Job ID = 6455007 SRX = SRX2618552 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T09:50:55 prefetch.2.10.7: 1) Downloading 'SRR5319106'... 2020-06-21T09:50:55 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T09:54:31 prefetch.2.10.7: HTTPS download succeed 2020-06-21T09:54:31 prefetch.2.10.7: 1) 'SRR5319106' was downloaded successfully 2020-06-21T09:54:31 prefetch.2.10.7: 'SRR5319106' has 0 unresolved dependencies Read 25009847 spots for SRR5319106/SRR5319106.sra Written 25009847 spots for SRR5319106/SRR5319106.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: 00:06:04 25009847 reads; of these: 25009847 (100.00%) were unpaired; of these: 2627464 (10.51%) aligned 0 times 17025446 (68.07%) aligned exactly 1 time 5356937 (21.42%) aligned >1 times 89.49% overall alignment rate Time searching: 00:06:04 Overall time: 00:06:04 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 12 files... [bam_rmdupse_core] 3020892 / 22382383 = 0.1350 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 19:08:25: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX2618552/SRX2618552.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX2618552/SRX2618552.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX2618552/SRX2618552.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX2618552/SRX2618552.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 19:08:25: #1 read tag files... INFO @ Sun, 21 Jun 2020 19:08:25: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 19:08:32: 1000000 INFO @ Sun, 21 Jun 2020 19:08:38: 2000000 INFO @ Sun, 21 Jun 2020 19:08:45: 3000000 INFO @ Sun, 21 Jun 2020 19:08:51: 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 19:08:55: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX2618552/SRX2618552.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX2618552/SRX2618552.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX2618552/SRX2618552.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX2618552/SRX2618552.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 19:08:55: #1 read tag files... INFO @ Sun, 21 Jun 2020 19:08:55: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 19:08:58: 5000000 INFO @ Sun, 21 Jun 2020 19:09:04: 1000000 INFO @ Sun, 21 Jun 2020 19:09:05: 6000000 INFO @ Sun, 21 Jun 2020 19:09:11: 2000000 INFO @ Sun, 21 Jun 2020 19:09:13: 7000000 INFO @ Sun, 21 Jun 2020 19:09:19: 3000000 INFO @ Sun, 21 Jun 2020 19:09:20: 8000000 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 19:09:26: 4000000 INFO @ Sun, 21 Jun 2020 19:09:26: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX2618552/SRX2618552.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX2618552/SRX2618552.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX2618552/SRX2618552.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX2618552/SRX2618552.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 19:09:26: #1 read tag files... INFO @ Sun, 21 Jun 2020 19:09:26: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 19:09:27: 9000000 INFO @ Sun, 21 Jun 2020 19:09:34: 5000000 INFO @ Sun, 21 Jun 2020 19:09:34: 1000000 INFO @ Sun, 21 Jun 2020 19:09:35: 10000000 INFO @ Sun, 21 Jun 2020 19:09:42: 6000000 INFO @ Sun, 21 Jun 2020 19:09:42: 2000000 INFO @ Sun, 21 Jun 2020 19:09:43: 11000000 INFO @ Sun, 21 Jun 2020 19:09:50: 7000000 INFO @ Sun, 21 Jun 2020 19:09:50: 3000000 INFO @ Sun, 21 Jun 2020 19:09:51: 12000000 INFO @ Sun, 21 Jun 2020 19:09:57: 8000000 INFO @ Sun, 21 Jun 2020 19:09:57: 4000000 INFO @ Sun, 21 Jun 2020 19:09:58: 13000000 INFO @ Sun, 21 Jun 2020 19:10:05: 9000000 INFO @ Sun, 21 Jun 2020 19:10:05: 5000000 INFO @ Sun, 21 Jun 2020 19:10:06: 14000000 INFO @ Sun, 21 Jun 2020 19:10:12: 10000000 INFO @ Sun, 21 Jun 2020 19:10:12: 6000000 INFO @ Sun, 21 Jun 2020 19:10:13: 15000000 INFO @ Sun, 21 Jun 2020 19:10:19: 7000000 INFO @ Sun, 21 Jun 