Job ID = 6454494 SRX = SRX2165278 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T09:26:29 prefetch.2.10.7: 1) Downloading 'SRR4244785'... 2020-06-21T09:26:29 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T09:30:25 prefetch.2.10.7: HTTPS download succeed 2020-06-21T09:30:26 prefetch.2.10.7: 'SRR4244785' is valid 2020-06-21T09:30:26 prefetch.2.10.7: 1) 'SRR4244785' was downloaded successfully Read 9072368 spots for SRR4244785/SRR4244785.sra Written 9072368 spots for SRR4244785/SRR4244785.sra 2020-06-21T09:31:03 prefetch.2.10.7: 1) Downloading 'SRR4244786'... 2020-06-21T09:31:03 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T09:32:39 prefetch.2.10.7: HTTPS download succeed 2020-06-21T09:32:39 prefetch.2.10.7: 'SRR4244786' is valid 2020-06-21T09:32:39 prefetch.2.10.7: 1) 'SRR4244786' was downloaded successfully Read 7304844 spots for SRR4244786/SRR4244786.sra Written 7304844 spots for SRR4244786/SRR4244786.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: 00:05:21 16377212 reads; of these: 16377212 (100.00%) were unpaired; of these: 5705641 (34.84%) aligned 0 times 7978137 (48.71%) aligned exactly 1 time 2693434 (16.45%) aligned >1 times 65.16% overall alignment rate Time searching: 00:05:21 Overall time: 00:05:21 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] 2720940 / 10671571 = 0.2550 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 18:42:12: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX2165278/SRX2165278.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX2165278/SRX2165278.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX2165278/SRX2165278.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX2165278/SRX2165278.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 18:42:12: #1 read tag files... INFO @ Sun, 21 Jun 2020 18:42:12: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 18:42:19: 1000000 INFO @ Sun, 21 Jun 2020 18:42:25: 2000000 INFO @ Sun, 21 Jun 2020 18:42:31: 3000000 INFO @ Sun, 21 Jun 2020 18:42:37: 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 18:42:42: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX2165278/SRX2165278.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX2165278/SRX2165278.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX2165278/SRX2165278.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX2165278/SRX2165278.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 18:42:42: #1 read tag files... INFO @ Sun, 21 Jun 2020 18:42:42: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 18:42:43: 5000000 INFO @ Sun, 21 Jun 2020 18:42:48: 1000000 INFO @ Sun, 21 Jun 2020 18:42:49: 6000000 INFO @ Sun, 21 Jun 2020 18:42:55: 2000000 INFO @ Sun, 21 Jun 2020 18:42:56: 7000000 INFO @ Sun, 21 Jun 2020 18:43:01: 3000000 INFO @ Sun, 21 Jun 2020 18:43:02: #1 tag size is determined as 75 bps INFO @ Sun, 21 Jun 2020 18:43:02: #1 tag size = 75 INFO @ Sun, 21 Jun 2020 18:43:02: #1 total tags in treatment: 7950631 INFO @ Sun, 21 Jun 2020 18:43:02: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 18:43:02: #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 18:43:02: #1 tags after filtering in treatment: 7950629 INFO @ Sun, 21 Jun 2020 18:43:02: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 18:43:02: #1 finished! INFO @ Sun, 21 Jun 2020 18:43:02: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 18:43:02: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 18:43:03: #2 number of paired peaks: 886 WARNING @ Sun, 21 Jun 2020 18:43:03: Fewer paired peaks (886) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 886 pairs to build model! INFO @ Sun, 21 Jun 2020 18:43:03: start model_add_line... INFO @ Sun, 21 Jun 2020 18:43:03: start X-correlation... INFO @ Sun, 21 Jun 2020 18:43:03: end of X-cor INFO @ Sun, 21 Jun 2020 18:43:03: #2 finished! INFO @ Sun, 21 Jun 2020 18:43:03: #2 predicted fragment length is 82 bps INFO @ Sun, 21 Jun 2020 18:43:03: #2 alternative fragment length(s) may be 82 bps INFO @ Sun, 21 Jun 2020 18:43:03: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX2165278/SRX2165278.05_model.r WARNING @ Sun, 21 Jun 2020 18:43:03: #2 Since the d (82) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 18:43:03: #2 You may need to consider one of the other alternative d(s): 82 WARNING @ Sun, 21 Jun 2020 18:43:03: #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 18:43:03: #3 Call peaks... INFO @ Sun, 21 Jun 2020 18:43:03: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 18:43:08: 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 18:43:12: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX2165278/SRX2165278.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX2165278/SRX2165278.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX2165278/SRX2165278.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX2165278/SRX2165278.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 18:43:12: #1 read tag files... INFO @ Sun, 21 Jun 2020 18:43:12: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 18:43:14: 5000000 INFO @ Sun, 21 Jun 2020 18:43:17: 1000000 INFO @ Sun, 21 Jun 2020 18:43:20: 6000000 INFO @ Sun, 21 Jun 2020 18:43:21: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 18:43:23: 2000000 INFO @ Sun, 21 Jun 2020 18:43:27: 7000000 INFO @ Sun, 21 Jun 2020 18:43:29: 3000000 INFO @ Sun, 21 Jun 2020 18:43:30: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX2165278/SRX2165278.05_peaks.xls INFO @ Sun, 21 Jun 2020 18:43:30: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX2165278/SRX2165278.