Job ID = 6452487 SRX = SRX013095 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T07:28:34 prefetch.2.10.7: 1) Downloading 'SRR030361'... 2020-06-21T07:28:34 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T07:30:08 prefetch.2.10.7: HTTPS download succeed 2020-06-21T07:30:08 prefetch.2.10.7: 'SRR030361' is valid 2020-06-21T07:30:08 prefetch.2.10.7: 1) 'SRR030361' was downloaded successfully Read 4509098 spots for SRR030361/SRR030361.sra Written 4509098 spots for SRR030361/SRR030361.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: 00:00:50 4509098 reads; of these: 4509098 (100.00%) were unpaired; of these: 1203072 (26.68%) aligned 0 times 1991523 (44.17%) aligned exactly 1 time 1314503 (29.15%) aligned >1 times 73.32% overall alignment rate Time searching: 00:00:50 Overall time: 00:00:50 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_rmdupse_core] 275374 / 3306026 = 0.0833 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 16:32:26: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX013095/SRX013095.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX013095/SRX013095.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX013095/SRX013095.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX013095/SRX013095.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 16:32:26: #1 read tag files... INFO @ Sun, 21 Jun 2020 16:32:26: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 16:32:32: 1000000 INFO @ Sun, 21 Jun 2020 16:32:37: 2000000 INFO @ Sun, 21 Jun 2020 16:32:43: 3000000 INFO @ Sun, 21 Jun 2020 16:32:43: #1 tag size is determined as 36 bps INFO @ Sun, 21 Jun 2020 16:32:43: #1 tag size = 36 INFO @ Sun, 21 Jun 2020 16:32:43: #1 total tags in treatment: 3030652 INFO @ Sun, 21 Jun 2020 16:32:43: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 16:32:43: #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 16:32:43: #1 tags after filtering in treatment: 3030617 INFO @ Sun, 21 Jun 2020 16:32:43: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 16:32:43: #1 finished! INFO @ Sun, 21 Jun 2020 16:32:43: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 16:32:43: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 16:32:43: #2 number of paired peaks: 1130 INFO @ Sun, 21 Jun 2020 16:32:43: start model_add_line... INFO @ Sun, 21 Jun 2020 16:32:43: start X-correlation... INFO @ Sun, 21 Jun 2020 16:32:43: end of X-cor INFO @ Sun, 21 Jun 2020 16:32:43: #2 finished! INFO @ Sun, 21 Jun 2020 16:32:43: #2 predicted fragment length is 113 bps INFO @ Sun, 21 Jun 2020 16:32:43: #2 alternative fragment length(s) may be 113,592 bps INFO @ Sun, 21 Jun 2020 16:32:43: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX013095/SRX013095.05_model.r INFO @ Sun, 21 Jun 2020 16:32:43: #3 Call peaks... INFO @ Sun, 21 Jun 2020 16:32:43: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 16:32:51: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 16:32:54: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX013095/SRX013095.05_peaks.xls INFO @ Sun, 21 Jun 2020 16:32:54: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX013095/SRX013095.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 16:32:54: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX013095/SRX013095.05_summits.bed INFO @ Sun, 21 Jun 2020 16:32:54: Done! 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 pass1 - making usageList (605 chroms): 1 millis pass2 - checking and writing primary data (1491 records, 4 fields): 18 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 16:32:56: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX013095/SRX013095.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX013095/SRX013095.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX013095/SRX013095.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX013095/SRX013095.