Job ID = 6457971 SRX = SRX4933879 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T12:03:19 prefetch.2.10.7: 1) Downloading 'SRR8107269'... 2020-06-21T12:03:19 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T12:14:45 prefetch.2.10.7: HTTPS download succeed 2020-06-21T12:14:45 prefetch.2.10.7: 1) 'SRR8107269' was downloaded successfully Read 53415299 spots for SRR8107269/SRR8107269.sra Written 53415299 spots for SRR8107269/SRR8107269.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: 00:14:01 53415299 reads; of these: 53415299 (100.00%) were unpaired; of these: 32584815 (61.00%) aligned 0 times 11732534 (21.96%) aligned exactly 1 time 9097950 (17.03%) aligned >1 times 39.00% overall alignment rate Time searching: 00:14:01 Overall time: 00:14:01 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 12 files... [bam_rmdupse_core] 18482170 / 20830484 = 0.8873 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 21:35:09: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX4933879/SRX4933879.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX4933879/SRX4933879.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX4933879/SRX4933879.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX4933879/SRX4933879.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 21:35:09: #1 read tag files... INFO @ Sun, 21 Jun 2020 21:35:09: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 21:35:16: 1000000 INFO @ Sun, 21 Jun 2020 21:35:23: 2000000 INFO @ Sun, 21 Jun 2020 21:35:25: #1 tag size is determined as 51 bps INFO @ Sun, 21 Jun 2020 21:35:25: #1 tag size = 51 INFO @ Sun, 21 Jun 2020 21:35:25: #1 total tags in treatment: 2348314 INFO @ Sun, 21 Jun 2020 21:35:25: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 21:35:25: #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 21:35:26: #1 tags after filtering in treatment: 2348209 INFO @ Sun, 21 Jun 2020 21:35:26: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 21:35:26: #1 finished! INFO @ Sun, 21 Jun 2020 21:35:26: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 21:35:26: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 21:35:26: #2 number of paired peaks: 5446 INFO @ Sun, 21 Jun 2020 21:35:26: start model_add_line... INFO @ Sun, 21 Jun 2020 21:35:26: start X-correlation... INFO @ Sun, 21 Jun 2020 21:35:26: end of X-cor INFO @ Sun, 21 Jun 2020 21:35:26: #2 finished! INFO @ Sun, 21 Jun 2020 21:35:26: #2 predicted fragment length is 106 bps INFO @ Sun, 21 Jun 2020 21:35:26: #2 alternative fragment length(s) may be 106 bps INFO @ Sun, 21 Jun 2020 21:35:26: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX4933879/SRX4933879.05_model.r INFO @ Sun, 21 Jun 2020 21:35:26: #3 Call peaks... INFO @ Sun, 21 Jun 2020 21:35:26: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 21:35:32: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 21:35:35: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX4933879/SRX4933879.05_peaks.xls INFO @ Sun, 21 Jun 2020 21:35:35: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX4933879/SRX4933879.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 21:35:35: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX4933879/SRX4933879.05_summits.bed INFO @ Sun, 21 Jun 2020 21:35:35: Done! pass1 - making usageList (931 chroms): 2 millis pass2 - checking and writing primary data (3924 records, 4 fields): 28 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 21:35:39: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX4933879/SRX4933879.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX4933879/SRX4933879.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX4933879/SRX4933879.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX4933879/SRX4933879.