Job ID = 6458455 SRX = SRX5232775 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T12:34:22 prefetch.2.10.7: 1) Downloading 'SRR8424027'... 2020-06-21T12:34:22 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T12:37:49 prefetch.2.10.7: HTTPS download succeed 2020-06-21T12:37:49 prefetch.2.10.7: 1) 'SRR8424027' was downloaded successfully 2020-06-21T12:37:49 prefetch.2.10.7: 'SRR8424027' has 0 unresolved dependencies Read 42375457 spots for SRR8424027/SRR8424027.sra Written 42375457 spots for SRR8424027/SRR8424027.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: 00:07:40 42375457 reads; of these: 42375457 (100.00%) were unpaired; of these: 22954454 (54.17%) aligned 0 times 15308266 (36.13%) aligned exactly 1 time 4112737 (9.71%) aligned >1 times 45.83% overall alignment rate Time searching: 00:07:40 Overall time: 00:07:40 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_sort_core] merging from 8 files... [bam_rmdupse_core] 14114248 / 19421003 = 0.7268 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 21:50:57: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX5232775/SRX5232775.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX5232775/SRX5232775.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX5232775/SRX5232775.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX5232775/SRX5232775.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 21:50:57: #1 read tag files... INFO @ Sun, 21 Jun 2020 21:50:57: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 21:51:03: 1000000 INFO @ Sun, 21 Jun 2020 21:51:08: 2000000 INFO @ Sun, 21 Jun 2020 21:51:14: 3000000 INFO @ Sun, 21 Jun 2020 21:51:19: 4000000 INFO @ Sun, 21 Jun 2020 21:51:25: 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 21:51:27: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 21:51:27: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 21:51:27: #1 total tags in treatment: 5306755 INFO @ Sun, 21 Jun 2020 21:51:27: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 21:51:27: #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 21:51:27: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX5232775/SRX5232775.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX5232775/SRX5232775.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX5232775/SRX5232775.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX5232775/SRX5232775.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 21:51:27: #1 read tag files... INFO @ Sun, 21 Jun 2020 21:51:27: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 21:51:27: #1 tags after filtering in treatment: 5306742 INFO @ Sun, 21 Jun 2020 21:51:27: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 21:51:27: #1 finished! INFO @ Sun, 21 Jun 2020 21:51:27: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 21:51:27: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 21:51:28: #2 number of paired peaks: 2672 INFO @ Sun, 21 Jun 2020 21:51:28: start model_add_line... INFO @ Sun, 21 Jun 2020 21:51:28: start X-correlation... INFO @ Sun, 21 Jun 2020 21:51:28: end of X-cor INFO @ Sun, 21 Jun 2020 21:51:28: #2 finished! INFO @ Sun, 21 Jun 2020 21:51:28: #2 predicted fragment length is 151 bps INFO @ Sun, 21 Jun 2020 21:51:28: #2 alternative fragment length(s) may be 151 bps INFO @ Sun, 21 Jun 2020 21:51:28: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX5232775/SRX5232775.05_model.r INFO @ Sun, 21 Jun 2020 21:51:28: #3 Call peaks... INFO @ Sun, 21 Jun 2020 21:51:28: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 21:51:32: 1000000 INFO @ Sun, 21 Jun 2020 21:51:37: 2000000 INFO @ Sun, 21 Jun 2020 21:51:41: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 21:51:42: 3000000 INFO @ Sun, 21 Jun 2020 21:51:47: 4000000 INFO @ Sun, 21 Jun 2020 21:51:47: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX5232775/SRX5232775.05_peaks.xls INFO @ Sun, 21 Jun 2020 21:51:47: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX5232775/SRX5232775.