Job ID = 11598008 sra ファイルのダウンロード中... Completed: 479275K bytes transferred in 9 seconds (399576K 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 20110391 spots for /home/okishinya/chipatlas/results/dm3/SRX4664663/SRR7813090.sra Written 20110391 spots for /home/okishinya/chipatlas/results/dm3/SRX4664663/SRR7813090.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: 00:08:20 20110391 reads; of these: 20110391 (100.00%) were unpaired; of these: 692471 (3.44%) aligned 0 times 13200723 (65.64%) aligned exactly 1 time 6217197 (30.92%) aligned >1 times 96.56% overall alignment rate Time searching: 00:08:21 Overall time: 00:08:21 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] 2819312 / 19417920 = 0.1452 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 @ Wed, 30 Jan 2019 17:01:17: # Command line: callpeak -t SRX4664663.bam -f BAM -g dm -n SRX4664663.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX4664663.05 # format = BAM # ChIP-seq file = ['SRX4664663.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 @ Wed, 30 Jan 2019 17:01:17: #1 read tag files... INFO @ Wed, 30 Jan 2019 17:01:17: #1 read treatment tags... INFO @ Wed, 30 Jan 2019 17:01:17: # Command line: callpeak -t SRX4664663.bam -f BAM -g dm -n SRX4664663.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX4664663.20 # format = BAM # ChIP-seq file = ['SRX4664663.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 @ Wed, 30 Jan 2019 17:01:17: #1 read tag files... INFO @ Wed, 30 Jan 2019 17:01:17: #1 read treatment tags... INFO @ Wed, 30 Jan 2019 17:01:17: # Command line: callpeak -t SRX4664663.bam -f BAM -g dm -n SRX4664663.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX4664663.10 # format = BAM # ChIP-seq file = ['SRX4664663.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 @ Wed, 30 Jan 2019 17:01:17: #1 read tag files... INFO @ Wed, 30 Jan 2019 17:01:17: #1 read treatment tags... INFO @ Wed, 30 Jan 2019 17:01:23: 1000000 INFO @ Wed, 30 Jan 2019 17:01:23: 1000000 INFO @ Wed, 30 Jan 2019 17:01:23: 1000000 INFO @ Wed, 30 Jan 2019 17:01:29: 2000000 INFO @ Wed, 30 Jan 2019 17:01:29: 2000000 INFO @ Wed, 30 Jan 2019 17:01:29: 2000000 INFO @ Wed, 30 Jan 2019 17:01:35: 3000000 INFO @ Wed, 30 Jan 2019 17:01:35: 3000000 INFO @ Wed, 30 Jan 2019 17:01:36: 3000000 INFO @ Wed, 30 Jan 2019 17:01:41: 4000000 INFO @ Wed, 30 Jan 2019 17:01:41: 4000000 INFO @ Wed, 30 Jan 2019 17:01:42: 4000000 INFO @ Wed, 30 Jan 2019 17:01:47: 5000000 INFO @ Wed, 30 Jan 2019 17:01:48: 5000000 INFO @ Wed, 30 Jan 2019 17:01:48: 5000000 INFO @ Wed, 30 Jan 2019 17:01:54: 6000000 INFO @ Wed, 30 Jan 2019 17:01:54: 6000000 INFO @ Wed, 30 Jan 2019 17:01:55: 6000000 INFO @ Wed, 30 Jan 2019 17:02:00: 7000000 INFO @ Wed, 30 Jan 2019 17:02:01: 7000000 INFO @ Wed, 30 Jan 2019 17:02:02: 7000000 INFO @ Wed, 30 Jan 2019 17:02:06: 8000000 INFO @ Wed, 30 Jan 2019 17:02:07: 8000000 INFO @ Wed, 30 Jan 2019 17:02:08: 8000000 INFO @ Wed, 30 Jan 2019 17:02:12: 9000000 INFO @ Wed, 30 Jan 2019 17:02:13: 9000000 INFO @ Wed, 30 Jan 2019 17:02:15: 9000000 INFO @ Wed, 30 Jan 2019 17:02:19: 10000000 INFO @ Wed, 30 Jan 2019 17:02:19: 10000000 INFO @ Wed, 30 Jan 2019 17:02:21: 10000000 INFO @ Wed, 30 Jan 2019 17:02:25: 11000000 INFO @ Wed, 30 Jan 2019 17:02:25: 11000000 INFO @ Wed, 30 Jan 2019 17:02:27: 11000000 INFO @ Wed, 30 Jan 2019 17:02:31: 12000000 INFO @ Wed, 30 Jan 2019 17:02:31: 12000000 INFO @ Wed, 30 Jan 2019 17:02:34: 12000000 INFO @ Wed, 30 