2020 19:10:19: 11000000 INFO @ Sun, 21 Jun 2020 19:10:21: 16000000 INFO @ Sun, 21 Jun 2020 19:10:27: 8000000 INFO @ Sun, 21 Jun 2020 19:10:27: 12000000 INFO @ Sun, 21 Jun 2020 19:10:29: 17000000 INFO @ Sun, 21 Jun 2020 19:10:34: 9000000 INFO @ Sun, 21 Jun 2020 19:10:34: 13000000 INFO @ Sun, 21 Jun 2020 19:10:36: 18000000 INFO @ Sun, 21 Jun 2020 19:10:41: 10000000 INFO @ Sun, 21 Jun 2020 19:10:42: 14000000 INFO @ Sun, 21 Jun 2020 19:10:44: 19000000 INFO @ Sun, 21 Jun 2020 19:10:47: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 19:10:47: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 19:10:47: #1 total tags in treatment: 19361491 INFO @ Sun, 21 Jun 2020 19:10:47: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 19:10:47: #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 19:10:47: #1 tags after filtering in treatment: 19361491 INFO @ Sun, 21 Jun 2020 19:10:47: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 19:10:47: #1 finished! INFO @ Sun, 21 Jun 2020 19:10:47: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 19:10:47: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 19:10:48: 11000000 INFO @ Sun, 21 Jun 2020 19:10:48: #2 number of paired peaks: 1121 INFO @ Sun, 21 Jun 2020 19:10:48: start model_add_line... INFO @ Sun, 21 Jun 2020 19:10:49: start X-correlation... INFO @ Sun, 21 Jun 2020 19:10:49: end of X-cor INFO @ Sun, 21 Jun 2020 19:10:49: #2 finished! INFO @ Sun, 21 Jun 2020 19:10:49: #2 predicted fragment length is 87 bps INFO @ Sun, 21 Jun 2020 19:10:49: #2 alternative fragment length(s) may be 4,87 bps INFO @ Sun, 21 Jun 2020 19:10:49: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX2618552/SRX2618552.05_model.r WARNING @ Sun, 21 Jun 2020 19:10:49: #2 Since the d (87) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 19:10:49: #2 You may need to consider one of the other alternative d(s): 4,87 WARNING @ Sun, 21 Jun 2020 19:10:49: #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 19:10:49: #3 Call peaks... INFO @ Sun, 21 Jun 2020 19:10:49: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 19:10:49: 15000000 INFO @ Sun, 21 Jun 2020 19:10:55: 12000000 INFO @ Sun, 21 Jun 2020 19:10:57: 16000000 INFO @ Sun, 21 Jun 2020 19:11:02: 13000000 INFO @ Sun, 21 Jun 2020 19:11:04: 17000000 INFO @ Sun, 21 Jun 2020 19:11:10: 14000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 19:11:11: 18000000 INFO @ Sun, 21 Jun 2020 19:11:17: 15000000 INFO @ Sun, 21 Jun 2020 19:11:19: 19000000 INFO @ Sun, 21 Jun 2020 19:11:22: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 19:11:22: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 19:11:22: #1 total tags in treatment: 19361491 INFO @ Sun, 21 Jun 2020 19:11:22: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 19:11:22: #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 19:11:22: #1 tags after filtering in treatment: 19361491 INFO @ Sun, 21 Jun 2020 19:11:22: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 19:11:22: #1 finished! INFO @ Sun, 21 Jun 2020 19:11:22: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 19:11:22: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 19:11:23: #2 number of paired peaks: 1121 INFO @ Sun, 21 Jun 2020 19:11:23: start model_add_line... INFO @ Sun, 21 Jun 2020 19:11:24: start X-correlation... INFO @ Sun, 21 Jun 2020 19:11:24: end of X-cor INFO @ Sun, 21 Jun 2020 19:11:24: #2 finished! INFO @ Sun, 21 Jun 2020 19:11:24: #2 predicted fragment length is 87 bps INFO @ Sun, 21 Jun 2020 19:11:24: #2 alternative fragment length(s) may be 4,87 bps INFO @ Sun, 21 Jun 2020 19:11:24: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX2618552/SRX2618552.10_model.r WARNING @ Sun, 21 Jun 2020 19:11:24: #2 Since the d (87) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 19:11:24: #2 You may need to consider one of the other alternative