Job ID = 11598006 sra ファイルのダウンロード中... Completed: 509234K bytes transferred in 9 seconds (431003K 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 21228103 spots for /home/okishinya/chipatlas/results/dm3/SRX4664661/SRR7813088.sra Written 21228103 spots for /home/okishinya/chipatlas/results/dm3/SRX4664661/SRR7813088.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: 00:09:16 21228103 reads; of these: 21228103 (100.00%) were unpaired; of these: 585183 (2.76%) aligned 0 times 13593103 (64.03%) aligned exactly 1 time 7049817 (33.21%) aligned >1 times 97.24% overall alignment rate Time searching: 00:09:16 Overall time: 00:09:16 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] 2848034 / 20642920 = 0.1380 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 17:02:33: # Command line: callpeak -t SRX4664661.bam -f BAM -g dm -n SRX4664661.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX4664661.20 # format = BAM # ChIP-seq file = ['SRX4664661.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 17:02:33: #1 read tag files... INFO @ Wed, 30 Jan 2019 17:02:33: #1 read treatment tags... INFO @ Wed, 30 Jan 2019 17:02:33: # Command line: callpeak -t SRX4664661.bam -f BAM -g dm -n SRX4664661.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX4664661.05 # format = BAM # ChIP-seq file = ['SRX4664661.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 17:02:33: #1 read tag files... INFO @ Wed, 30 Jan 2019 17:02:33: #1 read treatment tags... INFO @ Wed, 30 Jan 2019 17:02:33: # Command line: callpeak -t SRX4664661.bam -f BAM -g dm -n SRX4664661.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX4664661.10 # format = BAM # ChIP-seq file = ['SRX4664661.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 17:02:33: #1 read tag files... INFO @ Wed, 30 Jan 2019 17:02:33: #1 read treatment tags... INFO @ Wed, 30 Jan 2019 17:02:39: 1000000 INFO @ Wed, 30 Jan 2019 17:02:39: 1000000 INFO @ Wed, 30 Jan 2019 17:02:39: 1000000 INFO @ Wed, 30 Jan 2019 17:02:46: 2000000 INFO @ Wed, 30 Jan 2019 17:02:46: 2000000 INFO @ Wed, 30 Jan 2019 17:02:46: 2000000 INFO @ Wed, 30 Jan 2019 17:02:52: 3000000 INFO @ Wed, 30 Jan 2019 17:02:52: 3000000 INFO @ Wed, 30 Jan 2019 17:02:52: 3000000 INFO @ Wed, 30 Jan 2019 17:02:58: 4000000 INFO @ Wed, 30 Jan 2019 17:02:58: 4000000 INFO @ Wed, 30 Jan 2019 17:02:58: 4000000 INFO @ Wed, 30 Jan 2019 17:03:04: 5000000 INFO @ Wed, 30 Jan 2019 17:03:04: 5000000 INFO @ Wed, 30 Jan 2019 17:03:05: 5000000 INFO @ Wed, 30 Jan 2019 17:03:10: 6000000 INFO @ Wed, 30 Jan 2019 17:03:10: 6000000 INFO @ Wed, 30 Jan 2019 17:03:11: 6000000 INFO @ Wed, 30 Jan 2019 17:03:16: 7000000 INFO @ Wed, 30 Jan 2019 17:03:17: 7000000 INFO @ Wed, 30 Jan 2019 17:03:17: 7000000 INFO @ Wed, 30 Jan 2019 17:03:22: 8000000 INFO @ Wed, 30 Jan 2019 17:03:23: 8000000 INFO @ Wed, 30 Jan 2019 17:03:24: 8000000 INFO @ Wed, 30 Jan 2019 17:03:28: 9000000 INFO @ Wed, 30 Jan 2019 17:03:29: 9000000 INFO @ Wed, 30 Jan 2019 17:03:30: 9000000 INFO @ Wed, 30 Jan 2019 17:03:35: 10000000 INFO @ Wed, 30 Jan 2019 17:03:36: 10000000 INFO @ Wed, 30 Jan 2019 17:03:36: 10000000 INFO @ Wed, 30 Jan 2019 17:03:41: 11000000 INFO @ Wed, 30 Jan 2019 17:03:42: 11000000 INFO @ Wed, 30 Jan 2019 17:03:43: 11000000 INFO @ Wed, 30 Jan 2019 17:03:47: 12000000 INFO @ Wed, 30 Jan 2019 17:03:48: 12000000 INFO @ Wed, 30 Jan 2019 17:03:49: 12000000 INFO @ Wed, 30 Jan 2019 17:03:53: 13000000 INFO @ Wed, 30 Jan 2019 