Job ID = 6457079 SRX = SRX4375842 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T11:55:21 prefetch.2.10.7: 1) Downloading 'SRR7506496'... 2020-06-21T11:55:21 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T12:01:24 prefetch.2.10.7: HTTPS download succeed 2020-06-21T12:01:24 prefetch.2.10.7: 1) 'SRR7506496' was downloaded successfully Read 21971273 spots for SRR7506496/SRR7506496.sra Written 21971273 spots for SRR7506496/SRR7506496.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: 00:04:50 21971273 reads; of these: 21971273 (100.00%) were unpaired; of these: 1718327 (7.82%) aligned 0 times 16726296 (76.13%) aligned exactly 1 time 3526650 (16.05%) aligned >1 times 92.18% overall alignment rate Time searching: 00:04:50 Overall time: 00:04:50 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] 7331535 / 20252946 = 0.3620 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 21:13:45: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX4375842/SRX4375842.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX4375842/SRX4375842.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX4375842/SRX4375842.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX4375842/SRX4375842.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 21:13:45: #1 read tag files... INFO @ Sun, 21 Jun 2020 21:13:45: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 21:13:51: 1000000 INFO @ Sun, 21 Jun 2020 21:13:56: 2000000 INFO @ Sun, 21 Jun 2020 21:14:02: 3000000 INFO @ Sun, 21 Jun 2020 21:14:07: 4000000 INFO @ Sun, 21 Jun 2020 21:14:12: 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 21:14:15: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX4375842/SRX4375842.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX4375842/SRX4375842.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX4375842/SRX4375842.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX4375842/SRX4375842.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 21:14:15: #1 read tag files... INFO @ Sun, 21 Jun 2020 21:14:15: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 21:14:18: 6000000 INFO @ Sun, 21 Jun 2020 21:14:20: 1000000 INFO @ Sun, 21 Jun 2020 21:14:23: 7000000 INFO @ Sun, 21 Jun 2020 21:14:26: 2000000 INFO @ Sun, 21 Jun 2020 21:14:29: 8000000 INFO @ Sun, 21 Jun 2020 21:14:32: 3000000 INFO @ Sun, 21 Jun 2020 21:14:35: 9000000 INFO @ Sun, 21 Jun 2020 21:14:37: 4000000 INFO @ Sun, 21 Jun 2020 21:14:40: 10000000 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 21:14:43: 5000000 INFO @ Sun, 21 Jun 2020 21:14:45: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX4375842/SRX4375842.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX4375842/SRX4375842.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX4375842/SRX4375842.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX4375842/SRX4375842.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 21:14:45: #1 read tag files... INFO @ Sun, 21 Jun 2020 21:14:45: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 21:14:47: 11000000 INFO @ Sun, 21 Jun 2020 21:14:49: 6000000 INFO @ Sun, 21 Jun 2020 21:14:51: 1000000 INFO @ Sun, 21 Jun 2020 21:14:53: 12000000 INFO @ Sun, 21 Jun 2020 21:14:55: 7000000 INFO @ Sun, 21 Jun 2020 21:14:57: 2000000 INFO @ Sun, 21 Jun 2020 21:14:59: #1 tag size is determined as 51 bps INFO @ Sun, 21 Jun 2020 21:14:59: #1 tag size = 51 INFO @ Sun, 21 Jun 2020 21:14:59: #1 total tags in treatment: 12921411 INFO @ Sun, 21 Jun 2020 21:14:59: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 21:14:59: #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 21:15:00: #1 tags after filtering in treatment: 12921232 INFO @ Sun, 21 Jun 2020 21:15:00: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 21:15:00: #1 finished! INFO @ Sun, 21 Jun 2020 21:15:00: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 21:15:00: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 21:15:01: 8000000 INFO @ Sun, 21 Jun 2020 21:15:02: #2 number of paired peaks: 8700 INFO @ Sun, 21 Jun 2020 21:15:02: start model_add_line... INFO @ Sun, 21 Jun 2020 21:15:02: start X-correlation... INFO @ Sun, 21 Jun 2020 21:15:02: end of X-cor INFO @ Sun, 21 Jun 2020 21:15:02: #2 finished! INFO @ Sun, 21 Jun 2020 21:15:02: #2 predicted fragment length is 191 bps INFO @ Sun, 21 Jun 2020 21:15:02: #2 alternative fragment length(s) may be 191 bps INFO @ Sun, 21 Jun 2020 21:15:02: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX4375842/SRX4375842.05_model.r INFO @ Sun, 21 Jun 2020 21:15:02: #3 Call peaks... INFO @ Sun, 21 Jun 2020 21:15:02: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 21:15:03: 3000000 INFO @ Sun, 21 Jun 2020 21:15:07: 9000000 INFO @ Sun, 21 Jun 2020 21:15:09: 4000000 INFO @ Sun, 21 Jun 2020 21:15:12: 10000000 INFO @ Sun, 21 Jun 2020 21:15:15: 5000000 INFO @ Sun, 21 Jun 2020 21:15:19: 11000000 INFO @ Sun, 21 Jun 2020 