Job ID = 6454247 SRX = SRX193323 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T09:17:24 prefetch.2.10.7: 1) Downloading 'SRR585056'... 2020-06-21T09:17:24 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T09:19:39 prefetch.2.10.7: HTTPS download succeed 2020-06-21T09:19:40 prefetch.2.10.7: 'SRR585056' is valid 2020-06-21T09:19:40 prefetch.2.10.7: 1) 'SRR585056' was downloaded successfully Read 11319828 spots for SRR585056/SRR585056.sra Written 11319828 spots for SRR585056/SRR585056.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: 00:02:10 11319828 reads; of these: 11319828 (100.00%) were unpaired; of these: 4920442 (43.47%) aligned 0 times 5415091 (47.84%) aligned exactly 1 time 984295 (8.70%) aligned >1 times 56.53% overall alignment rate Time searching: 00:02:10 Overall time: 00:02:10 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] 2014285 / 6399386 = 0.3148 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 18:24:21: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX193323/SRX193323.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX193323/SRX193323.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX193323/SRX193323.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX193323/SRX193323.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 18:24:21: #1 read tag files... INFO @ Sun, 21 Jun 2020 18:24:21: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 18:24:27: 1000000 INFO @ Sun, 21 Jun 2020 18:24:32: 2000000 INFO @ Sun, 21 Jun 2020 18:24:37: 3000000 INFO @ Sun, 21 Jun 2020 18:24:43: 4000000 INFO @ Sun, 21 Jun 2020 18:24:45: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 18:24:45: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 18:24:45: #1 total tags in treatment: 4385101 INFO @ Sun, 21 Jun 2020 18:24:45: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 18:24:45: #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 18:24:45: #1 tags after filtering in treatment: 4384751 INFO @ Sun, 21 Jun 2020 18:24:45: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 18:24:45: #1 finished! INFO @ Sun, 21 Jun 2020 18:24:45: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 18:24:45: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 18:24:46: #2 number of paired peaks: 11890 INFO @ Sun, 21 Jun 2020 18:24:46: start model_add_line... INFO @ Sun, 21 Jun 2020 18:24:46: start X-correlation... INFO @ Sun, 21 Jun 2020 18:24:46: end of X-cor INFO @ Sun, 21 Jun 2020 18:24:46: #2 finished! INFO @ Sun, 21 Jun 2020 18:24:46: #2 predicted fragment length is 246 bps INFO @ Sun, 21 Jun 2020 18:24:46: #2 alternative fragment length(s) may be 246 bps INFO @ Sun, 21 Jun 2020 18:24:46: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX193323/SRX193323.05_model.r INFO @ Sun, 21 Jun 2020 18:24:46: #3 Call peaks... INFO @ Sun, 21 Jun 2020 18:24:46: #3 Pre-compute pvalue-qvalue table... 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 18:24:51: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX193323/SRX193323.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX193323/SRX193323.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX193323/SRX193323.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX193323/SRX193323.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 18:24:51: #1 read tag files... INFO @ Sun, 21 Jun 2020 18:24:51: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 18:24:57: 1000000 INFO @ Sun, 21 Jun 2020 18:25:00: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 18:25:02: 2000000 INFO @ Sun, 21 Jun 2020 18:25:07: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX193323/SRX193323.05_peaks.xls INFO @ Sun, 21 Jun 2020 18:25:07: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX193323/SRX193323.