Job ID = 6454117 SRX = SRX1837292 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T08:54:04 prefetch.2.10.7: 1) Downloading 'SRR3657648'... 2020-06-21T08:54:04 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T09:00:31 prefetch.2.10.7: HTTPS download succeed 2020-06-21T09:00:31 prefetch.2.10.7: 1) 'SRR3657648' was downloaded successfully Read 30561786 spots for SRR3657648/SRR3657648.sra Written 30561786 spots for SRR3657648/SRR3657648.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: 00:00:01 Time loading mirror index: 00:00:00 Multiseed full-index search: 00:12:54 30561786 reads; of these: 30561786 (100.00%) were unpaired; of these: 1243870 (4.07%) aligned 0 times 11172262 (36.56%) aligned exactly 1 time 18145654 (59.37%) aligned >1 times 95.93% overall alignment rate Time searching: 00:12:55 Overall time: 00:12:55 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] 14921950 / 29317916 = 0.5090 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 18:20:23: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX1837292/SRX1837292.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX1837292/SRX1837292.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX1837292/SRX1837292.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX1837292/SRX1837292.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 18:20:23: #1 read tag files... INFO @ Sun, 21 Jun 2020 18:20:23: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 18:20:28: 1000000 INFO @ Sun, 21 Jun 2020 18:20:33: 2000000 INFO @ Sun, 21 Jun 2020 18:20:38: 3000000 INFO @ Sun, 21 Jun 2020 18:20:43: 4000000 INFO @ Sun, 21 Jun 2020 18:20:48: 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 18:20:53: 6000000 INFO @ Sun, 21 Jun 2020 18:20:53: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX1837292/SRX1837292.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX1837292/SRX1837292.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX1837292/SRX1837292.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX1837292/SRX1837292.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 18:20:53: #1 read tag files... INFO @ Sun, 21 Jun 2020 18:20:53: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 18:20:58: 7000000 INFO @ Sun, 21 Jun 2020 18:20:58: 1000000 INFO @ Sun, 21 Jun 2020 18:21:03: 8000000 INFO @ Sun, 21 Jun 2020 18:21:04: 2000000 INFO @ Sun, 21 Jun 2020 18:21:08: 9000000 INFO @ Sun, 21 Jun 2020 18:21:09: 3000000 INFO @ Sun, 21 Jun 2020 18:21:13: 10000000 INFO @ Sun, 21 Jun 2020 18:21:14: 4000000 INFO @ Sun, 21 Jun 2020 18:21:18: 11000000 INFO @ Sun, 21 Jun 2020 18:21:19: 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 18:21:23: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX1837292/SRX1837292.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX1837292/SRX1837292.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX1837292/SRX1837292.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX1837292/SRX1837292.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 18:21:23: #1 read tag files... INFO @ Sun, 21 Jun 2020 18:21:23: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 18:21:24: 12000000 INFO @ Sun, 21 Jun 2020 18:21:24: 6000000 INFO @ Sun, 21 Jun 2020 18:21:29: 1000000 INFO @ Sun, 21 Jun 2020 18:21:29: 13000000 INFO @ Sun, 21 Jun 2020 18:21:29: 7000000 INFO @ Sun, 21 Jun 2020 18:21:34: 2000000 INFO @ Sun, 21 Jun 2020 18:21:34: 14000000 INFO @ Sun, 21 Jun 2020 18:21:35: 8000000 INFO @ Sun, 21 Jun 2020 18:21:36: #1 tag size is determined as 51 bps INFO @ Sun, 21 Jun 2020 18:21:36: #1 tag size = 51 INFO @ Sun, 21 Jun 2020 18:21:36: #1 total tags in treatment: 14395966 INFO @ Sun, 21 Jun 2020 18:21:36: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 18:21:36: #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 18:21:37: #1 tags after filtering in treatment: 14395933 INFO @ Sun, 21 Jun 2020 18:21:37: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 18:21:37: #1 finished! INFO @ Sun, 21 Jun 2020 18:21:37: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 18:21:37: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 18:21:38: #2 number of paired peaks: 4025 INFO @ Sun, 21 Jun 2020 18:21:38: start model_add_line... INFO @ Sun, 21 Jun 2020 18:21:39: start X-correlation... INFO @ Sun, 21 Jun 2020 18:21:39: end of X-cor INFO @ Sun, 21 Jun 2020 18:21:39: #2 finished! INFO @ Sun, 21 Jun 2020 18:21:39: #2 predicted fragment length is 54 bps INFO @ Sun, 21 Jun 2020 18:21:39: #2 alternative fragment length(s) may be 1,54 bps INFO @ Sun, 21 Jun 2020 18:21:39: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX1837292/SRX1837292.05_model.r WARNING @ Sun, 21 Jun 2020 18:21:39: #2 Since the d (54) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 18:21:39: #2 You may need to consider one of the other alternative d(s): 1,54 WARNING @ Sun, 21 Jun 2020 18:21:39: #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 18:21:39: #3 Call peaks... INFO @ Sun, 21 Jun 2020 18:21:39: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 18:21:39: 3000000 INFO @ Sun, 21 Jun 2020 18:21:40: 9000000 INFO @ Sun, 21 Jun 2020 18:21:44: 4000000 INFO @ Sun, 21 Jun 2020 18:21:45: 10000000 INFO @ Sun, 21 Jun 2020 18:21:49: 5000000 INFO @ Sun, 21 Jun 2020 18:21:51: 11000000 INFO @ Sun, 21 Jun 2020 18:21:54: 6000000 INFO @ Sun, 21 Jun 2020 18:21:56: 12000000 INFO @ Sun, 21 Jun 2020 18:21:59: 7000000 INFO @ Sun, 21 Jun 2020 18:22:01: 