Job ID = 6455523 SRX = SRX287853 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T10:29:21 prefetch.2.10.7: 1) Downloading 'SRR870042'... 2020-06-21T10:29:21 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T10:32:36 prefetch.2.10.7: HTTPS download succeed 2020-06-21T10:32:36 prefetch.2.10.7: 1) 'SRR870042' was downloaded successfully Read 17639345 spots for SRR870042/SRR870042.sra Written 17639345 spots for SRR870042/SRR870042.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: 00:06:23 17639345 reads; of these: 17639345 (100.00%) were unpaired; of these: 1423345 (8.07%) aligned 0 times 10544769 (59.78%) aligned exactly 1 time 5671231 (32.15%) aligned >1 times 91.93% overall alignment rate Time searching: 00:06:23 Overall time: 00:06:23 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] 3174866 / 16216000 = 0.1958 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 19:45:24: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX287853/SRX287853.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX287853/SRX287853.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX287853/SRX287853.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX287853/SRX287853.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 19:45:24: #1 read tag files... INFO @ Sun, 21 Jun 2020 19:45:24: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 19:45:31: 1000000 INFO @ Sun, 21 Jun 2020 19:45:38: 2000000 INFO @ Sun, 21 Jun 2020 19:45:45: 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 19:45:52: 4000000 INFO @ Sun, 21 Jun 2020 19:45:53: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX287853/SRX287853.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX287853/SRX287853.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX287853/SRX287853.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX287853/SRX287853.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 19:45:53: #1 read tag files... INFO @ Sun, 21 Jun 2020 19:45:53: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 19:45:59: 5000000 INFO @ Sun, 21 Jun 2020 19:46:01: 1000000 INFO @ Sun, 21 Jun 2020 19:46:07: 6000000 INFO @ Sun, 21 Jun 2020 19:46:09: 2000000 INFO @ Sun, 21 Jun 2020 19:46:15: 7000000 INFO @ Sun, 21 Jun 2020 19:46:16: 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 19:46:23: 8000000 INFO @ Sun, 21 Jun 2020 19:46:23: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX287853/SRX287853.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX287853/SRX287853.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX287853/SRX287853.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX287853/SRX287853.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 19:46:23: #1 read tag files... INFO @ Sun, 21 Jun 2020 19:46:23: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 19:46:24: 4000000 INFO @ Sun, 21 Jun 2020 19:46:31: 9000000 INFO @ Sun, 21 Jun 2020 19:46:31: 1000000 INFO @ Sun, 21 Jun 2020 19:46:32: 5000000 INFO @ Sun, 21 Jun 2020 19:46:39: 10000000 INFO @ Sun, 21 Jun 2020 19:46:40: 2000000 INFO @ Sun, 21 Jun 2020 19:46:40: 6000000 INFO @ Sun, 21 Jun 2020 19:46:48: 3000000 INFO @ Sun, 21 Jun 2020 19:46:48: 11000000 INFO @ Sun, 21 Jun 2020 19:46:48: 7000000 INFO @ Sun, 21 Jun 2020 19:46:56: 12000000 INFO @ Sun, 21 Jun 2020 19:46:56: 4000000 INFO @ Sun, 21 Jun 2020 19:46:57: 8000000 INFO @ Sun, 21 Jun 2020 19:47:04: 5000000 INFO @ Sun, 21 Jun 2020 19:47:04: 13000000 INFO @ Sun, 21 Jun 2020 19:47:05: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 19:47:05: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 19:47:05: #1 total tags in treatment: 13041134 INFO @ Sun, 21 Jun 2020 19:47:05: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 19:47:05: #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 19:47:05: 9000000 INFO @ Sun, 21 Jun 2020 19:47:06: #1 tags after filtering in treatment: 13041134 INFO @ Sun, 21 Jun 2020 19:47:06: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 19:47:06: #1 finished! INFO @ Sun, 21 Jun 2020 19:47:06: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 19:47:06: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 19:47:07: #2 number of paired peaks: 663 WARNING @ Sun, 21 Jun 2020 19:47:07: Fewer paired peaks (663) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 663 pairs to build model! INFO @ Sun, 21 Jun 2020 19:47:07: start model_add_line... INFO @ Sun, 21 Jun 2020 19:47:07: start X-correlation... INFO @ Sun, 21 Jun 2020 19:47:07: end of X-cor INFO @ Sun, 21 Jun 2020 19:47:07: #2 finished! INFO @ Sun, 21 Jun 2020 19:47:07: #2 predicted fragment length is 43 bps INFO @ Sun, 21 Jun 2020 19:47:07: #2 alternative fragment length(s) may be 4,43 bps INFO @ Sun, 21 Jun 2020 19:47:07: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX287853/SRX287853.05_model.r WARNING @ Sun, 21 Jun 2020 19:47:07: #2 Since the d (43) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 19:47:07: #2 You may need to consider one of the other alternative d(s): 4,43 WARNING @ Sun, 21 Jun 2020 19:47:07: #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 19:47:07: #3 Call peaks... INFO @ Sun, 21 Jun 2020 19:47:07: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 19:47:12: 6000000 INFO @ Sun, 21 Jun 2020 19:47:13: 10000000 INFO @ Sun, 21 Jun 2020 19:47:21: 7000000 INFO @ Sun, 21 Jun 2020 19:47:22: 11000000 INFO @ Sun, 21 Jun 2020 19:47:29: 8000000 INFO @ Sun, 21 Jun 2020 19:47:30: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 19:47:30: 