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 18:25:07: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX193323/SRX193323.05_summits.bed INFO @ Sun, 21 Jun 2020 18:25:07: Done! INFO @ Sun, 21 Jun 2020 18:25:07: 3000000 pass1 - making usageList (176 chroms): 1 millis pass2 - checking and writing primary data (7814 records, 4 fields): 14 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 18:25:13: 4000000 INFO @ Sun, 21 Jun 2020 18:25:15: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 18:25:15: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 18:25:15: #1 total tags in treatment: 4385101 INFO @ Sun, 21 Jun 2020 18:25:15: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 18:25:15: #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 18:25:15: #1 tags after filtering in treatment: 4384751 INFO @ Sun, 21 Jun 2020 18:25:15: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 18:25:15: #1 finished! INFO @ Sun, 21 Jun 2020 18:25:15: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 18:25:15: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 18:25:16: #2 number of paired peaks: 11890 INFO @ Sun, 21 Jun 2020 18:25:16: start model_add_line... INFO @ Sun, 21 Jun 2020 18:25:16: start X-correlation... INFO @ Sun, 21 Jun 2020 18:25:16: end of X-cor INFO @ Sun, 21 Jun 2020 18:25:16: #2 finished! INFO @ Sun, 21 Jun 2020 18:25:16: #2 predicted fragment length is 246 bps INFO @ Sun, 21 Jun 2020 18:25:16: #2 alternative fragment length(s) may be 246 bps INFO @ Sun, 21 Jun 2020 18:25:16: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX193323/SRX193323.10_model.r INFO @ Sun, 21 Jun 2020 18:25:16: #3 Call peaks... INFO @ Sun, 21 Jun 2020 18:25:16: #3 Pre-compute pvalue-qvalue table... 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 18:25:21: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX193323/SRX193323.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX193323/SRX193323.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX193323/SRX193323.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX193323/SRX193323.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 18:25:21: #1 read tag files... INFO @ Sun, 21 Jun 2020 18:25:21: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 18:25:27: 1000000 INFO @ Sun, 21 Jun 2020 18:25:31: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 18:25:33: 2000000 INFO @ Sun, 21 Jun 2020 18:25:37: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX193323/SRX193323.10_peaks.xls INFO @ Sun, 21 Jun 2020 18:25:37: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX193323/SRX193323.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 18:25:37: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX193323/SRX193323.10_summits.bed INFO @ Sun, 21 Jun 2020 18:25:37: Done! pass1 - making usageList (132 chroms): 2 millis pass2 - checking and writing primary data (7217 records, 4 fields): 13 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 18:25:39: 3000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 18:25:46: 4000000 INFO @ Sun, 21 Jun 2020 18:25:48: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 18:25:48: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 18:25:48: #1 total tags in treatment: 4385101 INFO @ Sun, 21 Jun 2020 18:25:48: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 18:25:48: #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 18:25:49: #1 tags after filtering in treatment: 4384751 INFO @ Sun, 21 Jun 2020 18:25:49: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 18:25:49: #1 finished! INFO @ Sun, 21 Jun 2020 18:25:49: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 18:25:49: #2 looking for paired plus/minus strand peaks... BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 18:25:50: #2 number of paired peaks: 11890 INFO @ Sun, 21 Jun 2020 18:25:50: start model_add_line... INFO @ Sun, 21 Jun 2020 18:25:50: start X-correlation... INFO @ Sun, 21 Jun 2020 18:25:50: end of X-cor INFO @ Sun, 21 Jun 2020 18:25:50: #2 finished! INFO @ Sun, 21 Jun 2020 18:25:50: #2 predicted fragment length is 246 bps INFO @ Sun, 21 Jun 2020 18:25:50: #2 alternative fragment length(s) may be 246 bps INFO @ Sun, 21 Jun 2020 18:25:50: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX193323/SRX193323.20_model.r INFO @ Sun, 21 Jun 2020 18:25:50: #3 Call peaks... INFO @ Sun, 21 Jun 2020 18:25:50: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 18:26:03: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 18:26:09: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX193323/SRX193323.20_peaks.xls INFO @ Sun, 21 Jun 2020 18:26:10: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX193323/SRX193323.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 18:26:10: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX193323/SRX193323.20_summits.bed INFO @ Sun, 21 Jun 2020 18:26:10: Done! pass1 - making usageList (99 chroms): 2 millis pass2 - checking and writing primary data (6148 records, 4 fields): 10 millis CompletedMACS2peakCalling