Job ID = 6455032 SRX = SRX2642383 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T09:33:55 prefetch.2.10.7: 1) Downloading 'SRR5345723'... 2020-06-21T09:33:55 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T09:35:03 prefetch.2.10.7: HTTPS download succeed 2020-06-21T09:35:03 prefetch.2.10.7: 'SRR5345723' is valid 2020-06-21T09:35:03 prefetch.2.10.7: 1) 'SRR5345723' was downloaded successfully 2020-06-21T09:35:03 prefetch.2.10.7: 'SRR5345723' has 0 unresolved dependencies Read 3448905 spots for SRR5345723/SRR5345723.sra Written 3448905 spots for SRR5345723/SRR5345723.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: 00:01:46 3448905 reads; of these: 3448905 (100.00%) were unpaired; of these: 567072 (16.44%) aligned 0 times 2074070 (60.14%) aligned exactly 1 time 807763 (23.42%) aligned >1 times 83.56% overall alignment rate Time searching: 00:01:46 Overall time: 00:01:46 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_rmdupse_core] 247085 / 2881833 = 0.0857 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 18:38:45: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX2642383/SRX2642383.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX2642383/SRX2642383.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX2642383/SRX2642383.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX2642383/SRX2642383.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 18:38:45: #1 read tag files... INFO @ Sun, 21 Jun 2020 18:38:45: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 18:38:53: 1000000 INFO @ Sun, 21 Jun 2020 18:39:01: 2000000 INFO @ Sun, 21 Jun 2020 18:39:07: #1 tag size is determined as 99 bps INFO @ Sun, 21 Jun 2020 18:39:07: #1 tag size = 99 INFO @ Sun, 21 Jun 2020 18:39:07: #1 total tags in treatment: 2634748 INFO @ Sun, 21 Jun 2020 18:39:07: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 18:39:07: #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 18:39:07: #1 tags after filtering in treatment: 2634701 INFO @ Sun, 21 Jun 2020 18:39:07: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 18:39:07: #1 finished! INFO @ Sun, 21 Jun 2020 18:39:07: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 18:39:07: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 18:39:07: #2 number of paired peaks: 559 WARNING @ Sun, 21 Jun 2020 18:39:07: Fewer paired peaks (559) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 559 pairs to build model! INFO @ Sun, 21 Jun 2020 18:39:07: start model_add_line... INFO @ Sun, 21 Jun 2020 18:39:07: start X-correlation... INFO @ Sun, 21 Jun 2020 18:39:07: end of X-cor INFO @ Sun, 21 Jun 2020 18:39:07: #2 finished! INFO @ Sun, 21 Jun 2020 18:39:07: #2 predicted fragment length is 98 bps INFO @ Sun, 21 Jun 2020 18:39:07: #2 alternative fragment length(s) may be 98 bps INFO @ Sun, 21 Jun 2020 18:39:07: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX2642383/SRX2642383.05_model.r WARNING @ Sun, 21 Jun 2020 18:39:07: #2 Since the d (98) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 18:39:07: #2 You may need to consider one of the other alternative d(s): 98 WARNING @ Sun, 21 Jun 2020 18:39:07: #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 18:39:07: #3 Call peaks... INFO @ Sun, 21 Jun 2020 18:39:07: #3 Pre-compute pvalue-qvalue table... 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 18:39:14: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 18:39:15: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX2642383/SRX2642383.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX2642383/SRX2642383.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX2642383/SRX2642383.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX2642383/SRX2642383.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 18:39:15: #1 read tag files... INFO @ Sun, 21 Jun 2020 18:39:15: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 18:39:18: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX2642383/SRX2642383.05_peaks.xls INFO @ Sun, 21 Jun 2020 18:39:18: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX2642383/SRX2642383.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 18:39:18: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX2642383/SRX2642383.05_summits.bed INFO @ Sun, 21 Jun 2020 18:39:18: Done! pass1 - making usageList (456 chroms): 1 millis pass2 - checking and writing primary data (956 records, 4 fields): 17 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 18:39:22: 1000000 INFO @ Sun, 21 Jun 2020 18:39:29: 2000000 INFO @ Sun, 21 Jun 2020 18:39:34: #1 tag size is determined as 99 bps INFO @ Sun, 21 Jun 2020 18:39:34: #1 tag size = 99 INFO @ Sun, 21 Jun 2020 18:39:34: #1 total tags in treatment: 2634748 INFO @ Sun, 21 Jun 2020 18:39:34: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 18:39:34: #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 18:39:34: #1 tags after filtering in