Job ID = 6455687 SRX = SRX287988 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T10:08:06 prefetch.2.10.7: 1) Downloading 'SRR870177'... 2020-06-21T10:08:06 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T10:11:30 prefetch.2.10.7: HTTPS download succeed 2020-06-21T10:11:30 prefetch.2.10.7: 1) 'SRR870177' was downloaded successfully Read 17133552 spots for SRR870177/SRR870177.sra Written 17133552 spots for SRR870177/SRR870177.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: 00:05:14 17133552 reads; of these: 17133552 (100.00%) were unpaired; of these: 963538 (5.62%) aligned 0 times 11195743 (65.34%) aligned exactly 1 time 4974271 (29.03%) aligned >1 times 94.38% overall alignment rate Time searching: 00:05:14 Overall time: 00:05:14 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] 2734728 / 16170014 = 0.1691 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 19:21:55: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX287988/SRX287988.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX287988/SRX287988.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX287988/SRX287988.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX287988/SRX287988.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 19:21:55: #1 read tag files... INFO @ Sun, 21 Jun 2020 19:21:55: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 19:22:01: 1000000 INFO @ Sun, 21 Jun 2020 19:22:06: 2000000 INFO @ Sun, 21 Jun 2020 19:22:12: 3000000 INFO @ Sun, 21 Jun 2020 19:22:18: 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 19:22:23: 5000000 INFO @ Sun, 21 Jun 2020 19:22:25: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX287988/SRX287988.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX287988/SRX287988.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX287988/SRX287988.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX287988/SRX287988.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 19:22:25: #1 read tag files... INFO @ Sun, 21 Jun 2020 19:22:25: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 19:22:30: 6000000 INFO @ Sun, 21 Jun 2020 19:22:32: 1000000 INFO @ Sun, 21 Jun 2020 19:22:36: 7000000 INFO @ Sun, 21 Jun 2020 19:22:38: 2000000 INFO @ Sun, 21 Jun 2020 19:22:43: 8000000 INFO @ Sun, 21 Jun 2020 19:22:45: 3000000 INFO @ Sun, 21 Jun 2020 19:22:49: 9000000 INFO @ Sun, 21 Jun 2020 19:22:52: 4000000 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 19:22:55: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX287988/SRX287988.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX287988/SRX287988.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX287988/SRX287988.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX287988/SRX287988.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 19:22:55: #1 read tag files... INFO @ Sun, 21 Jun 2020 19:22:55: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 19:22:56: 10000000 INFO @ Sun, 21 Jun 2020 19:22:58: 5000000 INFO @ Sun, 21 Jun 2020 19:23:02: 1000000 INFO @ Sun, 21 Jun 2020 19:23:03: 11000000 INFO @ Sun, 21 Jun 2020 19:23:05: 6000000 INFO @ Sun, 21 Jun 2020 19:23:08: 2000000 INFO @ Sun, 21 Jun 2020 19:23:09: 12000000 INFO @ Sun, 21 Jun 2020 19:23:11: 7000000 INFO @ Sun, 21 Jun 2020 19:23:15: 3000000 INFO @ Sun, 21 Jun 2020 19:23:16: 13000000 INFO @ Sun, 21 Jun 2020 19:23:18: 8000000 INFO @ Sun, 21 Jun 2020 19:23:19: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 19:23:19: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 19:23:19: #1 total tags in treatment: 13435286 INFO @ Sun, 21 Jun 2020 19:23:19: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 19:23:19: #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 19:23:19: #1 tags after filtering in treatment: 13435286 INFO @ Sun, 21 Jun 2020 19:23:19: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 19:23:19: #1 finished! INFO @ Sun, 21 Jun 2020 19:23:19: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 19:23:19: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 19:23:20: #2 number of paired peaks: 434 WARNING @ Sun, 21 Jun 2020 19:23:20: Fewer paired peaks (434) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 434 pairs to build model! INFO @ Sun, 21 Jun 2020 19:23:20: start model_add_line... INFO @ Sun, 21 Jun 2020 19:23:21: start X-correlation... INFO @ Sun, 21 Jun 2020 19:23:21: end of X-cor INFO @ Sun, 21 Jun 2020 19:23:21: #2 finished! INFO @ Sun, 21 Jun 2020 19:23:21: #2 predicted fragment length is 44 bps INFO @ Sun, 21 Jun 2020 19:23:21: #2 alternative fragment length(s) may be 4,44 bps INFO @ Sun, 21 Jun 2020 19:23:21: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX287988/SRX287988.05_model.r WARNING @ Sun, 21 Jun 2020 19:23:21: #2 Since the d (44) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 19:23:21: #2 You may need to consider one of the other alternative d(s): 4,44 WARNING @ Sun, 21 Jun 2020 19:23:21: #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 19:23:21: #3 Call peaks... INFO @ Sun, 21 Jun 2020 19:23:21: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 19:23:21: 4000000 INFO @ Sun, 21 Jun 2020 19:23:24: 9000000 INFO @ Sun, 21 Jun 2020 19:23:28: 5000000 INFO @ Sun, 21 Jun 2020 19:23:31: 10000000 INFO @ Sun, 21 Jun 2020 19:23:34: 6000000 INFO @ Sun, 21 Jun 2020 19:23:38: 11000000 INFO @ Sun, 21 Jun 2020 19:23:40: 7000000 INFO @ Sun, 21 Jun 2020 19:23:44: 12000000 INFO @ Sun, 21 Jun 2020 19:23:47: 8000000 INFO @ Sun, 21 Jun 2020 19:23:48: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 