Job ID = 2590479 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 8,581,094 reads read : 17,162,188 reads written : 8,581,094 reads 0-length : 8,581,094 spots read : 8,577,033 reads read : 17,154,066 reads written : 8,577,033 reads 0-length : 8,577,033 spots read : 8,610,938 reads read : 17,221,876 reads written : 8,610,938 reads 0-length : 8,610,938 spots read : 8,649,782 reads read : 17,299,564 reads written : 8,649,782 reads 0-length : 8,649,782 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: 00:00:01 Time loading mirror index: 00:00:00 Multiseed full-index search: 00:14:08 34418847 reads; of these: 34418847 (100.00%) were unpaired; of these: 1365399 (3.97%) aligned 0 times 24614493 (71.51%) aligned exactly 1 time 8438955 (24.52%) aligned >1 times 96.03% overall alignment rate Time searching: 00:14:09 Overall time: 00:14:09 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 16 files... [bam_rmdupse_core] 4696223 / 33053448 = 0.1421 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, 12 Aug 2019 22:26:29: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX3981709/SRX3981709.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX3981709/SRX3981709.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX3981709/SRX3981709.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX3981709/SRX3981709.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, 12 Aug 2019 22:26:29: #1 read tag files... INFO @ Mon, 12 Aug 2019 22:26:29: #1 read treatment tags... INFO @ Mon, 12 Aug 2019 22:26:30: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX3981709/SRX3981709.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX3981709/SRX3981709.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX3981709/SRX3981709.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX3981709/SRX3981709.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, 12 Aug 2019 22:26:30: #1 read tag files... INFO @ Mon, 12 Aug 2019 22:26:30: #1 read treatment tags... INFO @ Mon, 12 Aug 2019 22:26:31: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX3981709/SRX3981709.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX3981709/SRX3981709.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX3981709/SRX3981709.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX3981709/SRX3981709.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, 12 Aug 2019 22:26:31: #1 read tag files... INFO @ Mon, 12 Aug 2019 22:26:31: #1 read treatment tags... INFO @ Mon, 12 Aug 2019 22:26:37: 1000000 INFO @ Mon, 12 Aug 2019 22:26:38: 1000000 INFO @ Mon, 12 Aug 2019 22:26:40: 1000000 INFO @ Mon, 12 Aug 2019 22:26:45: 2000000 INFO @ Mon, 12 Aug 2019 22:26:46: 2000000 INFO @ Mon, 12 Aug 2019 22:26:48: 2000000 INFO @ Mon, 12 Aug 2019 22:26:54: 3000000 INFO @ Mon, 12 Aug 2019 22:26:55: 3000000 INFO @ Mon, 12 Aug 2019 22:26:57: 3000000 INFO @ Mon, 12 Aug 2019 22:27:02: 4000000 INFO @ Mon, 12 Aug 2019 22:27:03: 4000000 INFO @ Mon, 12 Aug 2019 22:27:05: 4000000 INFO @ Mon, 12 Aug 2019 22:27:10: 5000000 INFO @ Mon, 12 Aug 2019 22:27:11: 5000000 INFO @ Mon, 12 Aug 2019 22:27:14: 5000000 INFO @ Mon, 12 Aug 2019 22:27:18: 6000000 INFO @ Mon, 12 Aug 2019 22:27:19: 6000000 INFO @ Mon, 12 Aug 2019 22:27:22: 6000000 INFO @ Mon, 12 Aug 2019 22:27:26: 7000000 INFO @ Mon, 12 Aug 2019 22:27:27: 7000000 INFO @ Mon, 12 Aug 2019 22:27:31: 7000000 INFO @ Mon, 12 Aug 2019 22:27:35: 8000000 INFO @ Mon, 12 Aug 2019 22:27:36: 8000000 INFO @ Mon, 12 Aug 2019 22:27:39: 8000000 INFO @ Mon, 12 Aug 2019 22:27:43: 9000000 INFO @ Mon, 12 Aug 2019 22:27:44: 9000000 INFO @ Mon, 12 Aug 2019 22:27:48: 9000000 INFO @ Mon, 12 Aug 2019 22:27:51: 10000000 INFO @ Mon, 12 Aug 2019 22:27:52: 10000000 INFO @ Mon, 12 Aug 2019 22:27:56: 10000000 INFO @ Mon, 12 Aug 2019 22:27:59: 11000000 INFO @ Mon, 12 Aug 2019 22:28:00: 11000000 INFO @ Mon, 12 Aug 2019 22:28:04: 11000000 INFO @ Mon, 12 Aug 2019 22:28:06: 12000000 INFO @ Mon, 12 Aug 2019 22:28:07: 12000000 INFO @ Mon, 12 Aug 2019 22:28:13: 12000000 INFO @ Mon, 12 Aug 2019 22:28:14: 13000000 INFO @ Mon, 12 Aug 2019 22:28:14: 13000000 INFO @ Mon, 12 Aug 2019 22:28:21: 13000000 INFO @ Mon, 12 Aug 2019 22:28:22: 14000000 INFO @ Mon, 12 Aug 2019 22:28:22: 14000000 INFO @ Mon, 12 Aug 2019 22:28:29: 14000000 INFO @ Mon, 12 Aug 2019 22:28:30: 15000000 INFO @ Mon, 12 Aug 2019 22:28:30: 15000000 INFO @ Mon, 12 Aug 2019 22:28:38: 15000000 INFO @ Mon, 12 Aug 2019 22:28:38: 16000000 INFO @ Mon, 12 Aug 2019 22:28:38: 16000000 INFO @ Mon, 12 Aug 2019 22:28:46: 16000000 INFO @ Mon, 12 Aug 2019 22:28:46: 17000000 INFO @ Mon, 12 Aug 2019 22:28:46: 17000000 INFO @ Mon, 12 Aug 2019 22:28:54: 18000000 INFO @ Mon, 12 Aug 2019 22:28:54: 17000000 INFO @ Mon, 12 Aug 2019 22:28:55: 18000000 INFO @ Mon, 12 Aug 2019 22:29:02: 19000000 INFO @ Mon, 12 Aug 2019 22:29:02: 18000000 INFO @ Mon, 12 Aug 2019 22:29:03: 19000000 INFO @ Mon, 12 Aug 2019 22:29:10: 20000000 INFO @ Mon, 12 Aug 2019 22:29:10: 20000000 INFO @ Mon, 12 Aug 2019 22:29:11: 19000000 INFO @ Mon, 12 Aug 2019 22:29:17: 21000000 INFO @ Mon, 12 Aug 2019 22:29:17: 21000000 INFO @ Mon, 12 Aug 2019 22:29:19: 20000000 INFO @ Mon, 12 Aug 2019 22:29:24: 22000000 INFO @ Mon, 12 Aug 2019 22:29:24: 22000000 INFO @ Mon, 12 Aug 2019 22:29:27: 21000000 INFO @ Mon, 12 Aug 2019 22:29:31: 23000000 INFO @ Mon, 12 Aug 2019 22:29:31: 23000000 INFO @ Mon, 12 Aug 2019 22:29:35: 22000000 INFO @ Mon, 12 Aug 2019 22:29:37: 24000000 INFO @ Mon, 12 Aug 2019 22:29:38: 24000000 INFO @ Mon, 12 Aug 2019 22:29:44: 23000000 INFO @ Mon, 12 Aug 2019 22:29:44: 25000000 INFO @ Mon, 12 Aug 2019 22:29:45: 25000000 INFO @ Mon, 12 Aug 2019 22:29:51: 26000000 INFO @ Mon, 12 Aug 2019 22:29:52: 24000000 INFO @ Mon, 12 Aug 2019 22:29:52: 26000000 INFO @ Mon, 12 Aug 2019 22:29:57: 27000000 INFO @ Mon, 12 Aug 2019 22:30:00: 27000000 INFO @ Mon, 12 Aug 2019 22:30:00: 25000000 INFO @ Mon, 12 Aug 2019 22:30:04: 28000000 INFO @ Mon, 12 Aug 2019 22:30:07: #1 tag size is determined as 51 bps INFO @ Mon, 12 Aug 2019 22:30:07: #1 tag size = 51 INFO @ Mon, 12 Aug 2019 22:30:07: #1 total tags in treatment: 28357225 INFO @ Mon, 12 Aug 2019 22:30:07: #1 user defined the maximum tags... INFO @ Mon, 12 Aug 2019 22:30:07: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Mon, 12 Aug 2019 22:30:07: 28000000 INFO @ Mon, 12 Aug 2019 22:30:07: #1 tags after filtering in treatment: 28357225 INFO @ Mon, 12 Aug 2019 22:30:07: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 12 Aug 2019 22:30:07: #1 finished! INFO @ Mon, 12 Aug 2019 22:30:07: #2 Build Peak Model... INFO @ Mon, 12 Aug 2019 22:30:07: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 12 Aug 