treatment: 2634701 INFO @ Sun, 21 Jun 2020 18:39:34: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 18:39:34: #1 finished! INFO @ Sun, 21 Jun 2020 18:39:34: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 18:39:34: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 18:39:35: #2 number of paired peaks: 559 WARNING @ Sun, 21 Jun 2020 18:39:35: Fewer paired peaks (559) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 559 pairs to build model! INFO @ Sun, 21 Jun 2020 18:39:35: start model_add_line... INFO @ Sun, 21 Jun 2020 18:39:35: start X-correlation... INFO @ Sun, 21 Jun 2020 18:39:35: end of X-cor INFO @ Sun, 21 Jun 2020 18:39:35: #2 finished! INFO @ Sun, 21 Jun 2020 18:39:35: #2 predicted fragment length is 98 bps INFO @ Sun, 21 Jun 2020 18:39:35: #2 alternative fragment length(s) may be 98 bps INFO @ Sun, 21 Jun 2020 18:39:35: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX2642383/SRX2642383.10_model.r WARNING @ Sun, 21 Jun 2020 18:39:35: #2 Since the d (98) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 18:39:35: #2 You may need to consider one of the other alternative d(s): 98 WARNING @ Sun, 21 Jun 2020 18:39:35: #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 18:39:35: #3 Call peaks... INFO @ Sun, 21 Jun 2020 18:39:35: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 18:39:41: #3 Call peaks for each chromosome... 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 18:39:45: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX2642383/SRX2642383.10_peaks.xls INFO @ Sun, 21 Jun 2020 18:39:45: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX2642383/SRX2642383.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 18:39:45: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX2642383/SRX2642383.10_summits.bed INFO @ Sun, 21 Jun 2020 18:39:45: Done! pass1 - making usageList (346 chroms): 1 millis pass2 - checking and writing primary data (580 records, 4 fields): 13 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 18:39:45: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX2642383/SRX2642383.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX2642383/SRX2642383.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX2642383/SRX2642383.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX2642383/SRX2642383.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 18:39:45: #1 read tag files... INFO @ Sun, 21 Jun 2020 18:39:45: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 18:39:52: 1000000 INFO @ Sun, 21 Jun 2020 18:39:59: 2000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 18:40:04: #1 tag size is determined as 99 bps INFO @ Sun, 21 Jun 2020 18:40:04: #1 tag size = 99 INFO @ Sun, 21 Jun 2020 18:40:04: #1 total tags in treatment: 2634748 INFO @ Sun, 21 Jun 2020 18:40:04: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 18:40:04: #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 18:40:04: #1 tags after filtering in treatment: 2634701 INFO @ Sun, 21 Jun 2020 18:40:04: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 18:40:04: #1 finished! INFO @ Sun, 21 Jun 2020 18:40:04: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 18:40:04: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 18:40:04: #2 number of paired peaks: 559 WARNING @ Sun, 21 Jun 2020 18:40:04: Fewer paired peaks (559) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 559 pairs to build model! INFO @ Sun, 21 Jun 2020 18:40:04: start model_add_line... INFO @ Sun, 21 Jun 2020 18:40:04: start X-correlation... INFO @ Sun, 21 Jun 2020 18:40:04: end of X-cor INFO @ Sun, 21 Jun 2020 18:40:04: #2 finished! INFO @ Sun, 21 Jun 2020 18:40:04: #2 predicted fragment length is 98 bps INFO @ Sun, 21 Jun 2020 18:40:04: #2 alternative fragment length(s) may be 98 bps INFO @ Sun, 21 Jun 2020 18:40:04: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX2642383/SRX2642383.20_model.r WARNING @ Sun, 21 Jun 2020 18:40:04: #2 Since the d (98) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 18:40:04: #2 You may need to consider one of the other alternative d(s): 98 WARNING @ Sun, 21 Jun 2020 18:40:04: #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 18:40:04: #3 Call peaks... INFO @ Sun, 21 Jun 2020 18:40:04: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 18:40:11: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 18:40:14: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX2642383/SRX2642383.20_peaks.xls INFO @ Sun, 21 Jun 2020 18:40:14: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX2642383/SRX2642383.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 18:40:14: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX2642383/SRX2642383.20_summits.bed INFO @ Sun, 21 Jun 2020 18:40:14: Done! pass1 - making usageList (165 chroms): 1 millis pass2 - checking and writing primary data (240 records, 4 fields): 6 millis CompletedMACS2peakCalling