Job ID = 6456950 SRX = SRX4158177 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T11:17:12 prefetch.2.10.7: 1) Downloading 'SRR7253457'... 2020-06-21T11:17:12 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T11:18:56 prefetch.2.10.7: HTTPS download succeed 2020-06-21T11:18:57 prefetch.2.10.7: 'SRR7253457' is valid 2020-06-21T11:18:57 prefetch.2.10.7: 1) 'SRR7253457' was downloaded successfully Read 6995461 spots for SRR7253457/SRR7253457.sra Written 6995461 spots for SRR7253457/SRR7253457.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: 00:01:36 6995461 reads; of these: 6995461 (100.00%) were unpaired; of these: 301865 (4.32%) aligned 0 times 6257370 (89.45%) aligned exactly 1 time 436226 (6.24%) aligned >1 times 95.68% overall alignment rate Time searching: 00:01:36 Overall time: 00:01:36 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] 1168653 / 6693596 = 0.1746 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 20:22:55: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX4158177/SRX4158177.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX4158177/SRX4158177.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX4158177/SRX4158177.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX4158177/SRX4158177.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 20:22:55: #1 read tag files... INFO @ Sun, 21 Jun 2020 20:22:55: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 20:23:01: 1000000 INFO @ Sun, 21 Jun 2020 20:23:07: 2000000 INFO @ Sun, 21 Jun 2020 20:23:14: 3000000 INFO @ Sun, 21 Jun 2020 20:23:20: 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 20:23:25: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX4158177/SRX4158177.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX4158177/SRX4158177.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX4158177/SRX4158177.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX4158177/SRX4158177.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 20:23:25: #1 read tag files... INFO @ Sun, 21 Jun 2020 20:23:25: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 20:23:26: 5000000 INFO @ Sun, 21 Jun 2020 20:23:30: #1 tag size is determined as 49 bps INFO @ Sun, 21 Jun 2020 20:23:30: #1 tag size = 49 INFO @ Sun, 21 Jun 2020 20:23:30: #1 total tags in treatment: 5524943 INFO @ Sun, 21 Jun 2020 20:23:30: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 20:23:30: #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 20:23:30: #1 tags after filtering in treatment: 5524560 INFO @ Sun, 21 Jun 2020 20:23:30: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 20:23:30: #1 finished! INFO @ Sun, 21 Jun 2020 20:23:30: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 20:23:30: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 20:23:31: #2 number of paired peaks: 8774 INFO @ Sun, 21 Jun 2020 20:23:31: start model_add_line... INFO @ Sun, 21 Jun 2020 20:23:31: start X-correlation... INFO @ Sun, 21 Jun 2020 20:23:31: end of X-cor INFO @ Sun, 21 Jun 2020 20:23:31: #2 finished! INFO @ Sun, 21 Jun 2020 20:23:31: #2 predicted fragment length is 176 bps INFO @ Sun, 21 Jun 2020 20:23:31: #2 alternative fragment length(s) may be 176 bps INFO @ Sun, 21 Jun 2020 20:23:31: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX4158177/SRX4158177.05_model.r INFO @ Sun, 21 Jun 2020 20:23:31: #3 Call peaks... INFO @ Sun, 21 Jun 2020 20:23:31: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 20:23:31: 1000000 INFO @ Sun, 21 Jun 2020 20:23:37: 2000000 INFO @ Sun, 21 Jun 2020 20:23:43: 3000000 INFO @ Sun, 21 Jun 2020 20:23:45: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 20:23:48: 4000000 INFO @ Sun, 21 Jun 2020 20:23:52: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX4158177/SRX4158177.05_peaks.xls INFO @ Sun, 21 Jun 2020 20:23:52: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX4158177/SRX4158177.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 20:23:52: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX4158177/SRX4158177.05_summits.bed INFO @ Sun, 21 Jun 2020 20:23:52: Done! pass1 - making usageList (73 chroms): 1 millis pass2 - checking and writing primary data (6417 records, 4 fields): 10 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 20:23:54: 5000000 INFO @ Sun, 21 Jun 2020 20:23:55: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX4158177/SRX4158177.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX4158177/SRX4158177.