Job ID = 4178542 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 27,764,747 reads read : 27,764,747 reads written : 27,764,747 rm: cannot remove ‘[DSE]RR*’: 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: 00:07:36 27764747 reads; of these: 27764747 (100.00%) were unpaired; of these: 546412 (1.97%) aligned 0 times 21519412 (77.51%) aligned exactly 1 time 5698923 (20.53%) aligned >1 times 98.03% overall alignment rate Time searching: 00:07:36 Overall time: 00:07:36 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] 10616231 / 27218335 = 0.3900 in library ' ' BAM に変換しました。 Bed ファイルを作成中... INFO @ Thu, 05 Dec 2019 13:12:25: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX5736593/SRX5736593.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX5736593/SRX5736593.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX5736593/SRX5736593.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX5736593/SRX5736593.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 @ Thu, 05 Dec 2019 13:12:25: #1 read tag files... INFO @ Thu, 05 Dec 2019 13:12:25: #1 read treatment tags... INFO @ Thu, 05 Dec 2019 13:12:32: 1000000 INFO @ Thu, 05 Dec 2019 13:12:38: 2000000 INFO @ Thu, 05 Dec 2019 13:12:44: 3000000 INFO @ Thu, 05 Dec 2019 13:12:51: 4000000 INFO @ Thu, 05 Dec 2019 13:12:55: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX5736593/SRX5736593.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX5736593/SRX5736593.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX5736593/SRX5736593.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX5736593/SRX5736593.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 @ Thu, 05 Dec 2019 13:12:55: #1 read tag files... INFO @ Thu, 05 Dec 2019 13:12:55: #1 read treatment tags... INFO @ Thu, 05 Dec 2019 13:12:59: 5000000 INFO @ Thu, 05 Dec 2019 13:13:01: 1000000 INFO @ Thu, 05 Dec 2019 13:13:05: 6000000 INFO @ Thu, 05 Dec 2019 13:13:07: 2000000 INFO @ Thu, 05 Dec 2019 13:13:12: 7000000 INFO @ Thu, 05 Dec 2019 13:13:13: 3000000 INFO @ Thu, 05 Dec 2019 13:13:18: 4000000 INFO @ Thu, 05 Dec 2019 13:13:19: 8000000 BedGraph に変換中... INFO @ Thu, 05 Dec 2019 13:13:25: 5000000 INFO @ Thu, 05 Dec 2019 13:13:25: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX5736593/SRX5736593.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX5736593/SRX5736593.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX5736593/SRX5736593.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX5736593/SRX5736593.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 @ Thu, 05 Dec 2019 13:13:25: #1 read tag files... INFO @ Thu, 05 Dec 2019 13:13:25: #1 read treatment tags... INFO @ Thu, 05 Dec 2019 13:13:26: 9000000 INFO @ Thu, 05 Dec 2019 13:13:31: 6000000 INFO @ Thu, 05 Dec 2019 13:13:32: 1000000 INFO @ Thu, 05 Dec 2019 13:13:33: 10000000 INFO @ Thu, 05 Dec 2019 13:13:37: 7000000 INFO @ Thu, 05 Dec 2019 13:13:39: 2000000 INFO @ Thu, 05 Dec 2019 13:13:41: 11000000 INFO @ Thu, 05 Dec 2019 13:13:43: 8000000 INFO @ Thu, 05 Dec 2019 13:13:45: 3000000 INFO @ Thu, 05 Dec 2019 13:13:48: 12000000 INFO @ Thu, 05 Dec 2019 13:13:49: 9000000 INFO @ Thu, 05 Dec 2019 13:13:52: 4000000 INFO @ Thu, 05 Dec 2019 13:13:55: 10000000 INFO @ Thu, 05 Dec 2019 13:13:55: 13000000 INFO @ Thu, 05 Dec 2019 13:13:59: 5000000 INFO @ Thu, 05 Dec 2019 13:14:01: 11000000 INFO @ Thu, 05 Dec 2019 13:14:02: 14000000 INFO @ Thu, 05 Dec 2019 13:14:05: 6000000 INFO @ Thu, 05 Dec 2019 13:14:08: 12000000 INFO @ Thu, 05 Dec 2019 13:14:09: 15000000 INFO @ Thu, 05 Dec 2019 13:14:12: 7000000 INFO @ Thu, 05 Dec 2019 13:14:14: 13000000 INFO @ Thu, 05 Dec 2019 13:14:16: 16000000 INFO @ Thu, 05 Dec 2019 13:14:19: 8000000 INFO @ Thu, 05 Dec 2019 13:14:20: #1 tag size is determined as 50 bps INFO @ Thu, 05 Dec 2019 13:14:20: #1 tag size = 50 INFO @ Thu, 05 Dec 2019 13:14:20: #1 total tags in treatment: 16602104 INFO @ Thu, 05 Dec 2019 13:14:20: #1 user defined the maximum tags... INFO @ Thu, 05 Dec 2019 13:14:20: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Thu, 05 Dec 2019 13:14:20: #1 tags after filtering in treatment: 16602104 INFO @ Thu, 05 Dec 2019 13:14:20: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 05 Dec 2019 13:14:20: #1 finished! INFO @ Thu, 05 Dec 2019 13:14:20: #2 Build Peak Model... INFO @ Thu, 05 Dec 2019 13:14:20: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 05 Dec 2019 13:14:21: 14000000 INFO @ Thu, 05 Dec 2019 13:14:21: #2 number of paired peaks: 360 WARNING @ Thu, 05 Dec 2019 13:14:21: Fewer paired peaks (360) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 360 pairs to build model! INFO @ Thu, 05 Dec 2019 13:14:21: start model_add_line... INFO @ Thu, 05 Dec 2019 13:14:21: start X-correlation... INFO @ Thu, 05 Dec 2019 13:14:21: end of X-cor INFO @ Thu, 05 Dec 2019 13:14:21: #2 finished! INFO @ Thu, 05 Dec 2019 13:14:21: #2 predicted fragment length is 46 bps INFO @ Thu, 05 Dec 2019 13:14:21: #2 alternative fragment length(s) may be 21,46,63,67,86,107,139,166,194,286,313,408,432,490,516,536,592 bps INFO @ Thu, 05 Dec 2019 13:14:21: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX5736593/SRX5736593.05_model.r WARNING @ Thu, 05 Dec 2019 13:14:21: #2 Since the d (46) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 05 Dec 2019 13:14:21: #2 You may need to consider one of the other alternative d(s): 21,46,63,67,86,107,139,166,194,286,313,408,432,490,516,536,592 WARNING @ Thu, 05 Dec 2019 13:14:21: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Thu, 05 Dec 2019 13:14:21: #3 Call peaks... INFO @ Thu, 05 Dec 2019 13:14:21: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 05 Dec 2019 13:14:26: 9000000 INFO @ Thu, 05 Dec 2019 13:14:27: 15000000 INFO @ Thu, 05 Dec 2019 13:14:33: 10000000 INFO @ Thu, 05 Dec 2019 13:14:33: 16000000 INFO @ Thu, 05 Dec 2019 13:14:36: #1 tag size is determined as 50 bps INFO @ Thu, 05 Dec 2019 13:14:36: #1 tag size = 50 INFO @ Thu, 05 Dec 2019 13:14:36: #1 total tags in treatment: 16602104 INFO @ Thu, 05 Dec 2019 13:14:36: #1 user defined the maximum tags... INFO @ Thu, 05 Dec 2019 13:14:36: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Thu, 05 Dec 2019 13:14:37: #1 tags after filtering in treatment: 16602104 INFO @ Thu, 05 Dec 2019 13:14:37: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 05 Dec 2019 13:14:37: #1 finished! INFO @ Thu, 05 Dec 2019 13:14:37: #2 Build Peak Model... INFO @ Thu, 05 Dec 2019 13:14:37: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 05 Dec 2019 13:14:38: #2 number of paired peaks: 360 WARNING @ Thu, 05 Dec 2019 13:14:38: Fewer paired peaks (360) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 360 pairs to build model! INFO @ Thu, 05 Dec 2019 13:14:38: start model_add_line... INFO @ Thu, 05 Dec 2019 13:14:38: start X-correlation... INFO @ Thu, 05 Dec 2019 13:14:38: end of X-cor INFO @ Thu, 05 Dec 2019 13:14:38: #2 finished! INFO @ Thu, 05 Dec 2019 13:14:38: #2 predicted fragment length is 46 bps INFO @ Thu, 05 Dec 2019 13:14:38: #2 alternative fragment length(s) may be 21,46,63,67,86,107,139,166,194,286,313,408,432,490,516,536,592 bps INFO @ Thu, 05 Dec 2019 13:14:38: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX5736593/SRX5736593.10_model.r WARNING @ Thu, 05 Dec 2019 13:14:38: #2 Since the d (46) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 05 Dec 2019 13:14:38: #2 You may need to consider one of the other alternative d(s): 21,46,63,67,86,107,139,166,194,286,313,408,432,490,516,536,592 WARNING @ Thu, 05 Dec 2019 13:14:38: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Thu, 05 Dec 2019 13:14:38: #3 Call peaks... INFO @ Thu, 05 Dec 2019 13:14:38: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 05 Dec 2019 13:14:39: 11000000 INFO @ Thu, 05 Dec 2019 13:14:46: 12000000 INFO @ Thu, 05 Dec 2019 