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 18:43:30: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX2165278/SRX2165278.05_summits.bed INFO @ Sun, 21 Jun 2020 18:43:30: Done! pass1 - making usageList (628 chroms): 2 millis pass2 - checking and writing primary data (3111 records, 4 fields): 21 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 18:43:33: #1 tag size is determined as 75 bps INFO @ Sun, 21 Jun 2020 18:43:33: #1 tag size = 75 INFO @ Sun, 21 Jun 2020 18:43:33: #1 total tags in treatment: 7950631 INFO @ Sun, 21 Jun 2020 18:43:33: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 18:43:33: #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 18:43:34: #1 tags after filtering in treatment: 7950629 INFO @ Sun, 21 Jun 2020 18:43:34: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 18:43:34: #1 finished! INFO @ Sun, 21 Jun 2020 18:43:34: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 18:43:34: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 18:43:34: 4000000 INFO @ Sun, 21 Jun 2020 18:43:34: #2 number of paired peaks: 886 WARNING @ Sun, 21 Jun 2020 18:43:34: Fewer paired peaks (886) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 886 pairs to build model! INFO @ Sun, 21 Jun 2020 18:43:34: start model_add_line... INFO @ Sun, 21 Jun 2020 18:43:35: start X-correlation... INFO @ Sun, 21 Jun 2020 18:43:35: end of X-cor INFO @ Sun, 21 Jun 2020 18:43:35: #2 finished! INFO @ Sun, 21 Jun 2020 18:43:35: #2 predicted fragment length is 82 bps INFO @ Sun, 21 Jun 2020 18:43:35: #2 alternative fragment length(s) may be 82 bps INFO @ Sun, 21 Jun 2020 18:43:35: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX2165278/SRX2165278.10_model.r WARNING @ Sun, 21 Jun 2020 18:43:35: #2 Since the d (82) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 18:43:35: #2 You may need to consider one of the other alternative d(s): 82 WARNING @ Sun, 21 Jun 2020 18:43:35: #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 18:43:35: #3 Call peaks... INFO @ Sun, 21 Jun 2020 18:43:35: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 18:43:40: 5000000 INFO @ Sun, 21 Jun 2020 18:43:45: 6000000 INFO @ Sun, 21 Jun 2020 18:43:51: 7000000 INFO @ Sun, 21 Jun 2020 18:43:53: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 18:43:56: #1 tag size is determined as 75 bps INFO @ Sun, 21 Jun 2020 18:43:56: #1 tag size = 75 INFO @ Sun, 21 Jun 2020 18:43:56: #1 total tags in treatment: 7950631 INFO @ Sun, 21 Jun 2020 18:43:56: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 18:43:56: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 18:43:57: #1 tags after filtering in treatment: 7950629 INFO @ Sun, 21 Jun 2020 18:43:57: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 18:43:57: #1 finished! INFO @ Sun, 21 Jun 2020 18:43:57: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 18:43:57: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 18:43:57: #2 number of paired peaks: 886 WARNING @ Sun, 21 Jun 2020 18:43:57: Fewer paired peaks (886) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 886 pairs to build model! INFO @ Sun, 21 Jun 2020 18:43:57: start model_add_line... INFO @ Sun, 21 Jun 2020 18:43:57: start X-correlation... INFO @ Sun, 21 Jun 2020 18:43:57: end of X-cor INFO @ Sun, 21 Jun 2020 18:43:57: #2 finished! INFO @ Sun, 21 Jun 2020 18:43:57: #2 predicted fragment length is 82 bps INFO @ Sun, 21 Jun 2020 18:43:57: #2 alternative fragment length(s) may be 82 bps INFO @ Sun, 21 Jun 2020 18:43:57: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX2165278/SRX2165278.20_model.r WARNING @ Sun, 21 Jun 2020 18:43:57: #2 Since the d (82) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 18:43:57: #2 You may need to consider one of the other alternative d(s): 82 WARNING @ Sun, 21 Jun 2020 18:43:57: #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 18:43:57: #3 Call peaks... INFO @ Sun, 21 Jun 2020 18:43:57: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 18:44:02: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX2165278/SRX2165278.10_peaks.xls INFO @ Sun, 21 Jun 2020 18:44:02: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX2165278/SRX2165278.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 18:44:02: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX2165278/SRX2165278.10_summits.bed INFO @ Sun, 21 Jun 2020 18:44:02: Done! pass1 - making usageList (518 chroms): 2 millis pass2 - checking and writing primary data (1862 records, 4 fields): 16 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 18:44:14: #3 Call peaks for each chromosome... BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 18:44:23: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX2165278/SRX2165278.20_peaks.xls INFO @ Sun, 21 Jun 2020 18:44:23: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX2165278/SRX2165278.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 18:44:23: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX2165278/SRX2165278.20_summits.bed INFO @ Sun, 21 Jun 2020 18:44:23: Done! pass1 - making usageList (328 chroms): 1 millis pass2 - checking and writing primary data (823 records, 4 fields): 11 millis CompletedMACS2peakCalling