Jan 2019 17:02:37: 13000000 INFO @ Wed, 30 Jan 2019 17:02:38: 13000000 INFO @ Wed, 30 Jan 2019 17:02:40: 13000000 INFO @ Wed, 30 Jan 2019 17:02:44: 14000000 INFO @ Wed, 30 Jan 2019 17:02:44: 14000000 INFO @ Wed, 30 Jan 2019 17:02:47: 14000000 INFO @ Wed, 30 Jan 2019 17:02:50: 15000000 INFO @ Wed, 30 Jan 2019 17:02:50: 15000000 INFO @ Wed, 30 Jan 2019 17:02:53: 15000000 INFO @ Wed, 30 Jan 2019 17:02:56: 16000000 INFO @ Wed, 30 Jan 2019 17:02:56: 16000000 INFO @ Wed, 30 Jan 2019 17:03:00: #1 tag size is determined as 50 bps INFO @ Wed, 30 Jan 2019 17:03:00: #1 tag size = 50 INFO @ Wed, 30 Jan 2019 17:03:00: #1 total tags in treatment: 16598608 INFO @ Wed, 30 Jan 2019 17:03:00: #1 user defined the maximum tags... INFO @ Wed, 30 Jan 2019 17:03:00: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Wed, 30 Jan 2019 17:03:00: 16000000 INFO @ Wed, 30 Jan 2019 17:03:00: #1 tag size is determined as 50 bps INFO @ Wed, 30 Jan 2019 17:03:00: #1 tag size = 50 INFO @ Wed, 30 Jan 2019 17:03:00: #1 total tags in treatment: 16598608 INFO @ Wed, 30 Jan 2019 17:03:00: #1 user defined the maximum tags... INFO @ Wed, 30 Jan 2019 17:03:00: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Wed, 30 Jan 2019 17:03:00: #1 tags after filtering in treatment: 16598608 INFO @ Wed, 30 Jan 2019 17:03:00: #1 Redundant rate of treatment: 0.00 INFO @ Wed, 30 Jan 2019 17:03:00: #1 finished! INFO @ Wed, 30 Jan 2019 17:03:00: #2 Build Peak Model... INFO @ Wed, 30 Jan 2019 17:03:00: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 30 Jan 2019 17:03:00: #1 tags after filtering in treatment: 16598608 INFO @ Wed, 30 Jan 2019 17:03:00: #1 Redundant rate of treatment: 0.00 INFO @ Wed, 30 Jan 2019 17:03:00: #1 finished! INFO @ Wed, 30 Jan 2019 17:03:00: #2 Build Peak Model... INFO @ Wed, 30 Jan 2019 17:03:00: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 30 Jan 2019 17:03:01: #2 number of paired peaks: 1075 INFO @ Wed, 30 Jan 2019 17:03:01: start model_add_line... INFO @ Wed, 30 Jan 2019 17:03:01: start X-correlation... INFO @ Wed, 30 Jan 2019 17:03:02: end of X-cor INFO @ Wed, 30 Jan 2019 17:03:02: #2 finished! INFO @ Wed, 30 Jan 2019 17:03:02: #2 predicted fragment length is 71 bps INFO @ Wed, 30 Jan 2019 17:03:02: #2 alternative fragment length(s) may be 71 bps INFO @ Wed, 30 Jan 2019 17:03:02: #2.2 Generate R script for model : SRX4664663.10_model.r WARNING @ Wed, 30 Jan 2019 17:03:02: #2 Since the d (71) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Wed, 30 Jan 2019 17:03:02: #2 You may need to consider one of the other alternative d(s): 71 WARNING @ Wed, 30 Jan 2019 17:03:02: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Wed, 30 Jan 2019 17:03:02: #3 Call peaks... INFO @ Wed, 30 Jan 2019 17:03:02: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 30 Jan 2019 17:03:02: #2 number of paired peaks: 1075 INFO @ Wed, 30 Jan 2019 17:03:02: start model_add_line... INFO @ Wed, 30 Jan 2019 17:03:02: start X-correlation... INFO @ Wed, 30 Jan 2019 17:03:02: end of X-cor INFO @ Wed, 30 Jan 2019 17:03:02: #2 finished! INFO @ Wed, 30 Jan 2019 17:03:02: #2 predicted fragment length is 71 bps INFO @ Wed, 30 Jan 2019 17:03:02: #2 alternative fragment length(s) may be 71 bps INFO @ Wed, 30 Jan 2019 17:03:02: #2.2 Generate R script for model : SRX4664663.20_model.r WARNING @ Wed, 30 Jan 2019 17:03:02: #2 Since the d (71) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Wed, 30 Jan 2019 17:03:02: #2 You may need