13:14:52: #3 Call peaks for each chromosome... INFO @ Thu, 05 Dec 2019 13:14:53: 13000000 INFO @ Thu, 05 Dec 2019 13:15:00: 14000000 INFO @ Thu, 05 Dec 2019 13:15:06: 15000000 INFO @ Thu, 05 Dec 2019 13:15:07: #3 Call peaks for each chromosome... INFO @ Thu, 05 Dec 2019 13:15:10: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX5736593/SRX5736593.05_peaks.xls INFO @ Thu, 05 Dec 2019 13:15:10: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX5736593/SRX5736593.05_peaks.narrowPeak INFO @ Thu, 05 Dec 2019 13:15:10: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX5736593/SRX5736593.05_summits.bed INFO @ Thu, 05 Dec 2019 13:15:10: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (2750 records, 4 fields): 5 millis CompletedMACS2peakCalling INFO @ Thu, 05 Dec 2019 13:15:13: 16000000 INFO @ Thu, 05 Dec 2019 13:15:16: #1 tag size is determined as 50 bps INFO @ Thu, 05 Dec 2019 13:15:16: #1 tag size = 50 INFO @ Thu, 05 Dec 2019 13:15:16: #1 total tags in treatment: 16602104 INFO @ Thu, 05 Dec 2019 13:15:16: #1 user defined the maximum tags... INFO @ Thu, 05 Dec 2019 13:15:16: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Thu, 05 Dec 2019 13:15:16: #1 tags after filtering in treatment: 16602104 INFO @ Thu, 05 Dec 2019 13:15:16: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 05 Dec 2019 13:15:16: #1 finished! INFO @ Thu, 05 Dec 2019 13:15:16: #2 Build Peak Model... INFO @ Thu, 05 Dec 2019 13:15:16: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 05 Dec 2019 13:15:18: #2 number of paired peaks: 360 WARNING @ Thu, 05 Dec 2019 13:15:18: Fewer paired peaks (360) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 360 pairs to build model! INFO @ Thu, 05 Dec 2019 13:15:18: start model_add_line... INFO @ Thu, 05 Dec 2019 13:15:18: start X-correlation... INFO @ Thu, 05 Dec 2019 13:15:18: end of X-cor INFO @ Thu, 05 Dec 2019 13:15:18: #2 finished! INFO @ Thu, 05 Dec 2019 13:15:18: #2 predicted fragment length is 46 bps INFO @ Thu, 05 Dec 2019 13:15:18: #2 alternative fragment length(s) may be 21,46,63,67,86,107,139,166,194,286,313,408,432,490,516,536,592 bps INFO @ Thu, 05 Dec 2019 13:15:18: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX5736593/SRX5736593.20_model.r WARNING @ Thu, 05 Dec 2019 13:15:18: #2 Since the d (46) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 05 Dec 2019 13:15:18: #2 You may need to consider one of the other alternative d(s): 21,46,63,67,86,107,139,166,194,286,313,408,432,490,516,536,592 WARNING @ Thu, 05 Dec 2019 13:15:18: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Thu, 05 Dec 2019 13:15:18: #3 Call peaks... INFO @ Thu, 05 Dec 2019 13:15:18: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 05 Dec 2019 13:15:24: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX5736593/SRX5736593.10_peaks.xls INFO @ Thu, 05 Dec 2019 13:15:24: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX5736593/SRX5736593.10_peaks.narrowPeak INFO @ Thu, 05 Dec 2019 13:15:24: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX5736593/SRX5736593.10_summits.bed INFO @ Thu, 05 Dec 2019 13:15:24: Done! pass1 - making usageList (11 chroms): 0 millis pass2 - checking and writing primary data (721 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Thu, 05 Dec 2019 13:15:48: #3 Call peaks for each chromosome... INFO @ Thu, 05 Dec 2019 13:16:05: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX5736593/SRX5736593.20_peaks.xls INFO @ Thu, 05 Dec 2019 13:16:05: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX5736593/SRX5736593.20_peaks.narrowPeak INFO @ Thu, 05 Dec 2019 13:16:05: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX5736593/SRX5736593.20_summits.bed INFO @ Thu, 05 Dec 2019 13:16:05: Done! pass1 - making usageList (2 chroms): 1 millis pass2 - checking and writing primary data (60 records, 4 fields): 17 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。