Job ID = 6454580 SRX = SRX2325653 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T09:29:44 prefetch.2.10.7: 1) Downloading 'SRR4896341'... 2020-06-21T09:29:44 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T09:39:13 prefetch.2.10.7: HTTPS download succeed 2020-06-21T09:39:13 prefetch.2.10.7: 1) 'SRR4896341' was downloaded successfully 2020-06-21T09:39:13 prefetch.2.10.7: 'SRR4896341' has 0 unresolved dependencies Read 63124003 spots for SRR4896341/SRR4896341.sra Written 63124003 spots for SRR4896341/SRR4896341.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: 00:09:52 63124003 reads; of these: 63124003 (100.00%) were unpaired; of these: 54664747 (86.60%) aligned 0 times 6314890 (10.00%) aligned exactly 1 time 2144366 (3.40%) aligned >1 times 13.40% overall alignment rate Time searching: 00:09:52 Overall time: 00:09:52 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] 2532587 / 8459256 = 0.2994 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 18:55:37: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX2325653/SRX2325653.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX2325653/SRX2325653.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX2325653/SRX2325653.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX2325653/SRX2325653.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 18:55:37: #1 read tag files... INFO @ Sun, 21 Jun 2020 18:55:37: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 18:55:45: 1000000 INFO @ Sun, 21 Jun 2020 18:55:53: 2000000 INFO @ Sun, 21 Jun 2020 18:56:01: 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 18:56:06: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX2325653/SRX2325653.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX2325653/SRX2325653.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX2325653/SRX2325653.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX2325653/SRX2325653.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 18:56:06: #1 read tag files... INFO @ Sun, 21 Jun 2020 18:56:06: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 18:56:09: 4000000 INFO @ Sun, 21 Jun 2020 18:56:14: 1000000 INFO @ Sun, 21 Jun 2020 18:56:19: 5000000 INFO @ Sun, 21 Jun 2020 18:56:22: 2000000 INFO @ Sun, 21 Jun 2020 18:56:27: #1 tag size is determined as 76 bps INFO @ Sun, 21 Jun 2020 18:56:27: #1 tag size = 76 INFO @ Sun, 21 Jun 2020 18:56:27: #1 total tags in treatment: 5926669 INFO @ Sun, 21 Jun 2020 18:56:27: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 18:56:27: #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 18:56:27: #1 tags after filtering in treatment: 5926664 INFO @ Sun, 21 Jun 2020 18:56:27: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 18:56:27: #1 finished! INFO @ Sun, 21 Jun 2020 18:56:27: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 18:56:27: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 18:56:28: #2 number of paired peaks: 517 WARNING @ Sun, 21 Jun 2020 18:56:28: Fewer paired peaks (517) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 517 pairs to build model! INFO @ Sun, 21 Jun 2020 18:56:28: start model_add_line... INFO @ Sun, 21 Jun 2020 18:56:28: start X-correlation... INFO @ Sun, 21 Jun 2020 18:56:28: end of X-cor INFO @ Sun, 21 Jun 2020 18:56:28: #2 finished! INFO @ Sun, 21 Jun 2020 18:56:28: #2 predicted fragment length is 77 bps INFO @ Sun, 21 Jun 2020 18:56:28: #2 alternative fragment length(s) may be 77,554 bps INFO @ Sun, 21 Jun 2020 18:56:28: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX2325653/SRX2325653.05_model.r WARNING @ Sun, 21 Jun 2020 18:56:28: #2 Since the d (77) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 18:56:28: #2 You may need to consider one of the other alternative d(s): 77,554 WARNING @ Sun, 21 Jun 2020 18:56:28: #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 18:56:28: #3 Call peaks... INFO @ Sun, 21 Jun 2020 18:56:28: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 18:56:29: 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 18:56:36: 4000000 INFO @ Sun, 21 Jun 2020 18:56:38: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX2325653/SRX2325653.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX2325653/SRX2325653.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX2325653/SRX2325653.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX2325653/SRX2325653.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 18:56:38: #1 read tag files... INFO @ Sun, 21 Jun 2020 18:56:38: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 18:56:41: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 18:56:44: 5000000 INFO @ Sun, 21 Jun 2020 18:56:46: 1000000 INFO @ Sun, 21 Jun 2020 18:56:48: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX2325653/SRX2325653.05_peaks.xls INFO @ Sun, 21 Jun 2020 18:56:48: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX2325653/SRX2325653.