to consider one of the other alternative d(s): 71 WARNING @ Wed, 30 Jan 2019 17:03:02: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Wed, 30 Jan 2019 17:03:02: #3 Call peaks... INFO @ Wed, 30 Jan 2019 17:03:02: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 30 Jan 2019 17:03:04: #1 tag size is determined as 50 bps INFO @ Wed, 30 Jan 2019 17:03:04: #1 tag size = 50 INFO @ Wed, 30 Jan 2019 17:03:04: #1 total tags in treatment: 16598608 INFO @ Wed, 30 Jan 2019 17:03:04: #1 user defined the maximum tags... INFO @ Wed, 30 Jan 2019 17:03:04: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Wed, 30 Jan 2019 17:03:04: #1 tags after filtering in treatment: 16598608 INFO @ Wed, 30 Jan 2019 17:03:04: #1 Redundant rate of treatment: 0.00 INFO @ Wed, 30 Jan 2019 17:03:04: #1 finished! INFO @ Wed, 30 Jan 2019 17:03:04: #2 Build Peak Model... INFO @ Wed, 30 Jan 2019 17:03:04: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 30 Jan 2019 17:03:05: #2 number of paired peaks: 1075 INFO @ Wed, 30 Jan 2019 17:03:05: start model_add_line... INFO @ Wed, 30 Jan 2019 17:03:06: start X-correlation... INFO @ Wed, 30 Jan 2019 17:03:06: end of X-cor INFO @ Wed, 30 Jan 2019 17:03:06: #2 finished! INFO @ Wed, 30 Jan 2019 17:03:06: #2 predicted fragment length is 71 bps INFO @ Wed, 30 Jan 2019 17:03:06: #2 alternative fragment length(s) may be 71 bps INFO @ Wed, 30 Jan 2019 17:03:06: #2.2 Generate R script for model : SRX4664663.05_model.r WARNING @ Wed, 30 Jan 2019 17:03:06: #2 Since the d (71) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Wed, 30 Jan 2019 17:03:06: #2 You may need to consider one of the other alternative d(s): 71 WARNING @ Wed, 30 Jan 2019 17:03:06: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Wed, 30 Jan 2019 17:03:06: #3 Call peaks... INFO @ Wed, 30 Jan 2019 17:03:06: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 30 Jan 2019 17:03:36: #3 Call peaks for each chromosome... INFO @ Wed, 30 Jan 2019 17:03:37: #3 Call peaks for each chromosome... INFO @ Wed, 30 Jan 2019 17:03:39: #3 Call peaks for each chromosome... INFO @ Wed, 30 Jan 2019 17:03:55: #4 Write output xls file... SRX4664663.20_peaks.xls INFO @ Wed, 30 Jan 2019 17:03:55: #4 Write peak in narrowPeak format file... SRX4664663.20_peaks.narrowPeak INFO @ Wed, 30 Jan 2019 17:03:55: #4 Write summits bed file... SRX4664663.20_summits.bed INFO @ Wed, 30 Jan 2019 17:03:55: Done! pass1 - making usageList (13 chroms): 1 millis pass2 - checking and writing primary data (2070 records, 4 fields): 4 millis CompletedMACS2peakCalling INFO @ Wed, 30 Jan 2019 17:03:56: #4 Write output xls file... SRX4664663.10_peaks.xls INFO @ Wed, 30 Jan 2019 17:03:56: #4 Write peak in narrowPeak format file... SRX4664663.10_peaks.narrowPeak INFO @ Wed, 30 Jan 2019 17:03:56: #4 Write summits bed file... SRX4664663.10_summits.bed INFO @ Wed, 30 Jan 2019 17:03:56: Done! pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (3606 records, 4 fields): 6 millis CompletedMACS2peakCalling INFO @ Wed, 30 Jan 2019 17:04:00: #4 Write output xls file... SRX4664663.05_peaks.xls INFO @ Wed, 30 Jan 2019 17:04:01: #4 Write peak in narrowPeak format file... SRX4664663.05_peaks.narrowPeak INFO @ Wed, 30 Jan 2019 17:04:01: #4 Write summits bed file... SRX4664663.05_summits.bed INFO @ Wed, 30 Jan 2019 17:04:01: Done! pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (5460 records, 4 fields): 7 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。