Job ID = 6452996 SRX = SRX097295 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T08:07:33 prefetch.2.10.7: 1) Downloading 'SRR345248'... 2020-06-21T08:07:33 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T08:09:38 prefetch.2.10.7: HTTPS download succeed 2020-06-21T08:09:39 prefetch.2.10.7: 'SRR345248' is valid 2020-06-21T08:09:39 prefetch.2.10.7: 1) 'SRR345248' was downloaded successfully Read 21988686 spots for SRR345248/SRR345248.sra Written 21988686 spots for SRR345248/SRR345248.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: 00:03:32 21988686 reads; of these: 21988686 (100.00%) were unpaired; of these: 3231722 (14.70%) aligned 0 times 17465389 (79.43%) aligned exactly 1 time 1291575 (5.87%) aligned >1 times 85.30% overall alignment rate Time searching: 00:03:33 Overall time: 00:03:33 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] 5060422 / 18756964 = 0.2698 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 17:17:52: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX097295/SRX097295.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX097295/SRX097295.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX097295/SRX097295.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX097295/SRX097295.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 17:17:52: #1 read tag files... INFO @ Sun, 21 Jun 2020 17:17:52: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 17:17:58: 1000000 INFO @ Sun, 21 Jun 2020 17:18:04: 2000000 INFO @ Sun, 21 Jun 2020 17:18:10: 3000000 INFO @ Sun, 21 Jun 2020 17:18:16: 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 17:18:22: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX097295/SRX097295.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX097295/SRX097295.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX097295/SRX097295.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX097295/SRX097295.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 17:18:22: #1 read tag files... INFO @ Sun, 21 Jun 2020 17:18:22: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 17:18:23: 5000000 INFO @ Sun, 21 Jun 2020 17:18:28: 1000000 INFO @ Sun, 21 Jun 2020 17:18:30: 6000000 INFO @ Sun, 21 Jun 2020 17:18:34: 2000000 INFO @ Sun, 21 Jun 2020 17:18:36: 7000000 INFO @ Sun, 21 Jun 2020 17:18:40: 3000000 INFO @ Sun, 21 Jun 2020 17:18:43: 8000000 INFO @ Sun, 21 Jun 2020 17:18:46: 4000000 INFO @ Sun, 21 Jun 2020 17:18:50: 9000000 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 17:18:52: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX097295/SRX097295.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX097295/SRX097295.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX097295/SRX097295.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX097295/SRX097295.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 17:18:52: #1 read tag files... INFO @ Sun, 21 Jun 2020 17:18:52: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 17:18:53: 5000000 INFO @ Sun, 21 Jun 2020 17:18:57: 10000000 INFO @ Sun, 21 Jun 2020 17:18:58: 1000000 INFO @ Sun, 21 Jun 2020 17:18:59: 6000000 INFO @ Sun, 21 Jun 2020 17:19:03: 11000000 INFO @ Sun, 21 Jun 2020 17:19:05: 2000000 INFO @ Sun, 21 Jun 2020 17:19:06: 7000000 INFO @ Sun, 21 Jun 2020 17:19:10: 12000000 INFO @ Sun, 21 Jun 2020 17:19:11: 3000000 INFO @ Sun, 21 Jun 2020 17:19:12: 8000000 INFO @ Sun, 21 Jun 2020 17:19:17: 4000000 INFO @ Sun, 21 Jun 2020 17:19:17: 13000000 INFO @ Sun, 21 Jun 2020 17:19:18: 9000000 INFO @ Sun, 21 Jun 2020 17:19:22: #1 tag size is determined as 36 bps INFO @ Sun, 21 Jun 2020 17:19:22: #1 tag size = 36 INFO @ Sun, 21 Jun 2020 17:19:22: #1 total tags in treatment: 13696542 INFO @ Sun, 21 Jun 2020 17:19:22: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 17:19:22: #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 17:19:22: #1 tags after filtering in treatment: 13696344 INFO @ Sun, 21 Jun 2020 17:19:22: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 17:19:22: #1 finished! INFO @ Sun, 21 Jun 2020 17:19:22: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 17:19:22: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 17:19:23: #2 number of paired peaks: 724 WARNING @ Sun, 21 Jun 2020 17:19:23: Fewer paired peaks (724) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 724 pairs to build model! INFO @ Sun, 21 Jun 2020 17:19:23: start model_add_line... INFO @ Sun, 21 Jun 2020 17:19:24: start X-correlation... INFO @ Sun, 21 Jun 2020 17:19:24: end of X-cor INFO @ Sun, 21 Jun 2020 17:19:24: #2 finished! INFO @ Sun, 21 Jun 2020 17:19:24: #2 predicted fragment length is 137 bps INFO @ Sun, 21 Jun 2020 17:19:24: #2 alternative fragment length(s) may be 137 bps INFO @ Sun, 21 Jun 2020 17:19:24: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX097295/SRX097295.05_model.r INFO @ Sun, 21 Jun 2020 17:19:24: #3 Call peaks... INFO @ Sun, 21 Jun 2020 17:19:24: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 17:19:24: 5000000 INFO @ Sun, 21 Jun 2020 17:19:25: 10000000 INFO @ Sun, 21 Jun 2020 17:19:30: 6000000 INFO @ Sun, 21 Jun 2020 17:19:31: 11000000 INFO @ Sun, 21 Jun 2020 17:19:36: 7000000 INFO @ Sun, 21 