Job ID = 6455443 SRX = SRX287793 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T10:05:56 prefetch.2.10.7: 1) Downloading 'SRR869982'... 2020-06-21T10:05:56 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T10:08:27 prefetch.2.10.7: HTTPS download succeed 2020-06-21T10:08:28 prefetch.2.10.7: 'SRR869982' is valid 2020-06-21T10:08:28 prefetch.2.10.7: 1) 'SRR869982' was downloaded successfully Read 13809114 spots for SRR869982/SRR869982.sra Written 13809114 spots for SRR869982/SRR869982.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: 00:04:20 13809114 reads; of these: 13809114 (100.00%) were unpaired; of these: 756574 (5.48%) aligned 0 times 9039950 (65.46%) aligned exactly 1 time 4012590 (29.06%) aligned >1 times 94.52% overall alignment rate Time searching: 00:04:20 Overall time: 00:04:20 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] 2217100 / 13052540 = 0.1699 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 19:17:06: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX287793/SRX287793.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX287793/SRX287793.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX287793/SRX287793.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX287793/SRX287793.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 19:17:06: #1 read tag files... INFO @ Sun, 21 Jun 2020 19:17:06: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 19:17:13: 1000000 INFO @ Sun, 21 Jun 2020 19:17:20: 2000000 INFO @ Sun, 21 Jun 2020 19:17:27: 3000000 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 19:17:34: 4000000 INFO @ Sun, 21 Jun 2020 19:17:36: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX287793/SRX287793.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX287793/SRX287793.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX287793/SRX287793.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX287793/SRX287793.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 19:17:36: #1 read tag files... INFO @ Sun, 21 Jun 2020 19:17:36: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 19:17:42: 5000000 INFO @ Sun, 21 Jun 2020 19:17:44: 1000000 INFO @ Sun, 21 Jun 2020 19:17:49: 6000000 INFO @ Sun, 21 Jun 2020 19:17:52: 2000000 INFO @ Sun, 21 Jun 2020 19:17:57: 7000000 INFO @ Sun, 21 Jun 2020 19:18:00: 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 19:18:05: 8000000 INFO @ Sun, 21 Jun 2020 19:18:06: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX287793/SRX287793.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX287793/SRX287793.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX287793/SRX287793.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX287793/SRX287793.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 19:18:06: #1 read tag files... INFO @ Sun, 21 Jun 2020 19:18:06: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 19:18:08: 4000000 INFO @ Sun, 21 Jun 2020 19:18:13: 9000000 INFO @ Sun, 21 Jun 2020 19:18:14: 1000000 INFO @ Sun, 21 Jun 2020 19:18:16: 5000000 INFO @ Sun, 21 Jun 2020 19:18:21: 10000000 INFO @ Sun, 21 Jun 2020 19:18:21: 2000000 INFO @ Sun, 21 Jun 2020 19:18:25: 6000000 INFO @ Sun, 21 Jun 2020 19:18:28: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 19:18:28: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 19:18:28: #1 total tags in treatment: 10835440 INFO @ Sun, 21 Jun 2020 19:18:28: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 19:18:28: #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 19:18:29: #1 tags after filtering in treatment: 10835440 INFO @ Sun, 21 Jun 2020 19:18:29: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 19:18:29: #1 finished! INFO @ Sun, 21 Jun 2020 19:18:29: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 19:18:29: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 19:18:29: 3000000 INFO @ Sun, 21 Jun 2020 19:18:29: #2 number of paired peaks: 704 WARNING @ Sun, 21 Jun 2020 19:18:29: Fewer paired peaks (704) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 704 pairs to build model! INFO @ Sun, 21 Jun 2020 19:18:29: start model_add_line... INFO @ Sun, 21 Jun 2020 19:18:30: start X-correlation... INFO @ Sun, 21 Jun 2020 19:18:30: end of X-cor INFO @ Sun, 21 Jun 2020 19:18:30: #2 finished! INFO @ Sun, 21 Jun 2020 19:18:30: #2 predicted fragment length is 45 bps INFO @ Sun, 21 Jun 2020 19:18:30: #2 alternative fragment length(s) may be 4,45 bps INFO @ Sun, 21 Jun 2020 19:18:30: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX287793/SRX287793.05_model.r WARNING @ Sun, 21 Jun 2020 19:18:30: #2 Since the d (45) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 19:18:30: #2 You may need to consider one of the other alternative d(s): 4,45 WARNING @ Sun, 21 Jun 2020 19:18:30: #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 19:18:30: #3 Call peaks... INFO @ Sun, 21 Jun 2020 19:18:30: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 19:18:33: 7000000 INFO @ Sun, 21 Jun 2020 19:18:36: 4000000 INFO @ Sun, 21 Jun 2020 19:18:41: 8000000 INFO @ Sun, 21 Jun 2020 19:18:44: 5000000 INFO @ Sun, 21 Jun 2020 19:18:49: 9000000 INFO @ Sun, 21 Jun 2020 19:18:51: 6000000 INFO @ Sun, 21 Jun 2020 19:18:52: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 19:18:57: 10000000 INFO @ Sun, 21 Jun 2020 19:18:58: 7000000 INFO @ Sun, 21 Jun 2020 19:19:03: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX287793/SRX287793.05_peaks.xls INFO @ Sun, 21 Jun 2020 19:19:03: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX287793/SRX287793.