Job ID = 1295510 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 40,923,011 reads read : 40,923,011 reads written : 40,923,011 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: 00:10:36 40923011 reads; of these: 40923011 (100.00%) were unpaired; of these: 30646327 (74.89%) aligned 0 times 7363590 (17.99%) aligned exactly 1 time 2913094 (7.12%) aligned >1 times 25.11% overall alignment rate Time searching: 00:10:36 Overall time: 00:10:36 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 8 files... [bam_rmdupse_core] 2103004 / 10276684 = 0.2046 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 14:42:34: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX348466/SRX348466.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX348466/SRX348466.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX348466/SRX348466.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX348466/SRX348466.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 14:42:34: #1 read tag files... INFO @ Mon, 03 Jun 2019 14:42:34: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 14:42:34: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX348466/SRX348466.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX348466/SRX348466.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX348466/SRX348466.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX348466/SRX348466.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 14:42:34: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX348466/SRX348466.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX348466/SRX348466.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX348466/SRX348466.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX348466/SRX348466.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 14:42:34: #1 read tag files... INFO @ Mon, 03 Jun 2019 14:42:34: #1 read tag files... INFO @ Mon, 03 Jun 2019 14:42:34: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 14:42:34: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 14:42:45: 1000000 INFO @ Mon, 03 Jun 2019 14:42:45: 1000000 INFO @ Mon, 03 Jun 2019 14:42:46: 1000000 INFO @ Mon, 03 Jun 2019 14:42:55: 2000000 INFO @ Mon, 03 Jun 2019 14:42:56: 2000000 INFO @ Mon, 03 Jun 2019 14:42:57: 2000000 INFO @ Mon, 03 Jun 2019 14:43:04: 3000000 INFO @ Mon, 03 Jun 2019 14:43:04: 3000000 INFO @ Mon, 03 Jun 2019 14:43:08: 3000000 INFO @ Mon, 03 Jun 2019 14:43:13: 4000000 INFO @ Mon, 03 Jun 2019 14:43:13: 4000000 INFO @ Mon, 03 Jun 2019 14:43:19: 4000000 INFO @ Mon, 03 Jun 2019 14:43:22: 5000000 INFO @ Mon, 03 Jun 2019 14:43:22: 5000000 INFO @ Mon, 03 Jun 2019 14:43:30: 5000000 INFO @ Mon, 03 Jun 2019 14:43:30: 6000000 INFO @ Mon, 03 Jun 2019 14:43:31: 6000000 INFO @ Mon, 03 Jun 2019 14:43:39: 7000000 INFO @ Mon, 03 Jun 2019 14:43:39: 7000000 INFO @ Mon, 03 Jun 2019 14:43:41: 6000000 INFO @ Mon, 03 Jun 2019 14:43:47: 8000000 INFO @ Mon, 03 Jun 2019 14:43:48: 8000000 INFO @ Mon, 03 Jun 2019 14:43:49: #1 tag size is determined as 76 bps INFO @ Mon, 03 Jun 2019 14:43:49: #1 tag size = 76 INFO @ Mon, 03 Jun 2019 14:43:49: #1 total tags in treatment: 8173680 INFO @ Mon, 03 Jun 2019 14:43:49: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 14:43:49: #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 14:43:49: #1 tags after filtering in treatment: 8173680 INFO @ Mon, 03 Jun 2019 14:43:49: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 14:43:49: #1 finished! INFO @ Mon, 03 Jun 2019 14:43:49: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 14:43:49: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 14:43:49: #1 tag size is determined as 76 bps INFO @ Mon, 03 Jun 2019 14:43:49: #1 tag size = 76 INFO @ Mon, 03 Jun 2019 14:43:49: #1 total tags in treatment: 8173680 INFO @ Mon, 03 Jun 2019 14:43:49: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 14:43:49: #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 14:43:49: #1 tags after filtering in treatment: 8173680 INFO @ Mon, 03 Jun 2019 14:43:49: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 14:43:49: #1 finished! INFO @ Mon, 03 Jun 2019 14:43:49: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 14:43:49: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 14:43:50: #2 number of paired peaks: 159 WARNING @ Mon, 03 Jun 2019 14:43:50: Fewer paired peaks (159) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 159 pairs to build model! INFO @ Mon, 03 Jun 2019 14:43:50: start model_add_line... INFO @ Mon, 03 Jun 2019 14:43:50: start X-correlation... INFO @ Mon, 03 Jun 2019 14:43:50: end of X-cor INFO @ Mon, 03 Jun 2019 14:43:50: #2 finished! INFO @ Mon, 03 Jun 2019 14:43:50: #2 predicted fragment length is 86 bps INFO @ Mon, 03 Jun 2019 14:43:50: #2 alternative fragment length(s) may be 86 bps INFO @ Mon, 03 Jun 2019 14:43:50: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX348466/SRX348466.10_model.r WARNING @ Mon, 03 Jun 2019 14:43:50: #2 Since the d (86) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 03 Jun 2019 14:43:50: #2 