Job ID = 6458238 SRX = SRX495791 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T12:41:29 prefetch.2.10.7: 1) Downloading 'SRR1199489'... 2020-06-21T12:41:29 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T12:43:40 prefetch.2.10.7: HTTPS download succeed 2020-06-21T12:43:40 prefetch.2.10.7: 1) 'SRR1199489' was downloaded successfully Read 17643933 spots for SRR1199489/SRR1199489.sra Written 17643933 spots for SRR1199489/SRR1199489.sra 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: 00:05:15 17643933 reads; of these: 17643933 (100.00%) were unpaired; of these: 1075696 (6.10%) aligned 0 times 11627051 (65.90%) aligned exactly 1 time 4941186 (28.01%) aligned >1 times 93.90% overall alignment rate Time searching: 00:05:15 Overall time: 00:05:15 マッピングが完了しました。 samtools でBAM に変換中... [samopen] SAM header is present: 1870 sequences. [bam_sort_core] merging from 8 files... [bam_rmdupse_core] 4021188 / 16568237 = 0.2427 in library ' ' BAM に変換しました。 Bed ファイルを作成中... WARNING: Skipping mount /opt/pkg/singularity/3.5.2/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Sun, 21 Jun 2020 21:53:36: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX495791/SRX495791.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX495791/SRX495791.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX495791/SRX495791.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX495791/SRX495791.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 @ Sun, 21 Jun 2020 21:53:36: #1 read tag files... INFO @ Sun, 21 Jun 2020 21:53:36: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 21:53:42: 1000000 INFO @ Sun, 21 Jun 2020 21:53:48: 2000000 INFO @ Sun, 21 Jun 2020 21:53:54: 3000000 INFO @ Sun, 21 Jun 2020 21:54:00: 4000000 WARNING: Skipping mount /opt/pkg/singularity/3.5.2/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Sun, 21 Jun 2020 21:54:06: 5000000 INFO @ Sun, 21 Jun 2020 21:54:06: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX495791/SRX495791.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX495791/SRX495791.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX495791/SRX495791.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX495791/SRX495791.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 @ Sun, 21 Jun 2020 21:54:06: #1 read tag files... INFO @ Sun, 21 Jun 2020 21:54:06: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 21:54:13: 6000000 INFO @ Sun, 21 Jun 2020 21:54:15: 1000000 INFO @ Sun, 21 Jun 2020 21:54:20: 7000000 INFO @ Sun, 21 Jun 2020 21:54:23: 2000000 INFO @ Sun, 21 Jun 2020 21:54:28: 8000000 INFO @ Sun, 21 Jun 2020 21:54:31: 3000000 BedGraph に変換中... WARNING: Skipping mount /opt/pkg/singularity/3.5.2/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Sun, 21 Jun 2020 21:54:36: 9000000 INFO @ Sun, 21 Jun 2020 21:54:36: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX495791/SRX495791.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX495791/SRX495791.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX495791/SRX495791.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX495791/SRX495791.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 @ Sun, 21 Jun 2020 21:54:36: #1 read tag files... INFO @ Sun, 21 Jun 2020 21:54:36: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 21:54:39: 4000000 INFO @ Sun, 21 Jun 2020 21:54:44: 10000000 INFO @ Sun, 21 Jun 2020 21:54:45: 1000000 INFO @ Sun, 21 Jun 2020 21:54:48: 5000000 INFO @ Sun, 21 Jun 2020 21:54:51: 11000000 INFO @ Sun, 21 Jun 2020 21:54:54: 2000000 INFO @ Sun, 21 Jun 2020 21:54:57: 6000000 INFO @ Sun, 21 Jun 2020 21:54:59: 12000000 INFO @ Sun, 21 Jun 2020 21:55:03: 3000000 INFO @ Sun, 21 Jun 2020 21:55:03: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 21:55:03: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 21:55:03: #1 total tags in treatment: 12547049 INFO @ Sun, 21 Jun 2020 21:55:03: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 21:55:03: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sun, 21 Jun 2020 21:55:04: #1 tags after filtering in treatment: 12546982 INFO @ Sun, 21 Jun 2020 21:55:04: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 21:55:04: #1 finished! INFO @ Sun, 21 Jun 2020 21:55:04: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 21:55:04: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 21:55:05: #2 number of paired peaks: 219 WARNING @ Sun, 21 Jun 2020 21:55:05: Fewer paired peaks (219) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 219 pairs to build model! INFO @ Sun, 21 Jun 2020 21:55:05: start model_add_line... INFO @ Sun, 21 Jun 2020 21:55:05: start X-correlation... INFO @ Sun, 21 Jun 2020 21:55:05: end of X-cor INFO @ Sun, 21 Jun 2020 21:55:05: #2 finished! INFO @ Sun, 21 Jun 2020 21:55:05: #2 predicted fragment length is 57 bps INFO @ Sun, 21 Jun 2020 21:55:05: #2 alternative fragment length(s) may be 3,31,35,57,63,532,584 bps INFO @ Sun, 21 Jun 2020 21:55:05: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX495791/SRX495791.05_model.r WARNING @ Sun, 21 Jun 2020 21:55:05: #2 Since the d (57) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 21:55:05: #2 You may need to consider one of the other alternative d(s): 3,31,35,57,63,532,584 WARNING @ Sun, 21 Jun 2020 21:55:05: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sun, 21 Jun 2020 21:55:05: #3 Call peaks... INFO @ Sun, 21 Jun 2020 21:55:05: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 21:55:05: 7000000 INFO @ Sun, 21 Jun 2020 21:55:12: 4000000 INFO @ Sun, 21 Jun 2020 21:55:14: 8000000 INFO @ Sun, 21 Jun 2020 21:55:20: 5000000 INFO @ Sun, 21 Jun 2020 21:55:22: 9000000 INFO @ Sun, 21 Jun 2020 21:55:29: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 21:55:29: 6000000 INFO @ Sun, 21 Jun 2020 21:55:31: 10000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 21:55:38: 7000000 INFO @ Sun, 21 Jun 2020 21:55:39: 11000000 INFO @ Sun, 21 Jun 2020 21:55:41: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX495791/SRX495791.05_peaks.xls INFO @ Sun, 21 Jun 2020 21:55:41: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX495791/SRX495791.