Job ID = 10480655 sra ファイルのダウンロード中... Completed: 1731814K bytes transferred in 20 seconds (702543K 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... Written 52089097 spots for /home/okishinya/chipatlas/results/dm3/SRX2433655/SRR5118374.sra Written 52089097 spots total 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: 00:13:42 52089097 reads; of these: 52089097 (100.00%) were unpaired; of these: 35184161 (67.55%) aligned 0 times 7449411 (14.30%) aligned exactly 1 time 9455525 (18.15%) aligned >1 times 32.45% overall alignment rate Time searching: 00:13:42 Overall time: 00:13:42 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] 6056039 / 16904936 = 0.3582 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 @ Fri, 16 Mar 2018 07:39:44: # Command line: callpeak -t SRX2433655.bam -f BAM -g dm -n SRX2433655.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX2433655.20 # format = BAM # ChIP-seq file = ['SRX2433655.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 @ Fri, 16 Mar 2018 07:39:44: #1 read tag files... INFO @ Fri, 16 Mar 2018 07:39:44: #1 read treatment tags... INFO @ Fri, 16 Mar 2018 07:39:44: # Command line: callpeak -t SRX2433655.bam -f BAM -g dm -n SRX2433655.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX2433655.05 # format = BAM # ChIP-seq file = ['SRX2433655.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 @ Fri, 16 Mar 2018 07:39:44: #1 read tag files... INFO @ Fri, 16 Mar 2018 07:39:44: #1 read treatment tags... INFO @ Fri, 16 Mar 2018 07:39:44: # Command line: callpeak -t SRX2433655.bam -f BAM -g dm -n SRX2433655.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX2433655.10 # format = BAM # ChIP-seq file = ['SRX2433655.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 @ Fri, 16 Mar 2018 07:39:44: #1 read tag files... INFO @ Fri, 16 Mar 2018 07:39:44: #1 read treatment tags... INFO @ Fri, 16 Mar 2018 07:39:51: 1000000 INFO @ Fri, 16 Mar 2018 07:39:51: 1000000 INFO @ Fri, 16 Mar 2018 07:39:51: 1000000 INFO @ Fri, 16 Mar 2018 07:39:58: 2000000 INFO @ Fri, 16 Mar 2018 07:39:59: 2000000 INFO @ Fri, 16 Mar 2018 07:39:59: 2000000 INFO @ Fri, 16 Mar 2018 07:40:06: 3000000 INFO @ Fri, 16 Mar 2018 07:40:07: 3000000 INFO @ Fri, 16 Mar 2018 07:40:07: 3000000 INFO @ Fri, 16 Mar 2018 07:40:12: 4000000 INFO @ Fri, 16 Mar 2018 07:40:14: 4000000 INFO @ Fri, 16 Mar 2018 07:40:14: 4000000 INFO @ Fri, 16 Mar 2018 07:40:19: 5000000 INFO @ Fri, 16 Mar 2018 07:40:20: 5000000 INFO @ Fri, 16 Mar 2018 07:40:20: 5000000 INFO @ Fri, 16 Mar 2018 07:40:25: 6000000 INFO @ Fri, 16 Mar 2018 07:40:26: 6000000 INFO @ Fri, 16 Mar 2018 07:40:27: 6000000 INFO @ Fri, 16 Mar 2018 07:40:32: 7000000 INFO @ Fri, 16 Mar 2018 07:40:33: 7000000 INFO @ Fri, 16 Mar 2018 07:40:34: 7000000 INFO @ Fri, 16 Mar 2018 07:40:38: 8000000 INFO @ Fri, 16 Mar 2018 07:40:39: 8000000 INFO @ Fri, 16 Mar 2018 07:40:41: 8000000 INFO @ Fri, 16 Mar 2018 07:40:44: 9000000 INFO @ Fri, 16 Mar 2018 07:40:46: 9000000 INFO @ Fri, 16 Mar 2018 07:40:48: 9000000 INFO @ Fri, 16 Mar 2018 07:40:50: 10000000 INFO @ Fri, 16 Mar 2018 07:40:52: 10000000 INFO @ Fri, 16 Mar 2018 07:40:55: 10000000 INFO @ Fri, 16 Mar 2018 07:40:56: #1 tag size is