Job ID = 6456015 SRX = SRX3159472 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T10:35:30 prefetch.2.10.7: 1) Downloading 'SRR6004202'... 2020-06-21T10:35:30 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T10:38:08 prefetch.2.10.7: HTTPS download succeed 2020-06-21T10:38:08 prefetch.2.10.7: 'SRR6004202' is valid 2020-06-21T10:38:08 prefetch.2.10.7: 1) 'SRR6004202' was downloaded successfully 2020-06-21T10:38:08 prefetch.2.10.7: 'SRR6004202' has 0 unresolved dependencies Read 21548163 spots for SRR6004202/SRR6004202.sra Written 21548163 spots for SRR6004202/SRR6004202.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: 00:05:13 21548163 reads; of these: 21548163 (100.00%) were unpaired; of these: 1402215 (6.51%) aligned 0 times 17520792 (81.31%) aligned exactly 1 time 2625156 (12.18%) aligned >1 times 93.49% overall alignment rate Time searching: 00:05:13 Overall time: 00:05:13 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] 5673582 / 20145948 = 0.2816 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 19:48:40: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX3159472/SRX3159472.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX3159472/SRX3159472.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX3159472/SRX3159472.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX3159472/SRX3159472.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 19:48:40: #1 read tag files... INFO @ Sun, 21 Jun 2020 19:48:40: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 19:48:45: 1000000 INFO @ Sun, 21 Jun 2020 19:48:51: 2000000 INFO @ Sun, 21 Jun 2020 19:48:57: 3000000 INFO @ Sun, 21 Jun 2020 19:49:02: 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 19:49:08: 5000000 INFO @ Sun, 21 Jun 2020 19:49:10: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX3159472/SRX3159472.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX3159472/SRX3159472.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX3159472/SRX3159472.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX3159472/SRX3159472.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 19:49:10: #1 read tag files... INFO @ Sun, 21 Jun 2020 19:49:10: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 19:49:14: 6000000 INFO @ Sun, 21 Jun 2020 19:49:17: 1000000 INFO @ Sun, 21 Jun 2020 19:49:21: 7000000 INFO @ Sun, 21 Jun 2020 19:49:24: 2000000 INFO @ Sun, 21 Jun 2020 19:49:28: 8000000 INFO @ Sun, 21 Jun 2020 19:49:31: 3000000 INFO @ Sun, 21 Jun 2020 19:49:34: 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 19:49:39: 4000000 INFO @ Sun, 21 Jun 2020 19:49:40: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX3159472/SRX3159472.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX3159472/SRX3159472.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX3159472/SRX3159472.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX3159472/SRX3159472.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 19:49:40: #1 read tag files... INFO @ Sun, 21 Jun 2020 19:49:40: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 19:49:41: 10000000 INFO @ Sun, 21 Jun 2020 19:49:46: 5000000 INFO @ Sun, 21 Jun 2020 19:49:47: 1000000 INFO @ Sun, 21 Jun 2020 19:49:48: 11000000 INFO @ Sun, 21 Jun 2020 19:49:54: 6000000 INFO @ Sun, 21 Jun 2020 19:49:55: 2000000 INFO @ Sun, 21 Jun 2020 19:49:55: 12000000 INFO @ Sun, 21 Jun 2020 19:50:01: 7000000 INFO @ Sun, 21 Jun 2020 19:50:02: 3000000 INFO @ Sun, 21 Jun 2020 19:50:02: 13000000 INFO @ Sun, 21 Jun 2020 19:50:08: 8000000 INFO @ Sun, 21 Jun 2020 19:50:09: 14000000 INFO @ Sun, 21 Jun 2020 19:50:09: 4000000 INFO @ Sun, 21 Jun 2020 19:50:13: #1 tag size is determined as 51 bps INFO @ Sun, 21 Jun 2020 19:50:13: #1 tag size = 51 INFO @ Sun, 21 Jun 2020 19:50:13: #1 total tags in treatment: 14472366 INFO @ Sun, 21 Jun 2020 19:50:13: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 19:50:13: #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 19:50:13: #1 tags after filtering in treatment: 14472361 INFO @ Sun, 21 Jun 2020 19:50:13: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 19:50:13: #1 finished! INFO @ Sun, 21 Jun 2020 19:50:13: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 19:50:13: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 19:50:15: #2 number of paired peaks: 4210 INFO @ Sun, 21 Jun 2020 19:50:15: start model_add_line... INFO @ Sun, 21 Jun 2020 19:50:15: start X-correlation... INFO @ Sun, 21 Jun 2020 19:50:15: end of X-cor INFO @ Sun, 21 Jun 2020 19:50:15: #2 finished! INFO @ Sun, 21 Jun 2020 19:50:15: #2 predicted fragment length is 148 bps INFO @ Sun, 21 Jun 2020 19:50:15: #2 alternative fragment length(s) may be 148 bps INFO @ Sun, 21 Jun 2020 19:50:15: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX3159472/SRX3159472.05_model.r INFO @ Sun, 21 Jun 2020 19:50:15: #3 Call peaks... INFO @ Sun, 21 Jun 2020 19:50:15: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 19:50:16: 9000000 INFO @ Sun, 21 Jun 2020 19:50:16: 5000000 INFO @ Sun, 21 Jun 2020 19:50:23: 10000000 INFO @ Sun, 21 Jun 2020 19:50:24: 6000000 INFO @ Sun, 21 Jun 2020 19:50:31: 11000000 INFO @ Sun, 21 Jun 2020 19:50:31: 7000000 INFO @ Sun, 21 Jun 2020 19:50:38: 12000000 INFO @ Sun, 21 Jun 2020 19:50:38: 8000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 19:50:46: 9000000 INFO @ Sun, 21 Jun 2020 19:50:46: 13000000 INFO @ Sun, 21 Jun 2020 19:50:53: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 19:50:53: 10000000 INFO @ Sun, 21 Jun 2020 19:50:53: 14000000 INFO @ Sun, 21 Jun 2020 19:50:57: #1 tag size is determined as 51 bps INFO @ Sun, 21 Jun 2020 19:50:57: #1 tag size = 51 INFO @ Sun, 21 Jun 2020 19:50:57: #1 total tags in treatment: 14472366 INFO @ Sun, 21 Jun 2020 19:50:57: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 19:50:57: #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 19:50:57: #1 tags after filtering in treatment: 14472361 INFO @ Sun, 21 Jun 2020 19:50:57: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 19:50:57: #1 finished! INFO @ Sun, 21 Jun 2020 19:50:57: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 19:50:57: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 19:50:59: #2 number of paired peaks: 4210 INFO @ Sun, 21 Jun 2020 19:50:59: start model_add_line... INFO @ Sun, 21 Jun 2020 19:50:59: start X-correlation... INFO @ Sun, 21 Jun 2020 19:50:59: end of X-cor INFO @ Sun, 21 Jun 2020 19:50:59: #2 finished! INFO @ Sun, 21 Jun 2020 19:50:59: #2 predicted fragment length is 148 bps INFO @ Sun, 21 Jun 2020 19:50:59: #2 alternative fragment length(s) may be 148 bps INFO @ Sun, 21 Jun 2020 19:50:59: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX3159472/SRX3159472.10_model.r INFO @ Sun, 21 Jun 2020 19:50:59: #3 Call peaks... INFO @ Sun, 21 Jun 2020 19:50:59: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 19:51:00: 11000000 INFO @ Sun, 21 Jun 2020 19:51:07: 12000000 INFO @ Sun, 21 Jun 2020 19:51:12: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX3159472/SRX3159472.05_peaks.xls INFO @ Sun, 21 Jun 2020 19:51:12: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX3159472/SRX3159472.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 19:51:12: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX3159472/SRX3159472.05_summits.bed INFO @ Sun, 21 Jun 2020 19:51:12: Done! pass1 - making usageList (424 chroms): 3 millis pass2 - checking and writing primary data (8017 records, 4 fields): 22 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 19:51:14: 13000000 BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 19:51:21: 14000000 INFO @ Sun, 21 Jun 2020 19:51:25: #1 tag size is determined as 51 bps INFO @ Sun, 21 Jun 2020 19:51:25: #1 tag size = 51 INFO @ Sun, 21 Jun 2020 19:51:25: #1 total tags in treatment: 14472366 INFO @ Sun, 21 Jun 2020 19:51:25: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 19:51:25: #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 19:51:25: #1 tags after filtering in treatment: 14472361 INFO @ Sun, 21 Jun 2020 19:51:25: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 19:51:25: #1 finished! INFO @ Sun, 21 Jun 2020 19:51:25: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 19:51:25: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 19:51:27: #2 number of paired peaks: 4210 INFO @ Sun, 21 Jun 2020 19:51:27: start model_add_line... INFO @ Sun, 21 Jun 2020 19:51:27: start X-correlation... INFO @ Sun, 21 Jun 2020 19:51:27: end of X-cor INFO @ Sun, 21 Jun 2020 19:51:27: #2 finished! INFO @ Sun, 21 Jun 2020 19:51:27: #2 predicted fragment length is 148 bps INFO @ Sun, 21 Jun 2020 19:51:27: #2 alternative fragment length(s) may be 148 bps INFO @ Sun, 21 Jun 2020 19:51:27: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX3159472/SRX3159472.20_model.r INFO @ Sun, 21 Jun 2020 19:51:27: #3 Call peaks... INFO @ Sun, 21 Jun 2020 19:51:27: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 19:51:36: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 19:51:56: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX3159472/SRX3159472.10_peaks.xls INFO @ Sun, 21 Jun 2020 19:51:56: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX3159472/SRX3159472.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 19:51:56: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX3159472/SRX3159472.10_summits.bed INFO @ Sun, 21 Jun 2020 19:51:56: Done! pass1 - making usageList (331 chroms): 2 millis pass2 - checking and writing primary data (6757 records, 4 fields): 22 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 19:52:04: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 19:52:23: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX3159472/SRX3159472.20_peaks.xls INFO @ Sun, 21 Jun 2020 19:52:23: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX3159472/SRX3159472.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 19:52:23: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX3159472/SRX3159472.20_summits.bed INFO @ Sun, 21 Jun 2020 19:52:23: Done! pass1 - making usageList (161 chroms): 1 millis pass2 - checking and writing primary data (5365 records, 4 fields): 26 millis CompletedMACS2peakCalling