Job ID = 1307625 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 23,001,207 reads read : 46,002,414 reads written : 23,001,207 reads 0-length : 23,001,207 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: 00:18:33 23001207 reads; of these: 23001207 (100.00%) were unpaired; of these: 1369170 (5.95%) aligned 0 times 8012389 (34.83%) aligned exactly 1 time 13619648 (59.21%) aligned >1 times 94.05% overall alignment rate Time searching: 00:18:33 Overall time: 00:18:33 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] 7604222 / 21632037 = 0.3515 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 22:57:26: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX5343100/SRX5343100.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX5343100/SRX5343100.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX5343100/SRX5343100.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX5343100/SRX5343100.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 22:57:26: #1 read tag files... INFO @ Mon, 03 Jun 2019 22:57:26: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 22:57:26: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX5343100/SRX5343100.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX5343100/SRX5343100.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX5343100/SRX5343100.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX5343100/SRX5343100.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 22:57:26: #1 read tag files... INFO @ Mon, 03 Jun 2019 22:57:26: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 22:57:26: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX5343100/SRX5343100.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX5343100/SRX5343100.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX5343100/SRX5343100.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX5343100/SRX5343100.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 22:57:26: #1 read tag files... INFO @ Mon, 03 Jun 2019 22:57:26: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 22:57:37: 1000000 INFO @ Mon, 03 Jun 2019 22:57:37: 1000000 INFO @ Mon, 03 Jun 2019 22:57:37: 1000000 INFO @ Mon, 03 Jun 2019 22:57:46: 2000000 INFO @ Mon, 03 Jun 2019 22:57:47: 2000000 INFO @ Mon, 03 Jun 2019 22:57:47: 2000000 INFO @ Mon, 03 Jun 2019 22:57:54: 3000000 INFO @ Mon, 03 Jun 2019 22:57:56: 3000000 INFO @ Mon, 03 Jun 2019 22:57:56: 3000000 INFO @ Mon, 03 Jun 2019 22:58:03: 4000000 INFO @ Mon, 03 Jun 2019 22:58:06: 4000000 INFO @ Mon, 03 Jun 2019 22:58:06: 4000000 INFO @ Mon, 03 Jun 2019 22:58:11: 5000000 INFO @ Mon, 03 Jun 2019 22:58:15: 5000000 INFO @ Mon, 03 Jun 2019 22:58:16: 5000000 INFO @ Mon, 03 Jun 2019 22:58:20: 6000000 INFO @ Mon, 03 Jun 2019 22:58:25: 6000000 INFO @ Mon, 03 Jun 2019 22:58:27: 6000000 INFO @ Mon, 03 Jun 2019 22:58:28: 7000000 INFO @ Mon, 03 Jun 2019 22:58:35: 7000000 INFO @ Mon, 03 Jun 2019 22:58:36: 8000000 INFO @ Mon, 03 Jun 2019 22:58:37: 7000000 INFO @ Mon, 03 Jun 2019 22:58:44: 8000000 INFO @ Mon, 03 Jun 2019 22:58:45: 9000000 INFO @ Mon, 03 Jun 2019 22:58:47: 8000000 INFO @ Mon, 03 Jun 2019 22:58:54: 9000000 INFO @ Mon, 03 Jun 2019 22:58:55: 10000000 INFO @ Mon, 03 Jun 2019 22:58:58: 9000000 INFO @ Mon, 03 Jun 2019 22:59:04: 10000000 INFO @ Mon, 03 Jun 2019 22:59:05: 11000000 INFO @ Mon, 03 Jun 2019 22:59:09: 10000000 INFO @ Mon, 03 Jun 2019 22:59:14: 11000000 INFO @ Mon, 03 Jun 2019 22:59:14: 12000000 INFO @ Mon, 03 Jun 2019 22:59:21: 11000000 INFO @ Mon, 03 Jun 2019 22:59:23: 12000000 INFO @ Mon, 03 Jun 2019 22:59:24: 13000000 INFO @ Mon, 03 Jun 2019 22:59:31: 12000000 INFO @ Mon, 03 Jun 2019 22:59:34: 13000000 INFO @ Mon, 03 Jun 2019 22:59:34: 14000000 INFO @ Mon, 03 Jun 2019 22:59:34: #1 tag size is determined as 65 bps INFO @ Mon, 03 Jun 2019 22:59:34: #1 tag size = 65 INFO @ Mon, 03 Jun 2019 22:59:34: #1 total tags in treatment: 14027815 INFO @ Mon, 03 Jun 2019 22:59:34: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 22:59:34: #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 22:59:35: #1 tags after filtering in treatment: 14027815 INFO @ Mon, 03 Jun 2019 22:59:35: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 22:59:35: #1 finished! INFO @ Mon, 03 Jun 2019 22:59:35: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 22:59:35: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 22:59:36: #2 number of paired peaks: 1820 INFO @ Mon, 03 Jun 2019 22:59:36: start model_add_line... INFO @ Mon, 03 Jun 2019 22:59:36: start X-correlation... INFO @ Mon, 03 Jun 2019 22:59:36: end of X-cor INFO @ Mon, 03 Jun 2019 22:59:36: #2 finished! INFO @ Mon, 03 Jun 2019 22:59:36: #2 predicted fragment length is 67 bps INFO @ Mon, 03 Jun 2019 22:59:36: #2 alternative fragment length(s) may be 67 bps INFO @ Mon, 03 Jun 2019 22:59:36: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX5343100/SRX5343100.20_model.r WARNING @ Mon, 03 Jun 2019 22:59:36: #2 Since the d (67) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 03 Jun 2019 22:59:36: #2 You may need to consider one of the other alternative d(s): 67 WARNING @ Mon, 03 Jun 2019 22:59:36: #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 22:59:36: #3 Call peaks... INFO @ Mon, 03 Jun 2019 