Job ID = 1294481 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 18,630,340 reads read : 18,630,340 reads written : 18,630,340 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: 00:06:18 18630340 reads; of these: 18630340 (100.00%) were unpaired; of these: 1155493 (6.20%) aligned 0 times 15418406 (82.76%) aligned exactly 1 time 2056441 (11.04%) aligned >1 times 93.80% overall alignment rate Time searching: 00:06:18 Overall time: 00:06:18 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] 1255643 / 17474847 = 0.0719 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 08:37:37: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX287683/SRX287683.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX287683/SRX287683.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX287683/SRX287683.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX287683/SRX287683.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 08:37:37: #1 read tag files... INFO @ Mon, 03 Jun 2019 08:37:37: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 08:37:37: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX287683/SRX287683.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX287683/SRX287683.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX287683/SRX287683.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX287683/SRX287683.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 08:37:37: #1 read tag files... INFO @ Mon, 03 Jun 2019 08:37:37: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 08:37:37: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX287683/SRX287683.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX287683/SRX287683.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX287683/SRX287683.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX287683/SRX287683.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 08:37:37: #1 read tag files... INFO @ Mon, 03 Jun 2019 08:37:37: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 08:37:46: 1000000 INFO @ Mon, 03 Jun 2019 08:37:47: 1000000 INFO @ Mon, 03 Jun 2019 08:37:48: 1000000 INFO @ Mon, 03 Jun 2019 08:37:56: 2000000 INFO @ Mon, 03 Jun 2019 08:37:56: 2000000 INFO @ Mon, 03 Jun 2019 08:37:58: 2000000 INFO @ Mon, 03 Jun 2019 08:38:05: 3000000 INFO @ Mon, 03 Jun 2019 08:38:06: 3000000 INFO @ Mon, 03 Jun 2019 08:38:08: 3000000 INFO @ Mon, 03 Jun 2019 08:38:14: 4000000 INFO @ Mon, 03 Jun 2019 08:38:15: 4000000 INFO @ Mon, 03 Jun 2019 08:38:17: 4000000 INFO @ Mon, 03 Jun 2019 08:38:24: 5000000 INFO @ Mon, 03 Jun 2019 08:38:25: 5000000 INFO @ Mon, 03 Jun 2019 08:38:26: 5000000 INFO @ Mon, 03 Jun 2019 08:38:33: 6000000 INFO @ Mon, 03 Jun 2019 08:38:35: 6000000 INFO @ Mon, 03 Jun 2019 08:38:35: 6000000 INFO @ Mon, 03 Jun 2019 08:38:42: 7000000 INFO @ Mon, 03 Jun 2019 08:38:44: 7000000 INFO @ Mon, 03 Jun 2019 08:38:44: 7000000 INFO @ Mon, 03 Jun 2019 08:38:52: 8000000 INFO @ Mon, 03 Jun 2019 08:38:53: 8000000 INFO @ Mon, 03 Jun 2019 08:38:54: 8000000 INFO @ Mon, 03 Jun 2019 08:39:01: 9000000 INFO @ Mon, 03 Jun 2019 08:39:01: 9000000 INFO @ Mon, 03 Jun 2019 08:39:03: 9000000 INFO @ Mon, 03 Jun 2019 08:39:10: 10000000 INFO @ Mon, 03 Jun 2019 08:39:11: 10000000 INFO @ Mon, 03 Jun 2019 08:39:13: 10000000 INFO @ Mon, 03 Jun 2019 08:39:20: 11000000 INFO @ Mon, 03 Jun 2019 08:39:20: 11000000 INFO @ Mon, 03 Jun 2019 08:39:22: 11000000 INFO @ Mon, 03 Jun 2019 08:39:28: 12000000 INFO @ Mon, 03 Jun 2019 08:39:29: 12000000 INFO @ Mon, 03 Jun 2019 08:39:31: 12000000 INFO @ Mon, 03 Jun 2019 08:39:37: 13000000 INFO @ Mon, 03 Jun 2019 08:39:38: 13000000 INFO @ Mon, 03 Jun 2019 08:39:41: 13000000 INFO @ Mon, 03 Jun 2019 08:39:46: 14000000 INFO @ Mon, 03 Jun 2019 08:39:47: 14000000 INFO @ Mon, 03 Jun 2019 08:39:50: 14000000 INFO @ Mon, 03 Jun 2019 08:39:55: 15000000 INFO @ Mon, 03 Jun 2019 08:39:57: 15000000 INFO @ Mon, 03 Jun 2019 08:39:59: 15000000 INFO @ Mon, 03 Jun 2019 08:40:04: 16000000 INFO @ Mon, 03 Jun 2019 08:40:06: #1 tag size is determined as 50 bps INFO @ Mon, 03 Jun 2019 08:40:06: #1 tag size = 50 INFO @ Mon, 03 Jun 2019 08:40:06: #1 total tags in treatment: 16219204 INFO @ Mon, 03 Jun 2019 08:40:06: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 08:40:06: #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 08:40:06: 16000000 INFO @ Mon, 03 Jun 2019 08:40:06: #1 tags after filtering in treatment: 16219204 INFO @ Mon, 03 Jun 2019 08:40:06: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 08:40:06: #1 finished! INFO @ Mon, 03 Jun 2019 08:40:06: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 08:40:06: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 08:40:08: #2 number of paired peaks: 135 WARNING @ Mon, 03 Jun 2019 08:40:08: Fewer paired peaks (135) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 135 pairs to build model! INFO @ Mon, 03 Jun 2019 08:40:08: start model_add_line... INFO @ Mon, 03 Jun 2019 08:40:08: #1 tag size is determined as 50 bps INFO @ Mon, 03 Jun 2019 08:40:08: #1 tag size = 50 INFO @ Mon, 03 Jun 2019 08:40:08: #1 total tags in treatment: 16219204 INFO @ Mon, 03 Jun 2019 08:40:08: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 08:40:08: #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 08:40:08: start X-correlation... INFO @ Mon, 03 Jun 2019 08:40:08: end of X-cor INFO @ Mon, 03 Jun 2019 08:40:08: #2 finished! INFO @ Mon, 03 Jun 2019 08:40:08: #2 predicted fragment length is 74 bps INFO @ Mon, 03 Jun 2019 08:40:08: #2 alternative fragment length(s) may be 3,74,108,139,167,199,572 bps INFO @ Mon, 03 Jun 2019 