Job ID = 6459551 SRX = SRX699545 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T13:28:13 prefetch.2.10.7: 1) Downloading 'SRR1573544'... 2020-06-21T13:28:13 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T13:30:10 prefetch.2.10.7: HTTPS download succeed 2020-06-21T13:30:10 prefetch.2.10.7: 'SRR1573544' is valid 2020-06-21T13:30:10 prefetch.2.10.7: 1) 'SRR1573544' was downloaded successfully Read 11003368 spots for SRR1573544/SRR1573544.sra Written 11003368 spots for SRR1573544/SRR1573544.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: 00:01:21 11003368 reads; of these: 11003368 (100.00%) were unpaired; of these: 4976720 (45.23%) aligned 0 times 5322472 (48.37%) aligned exactly 1 time 704176 (6.40%) aligned >1 times 54.77% overall alignment rate Time searching: 00:01:21 Overall time: 00:01:21 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_rmdupse_core] 1027146 / 6026648 = 0.1704 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 22:33:48: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX699545/SRX699545.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX699545/SRX699545.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX699545/SRX699545.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX699545/SRX699545.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 22:33:48: #1 read tag files... INFO @ Sun, 21 Jun 2020 22:33:48: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 22:33:54: 1000000 INFO @ Sun, 21 Jun 2020 22:34:00: 2000000 INFO @ Sun, 21 Jun 2020 22:34:05: 3000000 INFO @ Sun, 21 Jun 2020 22:34:11: 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 22:34:17: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX699545/SRX699545.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX699545/SRX699545.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX699545/SRX699545.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX699545/SRX699545.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 22:34:17: #1 read tag files... INFO @ Sun, 21 Jun 2020 22:34:17: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 22:34:18: #1 tag size is determined as 36 bps INFO @ Sun, 21 Jun 2020 22:34:18: #1 tag size = 36 INFO @ Sun, 21 Jun 2020 22:34:18: #1 total tags in treatment: 4999502 INFO @ Sun, 21 Jun 2020 22:34:18: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 22:34:18: #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 22:34:18: #1 tags after filtering in treatment: 4999406 INFO @ Sun, 21 Jun 2020 22:34:18: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 22:34:18: #1 finished! INFO @ Sun, 21 Jun 2020 22:34:18: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 22:34:18: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 22:34:19: #2 number of paired peaks: 3742 INFO @ Sun, 21 Jun 2020 22:34:19: start model_add_line... INFO @ Sun, 21 Jun 2020 22:34:19: start X-correlation... INFO @ Sun, 21 Jun 2020 22:34:19: end of X-cor INFO @ Sun, 21 Jun 2020 22:34:19: #2 finished! INFO @ Sun, 21 Jun 2020 22:34:19: #2 predicted fragment length is 99 bps INFO @ Sun, 21 Jun 2020 22:34:19: #2 alternative fragment length(s) may be 99 bps INFO @ Sun, 21 Jun 2020 22:34:19: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX699545/SRX699545.05_model.r INFO @ Sun, 21 Jun 2020 22:34:19: #3 Call peaks... INFO @ Sun, 21 Jun 2020 22:34:19: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 22:34:24: 1000000 INFO @ Sun, 21 Jun 2020 22:34:30: 2000000 INFO @ Sun, 21 Jun 2020 22:34:31: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 22:34:36: 3000000 INFO @ Sun, 21 Jun 2020 22:34:37: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX699545/SRX699545.05_peaks.xls INFO @ Sun, 21 Jun 2020 22:34:37: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX699545/SRX699545.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 22:34:37: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX699545/SRX699545.05_summits.bed INFO @ Sun, 21 Jun 2020 22:34:37: Done! pass1 - making usageList (129 chroms): 2 millis pass2 - checking and writing primary data (8770 records, 4 fields): 13 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 22:34:41: 4000000 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 22:34:47: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX699545/SRX699545.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX699545/SRX699545.