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 21:35:39: #1 read tag files... INFO @ Sun, 21 Jun 2020 21:35:39: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 21:35:45: 1000000 INFO @ Sun, 21 Jun 2020 21:35:51: 2000000 INFO @ Sun, 21 Jun 2020 21:35:53: #1 tag size is determined as 51 bps INFO @ Sun, 21 Jun 2020 21:35:53: #1 tag size = 51 INFO @ Sun, 21 Jun 2020 21:35:53: #1 total tags in treatment: 2348314 INFO @ Sun, 21 Jun 2020 21:35:53: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 21:35:53: #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 21:35:54: #1 tags after filtering in treatment: 2348209 INFO @ Sun, 21 Jun 2020 21:35:54: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 21:35:54: #1 finished! INFO @ Sun, 21 Jun 2020 21:35:54: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 21:35:54: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 21:35:54: #2 number of paired peaks: 5446 INFO @ Sun, 21 Jun 2020 21:35:54: start model_add_line... INFO @ Sun, 21 Jun 2020 21:35:54: start X-correlation... INFO @ Sun, 21 Jun 2020 21:35:54: end of X-cor INFO @ Sun, 21 Jun 2020 21:35:54: #2 finished! INFO @ Sun, 21 Jun 2020 21:35:54: #2 predicted fragment length is 106 bps INFO @ Sun, 21 Jun 2020 21:35:54: #2 alternative fragment length(s) may be 106 bps INFO @ Sun, 21 Jun 2020 21:35:54: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX4933879/SRX4933879.10_model.r INFO @ Sun, 21 Jun 2020 21:35:54: #3 Call peaks... INFO @ Sun, 21 Jun 2020 21:35:54: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 21:36:00: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 21:36:03: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX4933879/SRX4933879.10_peaks.xls INFO @ Sun, 21 Jun 2020 21:36:03: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX4933879/SRX4933879.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 21:36:03: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX4933879/SRX4933879.10_summits.bed INFO @ Sun, 21 Jun 2020 21:36:03: Done! pass1 - making usageList (664 chroms): 1 millis pass2 - checking and writing primary data (1759 records, 4 fields): 20 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 21:36:09: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX4933879/SRX4933879.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX4933879/SRX4933879.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX4933879/SRX4933879.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX4933879/SRX4933879.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 21:36:09: #1 read tag files... INFO @ Sun, 21 Jun 2020 21:36:09: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 21:36:15: 1000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 21:36:21: 2000000 INFO @ Sun, 21 Jun 2020 21:36:23: #1 tag size is determined as 51 bps INFO @ Sun, 21 Jun 2020 21:36:23: #1 tag size = 51 INFO @ Sun, 21 Jun 2020 21:36:23: #1 total tags in treatment: 2348314 INFO @ Sun, 21 Jun 2020 21:36:23: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 21:36:23: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 21:36:24: #1 tags after filtering in treatment: 2348209 INFO @ Sun, 21 Jun 2020 21:36:24: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 21:36:24: #1 finished! INFO @ Sun, 21 Jun 2020 21:36:24: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 21:36:24: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 21:36:24: #2 number of paired peaks: 5446 INFO @ Sun, 21 Jun 2020 21:36:24: start model_add_line... INFO @ Sun, 21 Jun 2020 21:36:24: start X-correlation... INFO @ Sun, 21 Jun 2020 21:36:24: end of X-cor INFO @ Sun, 21 Jun 2020 21:36:24: #2 finished! INFO @ Sun, 21 Jun 2020 21:36:24: #2 predicted fragment length is 106 bps INFO @ Sun, 21 Jun 2020 21:36:24: #2 alternative fragment length(s) may be 106 bps INFO @ Sun, 21 Jun 2020 21:36:24: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX4933879/SRX4933879.20_model.r INFO @ Sun, 21 Jun 2020 21:36:24: #3 Call peaks... INFO @ Sun, 21 Jun 2020 21:36:24: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 21:36:30: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 21:36:33: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX4933879/SRX4933879.20_peaks.xls INFO @ Sun, 21 Jun 2020 21:36:33: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX4933879/SRX4933879.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 21:36:33: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX4933879/SRX4933879.20_summits.bed INFO @ Sun, 21 Jun 2020 21:36:33: Done! pass1 - making usageList (317 chroms): 1 millis pass2 - checking and writing primary data (623 records, 4 fields): 9 millis CompletedMACS2peakCalling