2019 22:30:09: 26000000 INFO @ Mon, 12 Aug 2019 22:30:09: #1 tag size is determined as 51 bps INFO @ Mon, 12 Aug 2019 22:30:09: #1 tag size = 51 INFO @ Mon, 12 Aug 2019 22:30:09: #1 total tags in treatment: 28357225 INFO @ Mon, 12 Aug 2019 22:30:09: #1 user defined the maximum tags... INFO @ Mon, 12 Aug 2019 22:30:09: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Mon, 12 Aug 2019 22:30:10: #2 number of paired peaks: 134 WARNING @ Mon, 12 Aug 2019 22:30:10: Fewer paired peaks (134) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 134 pairs to build model! INFO @ Mon, 12 Aug 2019 22:30:10: start model_add_line... INFO @ Mon, 12 Aug 2019 22:30:10: start X-correlation... INFO @ Mon, 12 Aug 2019 22:30:10: end of X-cor INFO @ Mon, 12 Aug 2019 22:30:10: #2 finished! INFO @ Mon, 12 Aug 2019 22:30:10: #2 predicted fragment length is 52 bps INFO @ Mon, 12 Aug 2019 22:30:10: #2 alternative fragment length(s) may be 2,52,595 bps INFO @ Mon, 12 Aug 2019 22:30:10: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX3981709/SRX3981709.10_model.r WARNING @ Mon, 12 Aug 2019 22:30:10: #2 Since the d (52) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 12 Aug 2019 22:30:10: #2 You may need to consider one of the other alternative d(s): 2,52,595 WARNING @ Mon, 12 Aug 2019 22:30:10: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Mon, 12 Aug 2019 22:30:10: #3 Call peaks... INFO @ Mon, 12 Aug 2019 22:30:10: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 12 Aug 2019 22:30:10: #1 tags after filtering in treatment: 28357225 INFO @ Mon, 12 Aug 2019 22:30:10: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 12 Aug 2019 22:30:10: #1 finished! INFO @ Mon, 12 Aug 2019 22:30:10: #2 Build Peak Model... INFO @ Mon, 12 Aug 2019 22:30:10: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 12 Aug 2019 22:30:12: #2 number of paired peaks: 134 WARNING @ Mon, 12 Aug 2019 22:30:12: Fewer paired peaks (134) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 134 pairs to build model! INFO @ Mon, 12 Aug 2019 22:30:12: start model_add_line... INFO @ Mon, 12 Aug 2019 22:30:13: start X-correlation... INFO @ Mon, 12 Aug 2019 22:30:13: end of X-cor INFO @ Mon, 12 Aug 2019 22:30:13: #2 finished! INFO @ Mon, 12 Aug 2019 22:30:13: #2 predicted fragment length is 52 bps INFO @ Mon, 12 Aug 2019 22:30:13: #2 alternative fragment length(s) may be 2,52,595 bps INFO @ Mon, 12 Aug 2019 22:30:13: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX3981709/SRX3981709.05_model.r WARNING @ Mon, 12 Aug 2019 22:30:13: #2 Since the d (52) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 12 Aug 2019 22:30:13: #2 You may need to consider one of the other alternative d(s): 2,52,595 WARNING @ Mon, 12 Aug 2019 22:30:13: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Mon, 12 Aug 2019 22:30:13: #3 Call peaks... INFO @ Mon, 12 Aug 2019 22:30:13: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 12 Aug 2019 22:30:17: 27000000 INFO @ Mon, 12 Aug 2019 22:30:25: 28000000 INFO @ Mon, 12 Aug 2019 22:30:28: #1 tag size is determined as 51 bps INFO @ Mon, 12 Aug 2019 22:30:28: #1 tag size = 51 INFO @ Mon, 12 Aug 2019 22:30:28: #1 total tags in treatment: 28357225 INFO @ Mon, 12 Aug 2019 22:30:28: #1 user defined the maximum tags... INFO @ Mon, 12 Aug 2019 