22:59:36: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 22:59:42: 13000000 INFO @ Mon, 03 Jun 2019 22:59:43: 14000000 INFO @ Mon, 03 Jun 2019 22:59:43: #1 tag size is determined as 65 bps INFO @ Mon, 03 Jun 2019 22:59:43: #1 tag size = 65 INFO @ Mon, 03 Jun 2019 22:59:43: #1 total tags in treatment: 14027815 INFO @ Mon, 03 Jun 2019 22:59:43: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 22:59:43: #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 22:59:44: #1 tags after filtering in treatment: 14027815 INFO @ Mon, 03 Jun 2019 22:59:44: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 22:59:44: #1 finished! INFO @ Mon, 03 Jun 2019 22:59:44: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 22:59:44: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 22:59:45: #2 number of paired peaks: 1820 INFO @ Mon, 03 Jun 2019 22:59:45: start model_add_line... INFO @ Mon, 03 Jun 2019 22:59:45: start X-correlation... INFO @ Mon, 03 Jun 2019 22:59:45: end of X-cor INFO @ Mon, 03 Jun 2019 22:59:45: #2 finished! INFO @ Mon, 03 Jun 2019 22:59:45: #2 predicted fragment length is 67 bps INFO @ Mon, 03 Jun 2019 22:59:45: #2 alternative fragment length(s) may be 67 bps INFO @ Mon, 03 Jun 2019 22:59:45: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX5343100/SRX5343100.10_model.r WARNING @ Mon, 03 Jun 2019 22:59:45: #2 Since the d (67) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 03 Jun 2019 22:59:45: #2 You may need to consider one of the other alternative d(s): 67 WARNING @ Mon, 03 Jun 2019 22:59:45: #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 22:59:45: #3 Call peaks... INFO @ Mon, 03 Jun 2019 22:59:45: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 22:59:52: 14000000 INFO @ Mon, 03 Jun 2019 22:59:52: #1 tag size is determined as 65 bps INFO @ Mon, 03 Jun 2019 22:59:52: #1 tag size = 65 INFO @ Mon, 03 Jun 2019 22:59:52: #1 total tags in treatment: 14027815 INFO @ Mon, 03 Jun 2019 22:59:52: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 22:59:52: #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 22:59:53: #1 tags after filtering in treatment: 14027815 INFO @ Mon, 03 Jun 2019 22:59:53: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 22:59:53: #1 finished! INFO @ Mon, 03 Jun 2019 22:59:53: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 22:59:53: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 22:59:54: #2 number of paired peaks: 1820 INFO @ Mon, 03 Jun 2019 22:59:54: start model_add_line... INFO @ Mon, 03 Jun 2019 22:59:54: start X-correlation... INFO @ Mon, 03 Jun 2019 22:59:54: end of X-cor INFO @ Mon, 03 Jun 2019 22:59:54: #2 finished! INFO @ Mon, 03 Jun 2019 22:59:54: #2 predicted fragment length is 67 bps INFO @ Mon, 03 Jun 2019 22:59:54: #2 alternative fragment length(s) may be 67 bps INFO @ Mon, 03 Jun 2019 22:59:54: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX5343100/SRX5343100.05_model.r WARNING @ Mon, 03 Jun 2019 22:59:54: #2 Since the d (67) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 03 Jun 2019 22:59:54: #2 You may need to consider one of the other alternative d(s): 67 WARNING @ Mon, 03 Jun 2019 22:59:54: #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 22:59:54: #3 Call peaks... INFO @ Mon, 03 Jun 2019 22:59:54: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 23:00:19: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 23:00:24: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 23:00:32: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 23:00:45: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX5343100/SRX5343100.20_peaks.xls INFO @ Mon, 03 Jun 2019 23:00:45: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX5343100/SRX5343100.20_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 23:00:45: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX5343100/SRX5343100.20_summits.bed INFO @ Mon, 03 Jun 2019 23:00:45: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX5343100/SRX5343100.10_peaks.xls INFO @ Mon, 03 Jun 2019 23:00:45: Done! INFO @ Mon, 03 Jun 2019 23:00:46: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX5343100/SRX5343100.10_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 23:00:46: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX5343100/SRX5343100.10_summits.bed INFO @ Mon, 03 Jun 2019 23:00:46: Done! pass1 - making usageList (13 chroms): 2 millis pass2 - checking and writing primary data (1615 records, 4 fields): 6 millis CompletedMACS2peakCalling pass1 - making usageList (14 chroms): 3 millis pass2 - checking and writing primary data (4422 records, 4 fields): 14 millis CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 23:00:52: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX5343100/SRX5343100.05_peaks.xls INFO @ Mon, 03 Jun 2019 23:00:52: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX5343100/SRX5343100.05_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 23:00:52: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX5343100/SRX5343100.05_summits.bed INFO @ Mon, 03 Jun 2019 23:00:52: Done! pass1 - making usageList (15 chroms): 3 millis pass2 - checking and writing primary data (11877 records, 4 fields): 34 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。