Job ID = 6453826 SRX = SRX151957 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T08:34:09 prefetch.2.10.7: 1) Downloading 'SRR504791'... 2020-06-21T08:34:09 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T08:34:57 prefetch.2.10.7: HTTPS download succeed 2020-06-21T08:34:57 prefetch.2.10.7: 'SRR504791' is valid 2020-06-21T08:34:57 prefetch.2.10.7: 1) 'SRR504791' was downloaded successfully Read 7895363 spots for SRR504791/SRR504791.sra Written 7895363 spots for SRR504791/SRR504791.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: 00:01:34 7895363 reads; of these: 7895363 (100.00%) were unpaired; of these: 391150 (4.95%) aligned 0 times 5708167 (72.30%) aligned exactly 1 time 1796046 (22.75%) aligned >1 times 95.05% overall alignment rate Time searching: 00:01:34 Overall time: 00:01:34 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_rmdupse_core] 1115663 / 7504213 = 0.1487 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 17:38:50: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX151957/SRX151957.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX151957/SRX151957.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX151957/SRX151957.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX151957/SRX151957.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 17:38:50: #1 read tag files... INFO @ Sun, 21 Jun 2020 17:38:50: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 17:38:54: 1000000 INFO @ Sun, 21 Jun 2020 17:38:59: 2000000 INFO @ Sun, 21 Jun 2020 17:39:04: 3000000 INFO @ Sun, 21 Jun 2020 17:39:09: 4000000 INFO @ Sun, 21 Jun 2020 17:39:13: 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 17:39:18: 6000000 INFO @ Sun, 21 Jun 2020 17:39:20: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX151957/SRX151957.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX151957/SRX151957.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX151957/SRX151957.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX151957/SRX151957.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 17:39:20: #1 read tag files... INFO @ Sun, 21 Jun 2020 17:39:20: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 17:39:20: #1 tag size is determined as 30 bps INFO @ Sun, 21 Jun 2020 17:39:20: #1 tag size = 30 INFO @ Sun, 21 Jun 2020 17:39:20: #1 total tags in treatment: 6388550 INFO @ Sun, 21 Jun 2020 17:39:20: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 17:39:20: #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 17:39:21: #1 tags after filtering in treatment: 6388523 INFO @ Sun, 21 Jun 2020 17:39:21: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 17:39:21: #1 finished! INFO @ Sun, 21 Jun 2020 17:39:21: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 17:39:21: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 17:39:21: #2 number of paired peaks: 2131 INFO @ Sun, 21 Jun 2020 17:39:21: start model_add_line... INFO @ Sun, 21 Jun 2020 17:39:21: start X-correlation... INFO @ Sun, 21 Jun 2020 17:39:21: end of X-cor INFO @ Sun, 21 Jun 2020 17:39:21: #2 finished! INFO @ Sun, 21 Jun 2020 17:39:21: #2 predicted fragment length is 112 bps INFO @ Sun, 21 Jun 2020 17:39:21: #2 alternative fragment length(s) may be 112 bps INFO @ Sun, 21 Jun 2020 17:39:21: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX151957/SRX151957.05_model.r INFO @ Sun, 21 Jun 2020 17:39:21: #3 Call peaks... INFO @ Sun, 21 Jun 2020 17:39:21: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 17:39:24: 1000000 INFO @ Sun, 21 Jun 2020 17:39:29: 2000000 INFO @ Sun, 21 Jun 2020 17:39:34: 3000000 INFO @ Sun, 21 Jun 2020 17:39:36: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 17:39:38: 4000000 INFO @ Sun, 21 Jun 2020 17:39:43: 5000000 INFO @ Sun, 21 Jun 2020 17:39:43: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX151957/SRX151957.05_peaks.xls INFO @ Sun, 21 Jun 2020 17:39:43: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX151957/SRX151957.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 17:39:43: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX151957/SRX151957.05_summits.bed INFO @ Sun, 21 Jun 2020 17:39:43: Done! pass1 - making usageList (526 chroms): 2 millis pass2 - checking and writing primary data (8648 records, 4 fields): 24 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 17:39:48: 6000000 INFO @ Sun, 21 Jun 2020 17:39:50: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX151957/SRX151957.