Job ID = 6453018 SRX = SRX099636 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T07:53:30 prefetch.2.10.7: 1) Downloading 'SRR350626'... 2020-06-21T07:53:30 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T07:55:29 prefetch.2.10.7: HTTPS download succeed 2020-06-21T07:55:29 prefetch.2.10.7: 'SRR350626' is valid 2020-06-21T07:55:29 prefetch.2.10.7: 1) 'SRR350626' was downloaded successfully Read 7419561 spots for SRR350626/SRR350626.sra Written 7419561 spots for SRR350626/SRR350626.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: 00:01:08 7419561 reads; of these: 7419561 (100.00%) were unpaired; of these: 4083660 (55.04%) aligned 0 times 1962195 (26.45%) aligned exactly 1 time 1373706 (18.51%) aligned >1 times 44.96% overall alignment rate Time searching: 00:01:08 Overall time: 00:01:08 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] 1344257 / 3335901 = 0.4030 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 16:58:06: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX099636/SRX099636.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX099636/SRX099636.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX099636/SRX099636.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX099636/SRX099636.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 16:58:06: #1 read tag files... INFO @ Sun, 21 Jun 2020 16:58:06: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 16:58:11: 1000000 INFO @ Sun, 21 Jun 2020 16:58:16: #1 tag size is determined as 39 bps INFO @ Sun, 21 Jun 2020 16:58:16: #1 tag size = 39 INFO @ Sun, 21 Jun 2020 16:58:16: #1 total tags in treatment: 1991644 INFO @ Sun, 21 Jun 2020 16:58:16: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 16:58:16: #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 16:58:16: #1 tags after filtering in treatment: 1991417 INFO @ Sun, 21 Jun 2020 16:58:16: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 16:58:16: #1 finished! INFO @ Sun, 21 Jun 2020 16:58:16: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 16:58:16: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 16:58:17: #2 number of paired peaks: 3004 INFO @ Sun, 21 Jun 2020 16:58:17: start model_add_line... INFO @ Sun, 21 Jun 2020 16:58:17: start X-correlation... INFO @ Sun, 21 Jun 2020 16:58:17: end of X-cor INFO @ Sun, 21 Jun 2020 16:58:17: #2 finished! INFO @ Sun, 21 Jun 2020 16:58:17: #2 predicted fragment length is 114 bps INFO @ Sun, 21 Jun 2020 16:58:17: #2 alternative fragment length(s) may be 114,587 bps INFO @ Sun, 21 Jun 2020 16:58:17: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX099636/SRX099636.05_model.r INFO @ Sun, 21 Jun 2020 16:58:17: #3 Call peaks... INFO @ Sun, 21 Jun 2020 16:58:17: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 16:58:21: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 16:58:24: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX099636/SRX099636.05_peaks.xls INFO @ Sun, 21 Jun 2020 16:58:24: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX099636/SRX099636.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 16:58:24: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX099636/SRX099636.05_summits.bed INFO @ Sun, 21 Jun 2020 16:58:24: Done! pass1 - making usageList (508 chroms): 1 millis pass2 - checking and writing primary data (2181 records, 4 fields): 15 millis CompletedMACS2peakCalling 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 16:58:36: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX099636/SRX099636.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX099636/SRX099636.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX099636/SRX099636.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX099636/SRX099636.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 16:58:36: #1 read tag files... INFO @ Sun, 21 Jun 2020 16:58:36: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 16:58:42: 1000000 INFO @ Sun, 21 Jun 2020 16:58:48: #1 tag size is determined as 39 bps INFO @ Sun, 21 Jun 2020 16:58:48: #1 tag size = 39 INFO @ Sun, 21 Jun 2020 16:58:48: #1 total tags in treatment: 1991644 INFO @ Sun, 21 Jun 2020 16:58:48: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 16:58:48: #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 16:58:48: #1 tags after filtering in treatment: 1991417 INFO @ Sun, 21 Jun 2020 16:58:48: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 16:58:48: #1 finished! INFO @ Sun, 21 Jun 2020 16:58:48: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 16:58:48: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 16:58:48: #2 number of paired peaks: 3004 INFO @ Sun, 21 Jun 2020 16:58:48: start model_add_line... INFO @ Sun, 21 Jun 2020 16:58:48: start X-correlation... INFO @ Sun, 21 Jun 2020 16:58:48: end of X-cor INFO @ Sun, 21 Jun 2020 16:58:48: #2 finished! INFO @ Sun, 21 Jun 2020 16:58:48: #2 predicted fragment length is 114 bps INFO @ Sun, 21 Jun 2020 16:58:48: #2 alternative fragment length(s) may be 114,587 bps INFO @ Sun, 21 Jun 2020 16:58:48: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX099636/SRX099636.10_model.r INFO @ Sun, 21 Jun 2020 16:58:48: #3 Call peaks... INFO @ Sun, 21 Jun 2020 16:58:48: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 16:58:53: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 16:58:55: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX099636/SRX099636.10_peaks.xls INFO @ Sun, 21 Jun 2020 16:58:55: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX099636/SRX099636.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 16:58:55: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX099636/SRX099636.10_summits.bed INFO @ Sun, 21 Jun 2020 16:58:55: Done! pass1 - making usageList (350 chroms): 1 millis pass2 - checking and writing primary data (1000 records, 4 fields): 11 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 16:59:06: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX099636/SRX099636.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX099636/SRX099636.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX099636/SRX099636.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX099636/SRX099636.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 16:59:06: #1 read tag files... INFO @ Sun, 21 Jun 2020 16:59:06: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 16:59:12: 1000000 BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 16:59:18: #1 tag size is determined as 39 bps INFO @ Sun, 21 Jun 2020 16:59:18: #1 tag size = 39 INFO @ Sun, 21 Jun 2020 16:59:18: #1 total tags in treatment: 1991644 INFO @ Sun, 21 Jun 2020 16:59:18: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 16:59:18: #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 16:59:18: #1 tags after filtering in treatment: 1991417 INFO @ Sun, 21 Jun 2020 16:59:18: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 16:59:18: #1 finished! INFO @ Sun, 21 Jun 2020 16:59:18: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 16:59:18: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 16:59:18: #2 number of paired peaks: 3004 INFO @ Sun, 21 Jun 2020 16:59:18: start model_add_line... INFO @ Sun, 21 Jun 2020 16:59:18: start X-correlation... INFO @ Sun, 21 Jun 2020 16:59:18: end of X-cor INFO @ Sun, 21 Jun 2020 16:59:18: #2 finished! INFO @ Sun, 21 Jun 2020 16:59:18: #2 predicted fragment length is 114 bps INFO @ Sun, 21 Jun 2020 16:59:18: #2 alternative fragment length(s) may be 114,587 bps INFO @ Sun, 21 Jun 2020 16:59:18: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX099636/SRX099636.20_model.r INFO @ Sun, 21 Jun 2020 16:59:18: #3 Call peaks... INFO @ Sun, 21 Jun 2020 16:59:18: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 16:59:23: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 16:59:25: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX099636/SRX099636.20_peaks.xls INFO @ Sun, 21 Jun 2020 16:59:25: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX099636/SRX099636.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 16:59:25: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX099636/SRX099636.20_summits.bed INFO @ Sun, 21 Jun 2020 16:59:25: Done! pass1 - making usageList (131 chroms): 1 millis pass2 - checking and writing primary data (323 records, 4 fields): 6 millis CompletedMACS2peakCalling