Job ID = 6458948 SRX = SRX5827819 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T12:48:40 prefetch.2.10.7: 1) Downloading 'SRR9051570'... 2020-06-21T12:48:40 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T12:50:23 prefetch.2.10.7: HTTPS download succeed 2020-06-21T12:50:24 prefetch.2.10.7: 'SRR9051570' is valid 2020-06-21T12:50:24 prefetch.2.10.7: 1) 'SRR9051570' was downloaded successfully 2020-06-21T12:50:24 prefetch.2.10.7: 'SRR9051570' has 0 unresolved dependencies Read 17877859 spots for SRR9051570/SRR9051570.sra Written 17877859 spots for SRR9051570/SRR9051570.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: 00:03:58 17877859 reads; of these: 17877859 (100.00%) were unpaired; of these: 3287597 (18.39%) aligned 0 times 12398836 (69.35%) aligned exactly 1 time 2191426 (12.26%) aligned >1 times 81.61% overall alignment rate Time searching: 00:03:58 Overall time: 00:03:58 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] 7791017 / 14590262 = 0.5340 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 21:58:59: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX5827819/SRX5827819.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX5827819/SRX5827819.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX5827819/SRX5827819.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX5827819/SRX5827819.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 21:58:59: #1 read tag files... INFO @ Sun, 21 Jun 2020 21:58:59: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 21:59:04: 1000000 INFO @ Sun, 21 Jun 2020 21:59:09: 2000000 INFO @ Sun, 21 Jun 2020 21:59:15: 3000000 INFO @ Sun, 21 Jun 2020 21:59:20: 4000000 INFO @ Sun, 21 Jun 2020 21:59:25: 5000000 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 21:59:29: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX5827819/SRX5827819.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX5827819/SRX5827819.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX5827819/SRX5827819.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX5827819/SRX5827819.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 21:59:29: #1 read tag files... INFO @ Sun, 21 Jun 2020 21:59:29: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 21:59:31: 6000000 INFO @ Sun, 21 Jun 2020 21:59:34: 1000000 INFO @ Sun, 21 Jun 2020 21:59:35: #1 tag size is determined as 51 bps INFO @ Sun, 21 Jun 2020 21:59:35: #1 tag size = 51 INFO @ Sun, 21 Jun 2020 21:59:35: #1 total tags in treatment: 6799245 INFO @ Sun, 21 Jun 2020 21:59:35: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 21:59:35: #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 21:59:36: #1 tags after filtering in treatment: 6799230 INFO @ Sun, 21 Jun 2020 21:59:36: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 21:59:36: #1 finished! INFO @ Sun, 21 Jun 2020 21:59:36: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 21:59:36: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 21:59:36: #2 number of paired peaks: 699 WARNING @ Sun, 21 Jun 2020 21:59:36: Fewer paired peaks (699) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 699 pairs to build model! INFO @ Sun, 21 Jun 2020 21:59:36: start model_add_line... INFO @ Sun, 21 Jun 2020 21:59:36: start X-correlation... INFO @ Sun, 21 Jun 2020 21:59:36: end of X-cor INFO @ Sun, 21 Jun 2020 21:59:36: #2 finished! INFO @ Sun, 21 Jun 2020 21:59:36: #2 predicted fragment length is 102 bps INFO @ Sun, 21 Jun 2020 21:59:36: #2 alternative fragment length(s) may be 102,570 bps INFO @ Sun, 21 Jun 2020 21:59:36: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX5827819/SRX5827819.05_model.r WARNING @ Sun, 21 Jun 2020 21:59:36: #2 Since the d (102) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 21:59:36: #2 You may need to consider one of the other alternative d(s): 102,570 WARNING @ Sun, 21 Jun 2020 21:59:36: #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 21:59:36: #3 Call peaks... INFO @ Sun, 21 Jun 2020 21:59:36: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 21:59:40: 2000000 INFO @ Sun, 21 Jun 2020 21:59:46: 3000000 INFO @ Sun, 21 Jun 2020 21:59:50: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 21:59:51: 4000000 INFO @ Sun, 21 Jun 2020 21:59:57: 5000000 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 21:59:58: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX5827819/SRX5827819.05_peaks.xls INFO @ Sun, 21 Jun 2020 21:59:58: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX5827819/SRX5827819.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 21:59:58: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX5827819/SRX5827819.05_summits.bed INFO @ Sun, 21 Jun 2020 21:59:58: Done! pass1 - making usageList (448 chroms): 2 millis pass2 - checking and writing primary data (2292 records, 4 fields): 13 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 21:59:59: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX5827819/SRX5827819.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX5827819/SRX5827819.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX5827819/SRX5827819.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX5827819/SRX5827819.