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 21:51:47: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX5232775/SRX5232775.05_summits.bed INFO @ Sun, 21 Jun 2020 21:51:47: Done! pass1 - making usageList (721 chroms): 1 millis pass2 - checking and writing primary data (3977 records, 4 fields): 22 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 21:51:52: 5000000 INFO @ Sun, 21 Jun 2020 21:51:54: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 21:51:54: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 21:51:54: #1 total tags in treatment: 5306755 INFO @ Sun, 21 Jun 2020 21:51:54: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 21:51:54: #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 21:51:54: #1 tags after filtering in treatment: 5306742 INFO @ Sun, 21 Jun 2020 21:51:54: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 21:51:54: #1 finished! INFO @ Sun, 21 Jun 2020 21:51:54: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 21:51:54: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 21:51:54: #2 number of paired peaks: 2672 INFO @ Sun, 21 Jun 2020 21:51:54: start model_add_line... INFO @ Sun, 21 Jun 2020 21:51:54: start X-correlation... INFO @ Sun, 21 Jun 2020 21:51:55: end of X-cor INFO @ Sun, 21 Jun 2020 21:51:55: #2 finished! INFO @ Sun, 21 Jun 2020 21:51:55: #2 predicted fragment length is 151 bps INFO @ Sun, 21 Jun 2020 21:51:55: #2 alternative fragment length(s) may be 151 bps INFO @ Sun, 21 Jun 2020 21:51:55: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX5232775/SRX5232775.10_model.r INFO @ Sun, 21 Jun 2020 21:51:55: #3 Call peaks... INFO @ Sun, 21 Jun 2020 21:51:55: #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 21:51:57: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX5232775/SRX5232775.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX5232775/SRX5232775.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX5232775/SRX5232775.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX5232775/SRX5232775.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 21:51:57: #1 read tag files... INFO @ Sun, 21 Jun 2020 21:51:57: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 21:52:02: 1000000 INFO @ Sun, 21 Jun 2020 21:52:07: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 21:52:07: 2000000 INFO @ Sun, 21 Jun 2020 21:52:12: 3000000 INFO @ Sun, 21 Jun 2020 21:52:13: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX5232775/SRX5232775.10_peaks.xls INFO @ Sun, 21 Jun 2020 21:52:13: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX5232775/SRX5232775.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 21:52:13: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX5232775/SRX5232775.10_summits.bed INFO @ Sun, 21 Jun 2020 21:52:13: Done! pass1 - making usageList (620 chroms): 2 millis pass2 - checking and writing primary data (3146 records, 4 fields): 19 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 21:52:17: 4000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 21:52:23: 5000000 INFO @ Sun, 21 Jun 2020 21:52:24: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 21:52:24: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 21:52:24: #1 total tags in treatment: 5306755 INFO @ Sun, 21 Jun 2020 21:52:24: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 21:52:24: #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 21:52:25: #1 tags after filtering in treatment: 5306742 INFO @ Sun, 21 Jun 2020 21:52:25: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 21:52:25: #1 finished! INFO @ Sun, 21 Jun 2020 21:52:25: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 21:52:25: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 21:52:25: #2 number of paired peaks: 2672 INFO @ Sun, 21 Jun 2020 21:52:25: start model_add_line... INFO @ Sun, 21 Jun 2020 21:52:25: start X-correlation... INFO @ Sun, 21 Jun 2020 21:52:25: end of X-cor INFO @ Sun, 21 Jun 2020 21:52:25: #2 finished! INFO @ Sun, 21 Jun 2020 21:52:25: #2 predicted fragment length is 151 bps INFO @ Sun, 21 Jun 2020 21:52:25: #2 alternative fragment length(s) may be 151 bps INFO @ Sun, 21 Jun 2020 21:52:25: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX5232775/SRX5232775.20_model.r INFO @ Sun, 21 Jun 2020 21:52:25: #3 Call peaks... INFO @ Sun, 21 Jun 2020 21:52:25: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 21:52:38: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 21:52:45: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX5232775/SRX5232775.20_peaks.xls INFO @ Sun, 21 Jun 2020 21:52:45: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX5232775/SRX5232775.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 21:52:45: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX5232775/SRX5232775.20_summits.bed INFO @ Sun, 21 Jun 2020 21:52:45: Done! pass1 - making usageList (472 chroms): 2 millis pass2 - checking and writing primary data (2249 records, 4 fields): 14 millis CompletedMACS2peakCalling