Job ID = 6459613 SRX = SRX7299238 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T13:29:46 prefetch.2.10.7: 1) Downloading 'SRR10620138'... 2020-06-21T13:29:46 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T13:31:30 prefetch.2.10.7: HTTPS download succeed 2020-06-21T13:31:31 prefetch.2.10.7: 'SRR10620138' is valid 2020-06-21T13:31:31 prefetch.2.10.7: 1) 'SRR10620138' was downloaded successfully 2020-06-21T13:31:31 prefetch.2.10.7: 'SRR10620138' has 0 unresolved dependencies Read 18887584 spots for SRR10620138/SRR10620138.sra Written 18887584 spots for SRR10620138/SRR10620138.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: 00:05:19 18887584 reads; of these: 18887584 (100.00%) were unpaired; of these: 880035 (4.66%) aligned 0 times 13312953 (70.49%) aligned exactly 1 time 4694596 (24.86%) aligned >1 times 95.34% overall alignment rate Time searching: 00:05:19 Overall time: 00:05:19 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] 3979096 / 18007549 = 0.2210 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 22:41:16: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX7299238/SRX7299238.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX7299238/SRX7299238.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX7299238/SRX7299238.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX7299238/SRX7299238.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 22:41:16: #1 read tag files... INFO @ Sun, 21 Jun 2020 22:41:16: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 22:41:22: 1000000 INFO @ Sun, 21 Jun 2020 22:41:28: 2000000 INFO @ Sun, 21 Jun 2020 22:41:35: 3000000 INFO @ Sun, 21 Jun 2020 22:41:41: 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 22:41:46: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX7299238/SRX7299238.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX7299238/SRX7299238.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX7299238/SRX7299238.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX7299238/SRX7299238.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 22:41:46: #1 read tag files... INFO @ Sun, 21 Jun 2020 22:41:46: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 22:41:47: 5000000 INFO @ Sun, 21 Jun 2020 22:41:53: 1000000 INFO @ Sun, 21 Jun 2020 22:41:54: 6000000 INFO @ Sun, 21 Jun 2020 22:41:59: 2000000 INFO @ Sun, 21 Jun 2020 22:42:02: 7000000 INFO @ Sun, 21 Jun 2020 22:42:06: 3000000 INFO @ Sun, 21 Jun 2020 22:42:08: 8000000 INFO @ Sun, 21 Jun 2020 22:42:13: 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 22:42:15: 9000000 INFO @ Sun, 21 Jun 2020 22:42:16: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX7299238/SRX7299238.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX7299238/SRX7299238.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX7299238/SRX7299238.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX7299238/SRX7299238.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 22:42:16: #1 read tag files... INFO @ Sun, 21 Jun 2020 22:42:16: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 22:42:20: 5000000 INFO @ Sun, 21 Jun 2020 22:42:23: 10000000 INFO @ Sun, 21 Jun 2020 22:42:23: 1000000 INFO @ Sun, 21 Jun 2020 22:42:28: 6000000 INFO @ Sun, 21 Jun 2020 22:42:30: 11000000 INFO @ Sun, 21 Jun 2020 22:42:30: 2000000 INFO @ Sun, 21 Jun 2020 22:42:35: 7000000 INFO @ Sun, 21 Jun 2020 22:42:37: 3000000 INFO @ Sun, 21 Jun 2020 22:42:38: 12000000 INFO @ Sun, 21 Jun 2020 22:42:42: 8000000 INFO @ Sun, 21 Jun 2020 22:42:44: 4000000 INFO @ Sun, 21 Jun 2020 22:42:45: 13000000 INFO @ Sun, 21 Jun 2020 22:42:49: 9000000 INFO @ Sun, 21 Jun 2020 22:42:51: 5000000 INFO @ Sun, 21 Jun 2020 22:42:53: 14000000 INFO @ Sun, 21 Jun 2020 22:42:53: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 22:42:53: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 22:42:53: #1 total tags in treatment: 14028453 INFO @ Sun, 21 Jun 2020 22:42:53: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 22:42:53: #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 22:42:53: #1 tags after filtering in treatment: 14028449 INFO @ Sun, 21 Jun 2020 22:42:53: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 22:42:53: #1 finished! INFO @ Sun, 21 Jun 2020 22:42:53: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 22:42:53: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 22:42:54: #2 number of paired peaks: 582 WARNING @ Sun, 21 Jun 2020 22:42:54: Fewer paired peaks (582) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 582 pairs to build model! INFO @ Sun, 21 Jun 2020 22:42:54: start model_add_line... INFO @ Sun, 21 Jun 2020 22:42:54: start X-correlation... INFO @ Sun, 21 Jun 2020 22:42:54: end of X-cor INFO @ Sun, 21 Jun 2020 22:42:54: #2 finished! INFO @ Sun, 21 Jun 2020 22:42:54: #2 predicted fragment length is 53 bps INFO @ Sun, 21 Jun 2020 22:42:54: #2 alternative fragment length(s) may be 4,53 bps INFO @ Sun, 21 Jun 2020 22:42:54: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX7299238/SRX7299238.05_model.r WARNING @ Sun, 21 Jun 2020 22:42:54: #2 Since the d (53) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 22:42:54: #2 You may need to consider one of the other alternative d(s): 4,53 WARNING @ Sun, 21 Jun 2020 22:42:54: #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 22:42:54: #3 Call peaks... INFO @ Sun, 21 Jun 2020 22:42:54: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 22:42:56: 10000000 INFO @ Sun, 21 Jun 2020 22:42:58: 6000000 INFO @ Sun, 21 Jun 2020 22:43:03: 11000000 INFO @ Sun, 21 Jun 2020 22:43:04: 7000000 INFO @ Sun, 21 Jun 2020 22:43:11: 8000000 INFO @ Sun, 21 Jun 2020 22:43:11: 