Job ID = 6457944 SRX = SRX4923188 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T12:24:49 prefetch.2.10.7: 1) Downloading 'SRR8096338'... 2020-06-21T12:24:49 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T12:28:04 prefetch.2.10.7: HTTPS download succeed 2020-06-21T12:28:04 prefetch.2.10.7: 1) 'SRR8096338' was downloaded successfully 2020-06-21T12:28:04 prefetch.2.10.7: 'SRR8096338' has 0 unresolved dependencies Read 33398729 spots for SRR8096338/SRR8096338.sra Written 33398729 spots for SRR8096338/SRR8096338.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: 00:06:38 33398729 reads; of these: 33398729 (100.00%) were unpaired; of these: 971693 (2.91%) aligned 0 times 27453235 (82.20%) aligned exactly 1 time 4973801 (14.89%) aligned >1 times 97.09% overall alignment rate Time searching: 00:06:38 Overall time: 00:06:38 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 16 files... [bam_rmdupse_core] 18650055 / 32427036 = 0.5751 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 21:40:51: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX4923188/SRX4923188.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX4923188/SRX4923188.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX4923188/SRX4923188.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX4923188/SRX4923188.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 21:40:51: #1 read tag files... INFO @ Sun, 21 Jun 2020 21:40:51: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 21:40:56: 1000000 INFO @ Sun, 21 Jun 2020 21:41:01: 2000000 INFO @ Sun, 21 Jun 2020 21:41:06: 3000000 INFO @ Sun, 21 Jun 2020 21:41:11: 4000000 INFO @ Sun, 21 Jun 2020 21:41:15: 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 21:41:20: 6000000 INFO @ Sun, 21 Jun 2020 21:41:21: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX4923188/SRX4923188.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX4923188/SRX4923188.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX4923188/SRX4923188.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX4923188/SRX4923188.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 21:41:21: #1 read tag files... INFO @ Sun, 21 Jun 2020 21:41:21: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 21:41:25: 7000000 INFO @ Sun, 21 Jun 2020 21:41:27: 1000000 INFO @ Sun, 21 Jun 2020 21:41:31: 8000000 INFO @ Sun, 21 Jun 2020 21:41:32: 2000000 INFO @ Sun, 21 Jun 2020 21:41:36: 9000000 INFO @ Sun, 21 Jun 2020 21:41:38: 3000000 INFO @ Sun, 21 Jun 2020 21:41:41: 10000000 INFO @ Sun, 21 Jun 2020 21:41:43: 4000000 INFO @ Sun, 21 Jun 2020 21:41:47: 11000000 INFO @ Sun, 21 Jun 2020 21:41:48: 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 21:41:52: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX4923188/SRX4923188.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX4923188/SRX4923188.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX4923188/SRX4923188.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX4923188/SRX4923188.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 21:41:52: #1 read tag files... INFO @ Sun, 21 Jun 2020 21:41:52: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 21:41:53: 12000000 INFO @ Sun, 21 Jun 2020 21:41:54: 6000000 INFO @ Sun, 21 Jun 2020 21:41:57: 1000000 INFO @ Sun, 21 Jun 2020 21:41:58: 13000000 INFO @ Sun, 21 Jun 2020 21:41:59: 7000000 INFO @ Sun, 21 Jun 2020 21:42:02: 2000000 INFO @ Sun, 21 Jun 2020 21:42:03: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 21:42:03: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 21:42:03: #1 total tags in treatment: 13776981 INFO @ Sun, 21 Jun 2020 21:42:03: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 21:42:03: #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 21:42:03: #1 tags after filtering in treatment: 13776846 INFO @ Sun, 21 Jun 2020 21:42:03: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 21:42:03: #1 finished! INFO @ Sun, 21 Jun 2020 21:42:03: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 21:42:03: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 21:42:05: 8000000 INFO @ Sun, 21 Jun 2020 21:42:05: #2 number of paired peaks: 13963 INFO @ Sun, 21 Jun 2020 21:42:05: start model_add_line... INFO @ Sun, 21 Jun 2020 21:42:05: start X-correlation... INFO @ Sun, 21 Jun 2020 21:42:05: end of X-cor INFO @ Sun, 21 Jun 2020 21:42:05: #2 finished! INFO @ Sun, 21 Jun 2020 21:42:05: #2 predicted fragment length is 119 bps INFO @ Sun, 21 Jun 2020 21:42:05: #2 alternative fragment length(s) may be 119 bps INFO @ Sun, 21 Jun 2020 21:42:05: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX4923188/SRX4923188.05_model.r INFO @ Sun, 21 Jun 2020 21:42:05: #3 Call peaks... INFO @ Sun, 21 Jun 2020 21:42:05: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 21:42:08: 3000000 INFO @ Sun, 21 Jun 2020 21:42:10: 9000000 INFO @ Sun, 21 Jun 2020 21:42:13: 4000000 INFO @ Sun, 21 Jun 2020 21:42:15: 10000000 INFO @ Sun, 21 Jun 2020 21:42:19: 5000000 INFO @ Sun, 21 Jun 2020 21:42:21: 11000000 INFO @ Sun, 21 Jun 2020 21:42:24: 6000000 INFO @ Sun, 21 Jun 2020 21:42:27: 12000000 INFO @ Sun, 21 Jun 2020 21:42:29: 7000000 INFO @ Sun, 21 Jun 2020 21:42:32: 13000000 INFO @ Sun, 21 Jun 2020 21:42:35: 8000000 INFO @ Sun, 21 Jun 2020 21:42:36: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 21:42:36: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 21:42:36: #1 total tags in treatment: 13776981 INFO @ Sun, 21 Jun 2020 21:42:36: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 21:42:36: #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 21:42:37: #1 tags after filtering in treatment: 13776846 INFO @ Sun, 21 Jun 2020 21:42:37: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 21:42:37: #1 finished! INFO @ Sun, 21 Jun 2020 21:42:37: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 21:42:37: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 21:42:37: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 21:42:39: #2 number of paired peaks: 13963 INFO @ Sun, 21 Jun 2020 21:42:39: start model_add_line... INFO @ Sun, 21 Jun 2020 21:42:39: start X-correlation... INFO @ Sun, 21 Jun 2020 21:42:39: end of X-cor INFO @ Sun, 21 Jun 2020 21:42:39: #2 finished! INFO @ Sun, 21 Jun 2020 21:42:39: #2 predicted fragment length is 119 bps INFO @ Sun, 21 Jun 2020 21:42:39: #2 alternative fragment length(s) may be 119 bps INFO @ Sun, 21 Jun 2020 21:42:39: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX4923188/SRX4923188.10_model.r INFO @ Sun, 21 Jun 2020 21:42:39: #3 Call peaks... INFO @ Sun, 21 Jun 2020 21:42:39: #3 Pre-compute pvalue-qvalue table... BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 21:42:40: 9000000 INFO @ Sun, 21 Jun 2020 21:42:45: 10000000 INFO @ Sun, 21 Jun 2020 21:42:50: 11000000 INFO @ Sun, 21 Jun 2020 21:42:53: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX4923188/SRX4923188.05_peaks.xls INFO @ Sun, 21 Jun 2020 21:42:53: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX4923188/SRX4923188.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 21:42:53: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX4923188/SRX4923188.05_summits.bed INFO @ Sun, 21 Jun 2020 21:42:53: Done! pass1 - making usageList (163 chroms): 2 millis pass2 - checking and writing primary data (11367 records, 4 fields): 16 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 21:42:55: 12000000 BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 21:43:00: 13000000 INFO @ Sun, 21 Jun 2020 21:43:05: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 21:43:05: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 21:43:05: #1 total tags in treatment: 13776981 INFO @ Sun, 21 Jun 2020 21:43:05: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 21:43:05: #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 21:43:05: #1 tags after filtering in treatment: 13776846 INFO @ Sun, 21 Jun 2020 21:43:05: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 21:43:05: #1 finished! INFO @ Sun, 21 Jun 2020 21:43:05: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 21:43:05: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 21:43:07: #2 number of paired peaks: 13963 INFO @ Sun, 21 Jun 2020 21:43:07: start model_add_line... INFO @ Sun, 21 Jun 2020 21:43:07: start X-correlation... INFO @ Sun, 21 Jun 2020 21:43:07: end of X-cor INFO @ Sun, 21 Jun 2020 21:43:07: #2 finished! INFO @ Sun, 21 Jun 2020 21:43:07: #2 predicted fragment length is 119 bps INFO @ Sun, 21 Jun 2020 21:43:07: #2 alternative fragment length(s) may be 119 bps INFO @ Sun, 21 Jun 2020 21:43:07: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX4923188/SRX4923188.20_model.r INFO @ Sun, 21 Jun 2020 21:43:07: #3 Call peaks... INFO @ Sun, 21 Jun 2020 21:43:07: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 21:43:12: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 21:43:27: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX4923188/SRX4923188.10_peaks.xls INFO @ Sun, 21 Jun 2020 21:43:28: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX4923188/SRX4923188.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 21:43:28: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX4923188/SRX4923188.10_summits.bed INFO @ Sun, 21 Jun 2020 21:43:28: Done! pass1 - making usageList (105 chroms): 2 millis pass2 - checking and writing primary data (9570 records, 4 fields): 13 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 21:43:41: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 21:43:56: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX4923188/SRX4923188.20_peaks.xls INFO @ Sun, 21 Jun 2020 21:43:56: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX4923188/SRX4923188.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 21:43:56: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX4923188/SRX4923188.20_summits.bed INFO @ Sun, 21 Jun 2020 21:43:56: Done! pass1 - making usageList (75 chroms): 1 millis pass2 - checking and writing primary data (7618 records, 4 fields): 11 millis CompletedMACS2peakCalling