22:30:28: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Mon, 12 Aug 2019 22:30:28: #1 tags after filtering in treatment: 28357225 INFO @ Mon, 12 Aug 2019 22:30:28: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 12 Aug 2019 22:30:28: #1 finished! INFO @ Mon, 12 Aug 2019 22:30:28: #2 Build Peak Model... INFO @ Mon, 12 Aug 2019 22:30:28: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 12 Aug 2019 22:30:31: #2 number of paired peaks: 134 WARNING @ Mon, 12 Aug 2019 22:30:31: Fewer paired peaks (134) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 134 pairs to build model! INFO @ Mon, 12 Aug 2019 22:30:31: start model_add_line... INFO @ Mon, 12 Aug 2019 22:30:31: start X-correlation... INFO @ Mon, 12 Aug 2019 22:30:31: end of X-cor INFO @ Mon, 12 Aug 2019 22:30:31: #2 finished! INFO @ Mon, 12 Aug 2019 22:30:31: #2 predicted fragment length is 52 bps INFO @ Mon, 12 Aug 2019 22:30:31: #2 alternative fragment length(s) may be 2,52,595 bps INFO @ Mon, 12 Aug 2019 22:30:31: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX3981709/SRX3981709.20_model.r WARNING @ Mon, 12 Aug 2019 22:30:31: #2 Since the d (52) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 12 Aug 2019 22:30:31: #2 You may need to consider one of the other alternative d(s): 2,52,595 WARNING @ Mon, 12 Aug 2019 22:30:31: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Mon, 12 Aug 2019 22:30:31: #3 Call peaks... INFO @ Mon, 12 Aug 2019 22:30:31: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 12 Aug 2019 22:31:15: #3 Call peaks for each chromosome... INFO @ Mon, 12 Aug 2019 22:31:19: #3 Call peaks for each chromosome... INFO @ Mon, 12 Aug 2019 22:31:36: #3 Call peaks for each chromosome... INFO @ Mon, 12 Aug 2019 22:31:48: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX3981709/SRX3981709.10_peaks.xls INFO @ Mon, 12 Aug 2019 22:31:48: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX3981709/SRX3981709.10_peaks.narrowPeak INFO @ Mon, 12 Aug 2019 22:31:48: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX3981709/SRX3981709.10_summits.bed INFO @ Mon, 12 Aug 2019 22:31:48: Done! pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (1480 records, 4 fields): 26 millis CompletedMACS2peakCalling INFO @ Mon, 12 Aug 2019 22:31:52: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX3981709/SRX3981709.05_peaks.xls INFO @ Mon, 12 Aug 2019 22:31:52: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX3981709/SRX3981709.05_peaks.narrowPeak INFO @ Mon, 12 Aug 2019 22:31:52: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX3981709/SRX3981709.05_summits.bed INFO @ Mon, 12 Aug 2019 22:31:52: Done! pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (2799 records, 4 fields): 10 millis CompletedMACS2peakCalling INFO @ Mon, 12 Aug 2019 22:32:11: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX3981709/SRX3981709.20_peaks.xls INFO @ Mon, 12 Aug 2019 22:32:11: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX3981709/SRX3981709.20_peaks.narrowPeak INFO @ Mon, 12 Aug 2019 22:32:11: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX3981709/SRX3981709.20_summits.bed INFO @ Mon, 12 Aug 2019 22:32:11: Done! pass1 - making usageList (11 chroms): 2 millis pass2 - checking and writing primary data (450 records, 4 fields): 2 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。