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 16:32:56: #1 read tag files... INFO @ Sun, 21 Jun 2020 16:32:56: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 16:33:01: 1000000 INFO @ Sun, 21 Jun 2020 16:33:06: 2000000 INFO @ Sun, 21 Jun 2020 16:33:12: 3000000 INFO @ Sun, 21 Jun 2020 16:33:12: #1 tag size is determined as 36 bps INFO @ Sun, 21 Jun 2020 16:33:12: #1 tag size = 36 INFO @ Sun, 21 Jun 2020 16:33:12: #1 total tags in treatment: 3030652 INFO @ Sun, 21 Jun 2020 16:33:12: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 16:33:12: #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 16:33:13: #1 tags after filtering in treatment: 3030617 INFO @ Sun, 21 Jun 2020 16:33:13: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 16:33:13: #1 finished! INFO @ Sun, 21 Jun 2020 16:33:13: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 16:33:13: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 16:33:13: #2 number of paired peaks: 1130 INFO @ Sun, 21 Jun 2020 16:33:13: start model_add_line... INFO @ Sun, 21 Jun 2020 16:33:13: start X-correlation... INFO @ Sun, 21 Jun 2020 16:33:13: end of X-cor INFO @ Sun, 21 Jun 2020 16:33:13: #2 finished! INFO @ Sun, 21 Jun 2020 16:33:13: #2 predicted fragment length is 113 bps INFO @ Sun, 21 Jun 2020 16:33:13: #2 alternative fragment length(s) may be 113,592 bps INFO @ Sun, 21 Jun 2020 16:33:13: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX013095/SRX013095.10_model.r INFO @ Sun, 21 Jun 2020 16:33:13: #3 Call peaks... INFO @ Sun, 21 Jun 2020 16:33:13: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 16:33:20: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 16:33:24: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX013095/SRX013095.10_peaks.xls INFO @ Sun, 21 Jun 2020 16:33:24: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX013095/SRX013095.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 16:33:24: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX013095/SRX013095.10_summits.bed INFO @ Sun, 21 Jun 2020 16:33:24: Done! pass1 - making usageList (319 chroms): 1 millis pass2 - checking and writing primary data (590 records, 4 fields): 9 millis CompletedMACS2peakCalling 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 16:33:26: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX013095/SRX013095.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX013095/SRX013095.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX013095/SRX013095.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX013095/SRX013095.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 16:33:26: #1 read tag files... INFO @ Sun, 21 Jun 2020 16:33:26: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 16:33:31: 1000000 INFO @ Sun, 21 Jun 2020 16:33:37: 2000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 16:33:42: 3000000 INFO @ Sun, 21 Jun 2020 16:33:43: #1 tag size is determined as 36 bps INFO @ Sun, 21 Jun 2020 16:33:43: #1 tag size = 36 INFO @ Sun, 21 Jun 2020 16:33:43: #1 total tags in treatment: 3030652 INFO @ Sun, 21 Jun 2020 16:33:43: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 16:33:43: #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 16:33:43: #1 tags after filtering in treatment: 3030617 INFO @ Sun, 21 Jun 2020 16:33:43: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 16:33:43: #1 finished! INFO @ Sun, 21 Jun 2020 16:33:43: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 16:33:43: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 16:33:43: #2 number of paired peaks: 1130 INFO @ Sun, 21 Jun 2020 16:33:43: start model_add_line... INFO @ Sun, 21 Jun 2020 16:33:43: start X-correlation... INFO @ Sun, 21 Jun 2020 16:33:43: end of X-cor INFO @ Sun, 21 Jun 2020 16:33:43: #2 finished! INFO @ Sun, 21 Jun 2020 16:33:43: #2 predicted fragment length is 113 bps INFO @ Sun, 21 Jun 2020 16:33:43: #2 alternative fragment length(s) may be 113,592 bps INFO @ Sun, 21 Jun 2020 16:33:43: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX013095/SRX013095.20_model.r INFO @ Sun, 21 Jun 2020 16:33:43: #3 Call peaks... INFO @ Sun, 21 Jun 2020 16:33:43: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 16:33:51: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 16:33:54: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX013095/SRX013095.20_peaks.xls INFO @ Sun, 21 Jun 2020 16:33:54: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX013095/SRX013095.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 16:33:54: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX013095/SRX013095.20_summits.bed INFO @ Sun, 21 Jun 2020 16:33:54: Done! pass1 - making usageList (161 chroms): 1 millis pass2 - checking and writing primary data (258 records, 4 fields): 6 millis CompletedMACS2peakCalling