determined as 51 bps INFO @ Fri, 16 Mar 2018 07:40:56: #1 tag size = 51 INFO @ Fri, 16 Mar 2018 07:40:56: #1 total tags in treatment: 10848897 INFO @ Fri, 16 Mar 2018 07:40:56: #1 user defined the maximum tags... INFO @ Fri, 16 Mar 2018 07:40:56: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 16 Mar 2018 07:40:56: #1 tags after filtering in treatment: 10848897 INFO @ Fri, 16 Mar 2018 07:40:56: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 16 Mar 2018 07:40:56: #1 finished! INFO @ Fri, 16 Mar 2018 07:40:56: #2 Build Peak Model... INFO @ Fri, 16 Mar 2018 07:40:56: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 16 Mar 2018 07:40:57: #2 number of paired peaks: 2526 INFO @ Fri, 16 Mar 2018 07:40:57: start model_add_line... INFO @ Fri, 16 Mar 2018 07:40:57: start X-correlation... INFO @ Fri, 16 Mar 2018 07:40:57: end of X-cor INFO @ Fri, 16 Mar 2018 07:40:57: #2 finished! INFO @ Fri, 16 Mar 2018 07:40:57: #2 predicted fragment length is 51 bps INFO @ Fri, 16 Mar 2018 07:40:57: #2 alternative fragment length(s) may be 4,51 bps INFO @ Fri, 16 Mar 2018 07:40:57: #2.2 Generate R script for model : SRX2433655.05_model.r WARNING @ Fri, 16 Mar 2018 07:40:57: #2 Since the d (51) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 16 Mar 2018 07:40:57: #2 You may need to consider one of the other alternative d(s): 4,51 WARNING @ Fri, 16 Mar 2018 07:40:57: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Fri, 16 Mar 2018 07:40:57: #3 Call peaks... INFO @ Fri, 16 Mar 2018 07:40:57: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 16 Mar 2018 07:40:57: #1 tag size is determined as 51 bps INFO @ Fri, 16 Mar 2018 07:40:57: #1 tag size = 51 INFO @ Fri, 16 Mar 2018 07:40:57: #1 total tags in treatment: 10848897 INFO @ Fri, 16 Mar 2018 07:40:57: #1 user defined the maximum tags... INFO @ Fri, 16 Mar 2018 07:40:57: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 16 Mar 2018 07:40:58: #1 tags after filtering in treatment: 10848897 INFO @ Fri, 16 Mar 2018 07:40:58: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 16 Mar 2018 07:40:58: #1 finished! INFO @ Fri, 16 Mar 2018 07:40:58: #2 Build Peak Model... INFO @ Fri, 16 Mar 2018 07:40:58: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 16 Mar 2018 07:40:59: #2 number of paired peaks: 2526 INFO @ Fri, 16 Mar 2018 07:40:59: start model_add_line... INFO @ Fri, 16 Mar 2018 07:40:59: start X-correlation... INFO @ Fri, 16 Mar 2018 07:40:59: end of X-cor INFO @ Fri, 16 Mar 2018 07:40:59: #2 finished! INFO @ Fri, 16 Mar 2018 07:40:59: #2 predicted fragment length is 51 bps INFO @ Fri, 16 Mar 2018 07:40:59: #2 alternative fragment length(s) may be 4,51 bps INFO @ Fri, 16 Mar 2018 07:40:59: #2.2 Generate R script for model : SRX2433655.10_model.r WARNING @ Fri, 16 Mar 2018 07:40:59: #2 Since the d (51) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 16 Mar 2018 07:40:59: #2 You may need to consider one of the other alternative d(s): 4,51 WARNING @ Fri, 16 Mar 2018 07:40:59: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Fri, 16 Mar 2018 07:40:59: #3 Call peaks... INFO @ Fri, 16 Mar 2018 07:40:59: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 16 Mar 