12000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 19:47:37: 9000000 INFO @ Sun, 21 Jun 2020 19:47:39: 13000000 INFO @ Sun, 21 Jun 2020 19:47:39: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 19:47:39: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 19:47:39: #1 total tags in treatment: 13041134 INFO @ Sun, 21 Jun 2020 19:47:39: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 19:47:39: #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 19:47:40: #1 tags after filtering in treatment: 13041134 INFO @ Sun, 21 Jun 2020 19:47:40: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 19:47:40: #1 finished! INFO @ Sun, 21 Jun 2020 19:47:40: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 19:47:40: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 19:47:41: #2 number of paired peaks: 663 WARNING @ Sun, 21 Jun 2020 19:47:41: Fewer paired peaks (663) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 663 pairs to build model! INFO @ Sun, 21 Jun 2020 19:47:41: start model_add_line... INFO @ Sun, 21 Jun 2020 19:47:41: start X-correlation... INFO @ Sun, 21 Jun 2020 19:47:41: end of X-cor INFO @ Sun, 21 Jun 2020 19:47:41: #2 finished! INFO @ Sun, 21 Jun 2020 19:47:41: #2 predicted fragment length is 43 bps INFO @ Sun, 21 Jun 2020 19:47:41: #2 alternative fragment length(s) may be 4,43 bps INFO @ Sun, 21 Jun 2020 19:47:41: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX287853/SRX287853.10_model.r WARNING @ Sun, 21 Jun 2020 19:47:41: #2 Since the d (43) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 19:47:41: #2 You may need to consider one of the other alternative d(s): 4,43 WARNING @ Sun, 21 Jun 2020 19:47:41: #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 19:47:41: #3 Call peaks... INFO @ Sun, 21 Jun 2020 19:47:41: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 19:47:42: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX287853/SRX287853.05_peaks.xls INFO @ Sun, 21 Jun 2020 19:47:42: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX287853/SRX287853.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 19:47:42: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX287853/SRX287853.05_summits.bed INFO @ Sun, 21 Jun 2020 19:47:42: Done! pass1 - making usageList (641 chroms): 1 millis pass2 - checking and writing primary data (2443 records, 4 fields): 43 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 19:47:45: 10000000 INFO @ Sun, 21 Jun 2020 19:47:54: 11000000 INFO @ Sun, 21 Jun 2020 19:48:02: 12000000 INFO @ Sun, 21 Jun 2020 19:48:04: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 19:48:11: 13000000 INFO @ Sun, 21 Jun 2020 19:48:11: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 19:48:11: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 19:48:11: #1 total tags in treatment: 13041134 INFO @ Sun, 21 Jun 2020 19:48:11: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 19:48:11: #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 19:48:12: #1 tags after filtering in treatment: 13041134 INFO @ Sun, 21 Jun 2020 19:48:12: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 19:48:12: #1 finished! INFO @ Sun, 21 Jun 2020 19:48:12: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 19:48:12: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 19:48:13: #2 number of paired peaks: 663 WARNING @ Sun, 21 Jun 2020 19:48:13: Fewer paired peaks (663) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 663 pairs to build model! INFO @ Sun, 21 Jun 2020 19:48:13: start model_add_line... INFO @ Sun, 21 Jun 2020 19:48:13: start X-correlation... INFO @ Sun, 21 Jun 2020 19:48:13: end of X-cor INFO @ Sun, 21 Jun 2020 19:48:13: #2 finished! INFO @ Sun, 21 Jun 2020 19:48:13: #2 predicted fragment length is 43 bps INFO @ Sun, 21 Jun 2020 19:48:13: #2 alternative fragment length(s) may be 4,43 bps INFO @ Sun, 21 Jun 2020 19:48:13: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX287853/SRX287853.20_model.r WARNING @ Sun, 21 Jun 2020 19:48:13: #2 Since the d (43) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 19:48:13: #2 You may need to consider one of the other alternative d(s): 4,43 WARNING @ Sun, 21 Jun 2020 19:48:13: #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 19:48:13: #3 Call peaks... INFO @ Sun, 21 Jun 2020 19:48:13: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 19:48:16: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX287853/SRX287853.10_peaks.xls INFO @ Sun, 21 Jun 2020 19:48:16: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX287853/SRX287853.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 19:48:16: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX287853/SRX287853.10_summits.bed INFO @ Sun, 21 Jun 2020 19:48:16: Done! pass1 - making usageList (529 chroms): 1 millis pass2 - checking and writing primary data (1988 records, 4 fields): 31 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 19:48:36: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 19:48:48: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX287853/SRX287853.20_peaks.xls INFO @ Sun, 21 Jun 2020 19:48:48: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX287853/SRX287853.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 19:48:48: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX287853/SRX287853.20_summits.bed INFO @ Sun, 21 Jun 2020 19:48:48: Done! pass1 - making usageList (353 chroms): 1 millis pass2 - checking and writing primary data (796 records, 4 fields): 21 millis CompletedMACS2peakCalling