Job ID = 6452691 SRX = SRX025491 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T07:42:36 prefetch.2.10.7: 1) Downloading 'SRR063894'... 2020-06-21T07:42:36 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T07:44:48 prefetch.2.10.7: HTTPS download succeed 2020-06-21T07:44:49 prefetch.2.10.7: 'SRR063894' is valid 2020-06-21T07:44:49 prefetch.2.10.7: 1) 'SRR063894' was downloaded successfully Read 11783956 spots for SRR063894/SRR063894.sra Written 11783956 spots for SRR063894/SRR063894.sra 2020-06-21T07:45:29 prefetch.2.10.7: 1) Downloading 'SRR063895'... 2020-06-21T07:45:29 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T07:46:47 prefetch.2.10.7: HTTPS download succeed 2020-06-21T07:46:48 prefetch.2.10.7: 'SRR063895' is valid 2020-06-21T07:46:48 prefetch.2.10.7: 1) 'SRR063895' was downloaded successfully Read 20760114 spots for SRR063895/SRR063895.sra Written 20760114 spots for SRR063895/SRR063895.sra fastq に変換しました。 bowtie でマッピング中... Time loading reference: 00:00:01 Time loading forward index: 00:00:00 Time loading mirror index: 00:00:00 Multiseed full-index search: 00:16:33 32544070 reads; of these: 32544070 (100.00%) were unpaired; of these: 1734774 (5.33%) aligned 0 times 7342576 (22.56%) aligned exactly 1 time 23466720 (72.11%) aligned >1 times 94.67% overall alignment rate Time searching: 00:16:34 Overall time: 00:16:34 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] 24543809 / 30809296 = 0.7966 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 17:08:09: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX025491/SRX025491.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX025491/SRX025491.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX025491/SRX025491.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX025491/SRX025491.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 17:08:09: #1 read tag files... INFO @ Sun, 21 Jun 2020 17:08:09: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 17:08:14: 1000000 INFO @ Sun, 21 Jun 2020 17:08:19: 2000000 INFO @ Sun, 21 Jun 2020 17:08:24: 3000000 INFO @ Sun, 21 Jun 2020 17:08:29: 4000000 INFO @ Sun, 21 Jun 2020 17:08:33: 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 17:08:38: 6000000 INFO @ Sun, 21 Jun 2020 17:08:39: #1 tag size is determined as 36 bps INFO @ Sun, 21 Jun 2020 17:08:39: #1 tag size = 36 INFO @ Sun, 21 Jun 2020 17:08:39: #1 total tags in treatment: 6265487 INFO @ Sun, 21 Jun 2020 17:08:39: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 17:08:39: #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 17:08:39: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX025491/SRX025491.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX025491/SRX025491.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX025491/SRX025491.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX025491/SRX025491.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 17:08:39: #1 read tag files... INFO @ Sun, 21 Jun 2020 17:08:39: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 17:08:39: #1 tags after filtering in treatment: 6265472 INFO @ Sun, 21 Jun 2020 17:08:40: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 17:08:40: #1 finished! INFO @ Sun, 21 Jun 2020 17:08:40: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 17:08:40: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 17:08:40: #2 number of paired peaks: 8002 INFO @ Sun, 21 Jun 2020 17:08:40: start model_add_line... INFO @ Sun, 21 Jun 2020 17:08:41: start X-correlation... INFO @ Sun, 21 Jun 2020 17:08:41: end of X-cor INFO @ Sun, 21 Jun 2020 17:08:41: #2 finished! INFO @ Sun, 21 Jun 2020 17:08:41: #2 predicted fragment length is 122 bps INFO @ Sun, 21 Jun 2020 17:08:41: #2 alternative fragment length(s) may be 3,122,142 bps INFO @ Sun, 21 Jun 2020 17:08:41: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX025491/SRX025491.05_model.r INFO @ Sun, 21 Jun 2020 17:08:41: #3 Call peaks... INFO @ Sun, 21 Jun 2020 17:08:41: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 17:08:44: 1000000 INFO @ Sun, 21 Jun 2020 17:08:49: 2000000 INFO @ Sun, 21 Jun 2020 17:08:53: 3000000 INFO @ Sun, 21 Jun 2020 17:08:55: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 17:08:58: 4000000 INFO @ Sun, 21 Jun 2020 17:09:02: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX025491/SRX025491.05_peaks.xls INFO @ Sun, 21 Jun 2020 17:09:02: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX025491/SRX025491.