13000000 INFO @ Sun, 21 Jun 2020 18:22:04: 8000000 INFO @ Sun, 21 Jun 2020 18:22:05: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 18:22:06: 14000000 INFO @ Sun, 21 Jun 2020 18:22:09: #1 tag size is determined as 51 bps INFO @ Sun, 21 Jun 2020 18:22:09: #1 tag size = 51 INFO @ Sun, 21 Jun 2020 18:22:09: #1 total tags in treatment: 14395966 INFO @ Sun, 21 Jun 2020 18:22:09: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 18:22:09: #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 18:22:09: #1 tags after filtering in treatment: 14395933 INFO @ Sun, 21 Jun 2020 18:22:09: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 18:22:09: #1 finished! INFO @ Sun, 21 Jun 2020 18:22:09: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 18:22:09: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 18:22:10: 9000000 INFO @ Sun, 21 Jun 2020 18:22:11: #2 number of paired peaks: 4025 INFO @ Sun, 21 Jun 2020 18:22:11: start model_add_line... INFO @ Sun, 21 Jun 2020 18:22:11: start X-correlation... INFO @ Sun, 21 Jun 2020 18:22:11: end of X-cor INFO @ Sun, 21 Jun 2020 18:22:11: #2 finished! INFO @ Sun, 21 Jun 2020 18:22:11: #2 predicted fragment length is 54 bps INFO @ Sun, 21 Jun 2020 18:22:11: #2 alternative fragment length(s) may be 1,54 bps INFO @ Sun, 21 Jun 2020 18:22:11: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX1837292/SRX1837292.10_model.r WARNING @ Sun, 21 Jun 2020 18:22:11: #2 Since the d (54) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 18:22:11: #2 You may need to consider one of the other alternative d(s): 1,54 WARNING @ Sun, 21 Jun 2020 18:22:11: #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 18:22:11: #3 Call peaks... INFO @ Sun, 21 Jun 2020 18:22:11: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 18:22:15: 10000000 INFO @ Sun, 21 Jun 2020 18:22:19: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX1837292/SRX1837292.05_peaks.xls INFO @ Sun, 21 Jun 2020 18:22:19: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX1837292/SRX1837292.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 18:22:19: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX1837292/SRX1837292.05_summits.bed INFO @ Sun, 21 Jun 2020 18:22:19: Done! pass1 - making usageList (1305 chroms): 2 millis pass2 - checking and writing primary data (6915 records, 4 fields): 41 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 18:22:20: 11000000 INFO @ Sun, 21 Jun 2020 18:22:25: 12000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 18:22:30: 13000000 INFO @ Sun, 21 Jun 2020 18:22:35: 14000000 INFO @ Sun, 21 Jun 2020 18:22:38: #1 tag size is determined as 51 bps INFO @ Sun, 21 Jun 2020 18:22:38: #1 tag size = 51 INFO @ Sun, 21 Jun 2020 18:22:38: #1 total tags in treatment: 14395966 INFO @ Sun, 21 Jun 2020 18:22:38: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 18:22:38: #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 18:22:38: #1 tags after filtering in treatment: 14395933 INFO @ Sun, 21 Jun 2020 18:22:38: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 18:22:38: #1 finished! INFO @ Sun, 21 Jun 2020 18:22:38: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 18:22:38: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 18:22:40: #2 number of paired peaks: 4025 INFO @ Sun, 21 Jun 2020 18:22:40: start model_add_line... INFO @ Sun, 21 Jun 2020 18:22:40: start X-correlation... INFO @ Sun, 21 Jun 2020 18:22:40: end of X-cor INFO @ Sun, 21 Jun 2020 18:22:40: #2 finished! INFO @ Sun, 21 Jun 2020 18:22:40: #2 predicted fragment length is 54 bps INFO @ Sun, 21 Jun 2020 18:22:40: #2 alternative fragment length(s) may be 1,54 bps INFO @ Sun, 21 Jun 2020 18:22:40: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX1837292/SRX1837292.20_model.r WARNING @ Sun, 21 Jun 2020 18:22:40: #2 Since the d (54) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 18:22:40: #2 You may need to consider one of the other alternative d(s): 1,54 WARNING @ Sun, 21 Jun 2020 18:22:40: #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 18:22:40: #3 Call peaks... INFO @ Sun, 21 Jun 2020 18:22:40: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 18:22:40: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 18:22:55: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX1837292/SRX1837292.10_peaks.xls INFO @ Sun, 21 Jun 2020 18:22:55: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX1837292/SRX1837292.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 18:22:55: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX1837292/SRX1837292.10_summits.bed INFO @ Sun, 21 Jun 2020 18:22:55: Done! pass1 - making usageList (954 chroms): 2 millis pass2 - checking and writing primary data (3509 records, 4 fields): 28 millis CompletedMACS2peakCalling BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 18:23:09: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 18:23:24: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX1837292/SRX1837292.20_peaks.xls INFO @ Sun, 21 Jun 2020 18:23:24: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX1837292/SRX1837292.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 18:23:24: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX1837292/SRX1837292.20_summits.bed INFO @ Sun, 21 Jun 2020 18:23:24: Done! pass1 - making usageList (637 chroms): 1 millis pass2 - checking and writing primary data (2214 records, 4 fields): 21 millis CompletedMACS2peakCalling