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX4158177/SRX4158177.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX4158177/SRX4158177.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 20:23:55: #1 read tag files... INFO @ Sun, 21 Jun 2020 20:23:55: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 20:23:57: #1 tag size is determined as 49 bps INFO @ Sun, 21 Jun 2020 20:23:57: #1 tag size = 49 INFO @ Sun, 21 Jun 2020 20:23:57: #1 total tags in treatment: 5524943 INFO @ Sun, 21 Jun 2020 20:23:57: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 20:23:57: #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 20:23:57: #1 tags after filtering in treatment: 5524560 INFO @ Sun, 21 Jun 2020 20:23:57: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 20:23:57: #1 finished! INFO @ Sun, 21 Jun 2020 20:23:57: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 20:23:57: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 20:23:58: #2 number of paired peaks: 8774 INFO @ Sun, 21 Jun 2020 20:23:58: start model_add_line... INFO @ Sun, 21 Jun 2020 20:23:58: start X-correlation... INFO @ Sun, 21 Jun 2020 20:23:58: end of X-cor INFO @ Sun, 21 Jun 2020 20:23:58: #2 finished! INFO @ Sun, 21 Jun 2020 20:23:58: #2 predicted fragment length is 176 bps INFO @ Sun, 21 Jun 2020 20:23:58: #2 alternative fragment length(s) may be 176 bps INFO @ Sun, 21 Jun 2020 20:23:58: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX4158177/SRX4158177.10_model.r INFO @ Sun, 21 Jun 2020 20:23:58: #3 Call peaks... INFO @ Sun, 21 Jun 2020 20:23:58: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 20:24:02: 1000000 INFO @ Sun, 21 Jun 2020 20:24:08: 2000000 INFO @ Sun, 21 Jun 2020 20:24:13: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 20:24:14: 3000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 20:24:20: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX4158177/SRX4158177.10_peaks.xls INFO @ Sun, 21 Jun 2020 20:24:20: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX4158177/SRX4158177.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 20:24:20: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX4158177/SRX4158177.10_summits.bed INFO @ Sun, 21 Jun 2020 20:24:20: Done! pass1 - making usageList (53 chroms): 1 millis pass2 - checking and writing primary data (5977 records, 4 fields): 9 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 20:24:21: 4000000 BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 20:24:27: 5000000 INFO @ Sun, 21 Jun 2020 20:24:31: #1 tag size is determined as 49 bps INFO @ Sun, 21 Jun 2020 20:24:31: #1 tag size = 49 INFO @ Sun, 21 Jun 2020 20:24:31: #1 total tags in treatment: 5524943 INFO @ Sun, 21 Jun 2020 20:24:31: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 20:24:31: #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 20:24:31: #1 tags after filtering in treatment: 5524560 INFO @ Sun, 21 Jun 2020 20:24:31: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 20:24:31: #1 finished! INFO @ Sun, 21 Jun 2020 20:24:31: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 20:24:31: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 20:24:32: #2 number of paired peaks: 8774 INFO @ Sun, 21 Jun 2020 20:24:32: start model_add_line... INFO @ Sun, 21 Jun 2020 20:24:32: start X-correlation... INFO @ Sun, 21 Jun 2020 20:24:32: end of X-cor INFO @ Sun, 21 Jun 2020 20:24:32: #2 finished! INFO @ Sun, 21 Jun 2020 20:24:32: #2 predicted fragment length is 176 bps INFO @ Sun, 21 Jun 2020 20:24:32: #2 alternative fragment length(s) may be 176 bps INFO @ Sun, 21 Jun 2020 20:24:32: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX4158177/SRX4158177.20_model.r INFO @ Sun, 21 Jun 2020 20:24:32: #3 Call peaks... INFO @ Sun, 21 Jun 2020 20:24:32: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 20:24:46: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 20:24:53: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX4158177/SRX4158177.20_peaks.xls INFO @ Sun, 21 Jun 2020 20:24:53: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX4158177/SRX4158177.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 20:24:53: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX4158177/SRX4158177.20_summits.bed INFO @ Sun, 21 Jun 2020 20:24:53: Done! pass1 - making usageList (38 chroms): 2 millis pass2 - checking and writing primary data (5129 records, 4 fields): 10 millis CompletedMACS2peakCalling