Job ID = 4178554 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 13,130,221 reads read : 26,260,442 reads written : 13,130,221 reads 0-length : 13,130,221 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: 00:03:08 13130221 reads; of these: 13130221 (100.00%) were unpaired; of these: 3327790 (25.34%) aligned 0 times 7731874 (58.89%) aligned exactly 1 time 2070557 (15.77%) aligned >1 times 74.66% overall alignment rate Time searching: 00:03:08 Overall time: 00:03:08 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_rmdupse_core] 5547367 / 9802431 = 0.5659 in library ' ' BAM に変換しました。 Bed ファイルを作成中... INFO @ Thu, 05 Dec 2019 13:10:18: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX5827826/SRX5827826.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX5827826/SRX5827826.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX5827826/SRX5827826.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX5827826/SRX5827826.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 13:10:18: #1 read tag files... INFO @ Thu, 05 Dec 2019 13:10:18: #1 read treatment tags... INFO @ Thu, 05 Dec 2019 13:10:23: 1000000 INFO @ Thu, 05 Dec 2019 13:10:29: 2000000 INFO @ Thu, 05 Dec 2019 13:10:34: 3000000 INFO @ Thu, 05 Dec 2019 13:10:39: 4000000 INFO @ Thu, 05 Dec 2019 13:10:41: #1 tag size is determined as 51 bps INFO @ Thu, 05 Dec 2019 13:10:41: #1 tag size = 51 INFO @ Thu, 05 Dec 2019 13:10:41: #1 total tags in treatment: 4255064 INFO @ Thu, 05 Dec 2019 13:10:41: #1 user defined the maximum tags... INFO @ Thu, 05 Dec 2019 13:10:41: #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 13:10:41: #1 tags after filtering in treatment: 4255064 INFO @ Thu, 05 Dec 2019 13:10:41: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 05 Dec 2019 13:10:41: #1 finished! INFO @ Thu, 05 Dec 2019 13:10:41: #2 Build Peak Model... INFO @ Thu, 05 Dec 2019 13:10:41: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 05 Dec 2019 13:10:41: #2 number of paired peaks: 642 WARNING @ Thu, 05 Dec 2019 13:10:41: Fewer paired peaks (642) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 642 pairs to build model! INFO @ Thu, 05 Dec 2019 13:10:41: start model_add_line... INFO @ Thu, 05 Dec 2019 13:10:41: start X-correlation... INFO @ Thu, 05 Dec 2019 13:10:41: end of X-cor INFO @ Thu, 05 Dec 2019 13:10:41: #2 finished! INFO @ Thu, 05 Dec 2019 13:10:41: #2 predicted fragment length is 100 bps INFO @ Thu, 05 Dec 2019 13:10:41: #2 alternative fragment length(s) may be 100 bps INFO @ Thu, 05 Dec 2019 13:10:41: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX5827826/SRX5827826.05_model.r WARNING @ Thu, 05 Dec 2019 13:10:41: #2 Since the d (100) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 05 Dec 2019 13:10:41: #2 You may need to consider one of the other alternative d(s): 100 WARNING @ Thu, 05 Dec 2019 13:10:41: #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 13:10:41: #3 Call peaks... INFO @ Thu, 05 Dec 2019 13:10:41: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 05 Dec 2019 13:10:48: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX5827826/SRX5827826.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX5827826/SRX5827826.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX5827826/SRX5827826.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX5827826/SRX5827826.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 13:10:48: #1 read tag files... INFO @ Thu, 05 Dec 2019 13:10:48: #1 read treatment tags... INFO @ Thu, 05 Dec 2019 13:10:49: #3 Call peaks for each chromosome... INFO @ Thu, 05 Dec 2019 13:10:53: 1000000 INFO @ Thu, 05 Dec 2019 13:10:54: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX5827826/SRX5827826.05_peaks.xls INFO @ Thu, 05 Dec 2019 13:10:54: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX5827826/SRX5827826.05_peaks.narrowPeak INFO @ Thu, 05 Dec 2019 13:10:54: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX5827826/SRX5827826.05_summits.bed INFO @ Thu, 05 Dec 2019 13:10:54: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (1471 records, 4 fields): 4 millis CompletedMACS2peakCalling INFO @ Thu, 05 Dec 2019 13:10:59: 2000000 INFO @ Thu, 05 Dec 2019 13:11:04: 3000000 INFO @ Thu, 05 Dec 2019 13:11:09: 4000000 INFO @ Thu, 05 Dec 2019 13:11:11: #1 tag size is determined as 51 bps INFO @ Thu, 05 Dec 2019 13:11:11: #1 tag size = 51 INFO @ Thu, 05 Dec 2019 13:11:11: #1 total tags in treatment: 4255064 INFO @ Thu, 05 Dec 2019 13:11:11: #1 user defined the maximum tags... INFO @ Thu, 05 Dec 2019 13:11:11: #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 13:11:11: #1 tags after filtering in treatment: 4255064 INFO @ Thu, 05 Dec 2019 13:11:11: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 05 Dec 2019 13:11:11: #1 finished! INFO @ Thu, 05 Dec 2019 13:11:11: #2 Build Peak Model... INFO @ Thu, 05 Dec 2019 13:11:11: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 05 Dec 2019 13:11:11: #2 number of paired peaks: 642 WARNING @ Thu, 05 Dec 2019 13:11:11: Fewer paired peaks (642) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 642 pairs to build model! INFO @ Thu, 05 Dec 2019 13:11:11: start model_add_line... INFO @ Thu, 05 Dec 2019 13:11:11: start X-correlation... INFO @ Thu, 05 Dec 2019 13:11:11: end of X-cor INFO @ Thu, 05 Dec 2019 13:11:11: #2 finished! INFO @ Thu, 05 Dec 2019 13:11:11: #2 predicted fragment length is 100 bps INFO @ Thu, 05 Dec 2019 13:11:11: #2 alternative fragment length(s) may be 100 bps INFO @ Thu, 05 Dec 2019 13:11:11: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX5827826/SRX5827826.10_model.r BedGraph に変換中... WARNING @ Thu, 05 Dec 2019 13:11:19: #2 Since the d (100) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 05 Dec 2019 13:11:19: #2 You may need to consider one of the other alternative d(s): 100 WARNING @ Thu, 05 Dec 2019 13:11:19: #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 13:11:19: #3 Call peaks... INFO @ Thu, 05 Dec 2019 13:11:19: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 05 Dec 2019 13:11:21: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX5827826/SRX5827826.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX5827826/SRX5827826.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX5827826/SRX5827826.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX5827826/SRX5827826.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 13:11:21: #1 read tag files... INFO @ Thu, 05 Dec 2019 13:11:21: #1 read treatment tags... INFO @ Thu, 05 Dec 2019 13:11:26: 1000000 INFO @ Thu, 05 Dec 2019 13:11:27: #3 Call peaks for each chromosome... INFO @ Thu, 05 Dec 2019 13:11:31: 2000000 INFO @ Thu, 05 Dec 2019 13:11:32: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX5827826/SRX5827826.10_peaks.xls INFO @ Thu, 05 Dec 2019 13:11:32: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX5827826/SRX5827826.10_peaks.narrowPeak INFO @ Thu, 05 Dec 2019 13:11:32: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX5827826/SRX5827826.10_summits.bed INFO @ Thu, 05 Dec 2019 13:11:32: Done! pass1 - making usageList (13 chroms): 1 millis pass2 - checking and writing primary data (947 records, 4 fields): 4 millis CompletedMACS2peakCalling INFO @ Thu, 05 Dec 2019 13:11:37: 3000000 INFO @ Thu, 05 Dec 2019 13:11:42: 4000000 INFO @ Thu, 05 Dec 2019 13:11:43: #1 tag size is determined as 51 bps INFO @ Thu, 05 Dec 2019 13:11:43: #1 tag size = 51 INFO @ Thu, 05 Dec 2019 13:11:43: #1 total tags in treatment: 4255064 INFO @ Thu, 05 Dec 2019 13:11:43: #1 user defined the maximum tags... INFO @ Thu, 05 Dec 2019 13:11:43: #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 13:11:43: #1 tags after filtering in treatment: 4255064 INFO @ Thu, 05 Dec 2019 13:11:43: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 05 Dec 2019 13:11:43: #1 finished! INFO @ Thu, 05 Dec 2019 13:11:43: #2 Build Peak Model... INFO @ Thu, 05 Dec 2019 13:11:43: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 05 Dec 2019 13:11:44: #2 number of paired peaks: 642 WARNING @ Thu, 05 Dec 2019 13:11:44: Fewer paired peaks (642) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 642 pairs to build model! INFO @ Thu, 05 Dec 2019 13:11:44: start model_add_line... INFO @ Thu, 05 Dec 2019 13:11:44: start X-correlation... INFO @ Thu, 05 Dec 2019 13:11:44: end of X-cor INFO @ Thu, 05 Dec 2019 13:11:44: #2 finished! INFO @ Thu, 05 Dec 2019 13:11:44: #2 predicted fragment length is 100 bps INFO @ Thu, 05 Dec 2019 13:11:44: #2 alternative fragment length(s) may be 100 bps INFO @ Thu, 05 Dec 2019 13:11:44: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX5827826/SRX5827826.20_model.r WARNING @ Thu, 05 Dec 2019 13:11:44: #2 Since the d (100) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 05 Dec 2019 13:11:44: #2 You may need to consider one of the other alternative d(s): 100 WARNING @ Thu, 05 Dec 2019 13:11:44: #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 13:11:44: #3 Call peaks... INFO @ Thu, 05 Dec 2019 13:11:44: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 05 Dec 2019 13:11:52: #3 Call peaks for each chromosome... INFO @ Thu, 05 Dec 2019 13:11:57: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX5827826/SRX5827826.20_peaks.xls INFO @ Thu, 05 Dec 2019 13:11:57: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX5827826/SRX5827826.20_peaks.narrowPeak INFO @ Thu, 05 Dec 2019 13:11:57: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX5827826/SRX5827826.20_summits.bed INFO @ Thu, 05 Dec 2019 13:11:57: Done! pass1 - making usageList (12 chroms): 1 millis pass2 - checking and writing primary data (560 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。