Job ID = 10480667 sra ファイルのダウンロード中... Completed: 633369K bytes transferred in 13 seconds (378158K 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 19375077 spots for /home/okishinya/chipatlas/results/dm3/SRX2832103/SRR5573767.sra Written 19375077 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: 00:08:25 19375077 reads; of these: 19375077 (100.00%) were unpaired; of these: 532551 (2.75%) aligned 0 times 12264117 (63.30%) aligned exactly 1 time 6578409 (33.95%) aligned >1 times 97.25% overall alignment rate Time searching: 00:08:25 Overall time: 00:08:25 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] 4635259 / 18842526 = 0.2460 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 07:39:55: # Command line: callpeak -t SRX2832103.bam -f BAM -g dm -n SRX2832103.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX2832103.10 # format = BAM # ChIP-seq file = ['SRX2832103.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 07:39:55: #1 read tag files... INFO @ Fri, 16 Mar 2018 07:39:55: #1 read treatment tags... INFO @ Fri, 16 Mar 2018 07:39:55: # Command line: callpeak -t SRX2832103.bam -f BAM -g dm -n SRX2832103.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX2832103.05 # format = BAM # ChIP-seq file = ['SRX2832103.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 07:39:55: #1 read tag files... INFO @ Fri, 16 Mar 2018 07:39:55: #1 read treatment tags... INFO @ Fri, 16 Mar 2018 07:39:55: # Command line: callpeak -t SRX2832103.bam -f BAM -g dm -n SRX2832103.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX2832103.20 # format = BAM # ChIP-seq file = ['SRX2832103.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 07:39:55: #1 read tag files... INFO @ Fri, 16 Mar 2018 07:39:55: #1 read treatment tags... INFO @ Fri, 16 Mar 2018 07:40:02: 1000000 INFO @ Fri, 16 Mar 2018 07:40:02: 1000000 INFO @ Fri, 16 Mar 2018 07:40:02: 1000000 INFO @ Fri, 16 Mar 2018 07:40:09: 2000000 INFO @ Fri, 16 Mar 2018 07:40:10: 2000000 INFO @ Fri, 16 Mar 2018 07:40:10: 2000000 INFO @ Fri, 16 Mar 2018 07:40:15: 3000000 INFO @ Fri, 16 Mar 2018 07:40:17: 3000000 INFO @ Fri, 16 Mar 2018 07:40:17: 3000000 INFO @ Fri, 16 Mar 2018 07:40:22: 4000000 INFO @ Fri, 16 Mar 2018 07:40:24: 4000000 INFO @ Fri, 16 Mar 2018 07:40:24: 4000000 INFO @ Fri, 16 Mar 2018 07:40:28: 5000000 INFO @ Fri, 16 Mar 2018 07:40:31: 5000000 INFO @ Fri, 16 Mar 2018 07:40:31: 5000000 INFO @ Fri, 16 Mar 2018 07:40:35: 6000000 INFO @ Fri, 16 Mar 2018 07:40:38: 6000000 INFO @ Fri, 16 Mar 2018 07:40:38: 6000000 INFO @ Fri, 16 Mar 2018 07:40:42: 7000000 INFO @ Fri, 16 Mar 2018 07:40:45: 7000000 INFO @ Fri, 16 Mar 2018 07:40:45: 7000000 INFO @ Fri, 16 Mar 2018 07:40:48: 8000000 INFO @ Fri, 16 Mar 2018 07:40:52: 8000000 INFO @ Fri, 16 Mar 2018 07:40:52: 8000000 INFO @ Fri, 16 Mar 2018 07:40:55: 9000000 INFO @ Fri, 16 Mar 2018 07:40:59: 9000000 INFO @ Fri, 16 Mar 2018 07:40:59: 9000000 INFO @ Fri, 16 Mar 2018 07:41:02: 10000000 INFO @ Fri, 16 Mar 2018 07:41:07: 10000000 INFO @ Fri, 16 Mar 2018 07:41:07: 10000000 INFO @ Fri, 16 Mar 2018 07:41:08: 11000000 INFO @ Fri, 16 Mar 2018 07:41:14: 11000000 INFO @ Fri, 16 Mar 2018 07:41:14: 11000000 INFO @ Fri, 16 Mar 2018 07:41:15: 12000000 INFO @ Fri, 16 Mar 2018 07:41:22: 13000000 INFO @ Fri, 16 Mar 2018 07:41:22: 12000000 