Job ID = 6454485 SRX = SRX2165272 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T09:15:39 prefetch.2.10.7: 1) Downloading 'SRR4244773'... 2020-06-21T09:15:39 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T09:17:53 prefetch.2.10.7: HTTPS download succeed 2020-06-21T09:17:53 prefetch.2.10.7: 'SRR4244773' is valid 2020-06-21T09:17:53 prefetch.2.10.7: 1) 'SRR4244773' was downloaded successfully Read 7665934 spots for SRR4244773/SRR4244773.sra Written 7665934 spots for SRR4244773/SRR4244773.sra 2020-06-21T09:18:28 prefetch.2.10.7: 1) Downloading 'SRR4244774'... 2020-06-21T09:18:28 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T09:20:37 prefetch.2.10.7: HTTPS download succeed 2020-06-21T09:20:38 prefetch.2.10.7: 'SRR4244774' is valid 2020-06-21T09:20:38 prefetch.2.10.7: 1) 'SRR4244774' was downloaded successfully Read 8488912 spots for SRR4244774/SRR4244774.sra Written 8488912 spots for SRR4244774/SRR4244774.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: 00:04:51 16154846 reads; of these: 16154846 (100.00%) were unpaired; of these: 5122040 (31.71%) aligned 0 times 8011854 (49.59%) aligned exactly 1 time 3020952 (18.70%) aligned >1 times 68.29% overall alignment rate Time searching: 00:04:51 Overall time: 00:04:51 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] 3667350 / 11032806 = 0.3324 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 18:29:31: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX2165272/SRX2165272.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX2165272/SRX2165272.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX2165272/SRX2165272.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX2165272/SRX2165272.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 18:29:31: #1 read tag files... INFO @ Sun, 21 Jun 2020 18:29:31: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 18:29:39: 1000000 INFO @ Sun, 21 Jun 2020 18:29:46: 2000000 INFO @ Sun, 21 Jun 2020 18:29:54: 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 18:30:01: 4000000 INFO @ Sun, 21 Jun 2020 18:30:01: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX2165272/SRX2165272.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX2165272/SRX2165272.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX2165272/SRX2165272.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX2165272/SRX2165272.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 18:30:01: #1 read tag files... INFO @ Sun, 21 Jun 2020 18:30:01: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 18:30:09: 5000000 INFO @ Sun, 21 Jun 2020 18:30:09: 1000000 INFO @ Sun, 21 Jun 2020 18:30:17: 2000000 INFO @ Sun, 21 Jun 2020 18:30:17: 6000000 INFO @ Sun, 21 Jun 2020 18:30:25: 3000000 INFO @ Sun, 21 Jun 2020 18:30:25: 7000000 INFO @ Sun, 21 Jun 2020 18:30:28: #1 tag size is determined as 67 bps INFO @ Sun, 21 Jun 2020 18:30:28: #1 tag size = 67 INFO @ Sun, 21 Jun 2020 18:30:28: #1 total tags in treatment: 7365456 INFO @ Sun, 21 Jun 2020 18:30:28: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 18:30:28: #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 18:30:28: #1 tags after filtering in treatment: 7365445 INFO @ Sun, 21 Jun 2020 18:30:28: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 18:30:28: #1 finished! INFO @ Sun, 21 Jun 2020 18:30:28: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 18:30:28: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 18:30:29: #2 number of paired peaks: 892 WARNING @ Sun, 21 Jun 2020 18:30:29: Fewer paired peaks (892) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 892 pairs to build model! INFO @ Sun, 21 Jun 2020 18:30:29: start model_add_line... BedGraph に変換中... INFO @ Sun, 21 Jun 2020 18:30:29: start X-correlation... INFO @ Sun, 21 Jun 2020 18:30:29: end of X-cor INFO @ Sun, 21 Jun 2020 18:30:29: #2 finished! INFO @ Sun, 21 Jun 2020 18:30:29: #2 predicted fragment length is 65 bps INFO @ Sun, 21 Jun 2020 18:30:29: #2 alternative fragment length(s) may be 4,65,564 bps INFO @ Sun, 21 Jun 2020 18:30:29: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX2165272/SRX2165272.05_model.r 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 WARNING @ Sun, 21 Jun 2020 18:30:29: #2 Since the d (65) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 18:30:29: #2 You may need to consider one of the other alternative d(s): 4,65,564 WARNING @ Sun, 21 Jun 2020 18:30:29: #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 18:30:29: #3 Call peaks... INFO @ Sun, 21 Jun 2020 18:30:29: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 18:30:31: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX2165272/SRX2165272.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX2165272/SRX2165272.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX2165272/SRX2165272.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX2165272/SRX2165272.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 18:30:31: #1 read tag files... INFO @ Sun, 21 Jun 2020 18:30:31: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 18:30:32: 4000000 INFO @ Sun, 21 Jun 2020 18:30:39: 1000000 INFO @ Sun, 21 Jun 2020 18:30:40: 5000000 INFO @ Sun, 21 Jun 2020 18:30:46: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 18:30:48: 2000000 INFO @ Sun, 21 Jun 2020 18:30:49: 6000000 INFO @ Sun, 21 Jun 2020 18:30:55: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX2165272/SRX2165272.05_peaks.xls INFO @ Sun, 21 Jun 2020 18:30:55: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX2165272/SRX2165272.