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 17:09:02: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX025491/SRX025491.05_summits.bed INFO @ Sun, 21 Jun 2020 17:09:02: Done! pass1 - making usageList (1121 chroms): 1 millis pass2 - checking and writing primary data (5235 records, 4 fields): 32 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 17:09:03: 5000000 INFO @ Sun, 21 Jun 2020 17:09:07: 6000000 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 17:09:09: #1 tag size is determined as 36 bps INFO @ Sun, 21 Jun 2020 17:09:09: #1 tag size = 36 INFO @ Sun, 21 Jun 2020 17:09:09: #1 total tags in treatment: 6265487 INFO @ Sun, 21 Jun 2020 17:09:09: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 17:09:09: #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 17:09:09: #1 tags after filtering in treatment: 6265472 INFO @ Sun, 21 Jun 2020 17:09:09: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 17:09:09: #1 finished! INFO @ Sun, 21 Jun 2020 17:09:09: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 17:09:09: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 17:09:09: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX025491/SRX025491.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX025491/SRX025491.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX025491/SRX025491.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX025491/SRX025491.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 17:09:09: #1 read tag files... INFO @ Sun, 21 Jun 2020 17:09:09: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 17:09:10: #2 number of paired peaks: 8002 INFO @ Sun, 21 Jun 2020 17:09:10: start model_add_line... INFO @ Sun, 21 Jun 2020 17:09:10: start X-correlation... INFO @ Sun, 21 Jun 2020 17:09:10: end of X-cor INFO @ Sun, 21 Jun 2020 17:09:10: #2 finished! INFO @ Sun, 21 Jun 2020 17:09:10: #2 predicted fragment length is 122 bps INFO @ Sun, 21 Jun 2020 17:09:10: #2 alternative fragment length(s) may be 3,122,142 bps INFO @ Sun, 21 Jun 2020 17:09:10: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX025491/SRX025491.10_model.r INFO @ Sun, 21 Jun 2020 17:09:10: #3 Call peaks... INFO @ Sun, 21 Jun 2020 17:09:10: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 17:09:14: 1000000 INFO @ Sun, 21 Jun 2020 17:09:19: 2000000 INFO @ Sun, 21 Jun 2020 17:09:23: 3000000 INFO @ Sun, 21 Jun 2020 17:09:25: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 17:09:28: 4000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 17:09:31: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX025491/SRX025491.10_peaks.xls INFO @ Sun, 21 Jun 2020 17:09:31: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX025491/SRX025491.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 17:09:32: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX025491/SRX025491.10_summits.bed INFO @ Sun, 21 Jun 2020 17:09:32: Done! pass1 - making usageList (992 chroms): 1 millis pass2 - checking and writing primary data (3061 records, 4 fields): 27 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 17:09:33: 5000000 INFO @ Sun, 21 Jun 2020 17:09:38: 6000000 INFO @ Sun, 21 Jun 2020 17:09:39: #1 tag size is determined as 36 bps INFO @ Sun, 21 Jun 2020 17:09:39: #1 tag size = 36 INFO @ Sun, 21 Jun 2020 17:09:39: #1 total tags in treatment: 6265487 INFO @ Sun, 21 Jun 2020 17:09:39: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 17:09:39: #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 17:09:39: #1 tags after filtering in treatment: 6265472 INFO @ Sun, 21 Jun 2020 17:09:39: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 17:09:39: #1 finished! INFO @ Sun, 21 Jun 2020 17:09:39: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 17:09:39: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 17:09:40: #2 number of paired peaks: 8002 INFO @ Sun, 21 Jun 2020 17:09:40: start model_add_line... INFO @ Sun, 21 Jun 2020 17:09:40: start X-correlation... INFO @ Sun, 21 Jun 2020 17:09:40: end of X-cor INFO @ Sun, 21 Jun 2020 17:09:40: #2 finished! INFO @ Sun, 21 Jun 2020 17:09:40: #2 predicted fragment length is 122 bps INFO @ Sun, 21 Jun 2020 17:09:40: #2 alternative fragment length(s) may be 3,122,142 bps INFO @ Sun, 21 Jun 2020 17:09:40: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX025491/SRX025491.20_model.r INFO @ Sun, 21 Jun 2020 17:09:40: #3 Call peaks... INFO @ Sun, 21 Jun 2020 17:09:40: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 17:09:55: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 17:10:01: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX025491/SRX025491.20_peaks.xls INFO @ Sun, 21 Jun 2020 17:10:01: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX025491/SRX025491.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 17:10:01: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX025491/SRX025491.20_summits.bed INFO @ Sun, 21 Jun 2020 17:10:01: Done! pass1 - making usageList (787 chroms): 1 millis pass2 - checking and writing primary data (1651 records, 4 fields): 21 millis CompletedMACS2peakCalling