Job ID = 6455888 SRX = SRX3020552 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T10:20:36 prefetch.2.10.7: 1) Downloading 'SRR5850468'... 2020-06-21T10:20:36 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T10:21:07 prefetch.2.10.7: HTTPS download succeed 2020-06-21T10:21:07 prefetch.2.10.7: 'SRR5850468' is valid 2020-06-21T10:21:07 prefetch.2.10.7: 1) 'SRR5850468' was downloaded successfully 2020-06-21T10:21:07 prefetch.2.10.7: 'SRR5850468' has 0 unresolved dependencies Read 4524256 spots for SRR5850468/SRR5850468.sra Written 4524256 spots for SRR5850468/SRR5850468.sra 2020-06-21T10:21:34 prefetch.2.10.7: 1) Downloading 'SRR5850469'... 2020-06-21T10:21:34 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T10:22:32 prefetch.2.10.7: HTTPS download succeed 2020-06-21T10:22:33 prefetch.2.10.7: 'SRR5850469' is valid 2020-06-21T10:22:33 prefetch.2.10.7: 1) 'SRR5850469' was downloaded successfully 2020-06-21T10:22:33 prefetch.2.10.7: 'SRR5850469' has 0 unresolved dependencies Read 4461378 spots for SRR5850469/SRR5850469.sra Written 4461378 spots for SRR5850469/SRR5850469.sra 2020-06-21T10:23:03 prefetch.2.10.7: 1) Downloading 'SRR5850470'... 2020-06-21T10:23:03 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T10:23:54 prefetch.2.10.7: HTTPS download succeed 2020-06-21T10:23:54 prefetch.2.10.7: 'SRR5850470' is valid 2020-06-21T10:23:54 prefetch.2.10.7: 1) 'SRR5850470' was downloaded successfully 2020-06-21T10:23:54 prefetch.2.10.7: 'SRR5850470' has 0 unresolved dependencies Read 4463707 spots for SRR5850470/SRR5850470.sra Written 4463707 spots for SRR5850470/SRR5850470.sra 2020-06-21T10:24:20 prefetch.2.10.7: 1) Downloading 'SRR5850471'... 2020-06-21T10:24:20 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T10:25:04 prefetch.2.10.7: HTTPS download succeed 2020-06-21T10:25:04 prefetch.2.10.7: 'SRR5850471' is valid 2020-06-21T10:25:04 prefetch.2.10.7: 1) 'SRR5850471' was downloaded successfully 2020-06-21T10:25:04 prefetch.2.10.7: 'SRR5850471' has 0 unresolved dependencies Read 4436186 spots for SRR5850471/SRR5850471.sra Written 4436186 spots for SRR5850471/SRR5850471.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: 00:05:02 17885527 reads; of these: 17885527 (100.00%) were unpaired; of these: 622026 (3.48%) aligned 0 times 11858772 (66.30%) aligned exactly 1 time 5404729 (30.22%) aligned >1 times 96.52% overall alignment rate Time searching: 00:05:02 Overall time: 00:05:02 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] 2947686 / 17263501 = 0.1707 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 19:34:23: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX3020552/SRX3020552.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX3020552/SRX3020552.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX3020552/SRX3020552.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX3020552/SRX3020552.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 19:34:23: #1 read tag files... INFO @ Sun, 21 Jun 2020 19:34:23: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 19:34:28: 1000000 INFO @ Sun, 21 Jun 2020 19:34:33: 2000000 INFO @ Sun, 21 Jun 2020 19:34:37: 3000000 INFO @ Sun, 21 Jun 2020 19:34:42: 4000000 INFO @ Sun, 21 Jun 2020 19:34:47: 5000000 INFO @ Sun, 21 Jun 2020 19:34:51: 6000000 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 19:34:53: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX3020552/SRX3020552.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX3020552/SRX3020552.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX3020552/SRX3020552.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX3020552/SRX3020552.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 19:34:53: #1 read tag files... INFO @ Sun, 21 Jun 2020 19:34:53: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 19:34:56: 7000000 INFO @ Sun, 21 Jun 2020 19:34:58: 1000000 INFO @ Sun, 21 Jun 2020 19:35:01: 8000000 INFO @ Sun, 21 Jun 2020 19:35:03: 2000000 INFO @ Sun, 21 Jun 2020 19:35:06: 9000000 INFO @ Sun, 21 Jun 2020 19:35:08: 3000000 INFO @ Sun, 21 Jun 2020 19:35:10: 10000000 INFO @ Sun, 21 Jun 2020 19:35:12: 4000000 INFO @ Sun, 21 Jun 2020 19:35:15: 11000000 INFO @ Sun, 21 Jun 2020 19:35:17: 5000000 INFO @ Sun, 21 Jun 2020 19:35:20: 12000000 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 19:35:22: 6000000 INFO @ Sun, 21 Jun 2020 19:35:24: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX3020552/SRX3020552.