Job ID = 1306894 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 9,372,883 reads read : 9,372,883 reads written : 9,372,883 rm: cannot remove ‘[DSE]RR*’: No such file or directory rm: cannot remove ‘fastqDump_tmp*’: No such file or directory 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: 00:07:51 9372883 reads; of these: 9372883 (100.00%) were unpaired; of these: 183959 (1.96%) aligned 0 times 2183416 (23.30%) aligned exactly 1 time 7005508 (74.74%) aligned >1 times 98.04% overall alignment rate Time searching: 00:07:51 Overall time: 00:07:51 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_rmdupse_core] 1491830 / 9188924 = 0.1624 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 @ Mon, 03 Jun 2019 22:14:09: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX511127/SRX511127.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX511127/SRX511127.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX511127/SRX511127.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX511127/SRX511127.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 @ Mon, 03 Jun 2019 22:14:09: #1 read tag files... INFO @ Mon, 03 Jun 2019 22:14:09: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 22:14:09: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX511127/SRX511127.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX511127/SRX511127.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX511127/SRX511127.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX511127/SRX511127.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 @ Mon, 03 Jun 2019 22:14:09: #1 read tag files... INFO @ Mon, 03 Jun 2019 22:14:09: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 22:14:09: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX511127/SRX511127.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX511127/SRX511127.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX511127/SRX511127.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX511127/SRX511127.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 @ Mon, 03 Jun 2019 22:14:09: #1 read tag files... INFO @ Mon, 03 Jun 2019 22:14:09: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 22:14:17: 1000000 INFO @ Mon, 03 Jun 2019 22:14:17: 1000000 INFO @ Mon, 03 Jun 2019 22:14:18: 1000000 INFO @ Mon, 03 Jun 2019 22:14:24: 2000000 INFO @ Mon, 03 Jun 2019 22:14:25: 2000000 INFO @ Mon, 03 Jun 2019 22:14:28: 2000000 INFO @ Mon, 03 Jun 2019 22:14:32: 3000000 INFO @ Mon, 03 Jun 2019 22:14:33: 3000000 INFO @ Mon, 03 Jun 2019 22:14:38: 3000000 INFO @ Mon, 03 Jun 2019 22:14:39: 4000000 INFO @ Mon, 03 Jun 2019 22:14:39: 4000000 INFO @ Mon, 03 Jun 2019 22:14:46: 5000000 INFO @ Mon, 03 Jun 2019 22:14:46: 5000000 INFO @ Mon, 03 Jun 2019 22:14:47: 4000000 INFO @ Mon, 03 Jun 2019 22:14:53: 6000000 INFO @ Mon, 03 Jun 2019 22:14:53: 6000000 INFO @ Mon, 03 Jun 2019 22:14:56: 5000000 INFO @ Mon, 03 Jun 2019 22:14:59: 7000000 INFO @ Mon, 03 Jun 2019 22:15:00: 7000000 INFO @ Mon, 03 Jun 2019 22:15:04: 6000000 INFO @ Mon, 03 Jun 2019 22:15:05: #1 tag size is determined as 50 bps INFO @ Mon, 03 Jun 2019 22:15:05: #1 tag size = 50 INFO @ Mon, 03 Jun 2019 22:15:05: #1 total tags in treatment: 7697094 INFO @ Mon, 03 Jun 2019 22:15:05: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 22:15:05: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Mon, 03 Jun 2019 22:15:05: #1 tags after filtering in treatment: 7697094 INFO @ Mon, 03 Jun 2019 22:15:05: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 22:15:05: #1 finished! INFO @ Mon, 03 Jun 2019 22:15:05: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 22:15:05: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 22:15:06: #1 tag size is determined as 50 bps INFO @ Mon, 03 Jun 2019 22:15:06: #1 tag size = 50 INFO @ Mon, 03 Jun 2019 22:15:06: #1 total tags in treatment: 7697094 INFO @ Mon, 03 Jun 2019 22:15:06: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 22:15:06: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Mon, 03 Jun 2019 22:15:06: #1 tags after filtering in treatment: 7697094 INFO @ Mon, 03 Jun 2019 22:15:06: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 22:15:06: #1 finished! INFO @ Mon, 03 Jun 2019 22:15:06: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 22:15:06: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 22:15:06: #2 number of paired peaks: 2108 INFO @ Mon, 03 Jun 2019 22:15:06: start model_add_line... INFO @ Mon, 03 Jun 2019 22:15:06: start X-correlation... INFO @ Mon, 03 Jun 2019 22:15:06: end of X-cor INFO @ Mon, 03 Jun 2019 22:15:06: #2 finished! INFO @ Mon, 03 Jun 2019 22:15:06: #2 predicted fragment length is 53 bps INFO @ Mon, 03 Jun 2019 22:15:06: #2 alternative fragment length(s) may be 53 bps INFO @ Mon, 03 Jun 2019 22:15:06: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX511127/SRX511127.10_model.r WARNING @ Mon, 