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 18:56:48: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX2325653/SRX2325653.05_summits.bed INFO @ Sun, 21 Jun 2020 18:56:48: Done! pass1 - making usageList (540 chroms): 1 millis pass2 - checking and writing primary data (1390 records, 4 fields): 18 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 18:56:51: #1 tag size is determined as 76 bps INFO @ Sun, 21 Jun 2020 18:56:51: #1 tag size = 76 INFO @ Sun, 21 Jun 2020 18:56:51: #1 total tags in treatment: 5926669 INFO @ Sun, 21 Jun 2020 18:56:51: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 18:56:51: #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 18:56:52: #1 tags after filtering in treatment: 5926664 INFO @ Sun, 21 Jun 2020 18:56:52: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 18:56:52: #1 finished! INFO @ Sun, 21 Jun 2020 18:56:52: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 18:56:52: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 18:56:52: #2 number of paired peaks: 517 WARNING @ Sun, 21 Jun 2020 18:56:52: Fewer paired peaks (517) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 517 pairs to build model! INFO @ Sun, 21 Jun 2020 18:56:52: start model_add_line... INFO @ Sun, 21 Jun 2020 18:56:52: start X-correlation... INFO @ Sun, 21 Jun 2020 18:56:52: end of X-cor INFO @ Sun, 21 Jun 2020 18:56:52: #2 finished! INFO @ Sun, 21 Jun 2020 18:56:52: #2 predicted fragment length is 77 bps INFO @ Sun, 21 Jun 2020 18:56:52: #2 alternative fragment length(s) may be 77,554 bps INFO @ Sun, 21 Jun 2020 18:56:52: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX2325653/SRX2325653.10_model.r WARNING @ Sun, 21 Jun 2020 18:56:52: #2 Since the d (77) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 18:56:52: #2 You may need to consider one of the other alternative d(s): 77,554 WARNING @ Sun, 21 Jun 2020 18:56:52: #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 18:56:52: #3 Call peaks... INFO @ Sun, 21 Jun 2020 18:56:52: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 18:56:54: 2000000 INFO @ Sun, 21 Jun 2020 18:57:03: 3000000 INFO @ Sun, 21 Jun 2020 18:57:06: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 18:57:11: 4000000 INFO @ Sun, 21 Jun 2020 18:57:13: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX2325653/SRX2325653.10_peaks.xls INFO @ Sun, 21 Jun 2020 18:57:13: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX2325653/SRX2325653.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 18:57:13: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX2325653/SRX2325653.10_summits.bed INFO @ Sun, 21 Jun 2020 18:57:13: Done! BedGraph に変換しました。 BigWig に変換中... pass1 - making usageList (365 chroms): 2 millis pass2 - checking and writing primary data (753 records, 4 fields): 11 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 18:57:19: 5000000 INFO @ Sun, 21 Jun 2020 18:57:27: #1 tag size is determined as 76 bps INFO @ Sun, 21 Jun 2020 18:57:27: #1 tag size = 76 INFO @ Sun, 21 Jun 2020 18:57:27: #1 total tags in treatment: 5926669 INFO @ Sun, 21 Jun 2020 18:57:27: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 18:57:27: #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 18:57:27: #1 tags after filtering in treatment: 5926664 INFO @ Sun, 21 Jun 2020 18:57:27: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 18:57:27: #1 finished! INFO @ Sun, 21 Jun 2020 18:57:27: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 18:57:27: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 18:57:27: #2 number of paired peaks: 517 WARNING @ Sun, 21 Jun 2020 18:57:27: Fewer paired peaks (517) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 517 pairs to build model! INFO @ Sun, 21 Jun 2020 18:57:27: start model_add_line... INFO @ Sun, 21 Jun 2020 18:57:27: start X-correlation... INFO @ Sun, 21 Jun 2020 18:57:27: end of X-cor INFO @ Sun, 21 Jun 2020 18:57:27: #2 finished! INFO @ Sun, 21 Jun 2020 18:57:27: #2 predicted fragment length is 77 bps INFO @ Sun, 21 Jun 2020 18:57:27: #2 alternative fragment length(s) may be 77,554 bps INFO @ Sun, 21 Jun 2020 18:57:27: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX2325653/SRX2325653.20_model.r WARNING @ Sun, 21 Jun 2020 18:57:27: #2 Since the d (77) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 18:57:27: #2 You may need to consider one of the other alternative d(s): 77,554 WARNING @ Sun, 21 Jun 2020 18:57:27: #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 18:57:27: #3 Call peaks... INFO @ Sun, 21 Jun 2020 18:57:27: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 18:57:42: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 18:57:49: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX2325653/SRX2325653.20_peaks.xls INFO @ Sun, 21 Jun 2020 18:57:49: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX2325653/SRX2325653.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 18:57:49: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX2325653/SRX2325653.20_summits.bed INFO @ Sun, 21 Jun 2020 18:57:49: Done! pass1 - making usageList (158 chroms): 1 millis pass2 - checking and writing primary data (282 records, 4 fields): 7 millis CompletedMACS2peakCalling