2018 07:41:01: #1 tag size is determined as 51 bps INFO @ Fri, 16 Mar 2018 07:41:01: #1 tag size = 51 INFO @ Fri, 16 Mar 2018 07:41:01: #1 total tags in treatment: 10848897 INFO @ Fri, 16 Mar 2018 07:41:01: #1 user defined the maximum tags... INFO @ Fri, 16 Mar 2018 07:41:01: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 16 Mar 2018 07:41:01: #1 tags after filtering in treatment: 10848897 INFO @ Fri, 16 Mar 2018 07:41:01: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 16 Mar 2018 07:41:01: #1 finished! INFO @ Fri, 16 Mar 2018 07:41:01: #2 Build Peak Model... INFO @ Fri, 16 Mar 2018 07:41:01: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 16 Mar 2018 07:41:02: #2 number of paired peaks: 2526 INFO @ Fri, 16 Mar 2018 07:41:02: start model_add_line... INFO @ Fri, 16 Mar 2018 07:41:02: start X-correlation... INFO @ Fri, 16 Mar 2018 07:41:02: end of X-cor INFO @ Fri, 16 Mar 2018 07:41:02: #2 finished! INFO @ Fri, 16 Mar 2018 07:41:02: #2 predicted fragment length is 51 bps INFO @ Fri, 16 Mar 2018 07:41:02: #2 alternative fragment length(s) may be 4,51 bps INFO @ Fri, 16 Mar 2018 07:41:02: #2.2 Generate R script for model : SRX2433655.20_model.r WARNING @ Fri, 16 Mar 2018 07:41:02: #2 Since the d (51) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 16 Mar 2018 07:41:02: #2 You may need to consider one of the other alternative d(s): 4,51 WARNING @ Fri, 16 Mar 2018 07:41:02: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Fri, 16 Mar 2018 07:41:02: #3 Call peaks... INFO @ Fri, 16 Mar 2018 07:41:02: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 16 Mar 2018 07:41:22: #3 Call peaks for each chromosome... INFO @ Fri, 16 Mar 2018 07:41:22: #3 Call peaks for each chromosome... INFO @ Fri, 16 Mar 2018 07:41:25: #3 Call peaks for each chromosome... INFO @ Fri, 16 Mar 2018 07:41:34: #4 Write output xls file... SRX2433655.05_peaks.xls INFO @ Fri, 16 Mar 2018 07:41:34: #4 Write peak in narrowPeak format file... SRX2433655.05_peaks.narrowPeak INFO @ Fri, 16 Mar 2018 07:41:34: #4 Write summits bed file... SRX2433655.05_summits.bed INFO @ Fri, 16 Mar 2018 07:41:34: Done! pass1 - making usageList (15 chroms): 3 millis pass2 - checking and writing primary data (10719 records, 4 fields): 13 millis CompletedMACS2peakCalling INFO @ Fri, 16 Mar 2018 07:41:35: #4 Write output xls file... SRX2433655.10_peaks.xls INFO @ Fri, 16 Mar 2018 07:41:35: #4 Write peak in narrowPeak format file... SRX2433655.10_peaks.narrowPeak INFO @ Fri, 16 Mar 2018 07:41:36: #4 Write summits bed file... SRX2433655.10_summits.bed INFO @ Fri, 16 Mar 2018 07:41:36: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (3983 records, 4 fields): 7 millis CompletedMACS2peakCalling INFO @ Fri, 16 Mar 2018 07:41:39: #4 Write output xls file... SRX2433655.20_peaks.xls INFO @ Fri, 16 Mar 2018 07:41:39: #4 Write peak in narrowPeak format file... SRX2433655.20_peaks.narrowPeak INFO @ Fri, 16 Mar 2018 07:41:39: #4 Write summits bed file... SRX2433655.20_summits.bed INFO @ Fri, 16 Mar 2018 07:41:39: Done! pass1 - making usageList (11 chroms): 1 millis pass2 - checking and writing primary data (1365 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。