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX3020552/SRX3020552.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX3020552/SRX3020552.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX3020552/SRX3020552.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 19:35:24: #1 read tag files... INFO @ Sun, 21 Jun 2020 19:35:24: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 19:35:25: 13000000 INFO @ Sun, 21 Jun 2020 19:35:26: 7000000 INFO @ Sun, 21 Jun 2020 19:35:28: 1000000 INFO @ Sun, 21 Jun 2020 19:35:30: 14000000 INFO @ Sun, 21 Jun 2020 19:35:31: 8000000 INFO @ Sun, 21 Jun 2020 19:35:31: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 19:35:31: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 19:35:31: #1 total tags in treatment: 14315815 INFO @ Sun, 21 Jun 2020 19:35:31: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 19:35:31: #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 19:35:32: #1 tags after filtering in treatment: 14315753 INFO @ Sun, 21 Jun 2020 19:35:32: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 19:35:32: #1 finished! INFO @ Sun, 21 Jun 2020 19:35:32: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 19:35:32: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 19:35:33: #2 number of paired peaks: 920 WARNING @ Sun, 21 Jun 2020 19:35:33: Fewer paired peaks (920) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 920 pairs to build model! INFO @ Sun, 21 Jun 2020 19:35:33: start model_add_line... INFO @ Sun, 21 Jun 2020 19:35:33: start X-correlation... INFO @ Sun, 21 Jun 2020 19:35:33: end of X-cor INFO @ Sun, 21 Jun 2020 19:35:33: #2 finished! INFO @ Sun, 21 Jun 2020 19:35:33: #2 predicted fragment length is 48 bps INFO @ Sun, 21 Jun 2020 19:35:33: #2 alternative fragment length(s) may be 2,48,510,547,567,584 bps INFO @ Sun, 21 Jun 2020 19:35:33: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX3020552/SRX3020552.05_model.r WARNING @ Sun, 21 Jun 2020 19:35:33: #2 Since the d (48) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 19:35:33: #2 You may need to consider one of the other alternative d(s): 2,48,510,547,567,584 WARNING @ Sun, 21 Jun 2020 19:35:33: #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 19:35:33: #3 Call peaks... INFO @ Sun, 21 Jun 2020 19:35:33: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 19:35:33: 2000000 INFO @ Sun, 21 Jun 2020 19:35:36: 9000000 INFO @ Sun, 21 Jun 2020 19:35:38: 3000000 INFO @ Sun, 21 Jun 2020 19:35:41: 10000000 INFO @ Sun, 21 Jun 2020 19:35:43: 4000000 INFO @ Sun, 21 Jun 2020 19:35:46: 11000000 INFO @ Sun, 21 Jun 2020 19:35:47: 5000000 INFO @ Sun, 21 Jun 2020 19:35:51: 12000000 INFO @ Sun, 21 Jun 2020 19:35:52: 6000000 INFO @ Sun, 21 Jun 2020 19:35:56: 13000000 INFO @ Sun, 21 Jun 2020 19:35:57: 7000000 INFO @ Sun, 21 Jun 2020 19:36:01: 14000000 INFO @ Sun, 21 Jun 2020 19:36:02: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 19:36:02: 8000000 INFO @ Sun, 21 Jun 2020 19:36:02: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 19:36:02: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 19:36:02: #1 total tags in treatment: 14315815 INFO @ Sun, 21 Jun 2020 19:36:02: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 19:36:02: #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 19:36:03: #1 tags after filtering in treatment: 14315753 INFO @ Sun, 21 Jun 2020 19:36:03: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 19:36:03: #1 finished! INFO @ Sun, 21 Jun 2020 19:36:03: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 19:36:03: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 19:36:04: #2 number of paired peaks: 920 WARNING @ Sun, 21 Jun 2020 19:36:04: Fewer paired peaks (920) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 920 pairs to build model! INFO @ Sun, 21 Jun 2020 19:36:04: start model_add_line... INFO @ Sun, 21 Jun 2020 19:36:04: start X-correlation... INFO @ Sun, 21 Jun 2020 19:36:04: end of X-cor INFO @ Sun, 21 Jun 2020 19:36:04: #2 finished! INFO @ Sun, 21 Jun 2020 19:36:04: #2 predicted fragment length is 48 bps INFO @ Sun, 21 Jun 2020 19:36:04: #2 alternative fragment length(s) may be 2,48,510,547,567,584 bps INFO @ Sun, 21 Jun 2020 