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX699545/SRX699545.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX699545/SRX699545.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 22:34:47: #1 read tag files... INFO @ Sun, 21 Jun 2020 22:34:47: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 22:34:48: #1 tag size is determined as 36 bps INFO @ Sun, 21 Jun 2020 22:34:48: #1 tag size = 36 INFO @ Sun, 21 Jun 2020 22:34:48: #1 total tags in treatment: 4999502 INFO @ Sun, 21 Jun 2020 22:34:48: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 22:34:48: #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 22:34:48: #1 tags after filtering in treatment: 4999406 INFO @ Sun, 21 Jun 2020 22:34:48: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 22:34:48: #1 finished! INFO @ Sun, 21 Jun 2020 22:34:48: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 22:34:48: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 22:34:49: #2 number of paired peaks: 3742 INFO @ Sun, 21 Jun 2020 22:34:49: start model_add_line... INFO @ Sun, 21 Jun 2020 22:34:49: start X-correlation... INFO @ Sun, 21 Jun 2020 22:34:49: end of X-cor INFO @ Sun, 21 Jun 2020 22:34:49: #2 finished! INFO @ Sun, 21 Jun 2020 22:34:49: #2 predicted fragment length is 99 bps INFO @ Sun, 21 Jun 2020 22:34:49: #2 alternative fragment length(s) may be 99 bps INFO @ Sun, 21 Jun 2020 22:34:49: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX699545/SRX699545.10_model.r INFO @ Sun, 21 Jun 2020 22:34:49: #3 Call peaks... INFO @ Sun, 21 Jun 2020 22:34:49: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 22:34:53: 1000000 INFO @ Sun, 21 Jun 2020 22:34:59: 2000000 INFO @ Sun, 21 Jun 2020 22:35:00: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 22:35:05: 3000000 INFO @ Sun, 21 Jun 2020 22:35:06: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX699545/SRX699545.10_peaks.xls INFO @ Sun, 21 Jun 2020 22:35:06: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX699545/SRX699545.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 22:35:06: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX699545/SRX699545.10_summits.bed INFO @ Sun, 21 Jun 2020 22:35:06: Done! pass1 - making usageList (115 chroms): 2 millis pass2 - checking and writing primary data (6121 records, 4 fields): 13 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 22:35:11: 4000000 INFO @ Sun, 21 Jun 2020 22:35:17: #1 tag size is determined as 36 bps INFO @ Sun, 21 Jun 2020 22:35:17: #1 tag size = 36 INFO @ Sun, 21 Jun 2020 22:35:17: #1 total tags in treatment: 4999502 INFO @ Sun, 21 Jun 2020 22:35:17: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 22:35:17: #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 22:35:17: #1 tags after filtering in treatment: 4999406 INFO @ Sun, 21 Jun 2020 22:35:17: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 22:35:17: #1 finished! INFO @ Sun, 21 Jun 2020 22:35:17: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 22:35:17: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 22:35:18: #2 number of paired peaks: 3742 INFO @ Sun, 21 Jun 2020 22:35:18: start model_add_line... INFO @ Sun, 21 Jun 2020 22:35:18: start X-correlation... INFO @ Sun, 21 Jun 2020 22:35:18: end of X-cor INFO @ Sun, 21 Jun 2020 22:35:18: #2 finished! INFO @ Sun, 21 Jun 2020 22:35:18: #2 predicted fragment length is 99 bps INFO @ Sun, 21 Jun 2020 22:35:18: #2 alternative fragment length(s) may be 99 bps INFO @ Sun, 21 Jun 2020 22:35:18: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX699545/SRX699545.20_model.r INFO @ Sun, 21 Jun 2020 22:35:18: #3 Call peaks... INFO @ Sun, 21 Jun 2020 22:35:18: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 22:35:30: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 22:35:35: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX699545/SRX699545.20_peaks.xls INFO @ Sun, 21 Jun 2020 22:35:35: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX699545/SRX699545.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 22:35:35: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX699545/SRX699545.20_summits.bed INFO @ Sun, 21 Jun 2020 22:35:35: Done! pass1 - making usageList (95 chroms): 1 millis pass2 - checking and writing primary data (3797 records, 4 fields): 7 millis CompletedMACS2peakCalling