17:03:55: 13000000 INFO @ Wed, 30 Jan 2019 17:03:55: 13000000 INFO @ Wed, 30 Jan 2019 17:03:59: 14000000 INFO @ Wed, 30 Jan 2019 17:04:01: 14000000 INFO @ Wed, 30 Jan 2019 17:04:01: 14000000 INFO @ Wed, 30 Jan 2019 17:04:06: 15000000 INFO @ Wed, 30 Jan 2019 17:04:07: 15000000 INFO @ Wed, 30 Jan 2019 17:04:08: 15000000 INFO @ Wed, 30 Jan 2019 17:04:12: 16000000 INFO @ Wed, 30 Jan 2019 17:04:14: 16000000 INFO @ Wed, 30 Jan 2019 17:04:14: 16000000 INFO @ Wed, 30 Jan 2019 17:04:18: 17000000 INFO @ Wed, 30 Jan 2019 17:04:20: 17000000 INFO @ Wed, 30 Jan 2019 17:04:21: 17000000 INFO @ Wed, 30 Jan 2019 17:04:23: #1 tag size is determined as 50 bps INFO @ Wed, 30 Jan 2019 17:04:23: #1 tag size = 50 INFO @ Wed, 30 Jan 2019 17:04:23: #1 total tags in treatment: 17794886 INFO @ Wed, 30 Jan 2019 17:04:23: #1 user defined the maximum tags... INFO @ Wed, 30 Jan 2019 17:04:23: #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 17:04:23: #1 tags after filtering in treatment: 17794886 INFO @ Wed, 30 Jan 2019 17:04:23: #1 Redundant rate of treatment: 0.00 INFO @ Wed, 30 Jan 2019 17:04:23: #1 finished! INFO @ Wed, 30 Jan 2019 17:04:23: #2 Build Peak Model... INFO @ Wed, 30 Jan 2019 17:04:23: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 30 Jan 2019 17:04:25: #2 number of paired peaks: 1025 INFO @ Wed, 30 Jan 2019 17:04:25: start model_add_line... INFO @ Wed, 30 Jan 2019 17:04:25: start X-correlation... INFO @ Wed, 30 Jan 2019 17:04:25: end of X-cor INFO @ Wed, 30 Jan 2019 17:04:25: #2 finished! INFO @ Wed, 30 Jan 2019 17:04:25: #2 predicted fragment length is 62 bps INFO @ Wed, 30 Jan 2019 17:04:25: #2 alternative fragment length(s) may be 3,62 bps INFO @ Wed, 30 Jan 2019 17:04:25: #2.2 Generate R script for model : SRX4664661.20_model.r WARNING @ Wed, 30 Jan 2019 17:04:25: #2 Since the d (62) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Wed, 30 Jan 2019 17:04:25: #2 You may need to consider one of the other alternative d(s): 3,62 WARNING @ Wed, 30 Jan 2019 17:04:25: #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 17:04:25: #3 Call peaks... INFO @ Wed, 30 Jan 2019 17:04:25: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 30 Jan 2019 17:04:25: #1 tag size is determined as 50 bps INFO @ Wed, 30 Jan 2019 17:04:25: #1 tag size = 50 INFO @ Wed, 30 Jan 2019 17:04:25: #1 total tags in treatment: 17794886 INFO @ Wed, 30 Jan 2019 17:04:25: #1 user defined the maximum tags... INFO @ Wed, 30 Jan 2019 17:04:25: #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 17:04:25: #1 tags after filtering in treatment: 17794886 INFO @ Wed, 30 Jan 2019 17:04:25: #1 Redundant rate of treatment: 0.00 INFO @ Wed, 30 Jan 2019 17:04:25: #1 finished! INFO @ Wed, 30 Jan 2019 17:04:25: #2 Build Peak Model... INFO @ Wed, 30 Jan 2019 17:04:25: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 30 Jan 2019 17:04:26: #1 tag size is determined as 50 bps INFO @ Wed, 30 Jan 2019 17:04:26: #1 tag size = 50 INFO @ Wed, 30 Jan 2019 17:04:26: #1 total tags in treatment: 17794886 INFO @ Wed, 30 Jan 2019 17:04:26: #1 user defined the maximum tags... INFO @ Wed, 30 Jan 2019 17:04:26: #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 17:04:26: #1 tags after filtering in treatment: 17794886 INFO @ Wed, 30 Jan 2019 17:04:26: #1 Redundant rate of treatment: 0.00 INFO @ Wed, 30 Jan 2019 17:04:26: #1 finished! INFO @ Wed, 30 Jan 2019 17:04:26: #2 Build Peak Model... INFO @ Wed, 30 Jan 2019 