Sun, 07 Oct 2018 20:52:07: 3000000 INFO @ Sun, 07 Oct 2018 20:52:09: 3000000 INFO @ Sun, 07 Oct 2018 20:52:15: 4000000 INFO @ Sun, 07 Oct 2018 20:52:15: 4000000 INFO @ Sun, 07 Oct 2018 20:52:18: 4000000 INFO @ Sun, 07 Oct 2018 20:52:23: 5000000 INFO @ Sun, 07 Oct 2018 20:52:23: 5000000 INFO @ Sun, 07 Oct 2018 20:52:27: 5000000 INFO @ Sun, 07 Oct 2018 20:52:31: 6000000 INFO @ Sun, 07 Oct 2018 20:52:31: 6000000 INFO @ Sun, 07 Oct 2018 20:52:36: 6000000 INFO @ Sun, 07 Oct 2018 20:52:40: 7000000 INFO @ Sun, 07 Oct 2018 20:52:40: 7000000 INFO @ Sun, 07 Oct 2018 20:52:46: 7000000 INFO @ Sun, 07 Oct 2018 20:52:48: 8000000 INFO @ Sun, 07 Oct 2018 20:52:48: 8000000 INFO @ Sun, 07 Oct 2018 20:52:55: 8000000 INFO @ Sun, 07 Oct 2018 20:52:56: 9000000 INFO @ Sun, 07 Oct 2018 20:52:56: 9000000 INFO @ Sun, 07 Oct 2018 20:53:04: 9000000 INFO @ Sun, 07 Oct 2018 20:53:04: 10000000 INFO @ Sun, 07 Oct 2018 20:53:04: 10000000 INFO @ Sun, 07 Oct 2018 20:53:12: 11000000 INFO @ Sun, 07 Oct 2018 20:53:12: 11000000 INFO @ Sun, 07 Oct 2018 20:53:13: 10000000 INFO @ Sun, 07 Oct 2018 20:53:20: 12000000 INFO @ Sun, 07 Oct 2018 20:53:20: 12000000 INFO @ Sun, 07 Oct 2018 20:53:22: 11000000 INFO @ Sun, 07 Oct 2018 20:53:28: 13000000 INFO @ Sun, 07 Oct 2018 20:53:28: 13000000 INFO @ Sun, 07 Oct 2018 20:53:30: 12000000 INFO @ Sun, 07 Oct 2018 20:53:36: 14000000 INFO @ Sun, 07 Oct 2018 20:53:36: 14000000 INFO @ Sun, 07 Oct 2018 20:53:39: 13000000 INFO @ Sun, 07 Oct 2018 20:53:44: 15000000 INFO @ Sun, 07 Oct 2018 20:53:44: 15000000 INFO @ Sun, 07 Oct 2018 20:53:48: 14000000 INFO @ Sun, 07 Oct 2018 20:53:49: #1 tag size is determined as 51 bps INFO @ Sun, 07 Oct 2018 20:53:49: #1 tag size = 51 INFO @ Sun, 07 Oct 2018 20:53:49: #1 total tags in treatment: 15656801 INFO @ Sun, 07 Oct 2018 20:53:49: #1 user defined the maximum tags... INFO @ Sun, 07 Oct 2018 20:53:49: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sun, 07 Oct 2018 20:53:49: #1 tag size is determined as 51 bps INFO @ Sun, 07 Oct 2018 20:53:49: #1 tag size = 51 INFO @ Sun, 07 Oct 2018 20:53:49: #1 total tags in treatment: 15656801 INFO @ Sun, 07 Oct 2018 20:53:49: #1 user defined the maximum tags... INFO @ Sun, 07 Oct 2018 20:53:49: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sun, 07 Oct 2018 20:53:50: #1 tags after filtering in treatment: 15656801 INFO @ Sun, 07 Oct 2018 20:53:50: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 07 Oct 2018 20:53:50: #1 finished! INFO @ Sun, 07 Oct 2018 20:53:50: #2 Build Peak Model... INFO @ Sun, 07 Oct 2018 20:53:50: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 07 Oct 2018 20:53:50: #1 tags after filtering in treatment: 15656801 INFO @ Sun, 07 Oct 2018 20:53:50: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 07 Oct 2018 20:53:50: #1 finished! INFO @ Sun, 07 Oct 2018 20:53:50: #2 Build Peak Model... INFO @ Sun, 07 Oct 2018 20:53:50: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 07 Oct 2018 20:53:51: #2 number of paired peaks: 1975 INFO @ Sun, 07 Oct 2018 20:53:51: start model_add_line... INFO @ Sun, 07 Oct 2018 20:53:51: #2 number of paired peaks: 1975 INFO @ Sun, 07 Oct 2018 20:53:51: start model_add_line... INFO @ Sun, 07 Oct 2018 20:53:51: start X-correlation... INFO @ Sun, 07 Oct 2018 20:53:51: start X-correlation... INFO @ Sun, 07 Oct 2018 20:53:52: end of X-cor INFO @ Sun, 07 Oct 2018 20:53:52: #2 finished! INFO @ Sun, 07 Oct 2018 20:53:52: end of X-cor INFO @ Sun, 07 Oct 2018 20:53:52: #2 predicted fragment length is 55 bps INFO @ Sun, 07 Oct 2018 20:53:52: #2 finished! INFO @ Sun, 07 Oct 2018 20:53:52: #2 alternative fragment length(s) may be 4,55 bps INFO @ Sun, 07 Oct 2018 20:53:52: #2 predicted fragment length is 55 bps INFO @ Sun, 07 Oct 2018 20:53:52: #2.2 Generate R script for model : SRX3630322.20_model.r INFO @ Sun, 07 Oct 2018 20:53:52: #2 alternative fragment length(s) may be 4,55 bps INFO @ Sun, 07 Oct 2018 20:53:52: #2.2 Generate R script for model : SRX3630322.05_model.r WARNING @ Sun, 07 Oct 2018 20:53:52: #2 Since the d (55) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 07 Oct 2018 20:53:52: #2 You may need to consider one of the other alternative d(s): 4,55 WARNING @ Sun, 07 Oct 2018 20:53:52: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sun, 07 Oct 2018 20:53:52: #3 Call peaks... WARNING @ Sun, 07 Oct 2018 20:53:52: #2 Since the d (55) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 07 Oct 2018 20:53:52: #2 You may need to consider one of the other alternative d(s): 4,55 WARNING @ Sun, 07 Oct 2018 20:53:52: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sun, 07 Oct 2018 20:53:52: #3 Call peaks... INFO @ Sun, 07 Oct 2018 20:53:52: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 07 Oct 2018 20:53:52: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 07 Oct 2018 20:53:55: 15000000 INFO @ Sun, 07 Oct 2018 20:54:00: #1 tag size is determined as 51 bps INFO @ Sun, 07 Oct 2018 20:54:00: #1 tag size = 51 INFO @ Sun, 07 Oct 2018 20:54:00: #1 total tags in treatment: 15656801 INFO @ Sun, 07 Oct 2018 20:54:00: #1 user defined the maximum tags... INFO @ Sun, 07 Oct 2018 20:54:00: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sun, 07 Oct 2018 20:54:00: #1 tags after filtering in treatment: 15656801 INFO @ Sun, 07 Oct 2018 20:54:00: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 07 Oct 2018 20:54:00: #1 finished! INFO @ Sun, 07 Oct 2018 20:54:00: #2 Build Peak Model... INFO @ Sun, 07 Oct 2018 20:54:00: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 07 Oct 2018 20:54:02: #2 number of paired peaks: 1975 INFO @ Sun, 07 Oct 2018 20:54:02: start model_add_line... INFO @ Sun, 07 Oct 2018 20:54:02: start X-correlation... INFO @ Sun, 07 Oct 2018 20:54:02: end of X-cor INFO @ Sun, 07 Oct 2018 20:54:02: #2 finished! INFO @ Sun, 07 Oct 2018 20:54:02: #2 predicted fragment length is 55 bps INFO @ Sun, 07 Oct 2018 20:54:02: #2 alternative fragment length(s) may be 4,55 bps INFO @ Sun, 07 Oct 2018 20:54:02: #2.2 Generate R script for model : SRX3630322.10_model.r WARNING @ Sun, 07 Oct 2018 20:54:02: #2 Since the d (55) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 07 Oct 2018 20:54:02: #2 You may need to consider one of the other alternative d(s): 4,55 WARNING @ Sun, 07 Oct 2018 20:54:02: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sun, 07 Oct 2018 20:54:02: #3 Call peaks... INFO @ Sun, 07 Oct 2018 20:54:02: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 07 Oct 2018 20:54:27: #3 Call peaks for each chromosome... INFO @ Sun, 07 Oct 2018 20:54:28: #3 Call peaks for each chromosome... INFO @ Sun, 07 Oct 2018 20:54:36: #3 Call peaks for each chromosome... INFO @ Sun, 07 Oct 2018 20:54:46: #4 Write output xls file... SRX3630322.20_peaks.xls INFO @ Sun, 07 Oct 2018 20:54:46: #4 Write peak in narrowPeak format file... SRX3630322.20_peaks.narrowPeak INFO @ Sun, 07 Oct 2018 20:54:46: #4 Write summits bed file... SRX3630322.20_summits.bed INFO @ Sun, 07 Oct 2018 20:54:46: Done! pass1 - making usageList (13 chroms): 1 millis pass2 - checking and writing primary data (1643 records, 4 fields): 5 millis CompletedMACS2peakCalling INFO @ Sun, 07 Oct 2018 20:54:48: #4 Write output xls file... SRX3630322.05_peaks.xls INFO @ Sun, 07 Oct 2018 20:54:48: #4 Write peak in narrowPeak format file... SRX3630322.05_peaks.narrowPeak INFO @ Sun, 07 Oct 2018 20:54:48: #4 Write summits bed file... SRX3630322.05_summits.bed INFO @ Sun, 07 Oct 2018 20:54:48: Done! pass1 - making usageList (14 chroms): 3 millis pass2 - checking and writing primary data (14503 records, 4 fields): 17 millis CompletedMACS2peakCalling INFO @ Sun, 07 Oct 2018 20:54:54: #4 Write output xls file... SRX3630322.10_peaks.xls INFO @ Sun, 07 Oct 2018 20:54:54: #4 Write peak in narrowPeak format file... SRX3630322.10_peaks.narrowPeak INFO @ Sun, 07 Oct 2018 20:54:54: #4 Write summits bed file... SRX3630322.10_summits.bed INFO @ Sun, 07 Oct 2018 20:54:54: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (5043 records, 4 fields): 9 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。