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 19:19:03: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX287793/SRX287793.05_summits.bed INFO @ Sun, 21 Jun 2020 19:19:03: Done! pass1 - making usageList (570 chroms): 2 millis pass2 - checking and writing primary data (2208 records, 4 fields): 18 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 19:19:04: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 19:19:04: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 19:19:04: #1 total tags in treatment: 10835440 INFO @ Sun, 21 Jun 2020 19:19:04: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 19:19:04: #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 19:19:04: #1 tags after filtering in treatment: 10835440 INFO @ Sun, 21 Jun 2020 19:19:04: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 19:19:04: #1 finished! INFO @ Sun, 21 Jun 2020 19:19:04: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 19:19:04: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 19:19:05: 8000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 19:19:05: #2 number of paired peaks: 704 WARNING @ Sun, 21 Jun 2020 19:19:05: Fewer paired peaks (704) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 704 pairs to build model! INFO @ Sun, 21 Jun 2020 19:19:05: start model_add_line... INFO @ Sun, 21 Jun 2020 19:19:05: start X-correlation... INFO @ Sun, 21 Jun 2020 19:19:05: end of X-cor INFO @ Sun, 21 Jun 2020 19:19:05: #2 finished! INFO @ Sun, 21 Jun 2020 19:19:05: #2 predicted fragment length is 45 bps INFO @ Sun, 21 Jun 2020 19:19:05: #2 alternative fragment length(s) may be 4,45 bps INFO @ Sun, 21 Jun 2020 19:19:05: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX287793/SRX287793.10_model.r WARNING @ Sun, 21 Jun 2020 19:19:05: #2 Since the d (45) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 19:19:05: #2 You may need to consider one of the other alternative d(s): 4,45 WARNING @ Sun, 21 Jun 2020 19:19:05: #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 19:19:05: #3 Call peaks... INFO @ Sun, 21 Jun 2020 19:19:05: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 19:19:11: 9000000 INFO @ Sun, 21 Jun 2020 19:19:17: 10000000 INFO @ Sun, 21 Jun 2020 19:19:22: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 19:19:22: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 19:19:22: #1 total tags in treatment: 10835440 INFO @ Sun, 21 Jun 2020 19:19:22: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 19:19:22: #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 19:19:22: #1 tags after filtering in treatment: 10835440 INFO @ Sun, 21 Jun 2020 19:19:22: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 19:19:22: #1 finished! INFO @ Sun, 21 Jun 2020 19:19:22: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 19:19:22: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 19:19:23: #2 number of paired peaks: 704 WARNING @ Sun, 21 Jun 2020 19:19:23: Fewer paired peaks (704) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 704 pairs to build model! INFO @ Sun, 21 Jun 2020 19:19:23: start model_add_line... INFO @ Sun, 21 Jun 2020 19:19:23: start X-correlation... INFO @ Sun, 21 Jun 2020 19:19:23: end of X-cor INFO @ Sun, 21 Jun 2020 19:19:23: #2 finished! INFO @ Sun, 21 Jun 2020 19:19:23: #2 predicted fragment length is 45 bps INFO @ Sun, 21 Jun 2020 19:19:23: #2 alternative fragment length(s) may be 4,45 bps INFO @ Sun, 21 Jun 2020 19:19:23: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX287793/SRX287793.20_model.r WARNING @ Sun, 21 Jun 2020 19:19:23: #2 Since the d (45) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 19:19:23: #2 You may need to consider one of the other alternative d(s): 4,45 WARNING @ Sun, 21 Jun 2020 19:19:23: #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 19:19:23: #3 Call peaks... INFO @ Sun, 21 Jun 2020 19:19:23: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 19:19:27: #3 Call peaks for each chromosome... BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 19:19:38: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX287793/SRX287793.10_peaks.xls INFO @ Sun, 21 Jun 2020 19:19:38: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX287793/SRX287793.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 19:19:38: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX287793/SRX287793.10_summits.bed INFO @ Sun, 21 Jun 2020 19:19:38: Done! pass1 - making usageList (489 chroms): 2 millis pass2 - checking and writing primary data (1818 records, 4 fields): 15 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 19:19:45: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 19:19:55: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX287793/SRX287793.20_peaks.xls INFO @ Sun, 21 Jun 2020 19:19:55: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX287793/SRX287793.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 19:19:55: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX287793/SRX287793.20_summits.bed INFO @ Sun, 21 Jun 2020 19:19:55: Done! pass1 - making usageList (338 chroms): 0 millis pass2 - checking and writing primary data (734 records, 4 fields): 11 millis CompletedMACS2peakCalling