Job ID = 1294250 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 21,933,505 reads read : 43,867,010 reads written : 21,933,505 reads 0-length : 21,933,505 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: 00:10:21 21933505 reads; of these: 21933505 (100.00%) were unpaired; of these: 818701 (3.73%) aligned 0 times 17159108 (78.23%) aligned exactly 1 time 3955696 (18.03%) aligned >1 times 96.27% overall alignment rate Time searching: 00:10:21 Overall time: 00:10:21 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 12 files... [bam_rmdupse_core] 5019191 / 21114804 = 0.2377 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 06:12:58: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX2035281/SRX2035281.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX2035281/SRX2035281.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX2035281/SRX2035281.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX2035281/SRX2035281.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 06:12:58: #1 read tag files... INFO @ Mon, 03 Jun 2019 06:12:58: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 06:12:58: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX2035281/SRX2035281.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX2035281/SRX2035281.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX2035281/SRX2035281.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX2035281/SRX2035281.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 06:12:58: #1 read tag files... INFO @ Mon, 03 Jun 2019 06:12:58: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 06:12:58: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX2035281/SRX2035281.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX2035281/SRX2035281.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX2035281/SRX2035281.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX2035281/SRX2035281.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 06:12:58: #1 read tag files... INFO @ Mon, 03 Jun 2019 06:12:58: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 06:13:06: 1000000 INFO @ Mon, 03 Jun 2019 06:13:08: 1000000 INFO @ Mon, 03 Jun 2019 06:13:10: 1000000 INFO @ Mon, 03 Jun 2019 06:13:15: 2000000 INFO @ Mon, 03 Jun 2019 06:13:17: 2000000 INFO @ Mon, 03 Jun 2019 06:13:20: 2000000 INFO @ Mon, 03 Jun 2019 06:13:23: 3000000 INFO @ Mon, 03 Jun 2019 06:13:27: 3000000 INFO @ Mon, 03 Jun 2019 06:13:31: 3000000 INFO @ Mon, 03 Jun 2019 06:13:31: 4000000 INFO @ Mon, 03 Jun 2019 06:13:36: 4000000 INFO @ Mon, 03 Jun 2019 06:13:39: 5000000 INFO @ Mon, 03 Jun 2019 06:13:42: 4000000 INFO @ Mon, 03 Jun 2019 06:13:45: 5000000 INFO @ Mon, 03 Jun 2019 06:13:48: 6000000 INFO @ Mon, 03 Jun 2019 06:13:52: 5000000 INFO @ Mon, 03 Jun 2019 06:13:55: 6000000 INFO @ Mon, 03 Jun 2019 06:13:56: 7000000 INFO @ Mon, 03 Jun 2019 06:14:03: 6000000 INFO @ Mon, 03 Jun 2019 06:14:04: 7000000 INFO @ Mon, 03 Jun 2019 06:14:04: 8000000 INFO @ Mon, 03 Jun 2019 06:14:12: 9000000 INFO @ Mon, 03 Jun 2019 06:14:13: 8000000 INFO @ Mon, 03 Jun 2019 06:14:13: 7000000 INFO @ Mon, 03 Jun 2019 06:14:21: 10000000 INFO @ Mon, 03 Jun 2019 06:14:22: 9000000 INFO @ Mon, 03 Jun 2019 06:14:24: 8000000 INFO @ Mon, 03 Jun 2019 06:14:29: 11000000 INFO @ Mon, 03 Jun 2019 06:14:31: 10000000 INFO @ Mon, 03 Jun 2019 06:14:34: 9000000 INFO @ Mon, 03 Jun 2019 06:14:37: 12000000 INFO @ Mon, 03 Jun 2019 06:14:40: 11000000 INFO @ Mon, 03 Jun 2019 06:14:45: 10000000 INFO @ Mon, 03 Jun 2019 06:14:46: 13000000 INFO @ Mon, 03 Jun 2019 06:14:49: 12000000 INFO @ Mon, 03 Jun 2019 06:14:54: 14000000 INFO @ Mon, 03 Jun 2019 06:14:55: 11000000 INFO @ Mon, 03 Jun 2019 06:14:59: 13000000 INFO @ Mon, 03 Jun 2019 06:15:02: 15000000 INFO @ Mon, 03 Jun 2019 06:15:06: 12000000 INFO @ Mon, 03 Jun 2019 06:15:08: 14000000 INFO @ Mon, 03 Jun 2019 06:15:10: 16000000 INFO @ Mon, 03 Jun 2019 06:15:11: #1 tag size is determined as 76 bps INFO @ Mon, 03 Jun 2019 06:15:11: #1 tag size = 76 INFO @ Mon, 03 Jun 2019 06:15:11: #1 total tags in treatment: 16095613 INFO @ Mon, 03 Jun 2019 06:15:11: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 06:15:11: #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 06:15:12: #1 tags after filtering in treatment: 16095613 INFO @ Mon, 03 Jun 2019 06:15:12: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 06:15:12: #1 finished! INFO @ Mon, 03 Jun 2019 06:15:12: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 06:15:12: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 06:15:13: #2 number of paired peaks: 3092 INFO @ Mon, 03 Jun 2019 06:15:13: start model_add_line... INFO @ Mon, 03 Jun 2019 06:15:14: start X-correlation... INFO @ Mon, 03 Jun 2019 06:15:14: end of X-cor INFO @ Mon, 03 Jun 2019 06:15:14: #2 finished! INFO @ Mon, 03 Jun 2019 06:15:14: #2 predicted fragment length is 138 bps INFO @ Mon, 03 Jun 2019 06:15:14: #2 alternative fragment length(s) may be 138 bps INFO @ Mon, 03 Jun 2019 06:15:14: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX2035281/SRX2035281.20_model.r WARNING @ Mon, 03 Jun 2019 06:15:14: #2 Since the d (138) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 03 Jun 2019 06:15:14: #2 You may need to consider one of the other alternative d(s): 138 WARNING @ Mon, 03 Jun 2019 06:15:14: #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 06:15:14: #3 Call peaks... INFO @ Mon, 03 Jun 2019 