19:23:51: 13000000 INFO @ Sun, 21 Jun 2020 19:23:53: 9000000 INFO @ Sun, 21 Jun 2020 19:23:54: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 19:23:54: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 19:23:54: #1 total tags in treatment: 13435286 INFO @ Sun, 21 Jun 2020 19:23:54: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 19:23:54: #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 19:23:54: #1 tags after filtering in treatment: 13435286 INFO @ Sun, 21 Jun 2020 19:23:54: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 19:23:54: #1 finished! INFO @ Sun, 21 Jun 2020 19:23:54: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 19:23:54: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 19:23:55: #2 number of paired peaks: 434 WARNING @ Sun, 21 Jun 2020 19:23:55: Fewer paired peaks (434) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 434 pairs to build model! INFO @ Sun, 21 Jun 2020 19:23:55: start model_add_line... INFO @ Sun, 21 Jun 2020 19:23:55: start X-correlation... INFO @ Sun, 21 Jun 2020 19:23:55: end of X-cor INFO @ Sun, 21 Jun 2020 19:23:55: #2 finished! INFO @ Sun, 21 Jun 2020 19:23:55: #2 predicted fragment length is 44 bps INFO @ Sun, 21 Jun 2020 19:23:55: #2 alternative fragment length(s) may be 4,44 bps INFO @ Sun, 21 Jun 2020 19:23:55: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX287988/SRX287988.10_model.r WARNING @ Sun, 21 Jun 2020 19:23:55: #2 Since the d (44) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 19:23:55: #2 You may need to consider one of the other alternative d(s): 4,44 WARNING @ Sun, 21 Jun 2020 19:23:55: #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 19:23:55: #3 Call peaks... INFO @ Sun, 21 Jun 2020 19:23:55: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 19:23:59: 10000000 INFO @ Sun, 21 Jun 2020 19:24:02: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX287988/SRX287988.05_peaks.xls INFO @ Sun, 21 Jun 2020 19:24:02: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX287988/SRX287988.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 19:24:02: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX287988/SRX287988.05_summits.bed INFO @ Sun, 21 Jun 2020 19:24:02: Done! pass1 - making usageList (613 chroms): 1 millis pass2 - checking and writing primary data (2442 records, 4 fields): 21 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 19:24:05: 11000000 INFO @ Sun, 21 Jun 2020 19:24:11: 12000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 19:24:17: 13000000 INFO @ Sun, 21 Jun 2020 19:24:19: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 19:24:19: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 19:24:19: #1 total tags in treatment: 13435286 INFO @ Sun, 21 Jun 2020 19:24:19: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 19:24:19: #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 19:24:20: #1 tags after filtering in treatment: 13435286 INFO @ Sun, 21 Jun 2020 19:24:20: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 19:24:20: #1 finished! INFO @ Sun, 21 Jun 2020 19:24:20: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 19:24:20: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 19:24:21: #2 number of paired peaks: 434 WARNING @ Sun, 21 Jun 2020 19:24:21: Fewer paired peaks (434) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 434 pairs to build model! INFO @ Sun, 21 Jun 2020 19:24:21: start model_add_line... INFO @ Sun, 21 Jun 2020 19:24:21: start X-correlation... INFO @ Sun, 21 Jun 2020 19:24:21: end of X-cor INFO @ Sun, 21 Jun 2020 19:24:21: #2 finished! INFO @ Sun, 21 Jun 2020 19:24:21: #2 predicted fragment length is 44 bps INFO @ Sun, 21 Jun 2020 19:24:21: #2 alternative fragment length(s) may be 4,44 bps INFO @ Sun, 21 Jun 2020 19:24:21: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX287988/SRX287988.20_model.r WARNING @ Sun, 21 Jun 2020 19:24:21: #2 Since the d (44) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 19:24:21: #2 You may need to consider one of the other alternative d(s): 4,44 WARNING @ Sun, 21 Jun 2020 19:24:21: #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 19:24:21: #3 Call peaks... INFO @ Sun, 21 Jun 2020 19:24:21: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 19:24:22: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 19:24:36: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX287988/SRX287988.10_peaks.xls INFO @ Sun, 21 Jun 2020 19:24:36: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX287988/SRX287988.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 19:24:36: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX287988/SRX287988.10_summits.bed INFO @ Sun, 21 Jun 2020 19:24:36: Done! pass1 - making usageList (507 chroms): 2 millis pass2 - checking and writing primary data (1745 records, 4 fields): 16 millis CompletedMACS2peakCalling BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 19:24:47: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 19:25:01: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX287988/SRX287988.20_peaks.xls INFO @ Sun, 21 Jun 2020 19:25:01: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX287988/SRX287988.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 19:25:01: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX287988/SRX287988.20_summits.bed INFO @ Sun, 21 Jun 2020 19:25:01: Done! pass1 - making usageList (280 chroms): 1 millis pass2 - checking and writing primary data (587 records, 4 fields): 11 millis CompletedMACS2peakCalling