Job ID = 6459482 SRX = SRX6827664 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T13:10:05 prefetch.2.10.7: 1) Downloading 'SRR10095444'... 2020-06-21T13:10:05 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T13:13:18 prefetch.2.10.7: HTTPS download succeed 2020-06-21T13:13:18 prefetch.2.10.7: 1) 'SRR10095444' was downloaded successfully Read 23302781 spots for SRR10095444/SRR10095444.sra Written 23302781 spots for SRR10095444/SRR10095444.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: 00:06:37 23302781 reads; of these: 23302781 (100.00%) were unpaired; of these: 877757 (3.77%) aligned 0 times 15332092 (65.80%) aligned exactly 1 time 7092932 (30.44%) aligned >1 times 96.23% overall alignment rate Time searching: 00:06:37 Overall time: 00:06:37 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] 4163999 / 22425024 = 0.1857 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 22:25:46: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX6827664/SRX6827664.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX6827664/SRX6827664.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX6827664/SRX6827664.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX6827664/SRX6827664.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 22:25:46: #1 read tag files... INFO @ Sun, 21 Jun 2020 22:25:46: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 22:25:51: 1000000 INFO @ Sun, 21 Jun 2020 22:25:55: 2000000 INFO @ Sun, 21 Jun 2020 22:26:00: 3000000 INFO @ Sun, 21 Jun 2020 22:26:05: 4000000 INFO @ Sun, 21 Jun 2020 22:26:10: 5000000 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 22:26:15: 6000000 INFO @ Sun, 21 Jun 2020 22:26:16: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX6827664/SRX6827664.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX6827664/SRX6827664.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX6827664/SRX6827664.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX6827664/SRX6827664.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 22:26:16: #1 read tag files... INFO @ Sun, 21 Jun 2020 22:26:16: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 22:26:20: 7000000 INFO @ Sun, 21 Jun 2020 22:26:21: 1000000 INFO @ Sun, 21 Jun 2020 22:26:25: 8000000 INFO @ Sun, 21 Jun 2020 22:26:26: 2000000 INFO @ Sun, 21 Jun 2020 22:26:30: 9000000 INFO @ Sun, 21 Jun 2020 22:26:31: 3000000 INFO @ Sun, 21 Jun 2020 22:26:35: 10000000 INFO @ Sun, 21 Jun 2020 22:26:35: 4000000 INFO @ Sun, 21 Jun 2020 22:26:40: 11000000 INFO @ Sun, 21 Jun 2020 22:26:40: 5000000 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 22:26:45: 12000000 INFO @ Sun, 21 Jun 2020 22:26:45: 6000000 INFO @ Sun, 21 Jun 2020 22:26:46: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX6827664/SRX6827664.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX6827664/SRX6827664.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX6827664/SRX6827664.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX6827664/SRX6827664.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 22:26:46: #1 read tag files... INFO @ Sun, 21 Jun 2020 22:26:46: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 22:26:50: 13000000 INFO @ Sun, 21 Jun 2020 22:26:50: 7000000 INFO @ Sun, 21 Jun 2020 22:26:52: 1000000 INFO @ Sun, 21 Jun 2020 22:26:55: 14000000 INFO @ Sun, 21 Jun 2020 22:26:55: 8000000 INFO @ Sun, 21 Jun 2020 22:26:57: 2000000 INFO @ Sun, 21 Jun 2020 22:27:00: 15000000 INFO @ Sun, 21 Jun 2020 22:27:00: 9000000 INFO @ Sun, 21 Jun 2020 22:27:03: 3000000 INFO @ Sun, 21 Jun 2020 22:27:05: 16000000 INFO @ Sun, 21 Jun 2020 22:27:05: 10000000 INFO @ Sun, 21 Jun 2020 22:27:09: 4000000 INFO @ Sun, 21 Jun 2020 22:27:10: 17000000 INFO @ Sun, 21 Jun 2020 22:27:11: 11000000 INFO @ Sun, 21 Jun 2020 22:27:15: 5000000 INFO @ Sun, 21 Jun 2020 22:27:15: 18000000 INFO @ Sun, 21 Jun 2020 22:27:16: 12000000 INFO @ Sun, 21 Jun 2020 22:27:17: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 22:27:17: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 22:27:17: #1 total tags in treatment: 18261025 INFO @ Sun, 21 Jun 2020 22:27:17: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 22:27:17: #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 22:27:17: #1 tags after filtering in treatment: 18260962 INFO @ Sun, 21 Jun 2020 22:27:17: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 22:27:17: #1 finished! INFO @ Sun, 21 Jun 2020 22:27:17: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 22:27:17: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 22:27:19: #2 number of paired peaks: 1031 INFO @ Sun, 21 Jun 2020 22:27:19: start model_add_line... INFO @ Sun, 21 Jun 2020 22:27:19: start X-correlation... INFO @ Sun, 21 Jun 2020 22:27:19: end of X-cor INFO @ Sun, 21 Jun 2020 22:27:19: #2 finished! INFO @ Sun, 21 Jun 2020 22:27:19: #2 predicted fragment length is 47 bps INFO @ Sun, 21 Jun 2020 22:27:19: #2 alternative fragment length(s) may be 1,47,580 bps INFO @ Sun, 21 Jun 2020 22:27:19: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX6827664/SRX6827664.05_model.r WARNING @ Sun, 21 Jun 2020 22:27:19: #2 Since the d (47) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 22:27:19: #2 You may need to consider one of the other alternative d(s): 1,47,580 WARNING @ Sun, 21 Jun 2020 22:27:19: #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 22:27:19: #3 Call peaks... INFO @ Sun, 21 Jun 2020 22:27:19: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 22:27:21: 13000000 INFO @ Sun, 21 Jun 2020 22:27:21: 6000000 INFO @ Sun, 21 Jun 2020 22:27:26: 14000000 INFO @ Sun, 21 Jun 2020 22:27:26: 7000000 INFO @ Sun, 21 Jun 2020 22:27:31: 15000000 INFO @ Sun, 21 Jun 2020 