Jun 2020 17:19:38: 12000000 INFO @ Sun, 21 Jun 2020 17:19:42: 8000000 INFO @ Sun, 21 Jun 2020 17:19:44: 13000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 17:19:48: #1 tag size is determined as 36 bps INFO @ Sun, 21 Jun 2020 17:19:48: #1 tag size = 36 INFO @ Sun, 21 Jun 2020 17:19:48: #1 total tags in treatment: 13696542 INFO @ Sun, 21 Jun 2020 17:19:48: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 17:19:48: #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 17:19:48: 9000000 INFO @ Sun, 21 Jun 2020 17:19:49: #1 tags after filtering in treatment: 13696344 INFO @ Sun, 21 Jun 2020 17:19:49: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 17:19:49: #1 finished! INFO @ Sun, 21 Jun 2020 17:19:49: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 17:19:49: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 17:19:50: #2 number of paired peaks: 724 WARNING @ Sun, 21 Jun 2020 17:19:50: Fewer paired peaks (724) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 724 pairs to build model! INFO @ Sun, 21 Jun 2020 17:19:50: start model_add_line... INFO @ Sun, 21 Jun 2020 17:19:50: start X-correlation... INFO @ Sun, 21 Jun 2020 17:19:50: end of X-cor INFO @ Sun, 21 Jun 2020 17:19:50: #2 finished! INFO @ Sun, 21 Jun 2020 17:19:50: #2 predicted fragment length is 137 bps INFO @ Sun, 21 Jun 2020 17:19:50: #2 alternative fragment length(s) may be 137 bps INFO @ Sun, 21 Jun 2020 17:19:50: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX097295/SRX097295.10_model.r INFO @ Sun, 21 Jun 2020 17:19:50: #3 Call peaks... INFO @ Sun, 21 Jun 2020 17:19:50: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 17:19:52: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 17:19:54: 10000000 INFO @ Sun, 21 Jun 2020 17:20:00: 11000000 INFO @ Sun, 21 Jun 2020 17:20:06: 12000000 INFO @ Sun, 21 Jun 2020 17:20:06: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX097295/SRX097295.05_peaks.xls INFO @ Sun, 21 Jun 2020 17:20:06: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX097295/SRX097295.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 17:20:06: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX097295/SRX097295.05_summits.bed INFO @ Sun, 21 Jun 2020 17:20:06: Done! pass1 - making usageList (28 chroms): 1 millis pass2 - checking and writing primary data (6224 records, 4 fields): 7 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 17:20:11: 13000000 INFO @ Sun, 21 Jun 2020 17:20:14: #1 tag size is determined as 36 bps INFO @ Sun, 21 Jun 2020 17:20:14: #1 tag size = 36 INFO @ Sun, 21 Jun 2020 17:20:14: #1 total tags in treatment: 13696542 INFO @ Sun, 21 Jun 2020 17:20:14: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 17:20:14: #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 17:20:15: #1 tags after filtering in treatment: 13696344 INFO @ Sun, 21 Jun 2020 17:20:15: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 17:20:15: #1 finished! INFO @ Sun, 21 Jun 2020 17:20:15: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 17:20:15: #2 looking for paired plus/minus strand peaks... BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 17:20:16: #2 number of paired peaks: 724 WARNING @ Sun, 21 Jun 2020 17:20:16: Fewer paired peaks (724) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 724 pairs to build model! INFO @ Sun, 21 Jun 2020 17:20:16: start model_add_line... INFO @ Sun, 21 Jun 2020 17:20:16: start X-correlation... INFO @ Sun, 21 Jun 2020 17:20:16: end of X-cor INFO @ Sun, 21 Jun 2020 17:20:16: #2 finished! INFO @ Sun, 21 Jun 2020 17:20:16: #2 predicted fragment length is 137 bps INFO @ Sun, 21 Jun 2020 17:20:16: #2 alternative fragment length(s) may be 137 bps INFO @ Sun, 21 Jun 2020 17:20:16: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX097295/SRX097295.20_model.r INFO @ Sun, 21 Jun 2020 17:20:16: #3 Call peaks... INFO @ Sun, 21 Jun 2020 17:20:16: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 17:20:20: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 17:20:36: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX097295/SRX097295.10_peaks.xls INFO @ Sun, 21 Jun 2020 17:20:36: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX097295/SRX097295.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 17:20:36: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX097295/SRX097295.10_summits.bed INFO @ Sun, 21 Jun 2020 17:20:36: Done! pass1 - making usageList (24 chroms): 1 millis pass2 - checking and writing primary data (3928 records, 4 fields): 5 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 17:20:44: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 17:20:59: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX097295/SRX097295.20_peaks.xls INFO @ Sun, 21 Jun 2020 17:20:59: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX097295/SRX097295.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 17:20:59: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX097295/SRX097295.20_summits.bed INFO @ Sun, 21 Jun 2020 17:20:59: Done! pass1 - making usageList (19 chroms): 1 millis pass2 - checking and writing primary data (2093 records, 4 fields): 4 millis CompletedMACS2peakCalling