INFO @ Fri, 16 Mar 2018 07:41:22: 12000000 INFO @ Fri, 16 Mar 2018 07:41:28: 14000000 INFO @ Fri, 16 Mar 2018 07:41:29: 13000000 INFO @ Fri, 16 Mar 2018 07:41:29: 13000000 INFO @ Fri, 16 Mar 2018 07:41:30: #1 tag size is determined as 50 bps INFO @ Fri, 16 Mar 2018 07:41:30: #1 tag size = 50 INFO @ Fri, 16 Mar 2018 07:41:30: #1 total tags in treatment: 14207267 INFO @ Fri, 16 Mar 2018 07:41:30: #1 user defined the maximum tags... INFO @ Fri, 16 Mar 2018 07:41:30: #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 07:41:30: #1 tags after filtering in treatment: 14207267 INFO @ Fri, 16 Mar 2018 07:41:30: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 16 Mar 2018 07:41:30: #1 finished! INFO @ Fri, 16 Mar 2018 07:41:30: #2 Build Peak Model... INFO @ Fri, 16 Mar 2018 07:41:30: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 16 Mar 2018 07:41:31: #2 number of paired peaks: 1460 INFO @ Fri, 16 Mar 2018 07:41:31: start model_add_line... INFO @ Fri, 16 Mar 2018 07:41:32: start X-correlation... INFO @ Fri, 16 Mar 2018 07:41:32: end of X-cor INFO @ Fri, 16 Mar 2018 07:41:32: #2 finished! INFO @ Fri, 16 Mar 2018 07:41:32: #2 predicted fragment length is 47 bps INFO @ Fri, 16 Mar 2018 07:41:32: #2 alternative fragment length(s) may be 2,47 bps INFO @ Fri, 16 Mar 2018 07:41:32: #2.2 Generate R script for model : SRX2832103.10_model.r WARNING @ Fri, 16 Mar 2018 07:41:32: #2 Since the d (47) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 16 Mar 2018 07:41:32: #2 You may need to consider one of the other alternative d(s): 2,47 WARNING @ Fri, 16 Mar 2018 07:41:32: #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 07:41:32: #3 Call peaks... INFO @ Fri, 16 Mar 2018 07:41:32: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 16 Mar 2018 07:41:36: 14000000 INFO @ Fri, 16 Mar 2018 07:41:36: 14000000 INFO @ Fri, 16 Mar 2018 07:41:38: #1 tag size is determined as 50 bps INFO @ Fri, 16 Mar 2018 07:41:38: #1 tag size = 50 INFO @ Fri, 16 Mar 2018 07:41:38: #1 total tags in treatment: 14207267 INFO @ Fri, 16 Mar 2018 07:41:38: #1 user defined the maximum tags... INFO @ Fri, 16 Mar 2018 07:41:38: #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 07:41:38: #1 tag size is determined as 50 bps INFO @ Fri, 16 Mar 2018 07:41:38: #1 tag size = 50 INFO @ Fri, 16 Mar 2018 07:41:38: #1 total tags in treatment: 14207267 INFO @ Fri, 16 Mar 2018 07:41:38: #1 user defined the maximum tags... INFO @ Fri, 16 Mar 2018 07:41:38: #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 07:41:38: #1 tags after filtering in treatment: 14207267 INFO @ Fri, 16 Mar 2018 07:41:38: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 16 Mar 2018 07:41:38: #1 finished! INFO @ Fri, 16 Mar 2018 07:41:38: #2 Build Peak Model... INFO @ Fri, 16 Mar 2018 07:41:38: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 16 Mar 2018 07:41:38: #1 tags after filtering in treatment: 14207267 INFO @ Fri, 16 Mar 2018 07:41:38: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 16 Mar 2018 07:41:38: #1 finished! INFO @ Fri, 16 Mar 2018 07:41:38: #2 Build Peak Model... INFO @ Fri, 16 Mar 2018 07:41:38: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 16 Mar 2018 07:41:39: #2 number of paired peaks: 1460 INFO @ Fri, 16 Mar 2018 07:41:39: start model_add_line... INFO @ Fri, 16 Mar 2018 07:41:39: #2 number of paired peaks: 1460 INFO @ Fri, 16 Mar 2018 07:41:39: start model_add_line... INFO @ Fri, 16 Mar 2018 07:41:39: start X-correlation... INFO @ Fri, 16 Mar 2018 07:41:39: end of X-cor INFO @ Fri, 16 Mar 2018 07:41:39: #2 finished! INFO @ Fri, 16 Mar 2018 07:41:39: #2 predicted fragment length is 47 bps INFO @ Fri, 16 Mar 2018 07:41:39: #2 alternative fragment length(s) may be 2,47 bps INFO @ Fri, 16 Mar 2018 07:41:39: #2.2 Generate R script for model : SRX2832103.20_model.r WARNING @ Fri, 16 Mar 2018 07:41:39: #2 Since the d (47) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 16 Mar 2018 07:41:39: #2 You may need to consider one of the other alternative d(s): 2,47 WARNING @ Fri, 16 Mar 2018 07:41:39: #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 07:41:39: #3 Call peaks... INFO @ Fri, 16 Mar 2018 07:41:39: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 16 Mar 2018 07:41:39: start X-correlation... INFO @ Fri, 16 Mar 2018 07:41:39: end of X-cor INFO @ Fri, 16 Mar 2018 07:41:39: #2 finished! INFO @ Fri, 16 Mar 2018 07:41:39: #2 predicted fragment length is 47 bps INFO @ Fri, 16 Mar 2018 07:41:39: #2 alternative fragment length(s) may be 2,47 bps INFO @ Fri, 16 Mar 2018 07:41:39: #2.2 Generate R script for model : SRX2832103.05_model.r WARNING @ Fri, 16 Mar 2018 07:41:39: #2 Since the d (47) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 16 Mar 2018 07:41:39: #2 You may need to consider one of the other alternative d(s): 2,47 WARNING @ Fri, 16 Mar 2018 07:41:39: #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 07:41:39: #3 Call peaks... INFO @ Fri, 16 Mar 2018 07:41:39: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 16 Mar 2018 07:42:02: #3 Call peaks for each chromosome... INFO @ Fri, 16 Mar 2018 07:42:12: #3 Call peaks for each chromosome... INFO @ Fri, 16 Mar 2018 07:42:12: #3 Call peaks for each chromosome... INFO @ Fri, 16 Mar 2018 07:42:17: #4 Write output xls file... SRX2832103.10_peaks.xls INFO @ Fri, 16 Mar 2018 07:42:17: #4 Write peak in narrowPeak format file... SRX2832103.10_peaks.narrowPeak INFO @ Fri, 16 Mar 2018 07:42:17: #4 Write summits bed file... SRX2832103.10_summits.bed INFO @ Fri, 16 Mar 2018 07:42:17: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (2708 records, 4 fields): 5 millis CompletedMACS2peakCalling INFO @ Fri, 16 Mar 2018 07:42:28: #4 Write output xls file... SRX2832103.20_peaks.xls INFO @ Fri, 16 Mar 2018 07:42:28: #4 Write peak in narrowPeak format file... SRX2832103.20_peaks.narrowPeak INFO @ Fri, 16 Mar 2018 07:42:28: #4 Write summits bed file... SRX2832103.20_summits.bed INFO @ Fri, 16 Mar 2018 07:42:28: Done! pass1 - making usageList (10 chroms): 1 millis pass2 - checking and writing primary data (1422 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Fri, 16 Mar 2018 07:42:28: #4 Write output xls file... SRX2832103.05_peaks.xls INFO @ Fri, 16 Mar 2018 07:42:28: #4 Write peak in narrowPeak format file... SRX2832103.05_peaks.narrowPeak INFO @ Fri, 16 Mar 2018 07:42:28: #4 Write summits bed file... SRX2832103.05_summits.bed INFO @ Fri, 16 Mar 2018 07:42:28: Done! pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (3919 records, 4 fields): 26 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。