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 21:55:41: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX495791/SRX495791.05_summits.bed INFO @ Sun, 21 Jun 2020 21:55:41: Done! pass1 - making usageList (557 chroms): 1 millis pass2 - checking and writing primary data (1988 records, 4 fields): 17 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 21:55:47: 8000000 INFO @ Sun, 21 Jun 2020 21:55:48: 12000000 INFO @ Sun, 21 Jun 2020 21:55:52: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 21:55:52: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 21:55:52: #1 total tags in treatment: 12547049 INFO @ Sun, 21 Jun 2020 21:55:52: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 21:55:52: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sun, 21 Jun 2020 21:55:53: #1 tags after filtering in treatment: 12546982 INFO @ Sun, 21 Jun 2020 21:55:53: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 21:55:53: #1 finished! INFO @ Sun, 21 Jun 2020 21:55:53: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 21:55:53: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 21:55:54: #2 number of paired peaks: 219 WARNING @ Sun, 21 Jun 2020 21:55:54: Fewer paired peaks (219) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 219 pairs to build model! INFO @ Sun, 21 Jun 2020 21:55:54: start model_add_line... INFO @ Sun, 21 Jun 2020 21:55:54: start X-correlation... INFO @ Sun, 21 Jun 2020 21:55:54: end of X-cor INFO @ Sun, 21 Jun 2020 21:55:54: #2 finished! INFO @ Sun, 21 Jun 2020 21:55:54: #2 predicted fragment length is 57 bps INFO @ Sun, 21 Jun 2020 21:55:54: #2 alternative fragment length(s) may be 3,31,35,57,63,532,584 bps INFO @ Sun, 21 Jun 2020 21:55:54: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX495791/SRX495791.10_model.r WARNING @ Sun, 21 Jun 2020 21:55:54: #2 Since the d (57) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 21:55:54: #2 You may need to consider one of the other alternative d(s): 3,31,35,57,63,532,584 WARNING @ Sun, 21 Jun 2020 21:55:54: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sun, 21 Jun 2020 21:55:54: #3 Call peaks... INFO @ Sun, 21 Jun 2020 21:55:54: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 21:55:55: 9000000 BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 21:56:03: 10000000 INFO @ Sun, 21 Jun 2020 21:56:10: 11000000 INFO @ Sun, 21 Jun 2020 21:56:18: 12000000 INFO @ Sun, 21 Jun 2020 21:56:19: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 21:56:22: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 21:56:22: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 21:56:22: #1 total tags in treatment: 12547049 INFO @ Sun, 21 Jun 2020 21:56:22: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 21:56:22: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sun, 21 Jun 2020 21:56:22: #1 tags after filtering in treatment: 12546982 INFO @ Sun, 21 Jun 2020 21:56:22: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 21:56:22: #1 finished! INFO @ Sun, 21 Jun 2020 21:56:22: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 21:56:22: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 21:56:23: #2 number of paired peaks: 219 WARNING @ Sun, 21 Jun 2020 21:56:23: Fewer paired peaks (219) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 219 pairs to build model! INFO @ Sun, 21 Jun 2020 21:56:23: start model_add_line... INFO @ Sun, 21 Jun 2020 21:56:23: start X-correlation... INFO @ Sun, 21 Jun 2020 21:56:23: end of X-cor INFO @ Sun, 21 Jun 2020 21:56:23: #2 finished! INFO @ Sun, 21 Jun 2020 21:56:23: #2 predicted fragment length is 57 bps INFO @ Sun, 21 Jun 2020 21:56:23: #2 alternative fragment length(s) may be 3,31,35,57,63,532,584 bps INFO @ Sun, 21 Jun 2020 21:56:23: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX495791/SRX495791.20_model.r WARNING @ Sun, 21 Jun 2020 21:56:23: #2 Since the d (57) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 21:56:23: #2 You may need to consider one of the other alternative d(s): 3,31,35,57,63,532,584 WARNING @ Sun, 21 Jun 2020 21:56:23: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sun, 21 Jun 2020 21:56:23: #3 Call peaks... INFO @ Sun, 21 Jun 2020 21:56:23: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 21:56:30: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX495791/SRX495791.10_peaks.xls INFO @ Sun, 21 Jun 2020 21:56:30: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX495791/SRX495791.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 21:56:30: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX495791/SRX495791.10_summits.bed INFO @ Sun, 21 Jun 2020 21:56:30: Done! pass1 - making usageList (326 chroms): 1 millis pass2 - checking and writing primary data (759 records, 4 fields): 10 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 21:56:48: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 21:57:00: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX495791/SRX495791.20_peaks.xls INFO @ Sun, 21 Jun 2020 21:57:00: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX495791/SRX495791.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 21:57:00: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX495791/SRX495791.20_summits.bed INFO @ Sun, 21 Jun 2020 21:57:00: Done! pass1 - making usageList (95 chroms): 1 millis pass2 - checking and writing primary data (182 records, 4 fields): 3 millis CompletedMACS2peakCalling