12000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 22:43:17: 9000000 INFO @ Sun, 21 Jun 2020 22:43:18: 13000000 INFO @ Sun, 21 Jun 2020 22:43:20: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 22:43:24: 10000000 INFO @ Sun, 21 Jun 2020 22:43:25: 14000000 INFO @ Sun, 21 Jun 2020 22:43:26: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 22:43:26: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 22:43:26: #1 total tags in treatment: 14028453 INFO @ Sun, 21 Jun 2020 22:43:26: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 22:43:26: #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 22:43:26: #1 tags after filtering in treatment: 14028449 INFO @ Sun, 21 Jun 2020 22:43:26: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 22:43:26: #1 finished! INFO @ Sun, 21 Jun 2020 22:43:26: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 22:43:26: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 22:43:27: #2 number of paired peaks: 582 WARNING @ Sun, 21 Jun 2020 22:43:27: Fewer paired peaks (582) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 582 pairs to build model! INFO @ Sun, 21 Jun 2020 22:43:27: start model_add_line... INFO @ Sun, 21 Jun 2020 22:43:27: start X-correlation... INFO @ Sun, 21 Jun 2020 22:43:27: end of X-cor INFO @ Sun, 21 Jun 2020 22:43:27: #2 finished! INFO @ Sun, 21 Jun 2020 22:43:27: #2 predicted fragment length is 53 bps INFO @ Sun, 21 Jun 2020 22:43:27: #2 alternative fragment length(s) may be 4,53 bps INFO @ Sun, 21 Jun 2020 22:43:27: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX7299238/SRX7299238.10_model.r WARNING @ Sun, 21 Jun 2020 22:43:27: #2 Since the d (53) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 22:43:27: #2 You may need to consider one of the other alternative d(s): 4,53 WARNING @ Sun, 21 Jun 2020 22:43:27: #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 22:43:27: #3 Call peaks... INFO @ Sun, 21 Jun 2020 22:43:27: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 22:43:30: 11000000 INFO @ Sun, 21 Jun 2020 22:43:34: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX7299238/SRX7299238.05_peaks.xls INFO @ Sun, 21 Jun 2020 22:43:34: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX7299238/SRX7299238.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 22:43:34: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX7299238/SRX7299238.05_summits.bed INFO @ Sun, 21 Jun 2020 22:43:34: Done! pass1 - making usageList (639 chroms): 2 millis pass2 - checking and writing primary data (3932 records, 4 fields): 20 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 22:43:36: 12000000 INFO @ Sun, 21 Jun 2020 22:43:42: 13000000 INFO @ Sun, 21 Jun 2020 22:43:48: 14000000 INFO @ Sun, 21 Jun 2020 22:43:48: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 22:43:48: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 22:43:48: #1 total tags in treatment: 14028453 INFO @ Sun, 21 Jun 2020 22:43:48: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 22:43:48: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 22:43:49: #1 tags after filtering in treatment: 14028449 INFO @ Sun, 21 Jun 2020 22:43:49: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 22:43:49: #1 finished! INFO @ Sun, 21 Jun 2020 22:43:49: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 22:43:49: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 22:43:50: #2 number of paired peaks: 582 WARNING @ Sun, 21 Jun 2020 22:43:50: Fewer paired peaks (582) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 582 pairs to build model! INFO @ Sun, 21 Jun 2020 22:43:50: start model_add_line... INFO @ Sun, 21 Jun 2020 22:43:50: start X-correlation... INFO @ Sun, 21 Jun 2020 22:43:50: end of X-cor INFO @ Sun, 21 Jun 2020 22:43:50: #2 finished! INFO @ Sun, 21 Jun 2020 22:43:50: #2 predicted fragment length is 53 bps INFO @ Sun, 21 Jun 2020 22:43:50: #2 alternative fragment length(s) may be 4,53 bps INFO @ Sun, 21 Jun 2020 22:43:50: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX7299238/SRX7299238.20_model.r WARNING @ Sun, 21 Jun 2020 22:43:50: #2 Since the d (53) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 22:43:50: #2 You may need to consider one of the other alternative d(s): 4,53 WARNING @ Sun, 21 Jun 2020 22:43:50: #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 22:43:50: #3 Call peaks... INFO @ Sun, 21 Jun 2020 22:43:50: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 22:43:53: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 22:44:07: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX7299238/SRX7299238.10_peaks.xls INFO @ Sun, 21 Jun 2020 22:44:07: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX7299238/SRX7299238.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 22:44:07: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX7299238/SRX7299238.10_summits.bed INFO @ Sun, 21 Jun 2020 22:44:07: Done! pass1 - making usageList (492 chroms): 2 millis pass2 - checking and writing primary data (2238 records, 4 fields): 15 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 22:44:16: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 22:44:29: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX7299238/SRX7299238.20_peaks.xls INFO @ Sun, 21 Jun 2020 22:44:29: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX7299238/SRX7299238.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 22:44:29: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX7299238/SRX7299238.20_summits.bed INFO @ Sun, 21 Jun 2020 22:44:29: Done! pass1 - making usageList (348 chroms): 1 millis pass2 - checking and writing primary data (925 records, 4 fields): 10 millis CompletedMACS2peakCalling