08:40:08: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX287683/SRX287683.20_model.r WARNING @ Mon, 03 Jun 2019 08:40:08: #2 Since the d (74) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 03 Jun 2019 08:40:08: #2 You may need to consider one of the other alternative d(s): 3,74,108,139,167,199,572 WARNING @ Mon, 03 Jun 2019 08:40:08: #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 08:40:08: #3 Call peaks... INFO @ Mon, 03 Jun 2019 08:40:08: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 08:40:08: #1 tags after filtering in treatment: 16219204 INFO @ Mon, 03 Jun 2019 08:40:08: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 08:40:08: #1 finished! INFO @ Mon, 03 Jun 2019 08:40:08: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 08:40:08: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 08:40:09: 16000000 INFO @ Mon, 03 Jun 2019 08:40:10: #2 number of paired peaks: 135 WARNING @ Mon, 03 Jun 2019 08:40:10: Fewer paired peaks (135) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 135 pairs to build model! INFO @ Mon, 03 Jun 2019 08:40:10: start model_add_line... INFO @ Mon, 03 Jun 2019 08:40:10: start X-correlation... INFO @ Mon, 03 Jun 2019 08:40:10: end of X-cor INFO @ Mon, 03 Jun 2019 08:40:10: #2 finished! INFO @ Mon, 03 Jun 2019 08:40:10: #2 predicted fragment length is 74 bps INFO @ Mon, 03 Jun 2019 08:40:10: #2 alternative fragment length(s) may be 3,74,108,139,167,199,572 bps INFO @ Mon, 03 Jun 2019 08:40:10: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX287683/SRX287683.05_model.r WARNING @ Mon, 03 Jun 2019 08:40:10: #2 Since the d (74) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 03 Jun 2019 08:40:10: #2 You may need to consider one of the other alternative d(s): 3,74,108,139,167,199,572 WARNING @ Mon, 03 Jun 2019 08:40:10: #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 08:40:10: #3 Call peaks... INFO @ Mon, 03 Jun 2019 08:40:10: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 08:40:11: #1 tag size is determined as 50 bps INFO @ Mon, 03 Jun 2019 08:40:11: #1 tag size = 50 INFO @ Mon, 03 Jun 2019 08:40:11: #1 total tags in treatment: 16219204 INFO @ Mon, 03 Jun 2019 08:40:11: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 08:40:11: #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 08:40:11: #1 tags after filtering in treatment: 16219204 INFO @ Mon, 03 Jun 2019 08:40:11: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 08:40:11: #1 finished! INFO @ Mon, 03 Jun 2019 08:40:11: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 08:40:11: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 08:40:13: #2 number of paired peaks: 135 WARNING @ Mon, 03 Jun 2019 08:40:13: Fewer paired peaks (135) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 135 pairs to build model! INFO @ Mon, 03 Jun 2019 08:40:13: start model_add_line... INFO @ Mon, 03 Jun 2019 08:40:13: start X-correlation... INFO @ Mon, 03 Jun 2019 08:40:13: end of X-cor INFO @ Mon, 03 Jun 2019 08:40:13: #2 finished! INFO @ Mon, 03 Jun 2019 08:40:13: #2 predicted fragment length is 74 bps INFO @ Mon, 03 Jun 2019 08:40:13: #2 alternative fragment length(s) may be 3,74,108,139,167,199,572 bps INFO @ Mon, 03 Jun 2019 08:40:13: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX287683/SRX287683.10_model.r WARNING @ Mon, 03 Jun 2019 08:40:13: #2 Since the d (74) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 03 Jun 2019 08:40:13: #2 You may need to consider one of the other alternative d(s): 3,74,108,139,167,199,572 WARNING @ Mon, 03 Jun 2019 08:40:13: #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 08:40:13: #3 Call peaks... INFO @ Mon, 03 Jun 2019 08:40:13: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 08:40:57: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 08:40:59: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 08:41:02: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 08:41:21: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX287683/SRX287683.20_peaks.xls INFO @ Mon, 03 Jun 2019 08:41:21: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX287683/SRX287683.20_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 08:41:21: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX287683/SRX287683.20_summits.bed INFO @ Mon, 03 Jun 2019 08:41:21: Done! pass1 - making usageList (8 chroms): 1 millis pass2 - checking and writing primary data (142 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 08:41:23: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX287683/SRX287683.05_peaks.xls INFO @ Mon, 03 Jun 2019 08:41:23: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX287683/SRX287683.05_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 08:41:23: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX287683/SRX287683.05_summits.bed INFO @ Mon, 03 Jun 2019 08:41:23: Done! pass1 - making usageList (13 chroms): 1 millis pass2 - checking and writing primary data (1322 records, 4 fields): 6 millis CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 08:41:27: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX287683/SRX287683.10_peaks.xls INFO @ Mon, 03 Jun 2019 08:41:27: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX287683/SRX287683.10_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 08:41:27: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX287683/SRX287683.10_summits.bed INFO @ Mon, 03 Jun 2019 08:41:27: Done! pass1 - making usageList (12 chroms): 1 millis pass2 - checking and writing primary data (419 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。