19:36:04: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX3020552/SRX3020552.10_model.r WARNING @ Sun, 21 Jun 2020 19:36:04: #2 Since the d (48) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 19:36:04: #2 You may need to consider one of the other alternative d(s): 2,48,510,547,567,584 WARNING @ Sun, 21 Jun 2020 19:36:04: #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 19:36:04: #3 Call peaks... INFO @ Sun, 21 Jun 2020 19:36:04: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 19:36:06: 9000000 INFO @ Sun, 21 Jun 2020 19:36:11: 10000000 INFO @ Sun, 21 Jun 2020 19:36:16: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX3020552/SRX3020552.05_peaks.xls INFO @ Sun, 21 Jun 2020 19:36:16: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX3020552/SRX3020552.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 19:36:16: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX3020552/SRX3020552.05_summits.bed INFO @ Sun, 21 Jun 2020 19:36:16: Done! INFO @ Sun, 21 Jun 2020 19:36:16: 11000000 pass1 - making usageList (609 chroms): 1 millis pass2 - checking and writing primary data (2817 records, 4 fields): 19 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 19:36:21: 12000000 INFO @ Sun, 21 Jun 2020 19:36:26: 13000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 19:36:31: 14000000 INFO @ Sun, 21 Jun 2020 19:36:33: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 19:36:33: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 19:36:33: #1 total tags in treatment: 14315815 INFO @ Sun, 21 Jun 2020 19:36:33: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 19:36:33: #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 19:36:33: #1 tags after filtering in treatment: 14315753 INFO @ Sun, 21 Jun 2020 19:36:33: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 19:36:33: #1 finished! INFO @ Sun, 21 Jun 2020 19:36:33: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 19:36:33: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 19:36:33: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 19:36:34: #2 number of paired peaks: 920 WARNING @ Sun, 21 Jun 2020 19:36:34: Fewer paired peaks (920) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 920 pairs to build model! INFO @ Sun, 21 Jun 2020 19:36:34: start model_add_line... INFO @ Sun, 21 Jun 2020 19:36:34: start X-correlation... INFO @ Sun, 21 Jun 2020 19:36:34: end of X-cor INFO @ Sun, 21 Jun 2020 19:36:34: #2 finished! INFO @ Sun, 21 Jun 2020 19:36:34: #2 predicted fragment length is 48 bps INFO @ Sun, 21 Jun 2020 19:36:34: #2 alternative fragment length(s) may be 2,48,510,547,567,584 bps INFO @ Sun, 21 Jun 2020 19:36:34: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX3020552/SRX3020552.20_model.r WARNING @ Sun, 21 Jun 2020 19:36:34: #2 Since the d (48) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 19:36:34: #2 You may need to consider one of the other alternative d(s): 2,48,510,547,567,584 WARNING @ Sun, 21 Jun 2020 19:36:34: #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 19:36:34: #3 Call peaks... INFO @ Sun, 21 Jun 2020 19:36:34: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 19:36:48: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX3020552/SRX3020552.10_peaks.xls INFO @ Sun, 21 Jun 2020 19:36:48: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX3020552/SRX3020552.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 19:36:48: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX3020552/SRX3020552.10_summits.bed INFO @ Sun, 21 Jun 2020 19:36:48: Done! pass1 - making usageList (494 chroms): 2 millis pass2 - checking and writing primary data (1690 records, 4 fields): 14 millis CompletedMACS2peakCalling BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 19:37:03: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 19:37:18: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX3020552/SRX3020552.20_peaks.xls INFO @ Sun, 21 Jun 2020 19:37:18: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX3020552/SRX3020552.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 19:37:18: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX3020552/SRX3020552.20_summits.bed INFO @ Sun, 21 Jun 2020 19:37:18: Done! pass1 - making usageList (261 chroms): 1 millis pass2 - checking and writing primary data (599 records, 4 fields): 8 millis CompletedMACS2peakCalling