17:04:26: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 30 Jan 2019 17:04:27: #2 number of paired peaks: 1025 INFO @ Wed, 30 Jan 2019 17:04:27: start model_add_line... INFO @ Wed, 30 Jan 2019 17:04:27: start X-correlation... INFO @ Wed, 30 Jan 2019 17:04:27: end of X-cor INFO @ Wed, 30 Jan 2019 17:04:27: #2 finished! INFO @ Wed, 30 Jan 2019 17:04:27: #2 predicted fragment length is 62 bps INFO @ Wed, 30 Jan 2019 17:04:27: #2 alternative fragment length(s) may be 3,62 bps INFO @ Wed, 30 Jan 2019 17:04:27: #2.2 Generate R script for model : SRX4664661.05_model.r WARNING @ Wed, 30 Jan 2019 17:04:27: #2 Since the d (62) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Wed, 30 Jan 2019 17:04:27: #2 You may need to consider one of the other alternative d(s): 3,62 WARNING @ Wed, 30 Jan 2019 17:04:27: #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 17:04:27: #3 Call peaks... INFO @ Wed, 30 Jan 2019 17:04:27: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 30 Jan 2019 17:04:28: #2 number of paired peaks: 1025 INFO @ Wed, 30 Jan 2019 17:04:28: start model_add_line... INFO @ Wed, 30 Jan 2019 17:04:28: start X-correlation... INFO @ Wed, 30 Jan 2019 17:04:28: end of X-cor INFO @ Wed, 30 Jan 2019 17:04:28: #2 finished! INFO @ Wed, 30 Jan 2019 17:04:28: #2 predicted fragment length is 62 bps INFO @ Wed, 30 Jan 2019 17:04:28: #2 alternative fragment length(s) may be 3,62 bps INFO @ Wed, 30 Jan 2019 17:04:28: #2.2 Generate R script for model : SRX4664661.10_model.r WARNING @ Wed, 30 Jan 2019 17:04:28: #2 Since the d (62) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Wed, 30 Jan 2019 17:04:28: #2 You may need to consider one of the other alternative d(s): 3,62 WARNING @ Wed, 30 Jan 2019 17:04:28: #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 17:04:28: #3 Call peaks... INFO @ Wed, 30 Jan 2019 17:04:28: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 30 Jan 2019 17:05:03: #3 Call peaks for each chromosome... INFO @ Wed, 30 Jan 2019 17:05:04: #3 Call peaks for each chromosome... INFO @ Wed, 30 Jan 2019 17:05:06: #3 Call peaks for each chromosome... INFO @ Wed, 30 Jan 2019 17:05:25: #4 Write output xls file... SRX4664661.05_peaks.xls INFO @ Wed, 30 Jan 2019 17:05:25: #4 Write peak in narrowPeak format file... SRX4664661.05_peaks.narrowPeak INFO @ Wed, 30 Jan 2019 17:05:25: #4 Write summits bed file... SRX4664661.05_summits.bed INFO @ Wed, 30 Jan 2019 17:05:25: Done! pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (4892 records, 4 fields): 7 millis CompletedMACS2peakCalling INFO @ Wed, 30 Jan 2019 17:05:26: #4 Write output xls file... SRX4664661.20_peaks.xls INFO @ Wed, 30 Jan 2019 17:05:26: #4 Write peak in narrowPeak format file... SRX4664661.20_peaks.narrowPeak INFO @ Wed, 30 Jan 2019 17:05:26: #4 Write summits bed file... SRX4664661.20_summits.bed INFO @ Wed, 30 Jan 2019 17:05:26: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (1850 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Wed, 30 Jan 2019 17:05:27: #4 Write output xls file... SRX4664661.10_peaks.xls INFO @ Wed, 30 Jan 2019 17:05:27: #4 Write peak in narrowPeak format file... SRX4664661.10_peaks.narrowPeak INFO @ Wed, 30 Jan 2019 17:05:27: #4 Write summits bed file... SRX4664661.10_summits.bed INFO @ Wed, 30 Jan 2019 17:05:27: Done! pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (3132 records, 4 fields): 6 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。