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX151957/SRX151957.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX151957/SRX151957.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX151957/SRX151957.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 17:39:50: #1 read tag files... INFO @ Sun, 21 Jun 2020 17:39:50: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 17:39:50: #1 tag size is determined as 30 bps INFO @ Sun, 21 Jun 2020 17:39:50: #1 tag size = 30 INFO @ Sun, 21 Jun 2020 17:39:50: #1 total tags in treatment: 6388550 INFO @ Sun, 21 Jun 2020 17:39:50: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 17:39:50: #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 17:39:50: #1 tags after filtering in treatment: 6388523 INFO @ Sun, 21 Jun 2020 17:39:50: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 17:39:50: #1 finished! INFO @ Sun, 21 Jun 2020 17:39:50: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 17:39:50: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 17:39:51: #2 number of paired peaks: 2131 INFO @ Sun, 21 Jun 2020 17:39:51: start model_add_line... INFO @ Sun, 21 Jun 2020 17:39:51: start X-correlation... INFO @ Sun, 21 Jun 2020 17:39:51: end of X-cor INFO @ Sun, 21 Jun 2020 17:39:51: #2 finished! INFO @ Sun, 21 Jun 2020 17:39:51: #2 predicted fragment length is 112 bps INFO @ Sun, 21 Jun 2020 17:39:51: #2 alternative fragment length(s) may be 112 bps INFO @ Sun, 21 Jun 2020 17:39:51: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX151957/SRX151957.10_model.r INFO @ Sun, 21 Jun 2020 17:39:51: #3 Call peaks... INFO @ Sun, 21 Jun 2020 17:39:51: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 17:39:54: 1000000 INFO @ Sun, 21 Jun 2020 17:39:59: 2000000 INFO @ Sun, 21 Jun 2020 17:40:04: 3000000 INFO @ Sun, 21 Jun 2020 17:40:06: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 17:40:09: 4000000 INFO @ Sun, 21 Jun 2020 17:40:13: 5000000 INFO @ Sun, 21 Jun 2020 17:40:13: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX151957/SRX151957.10_peaks.xls INFO @ Sun, 21 Jun 2020 17:40:13: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX151957/SRX151957.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 17:40:13: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX151957/SRX151957.10_summits.bed INFO @ Sun, 21 Jun 2020 17:40:13: Done! pass1 - making usageList (299 chroms): 1 millis pass2 - checking and writing primary data (4636 records, 4 fields): 13 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 17:40:18: 6000000 INFO @ Sun, 21 Jun 2020 17:40:20: #1 tag size is determined as 30 bps INFO @ Sun, 21 Jun 2020 17:40:20: #1 tag size = 30 INFO @ Sun, 21 Jun 2020 17:40:20: #1 total tags in treatment: 6388550 INFO @ Sun, 21 Jun 2020 17:40:20: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 17:40:20: #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 17:40:21: #1 tags after filtering in treatment: 6388523 INFO @ Sun, 21 Jun 2020 17:40:21: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 17:40:21: #1 finished! INFO @ Sun, 21 Jun 2020 17:40:21: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 17:40:21: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 17:40:21: #2 number of paired peaks: 2131 INFO @ Sun, 21 Jun 2020 17:40:21: start model_add_line... INFO @ Sun, 21 Jun 2020 17:40:21: start X-correlation... INFO @ Sun, 21 Jun 2020 17:40:21: end of X-cor INFO @ Sun, 21 Jun 2020 17:40:21: #2 finished! INFO @ Sun, 21 Jun 2020 17:40:21: #2 predicted fragment length is 112 bps INFO @ Sun, 21 Jun 2020 17:40:21: #2 alternative fragment length(s) may be 112 bps INFO @ Sun, 21 Jun 2020 17:40:21: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX151957/SRX151957.20_model.r INFO @ Sun, 21 Jun 2020 17:40:21: #3 Call peaks... INFO @ Sun, 21 Jun 2020 17:40:21: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 17:40:36: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 17:40:44: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX151957/SRX151957.20_peaks.xls INFO @ Sun, 21 Jun 2020 17:40:44: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX151957/SRX151957.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 17:40:44: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX151957/SRX151957.20_summits.bed INFO @ Sun, 21 Jun 2020 17:40:44: Done! pass1 - making usageList (149 chroms): 1 millis pass2 - checking and writing primary data (1724 records, 4 fields): 7 millis CompletedMACS2peakCalling