06:15:14: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 06:15:17: 13000000 INFO @ Mon, 03 Jun 2019 06:15:17: 15000000 INFO @ Mon, 03 Jun 2019 06:15:26: 16000000 INFO @ Mon, 03 Jun 2019 06:15:27: #1 tag size is determined as 76 bps INFO @ Mon, 03 Jun 2019 06:15:27: #1 tag size = 76 INFO @ Mon, 03 Jun 2019 06:15:27: #1 total tags in treatment: 16095613 INFO @ Mon, 03 Jun 2019 06:15:27: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 06:15:27: #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 06:15:27: #1 tags after filtering in treatment: 16095613 INFO @ Mon, 03 Jun 2019 06:15:27: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 06:15:27: #1 finished! INFO @ Mon, 03 Jun 2019 06:15:27: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 06:15:27: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 06:15:27: 14000000 INFO @ Mon, 03 Jun 2019 06:15:29: #2 number of paired peaks: 3092 INFO @ Mon, 03 Jun 2019 06:15:29: start model_add_line... INFO @ Mon, 03 Jun 2019 06:15:29: start X-correlation... INFO @ Mon, 03 Jun 2019 06:15:29: end of X-cor INFO @ Mon, 03 Jun 2019 06:15:29: #2 finished! INFO @ Mon, 03 Jun 2019 06:15:29: #2 predicted fragment length is 138 bps INFO @ Mon, 03 Jun 2019 06:15:29: #2 alternative fragment length(s) may be 138 bps INFO @ Mon, 03 Jun 2019 06:15:29: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX2035281/SRX2035281.10_model.r WARNING @ Mon, 03 Jun 2019 06:15:29: #2 Since the d (138) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 03 Jun 2019 06:15:29: #2 You may need to consider one of the other alternative d(s): 138 WARNING @ Mon, 03 Jun 2019 06:15:29: #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 06:15:29: #3 Call peaks... INFO @ Mon, 03 Jun 2019 06:15:29: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 06:15:38: 15000000 INFO @ Mon, 03 Jun 2019 06:15:48: 16000000 INFO @ Mon, 03 Jun 2019 06:15:49: #1 tag size is determined as 76 bps INFO @ Mon, 03 Jun 2019 06:15:49: #1 tag size = 76 INFO @ Mon, 03 Jun 2019 06:15:49: #1 total tags in treatment: 16095613 INFO @ Mon, 03 Jun 2019 06:15:49: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 06:15:49: #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 06:15:49: #1 tags after filtering in treatment: 16095613 INFO @ Mon, 03 Jun 2019 06:15:49: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 06:15:49: #1 finished! INFO @ Mon, 03 Jun 2019 06:15:49: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 06:15:49: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 06:15:51: #2 number of paired peaks: 3092 INFO @ Mon, 03 Jun 2019 06:15:51: start model_add_line... INFO @ Mon, 03 Jun 2019 06:15:51: start X-correlation... INFO @ Mon, 03 Jun 2019 06:15:51: end of X-cor INFO @ Mon, 03 Jun 2019 06:15:51: #2 finished! INFO @ Mon, 03 Jun 2019 06:15:51: #2 predicted fragment length is 138 bps INFO @ Mon, 03 Jun 2019 06:15:51: #2 alternative fragment length(s) may be 138 bps INFO @ Mon, 03 Jun 2019 06:15:51: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX2035281/SRX2035281.05_model.r WARNING @ Mon, 03 Jun 2019 06:15:51: #2 Since the d (138) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 03 Jun 2019 06:15:51: #2 You may need to consider one of the other alternative d(s): 138 WARNING @ Mon, 03 Jun 2019 06:15:51: #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 06:15:51: #3 Call peaks... INFO @ Mon, 03 Jun 2019 06:15:51: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 06:16:02: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 06:16:17: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 06:16:27: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX2035281/SRX2035281.20_peaks.xls INFO @ Mon, 03 Jun 2019 06:16:27: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX2035281/SRX2035281.20_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 06:16:27: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX2035281/SRX2035281.20_summits.bed INFO @ Mon, 03 Jun 2019 06:16:27: Done! pass1 - making usageList (14 chroms): 4 millis pass2 - checking and writing primary data (7575 records, 4 fields): 17 millis CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 06:16:39: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 06:16:42: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX2035281/SRX2035281.10_peaks.xls INFO @ Mon, 03 Jun 2019 06:16:42: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX2035281/SRX2035281.10_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 06:16:42: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX2035281/SRX2035281.10_summits.bed INFO @ Mon, 03 Jun 2019 06:16:42: Done! pass1 - making usageList (14 chroms): 2 millis pass2 - checking and writing primary data (11050 records, 4 fields): 16 millis CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 06:17:03: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX2035281/SRX2035281.05_peaks.xls INFO @ Mon, 03 Jun 2019 06:17:03: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX2035281/SRX2035281.05_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 06:17:03: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX2035281/SRX2035281.05_summits.bed INFO @ Mon, 03 Jun 2019 06:17:03: Done! pass1 - making usageList (15 chroms): 3 millis pass2 - checking and writing primary data (14413 records, 4 fields): 19 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。