22:27:32: 8000000 INFO @ Sun, 21 Jun 2020 22:27:36: 16000000 INFO @ Sun, 21 Jun 2020 22:27:38: 9000000 INFO @ Sun, 21 Jun 2020 22:27:41: 17000000 INFO @ Sun, 21 Jun 2020 22:27:44: 10000000 INFO @ Sun, 21 Jun 2020 22:27:46: 18000000 INFO @ Sun, 21 Jun 2020 22:27:48: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 22:27:48: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 22:27:48: #1 total tags in treatment: 18261025 INFO @ Sun, 21 Jun 2020 22:27:48: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 22:27:48: #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 22:27:48: #1 tags after filtering in treatment: 18260962 INFO @ Sun, 21 Jun 2020 22:27:48: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 22:27:48: #1 finished! INFO @ Sun, 21 Jun 2020 22:27:48: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 22:27:48: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 22:27:50: 11000000 INFO @ Sun, 21 Jun 2020 22:27:50: #2 number of paired peaks: 1031 INFO @ Sun, 21 Jun 2020 22:27:50: start model_add_line... INFO @ Sun, 21 Jun 2020 22:27:50: start X-correlation... INFO @ Sun, 21 Jun 2020 22:27:50: end of X-cor INFO @ Sun, 21 Jun 2020 22:27:50: #2 finished! INFO @ Sun, 21 Jun 2020 22:27:50: #2 predicted fragment length is 47 bps INFO @ Sun, 21 Jun 2020 22:27:50: #2 alternative fragment length(s) may be 1,47,580 bps INFO @ Sun, 21 Jun 2020 22:27:50: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX6827664/SRX6827664.10_model.r WARNING @ Sun, 21 Jun 2020 22:27:50: #2 Since the d (47) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 22:27:50: #2 You may need to consider one of the other alternative d(s): 1,47,580 WARNING @ Sun, 21 Jun 2020 22:27:50: #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 22:27:50: #3 Call peaks... INFO @ Sun, 21 Jun 2020 22:27:50: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 22:27:54: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 22:27:56: 12000000 INFO @ Sun, 21 Jun 2020 22:28:01: 13000000 INFO @ Sun, 21 Jun 2020 22:28:07: 14000000 INFO @ Sun, 21 Jun 2020 22:28:12: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX6827664/SRX6827664.05_peaks.xls INFO @ Sun, 21 Jun 2020 22:28:12: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX6827664/SRX6827664.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 22:28:12: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX6827664/SRX6827664.05_summits.bed INFO @ Sun, 21 Jun 2020 22:28:12: Done! pass1 - making usageList (615 chroms): 1 millis pass2 - checking and writing primary data (2924 records, 4 fields): 20 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 22:28:13: 15000000 INFO @ Sun, 21 Jun 2020 22:28:19: 16000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 22:28:25: 17000000 INFO @ Sun, 21 Jun 2020 22:28:27: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 22:28:31: 18000000 INFO @ Sun, 21 Jun 2020 22:28:32: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 22:28:32: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 22:28:32: #1 total tags in treatment: 18261025 INFO @ Sun, 21 Jun 2020 22:28:32: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 22:28:32: #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 22:28:33: #1 tags after filtering in treatment: 18260962 INFO @ Sun, 21 Jun 2020 22:28:33: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 22:28:33: #1 finished! INFO @ Sun, 21 Jun 2020 22:28:33: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 22:28:33: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 22:28:34: #2 number of paired peaks: 1031 INFO @ Sun, 21 Jun 2020 22:28:34: start model_add_line... INFO @ Sun, 21 Jun 2020 22:28:34: start X-correlation... INFO @ Sun, 21 Jun 2020 22:28:34: end of X-cor INFO @ Sun, 21 Jun 2020 22:28:34: #2 finished! INFO @ Sun, 21 Jun 2020 22:28:34: #2 predicted fragment length is 47 bps INFO @ Sun, 21 Jun 2020 22:28:34: #2 alternative fragment length(s) may be 1,47,580 bps INFO @ Sun, 21 Jun 2020 22:28:34: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX6827664/SRX6827664.20_model.r WARNING @ Sun, 21 Jun 2020 22:28:34: #2 Since the d (47) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 22:28:34: #2 You may need to consider one of the other alternative d(s): 1,47,580 WARNING @ Sun, 21 Jun 2020 22:28:34: #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 22:28:34: #3 Call peaks... INFO @ Sun, 21 Jun 2020 22:28:34: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 22:28:45: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX6827664/SRX6827664.10_peaks.xls INFO @ Sun, 21 Jun 2020 22:28:45: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX6827664/SRX6827664.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 22:28:45: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX6827664/SRX6827664.10_summits.bed INFO @ Sun, 21 Jun 2020 22:28:45: Done! pass1 - making usageList (521 chroms): 1 millis pass2 - checking and writing primary data (2165 records, 4 fields): 17 millis CompletedMACS2peakCalling BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 22:29:13: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 22:29:32: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX6827664/SRX6827664.20_peaks.xls INFO @ Sun, 21 Jun 2020 22:29:32: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX6827664/SRX6827664.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 22:29:32: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX6827664/SRX6827664.20_summits.bed INFO @ Sun, 21 Jun 2020 22:29:32: Done! pass1 - making usageList (359 chroms): 2 millis pass2 - checking and writing primary data (895 records, 4 fields): 11 millis CompletedMACS2peakCalling