d(s): 4,87 WARNING @ Sun, 21 Jun 2020 19:11:24: #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 19:11:24: #3 Call peaks... INFO @ Sun, 21 Jun 2020 19:11:24: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 19:11:24: 16000000 INFO @ Sun, 21 Jun 2020 19:11:29: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 19:11:31: 17000000 INFO @ Sun, 21 Jun 2020 19:11:38: 18000000 INFO @ Sun, 21 Jun 2020 19:11:44: 19000000 INFO @ Sun, 21 Jun 2020 19:11:47: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 19:11:47: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 19:11:47: #1 total tags in treatment: 19361491 INFO @ Sun, 21 Jun 2020 19:11:47: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 19:11:47: #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 19:11:47: #1 tags after filtering in treatment: 19361491 INFO @ Sun, 21 Jun 2020 19:11:47: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 19:11:47: #1 finished! INFO @ Sun, 21 Jun 2020 19:11:47: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 19:11:47: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 19:11:49: #2 number of paired peaks: 1121 INFO @ Sun, 21 Jun 2020 19:11:49: start model_add_line... INFO @ Sun, 21 Jun 2020 19:11:49: start X-correlation... INFO @ Sun, 21 Jun 2020 19:11:49: end of X-cor INFO @ Sun, 21 Jun 2020 19:11:49: #2 finished! INFO @ Sun, 21 Jun 2020 19:11:49: #2 predicted fragment length is 87 bps INFO @ Sun, 21 Jun 2020 19:11:49: #2 alternative fragment length(s) may be 4,87 bps INFO @ Sun, 21 Jun 2020 19:11:49: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX2618552/SRX2618552.20_model.r WARNING @ Sun, 21 Jun 2020 19:11:49: #2 Since the d (87) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 19:11:49: #2 You may need to consider one of the other alternative d(s): 4,87 WARNING @ Sun, 21 Jun 2020 19:11:49: #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 19:11:49: #3 Call peaks... INFO @ Sun, 21 Jun 2020 19:11:49: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 19:11:49: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX2618552/SRX2618552.05_peaks.xls INFO @ Sun, 21 Jun 2020 19:11:49: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX2618552/SRX2618552.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 19:11:49: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX2618552/SRX2618552.05_summits.bed INFO @ Sun, 21 Jun 2020 19:11:49: Done! BigWig に変換しました。 pass1 - making usageList (626 chroms): 2 millis pass2 - checking and writing primary data (9252 records, 4 fields): 29 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 19:12:04: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 19:12:25: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX2618552/SRX2618552.10_peaks.xls INFO @ Sun, 21 Jun 2020 19:12:25: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX2618552/SRX2618552.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 19:12:25: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX2618552/SRX2618552.10_summits.bed INFO @ Sun, 21 Jun 2020 19:12:25: Done! pass1 - making usageList (521 chroms): 2 millis pass2 - checking and writing primary data (6052 records, 4 fields): 20 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 19:12:28: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 19:12:47: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX2618552/SRX2618552.20_peaks.xls INFO @ Sun, 21 Jun 2020 19:12:47: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX2618552/SRX2618552.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 19:12:47: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX2618552/SRX2618552.20_summits.bed INFO @ Sun, 21 Jun 2020 19:12:47: Done! pass1 - making usageList (441 chroms): 1 millis pass2 - checking and writing primary data (3133 records, 4 fields): 15 millis CompletedMACS2peakCalling