You may need to consider one of the other alternative d(s): 86 WARNING @ Mon, 03 Jun 2019 14:43:50: #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 14:43:50: #3 Call peaks... INFO @ Mon, 03 Jun 2019 14:43:50: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 14:43:50: #2 number of paired peaks: 159 WARNING @ Mon, 03 Jun 2019 14:43:50: Fewer paired peaks (159) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 159 pairs to build model! INFO @ Mon, 03 Jun 2019 14:43:50: start model_add_line... INFO @ Mon, 03 Jun 2019 14:43:50: start X-correlation... INFO @ Mon, 03 Jun 2019 14:43:50: end of X-cor INFO @ Mon, 03 Jun 2019 14:43:50: #2 finished! INFO @ Mon, 03 Jun 2019 14:43:50: #2 predicted fragment length is 86 bps INFO @ Mon, 03 Jun 2019 14:43:50: #2 alternative fragment length(s) may be 86 bps INFO @ Mon, 03 Jun 2019 14:43:50: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX348466/SRX348466.05_model.r WARNING @ Mon, 03 Jun 2019 14:43:50: #2 Since the d (86) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 03 Jun 2019 14:43:50: #2 You may need to consider one of the other alternative d(s): 86 WARNING @ Mon, 03 Jun 2019 14:43:50: #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 14:43:50: #3 Call peaks... INFO @ Mon, 03 Jun 2019 14:43:50: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 14:43:52: 7000000 INFO @ Mon, 03 Jun 2019 14:44:03: 8000000 INFO @ Mon, 03 Jun 2019 14:44:04: #1 tag size is determined as 76 bps INFO @ Mon, 03 Jun 2019 14:44:04: #1 tag size = 76 INFO @ Mon, 03 Jun 2019 14:44:04: #1 total tags in treatment: 8173680 INFO @ Mon, 03 Jun 2019 14:44:04: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 14:44:04: #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 14:44:04: #1 tags after filtering in treatment: 8173680 INFO @ Mon, 03 Jun 2019 14:44:04: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 14:44:04: #1 finished! INFO @ Mon, 03 Jun 2019 14:44:04: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 14:44:04: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 14:44:05: #2 number of paired peaks: 159 WARNING @ Mon, 03 Jun 2019 14:44:05: Fewer paired peaks (159) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 159 pairs to build model! INFO @ Mon, 03 Jun 2019 14:44:05: start model_add_line... INFO @ Mon, 03 Jun 2019 14:44:05: start X-correlation... INFO @ Mon, 03 Jun 2019 14:44:05: end of X-cor INFO @ Mon, 03 Jun 2019 14:44:05: #2 finished! INFO @ Mon, 03 Jun 2019 14:44:05: #2 predicted fragment length is 86 bps INFO @ Mon, 03 Jun 2019 14:44:05: #2 alternative fragment length(s) may be 86 bps INFO @ Mon, 03 Jun 2019 14:44:05: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX348466/SRX348466.20_model.r WARNING @ Mon, 03 Jun 2019 14:44:05: #2 Since the d (86) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 03 Jun 2019 14:44:05: #2 You may need to consider one of the other alternative d(s): 86 WARNING @ Mon, 03 Jun 2019 14:44:05: #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 14:44:05: #3 Call peaks... INFO @ Mon, 03 Jun 2019 14:44:05: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 14:44:13: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 14:44:14: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 14:44:25: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX348466/SRX348466.10_peaks.xls INFO @ Mon, 03 Jun 2019 14:44:25: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX348466/SRX348466.10_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 14:44:25: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX348466/SRX348466.10_summits.bed INFO @ Mon, 03 Jun 2019 14:44:25: Done! pass1 - making usageList (15 chroms): 2 millis pass2 - checking and writing primary data (1757 records, 4 fields): 25 millis CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 14:44:26: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX348466/SRX348466.05_peaks.xls INFO @ Mon, 03 Jun 2019 14:44:26: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX348466/SRX348466.05_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 14:44:26: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX348466/SRX348466.05_summits.bed INFO @ Mon, 03 Jun 2019 14:44:26: Done! pass1 - making usageList (15 chroms): 3 millis pass2 - checking and writing primary data (3945 records, 4 fields): 11 millis CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 14:44:29: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 14:44:41: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX348466/SRX348466.20_peaks.xls INFO @ Mon, 03 Jun 2019 14:44:41: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX348466/SRX348466.20_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 14:44:41: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX348466/SRX348466.20_summits.bed INFO @ Mon, 03 Jun 2019 14:44:41: Done! pass1 - making usageList (12 chroms): 1 millis pass2 - checking and writing primary data (845 records, 4 fields): 5 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。