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 18:30:55: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX2165272/SRX2165272.05_summits.bed INFO @ Sun, 21 Jun 2020 18:30:55: Done! pass1 - making usageList (642 chroms): 1 millis pass2 - checking and writing primary data (2193 records, 4 fields): 21 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 18:30:56: 3000000 INFO @ Sun, 21 Jun 2020 18:30:57: 7000000 INFO @ Sun, 21 Jun 2020 18:31:00: #1 tag size is determined as 67 bps INFO @ Sun, 21 Jun 2020 18:31:00: #1 tag size = 67 INFO @ Sun, 21 Jun 2020 18:31:00: #1 total tags in treatment: 7365456 INFO @ Sun, 21 Jun 2020 18:31:00: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 18:31:00: #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 18:31:01: #1 tags after filtering in treatment: 7365445 INFO @ Sun, 21 Jun 2020 18:31:01: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 18:31:01: #1 finished! INFO @ Sun, 21 Jun 2020 18:31:01: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 18:31:01: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 18:31:01: #2 number of paired peaks: 892 WARNING @ Sun, 21 Jun 2020 18:31:01: Fewer paired peaks (892) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 892 pairs to build model! INFO @ Sun, 21 Jun 2020 18:31:01: start model_add_line... INFO @ Sun, 21 Jun 2020 18:31:01: start X-correlation... INFO @ Sun, 21 Jun 2020 18:31:01: end of X-cor INFO @ Sun, 21 Jun 2020 18:31:01: #2 finished! INFO @ Sun, 21 Jun 2020 18:31:01: #2 predicted fragment length is 65 bps INFO @ Sun, 21 Jun 2020 18:31:01: #2 alternative fragment length(s) may be 4,65,564 bps INFO @ Sun, 21 Jun 2020 18:31:01: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX2165272/SRX2165272.10_model.r WARNING @ Sun, 21 Jun 2020 18:31:01: #2 Since the d (65) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 18:31:01: #2 You may need to consider one of the other alternative d(s): 4,65,564 WARNING @ Sun, 21 Jun 2020 18:31:01: #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 18:31:01: #3 Call peaks... INFO @ Sun, 21 Jun 2020 18:31:01: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 18:31:03: 4000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 18:31:11: 5000000 INFO @ Sun, 21 Jun 2020 18:31:18: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 18:31:19: 6000000 INFO @ Sun, 21 Jun 2020 18:31:26: 7000000 INFO @ Sun, 21 Jun 2020 18:31:27: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX2165272/SRX2165272.10_peaks.xls INFO @ Sun, 21 Jun 2020 18:31:27: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX2165272/SRX2165272.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 18:31:27: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX2165272/SRX2165272.10_summits.bed INFO @ Sun, 21 Jun 2020 18:31:27: Done! pass1 - making usageList (516 chroms): 1 millis pass2 - checking and writing primary data (1484 records, 4 fields): 16 millis CompletedMACS2peakCalling BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 18:31:29: #1 tag size is determined as 67 bps INFO @ Sun, 21 Jun 2020 18:31:29: #1 tag size = 67 INFO @ Sun, 21 Jun 2020 18:31:29: #1 total tags in treatment: 7365456 INFO @ Sun, 21 Jun 2020 18:31:29: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 18:31:29: #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 18:31:30: #1 tags after filtering in treatment: 7365445 INFO @ Sun, 21 Jun 2020 18:31:30: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 18:31:30: #1 finished! INFO @ Sun, 21 Jun 2020 18:31:30: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 18:31:30: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 18:31:30: #2 number of paired peaks: 892 WARNING @ Sun, 21 Jun 2020 18:31:30: Fewer paired peaks (892) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 892 pairs to build model! INFO @ Sun, 21 Jun 2020 18:31:30: start model_add_line... INFO @ Sun, 21 Jun 2020 18:31:30: start X-correlation... INFO @ Sun, 21 Jun 2020 18:31:30: end of X-cor INFO @ Sun, 21 Jun 2020 18:31:30: #2 finished! INFO @ Sun, 21 Jun 2020 18:31:30: #2 predicted fragment length is 65 bps INFO @ Sun, 21 Jun 2020 18:31:30: #2 alternative fragment length(s) may be 4,65,564 bps INFO @ Sun, 21 Jun 2020 18:31:30: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX2165272/SRX2165272.20_model.r WARNING @ Sun, 21 Jun 2020 18:31:30: #2 Since the d (65) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 18:31:30: #2 You may need to consider one of the other alternative d(s): 4,65,564 WARNING @ Sun, 21 Jun 2020 18:31:30: #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 18:31:30: #3 Call peaks... INFO @ Sun, 21 Jun 2020 18:31:30: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 18:31:48: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 18:31:56: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX2165272/SRX2165272.20_peaks.xls INFO @ Sun, 21 Jun 2020 18:31:56: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX2165272/SRX2165272.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 18:31:56: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX2165272/SRX2165272.20_summits.bed INFO @ Sun, 21 Jun 2020 18:31:56: Done! pass1 - making usageList (319 chroms): 1 millis pass2 - checking and writing primary data (591 records, 4 fields): 11 millis CompletedMACS2peakCalling