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 21:59:59: #1 read tag files... INFO @ Sun, 21 Jun 2020 21:59:59: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 22:00:03: 6000000 INFO @ Sun, 21 Jun 2020 22:00:04: 1000000 INFO @ Sun, 21 Jun 2020 22:00:07: #1 tag size is determined as 51 bps INFO @ Sun, 21 Jun 2020 22:00:07: #1 tag size = 51 INFO @ Sun, 21 Jun 2020 22:00:07: #1 total tags in treatment: 6799245 INFO @ Sun, 21 Jun 2020 22:00:07: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 22:00:07: #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 22:00:07: #1 tags after filtering in treatment: 6799230 INFO @ Sun, 21 Jun 2020 22:00:07: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 22:00:07: #1 finished! INFO @ Sun, 21 Jun 2020 22:00:07: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 22:00:07: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 22:00:08: #2 number of paired peaks: 699 WARNING @ Sun, 21 Jun 2020 22:00:08: Fewer paired peaks (699) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 699 pairs to build model! INFO @ Sun, 21 Jun 2020 22:00:08: start model_add_line... INFO @ Sun, 21 Jun 2020 22:00:08: start X-correlation... INFO @ Sun, 21 Jun 2020 22:00:08: end of X-cor INFO @ Sun, 21 Jun 2020 22:00:08: #2 finished! INFO @ Sun, 21 Jun 2020 22:00:08: #2 predicted fragment length is 102 bps INFO @ Sun, 21 Jun 2020 22:00:08: #2 alternative fragment length(s) may be 102,570 bps INFO @ Sun, 21 Jun 2020 22:00:08: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX5827819/SRX5827819.10_model.r WARNING @ Sun, 21 Jun 2020 22:00:08: #2 Since the d (102) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 22:00:08: #2 You may need to consider one of the other alternative d(s): 102,570 WARNING @ Sun, 21 Jun 2020 22:00:08: #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 22:00:08: #3 Call peaks... INFO @ Sun, 21 Jun 2020 22:00:08: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 22:00:10: 2000000 INFO @ Sun, 21 Jun 2020 22:00:15: 3000000 INFO @ Sun, 21 Jun 2020 22:00:19: 4000000 INFO @ Sun, 21 Jun 2020 22:00:23: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 22:00:24: 5000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 22:00:29: 6000000 INFO @ Sun, 21 Jun 2020 22:00:30: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX5827819/SRX5827819.10_peaks.xls INFO @ Sun, 21 Jun 2020 22:00:30: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX5827819/SRX5827819.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 22:00:30: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX5827819/SRX5827819.10_summits.bed INFO @ Sun, 21 Jun 2020 22:00:30: Done! pass1 - making usageList (301 chroms): 1 millis pass2 - checking and writing primary data (929 records, 4 fields): 10 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 22:00:34: #1 tag size is determined as 51 bps INFO @ Sun, 21 Jun 2020 22:00:34: #1 tag size = 51 INFO @ Sun, 21 Jun 2020 22:00:34: #1 total tags in treatment: 6799245 INFO @ Sun, 21 Jun 2020 22:00:34: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 22:00:34: #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 22:00:34: #1 tags after filtering in treatment: 6799230 INFO @ Sun, 21 Jun 2020 22:00:34: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 22:00:34: #1 finished! INFO @ Sun, 21 Jun 2020 22:00:34: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 22:00:34: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 22:00:34: #2 number of paired peaks: 699 WARNING @ Sun, 21 Jun 2020 22:00:34: Fewer paired peaks (699) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 699 pairs to build model! INFO @ Sun, 21 Jun 2020 22:00:34: start model_add_line... INFO @ Sun, 21 Jun 2020 22:00:34: start X-correlation... INFO @ Sun, 21 Jun 2020 22:00:34: end of X-cor INFO @ Sun, 21 Jun 2020 22:00:34: #2 finished! INFO @ Sun, 21 Jun 2020 22:00:34: #2 predicted fragment length is 102 bps INFO @ Sun, 21 Jun 2020 22:00:34: #2 alternative fragment length(s) may be 102,570 bps INFO @ Sun, 21 Jun 2020 22:00:34: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX5827819/SRX5827819.20_model.r WARNING @ Sun, 21 Jun 2020 22:00:34: #2 Since the d (102) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 22:00:34: #2 You may need to consider one of the other alternative d(s): 102,570 WARNING @ Sun, 21 Jun 2020 22:00:34: #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 22:00:34: #3 Call peaks... INFO @ Sun, 21 Jun 2020 22:00:34: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 22:00:50: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 22:00:57: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX5827819/SRX5827819.20_peaks.xls INFO @ Sun, 21 Jun 2020 22:00:57: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX5827819/SRX5827819.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 22:00:57: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX5827819/SRX5827819.20_summits.bed INFO @ Sun, 21 Jun 2020 22:00:57: Done! pass1 - making usageList (125 chroms): 1 millis pass2 - checking and writing primary data (306 records, 4 fields): 7 millis CompletedMACS2peakCalling