21:15:20: 6000000 INFO @ Sun, 21 Jun 2020 21:15:24: 12000000 INFO @ Sun, 21 Jun 2020 21:15:26: 7000000 INFO @ Sun, 21 Jun 2020 21:15:30: #1 tag size is determined as 51 bps INFO @ Sun, 21 Jun 2020 21:15:30: #1 tag size = 51 INFO @ Sun, 21 Jun 2020 21:15:30: #1 total tags in treatment: 12921411 INFO @ Sun, 21 Jun 2020 21:15:30: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 21:15:30: #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 21:15:30: #1 tags after filtering in treatment: 12921232 INFO @ Sun, 21 Jun 2020 21:15:30: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 21:15:30: #1 finished! INFO @ Sun, 21 Jun 2020 21:15:30: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 21:15:30: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 21:15:31: 8000000 INFO @ Sun, 21 Jun 2020 21:15:32: #2 number of paired peaks: 8700 INFO @ Sun, 21 Jun 2020 21:15:32: start model_add_line... INFO @ Sun, 21 Jun 2020 21:15:32: start X-correlation... INFO @ Sun, 21 Jun 2020 21:15:32: end of X-cor INFO @ Sun, 21 Jun 2020 21:15:32: #2 finished! INFO @ Sun, 21 Jun 2020 21:15:32: #2 predicted fragment length is 191 bps INFO @ Sun, 21 Jun 2020 21:15:32: #2 alternative fragment length(s) may be 191 bps INFO @ Sun, 21 Jun 2020 21:15:32: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX4375842/SRX4375842.10_model.r INFO @ Sun, 21 Jun 2020 21:15:32: #3 Call peaks... INFO @ Sun, 21 Jun 2020 21:15:32: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 21:15:36: 9000000 INFO @ Sun, 21 Jun 2020 21:15:42: 10000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 21:15:48: 11000000 INFO @ Sun, 21 Jun 2020 21:15:49: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 21:15:53: 12000000 INFO @ Sun, 21 Jun 2020 21:15:58: #1 tag size is determined as 51 bps INFO @ Sun, 21 Jun 2020 21:15:58: #1 tag size = 51 INFO @ Sun, 21 Jun 2020 21:15:58: #1 total tags in treatment: 12921411 INFO @ Sun, 21 Jun 2020 21:15:58: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 21:15:58: #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 21:15:59: #1 tags after filtering in treatment: 12921232 INFO @ Sun, 21 Jun 2020 21:15:59: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 21:15:59: #1 finished! INFO @ Sun, 21 Jun 2020 21:15:59: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 21:15:59: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 21:16:01: #2 number of paired peaks: 8700 INFO @ Sun, 21 Jun 2020 21:16:01: start model_add_line... INFO @ Sun, 21 Jun 2020 21:16:01: start X-correlation... INFO @ Sun, 21 Jun 2020 21:16:01: end of X-cor INFO @ Sun, 21 Jun 2020 21:16:01: #2 finished! INFO @ Sun, 21 Jun 2020 21:16:01: #2 predicted fragment length is 191 bps INFO @ Sun, 21 Jun 2020 21:16:01: #2 alternative fragment length(s) may be 191 bps INFO @ Sun, 21 Jun 2020 21:16:01: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX4375842/SRX4375842.20_model.r INFO @ Sun, 21 Jun 2020 21:16:01: #3 Call peaks... INFO @ Sun, 21 Jun 2020 21:16:01: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 21:16:04: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX4375842/SRX4375842.05_peaks.xls INFO @ Sun, 21 Jun 2020 21:16:04: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX4375842/SRX4375842.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 21:16:04: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX4375842/SRX4375842.05_summits.bed INFO @ Sun, 21 Jun 2020 21:16:04: Done! pass1 - making usageList (168 chroms): 2 millis pass2 - checking and writing primary data (11351 records, 4 fields): 24 millis CompletedMACS2peakCalling BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 21:16:19: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 21:16:33: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX4375842/SRX4375842.10_peaks.xls INFO @ Sun, 21 Jun 2020 21:16:33: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX4375842/SRX4375842.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 21:16:33: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX4375842/SRX4375842.10_summits.bed INFO @ Sun, 21 Jun 2020 21:16:33: Done! pass1 - making usageList (143 chroms): 3 millis pass2 - checking and writing primary data (8587 records, 4 fields): 19 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 21:16:48: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 21:17:02: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX4375842/SRX4375842.20_peaks.xls INFO @ Sun, 21 Jun 2020 21:17:02: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX4375842/SRX4375842.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 21:17:02: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX4375842/SRX4375842.20_summits.bed INFO @ Sun, 21 Jun 2020 21:17:02: Done! pass1 - making usageList (107 chroms): 2 millis pass2 - checking and writing primary data (6019 records, 4 fields): 14 millis CompletedMACS2peakCalling