03 Jun 2019 22:15:06: #2 Since the d (53) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 03 Jun 2019 22:15:06: #2 You may need to consider one of the other alternative d(s): 53 WARNING @ Mon, 03 Jun 2019 22:15:06: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Mon, 03 Jun 2019 22:15:06: #3 Call peaks... INFO @ Mon, 03 Jun 2019 22:15:06: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 22:15:07: #2 number of paired peaks: 2108 INFO @ Mon, 03 Jun 2019 22:15:07: start model_add_line... INFO @ Mon, 03 Jun 2019 22:15:07: start X-correlation... INFO @ Mon, 03 Jun 2019 22:15:07: end of X-cor INFO @ Mon, 03 Jun 2019 22:15:07: #2 finished! INFO @ Mon, 03 Jun 2019 22:15:07: #2 predicted fragment length is 53 bps INFO @ Mon, 03 Jun 2019 22:15:07: #2 alternative fragment length(s) may be 53 bps INFO @ Mon, 03 Jun 2019 22:15:07: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX511127/SRX511127.05_model.r WARNING @ Mon, 03 Jun 2019 22:15:07: #2 Since the d (53) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 03 Jun 2019 22:15:07: #2 You may need to consider one of the other alternative d(s): 53 WARNING @ Mon, 03 Jun 2019 22:15:07: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Mon, 03 Jun 2019 22:15:07: #3 Call peaks... INFO @ Mon, 03 Jun 2019 22:15:07: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 22:15:13: 7000000 INFO @ Mon, 03 Jun 2019 22:15:20: #1 tag size is determined as 50 bps INFO @ Mon, 03 Jun 2019 22:15:20: #1 tag size = 50 INFO @ Mon, 03 Jun 2019 22:15:20: #1 total tags in treatment: 7697094 INFO @ Mon, 03 Jun 2019 22:15:20: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 22:15:20: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Mon, 03 Jun 2019 22:15:20: #1 tags after filtering in treatment: 7697094 INFO @ Mon, 03 Jun 2019 22:15:20: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 22:15:20: #1 finished! INFO @ Mon, 03 Jun 2019 22:15:20: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 22:15:20: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 22:15:21: #2 number of paired peaks: 2108 INFO @ Mon, 03 Jun 2019 22:15:21: start model_add_line... INFO @ Mon, 03 Jun 2019 22:15:21: start X-correlation... INFO @ Mon, 03 Jun 2019 22:15:21: end of X-cor INFO @ Mon, 03 Jun 2019 22:15:21: #2 finished! INFO @ Mon, 03 Jun 2019 22:15:21: #2 predicted fragment length is 53 bps INFO @ Mon, 03 Jun 2019 22:15:21: #2 alternative fragment length(s) may be 53 bps INFO @ Mon, 03 Jun 2019 22:15:21: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX511127/SRX511127.20_model.r WARNING @ Mon, 03 Jun 2019 22:15:21: #2 Since the d (53) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 03 Jun 2019 22:15:21: #2 You may need to consider one of the other alternative d(s): 53 WARNING @ Mon, 03 Jun 2019 22:15:21: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Mon, 03 Jun 2019 22:15:21: #3 Call peaks... INFO @ Mon, 03 Jun 2019 22:15:21: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 22:15:28: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 22:15:28: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 22:15:39: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX511127/SRX511127.10_peaks.xls INFO @ Mon, 03 Jun 2019 22:15:39: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX511127/SRX511127.10_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 22:15:39: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX511127/SRX511127.10_summits.bed INFO @ Mon, 03 Jun 2019 22:15:39: Done! INFO @ Mon, 03 Jun 2019 22:15:39: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX511127/SRX511127.05_peaks.xls INFO @ Mon, 03 Jun 2019 22:15:39: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX511127/SRX511127.05_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 22:15:39: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX511127/SRX511127.05_summits.bed pass1 - making usageList (13 chroms): 3 millis pass2 - checking and writing primary data (2047 records, 4 fields): 6 millis INFO @ Mon, 03 Jun 2019 22:15:39: Done! CompletedMACS2peakCalling pass1 - making usageList (14 chroms): 4 millis pass2 - checking and writing primary data (5323 records, 4 fields): 11 millis CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 22:15:45: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 22:15:59: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX511127/SRX511127.20_peaks.xls INFO @ Mon, 03 Jun 2019 22:15:59: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX511127/SRX511127.20_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 22:15:59: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX511127/SRX511127.20_summits.bed INFO @ Mon, 03 Jun 2019 22:15:59: Done! pass1 - making usageList (12 chroms): 2 millis pass2 - checking and writing primary data (1225 records, 4 fields): 4 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。