Job ID = 6457806 SRX = SRX4798851 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T12:03:04 prefetch.2.10.7: 1) Downloading 'SRR7965218'... 2020-06-21T12:03:04 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T12:04:47 prefetch.2.10.7: HTTPS download succeed 2020-06-21T12:04:47 prefetch.2.10.7: 'SRR7965218' is valid 2020-06-21T12:04:47 prefetch.2.10.7: 1) 'SRR7965218' was downloaded successfully Read 10703557 spots for SRR7965218/SRR7965218.sra Written 10703557 spots for SRR7965218/SRR7965218.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: 00:01:25 10703557 reads; of these: 10703557 (100.00%) were unpaired; of these: 4806181 (44.90%) aligned 0 times 5624745 (52.55%) aligned exactly 1 time 272631 (2.55%) aligned >1 times 55.10% overall alignment rate Time searching: 00:01:25 Overall time: 00:01:25 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] 1783523 / 5897376 = 0.3024 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 21:08:40: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX4798851/SRX4798851.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX4798851/SRX4798851.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX4798851/SRX4798851.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX4798851/SRX4798851.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 21:08:40: #1 read tag files... INFO @ Sun, 21 Jun 2020 21:08:40: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 21:08:46: 1000000 INFO @ Sun, 21 Jun 2020 21:08:53: 2000000 INFO @ Sun, 21 Jun 2020 21:09:00: 3000000 INFO @ Sun, 21 Jun 2020 21:09:07: 4000000 INFO @ Sun, 21 Jun 2020 21:09:08: #1 tag size is determined as 51 bps INFO @ Sun, 21 Jun 2020 21:09:08: #1 tag size = 51 INFO @ Sun, 21 Jun 2020 21:09:08: #1 total tags in treatment: 4113853 INFO @ Sun, 21 Jun 2020 21:09:08: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 21:09:08: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) 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 21:09:08: #1 tags after filtering in treatment: 4113380 INFO @ Sun, 21 Jun 2020 21:09:08: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 21:09:08: #1 finished! INFO @ Sun, 21 Jun 2020 21:09:08: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 21:09:08: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 21:09:09: #2 number of paired peaks: 6158 INFO @ Sun, 21 Jun 2020 21:09:09: start model_add_line... INFO @ Sun, 21 Jun 2020 21:09:09: start X-correlation... INFO @ Sun, 21 Jun 2020 21:09:09: end of X-cor INFO @ Sun, 21 Jun 2020 21:09:09: #2 finished! INFO @ Sun, 21 Jun 2020 21:09:09: #2 predicted fragment length is 178 bps INFO @ Sun, 21 Jun 2020 21:09:09: #2 alternative fragment length(s) may be 178 bps INFO @ Sun, 21 Jun 2020 21:09:09: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX4798851/SRX4798851.05_model.r INFO @ Sun, 21 Jun 2020 21:09:09: #3 Call peaks... INFO @ Sun, 21 Jun 2020 21:09:09: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 21:09:10: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX4798851/SRX4798851.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX4798851/SRX4798851.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX4798851/SRX4798851.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX4798851/SRX4798851.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 21:09:10: #1 read tag files... INFO @ Sun, 21 Jun 2020 21:09:10: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 21:09:16: 1000000 INFO @ Sun, 21 Jun 2020 21:09:21: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 21:09:22: 2000000 INFO @ Sun, 21 Jun 2020 21:09:27: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX4798851/SRX4798851.05_peaks.xls INFO @ Sun, 21 Jun 2020 21:09:27: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX4798851/SRX4798851.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 21:09:27: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX4798851/SRX4798851.05_summits.bed INFO @ Sun, 21 Jun 2020 21:09:27: Done! pass1 - making usageList (38 chroms): 2 millis pass2 - checking and writing primary data (8600 records, 4 fields): 10 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 21:09:28: 3000000 INFO @ Sun, 21 Jun 2020 21:09:35: 4000000 INFO @ Sun, 21 Jun 2020 21:09:36: #1 tag size is determined as 51 bps INFO @ Sun, 21 Jun 2020 21:09:36: #1 tag size = 51 INFO @ Sun, 21 Jun 2020 21:09:36: #1 total tags in treatment: 4113853 INFO @ Sun, 21 Jun 2020 21:09:36: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 21:09:36: #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 21:09:36: #1 tags after filtering in treatment: 4113380 INFO @ Sun, 21 Jun 2020 21:09:36: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 21:09:36: #1 finished! INFO @ Sun, 21 Jun 2020 21:09:36: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 21:09:36: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 21:09:37: #2 number of paired peaks: 6158 INFO @ Sun, 21 Jun 2020 21:09:37: start model_add_line... INFO @ Sun, 21 Jun 2020 21:09:37: start X-correlation... INFO @ Sun, 21 Jun 2020 21:09:37: end of X-cor INFO @ Sun, 21 Jun 2020 21:09:37: #2 finished! INFO @ Sun, 21 Jun 2020 21:09:37: #2 predicted fragment length is 178 bps INFO @ Sun, 21 Jun 2020 21:09:37: #2 alternative fragment length(s) may be 178 bps INFO @ Sun, 21 Jun 2020 21:09:37: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX4798851/SRX4798851.10_model.r INFO @ Sun, 21 Jun 2020 21:09:37: #3 Call peaks... INFO @ Sun, 21 Jun 2020 21:09:37: #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 21:09:40: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX4798851/SRX4798851.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX4798851/SRX4798851.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX4798851/SRX4798851.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX4798851/SRX4798851.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 21:09:40: #1 read tag files... INFO @ Sun, 21 Jun 2020 21:09:40: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 21:09:46: 1000000 INFO @ Sun, 21 Jun 2020 21:09:48: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 21:09:52: 2000000 INFO @ Sun, 21 Jun 2020 21:09:53: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX4798851/SRX4798851.10_peaks.xls INFO @ Sun, 21 Jun 2020 21:09:53: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX4798851/SRX4798851.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 21:09:53: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX4798851/SRX4798851.10_summits.bed INFO @ Sun, 21 Jun 2020 21:09:53: Done! pass1 - making usageList (31 chroms): 1 millis pass2 - checking and writing primary data (6024 records, 4 fields): 7 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 21:09:59: 3000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 21:10:05: 4000000 INFO @ Sun, 21 Jun 2020 21:10:06: #1 tag size is determined as 51 bps INFO @ Sun, 21 Jun 2020 21:10:06: #1 tag size = 51 INFO @ Sun, 21 Jun 2020 21:10:06: #1 total tags in treatment: 4113853 INFO @ Sun, 21 Jun 2020 21:10:06: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 21:10:06: #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 21:10:07: #1 tags after filtering in treatment: 4113380 INFO @ Sun, 21 Jun 2020 21:10:07: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 21:10:07: #1 finished! INFO @ Sun, 21 Jun 2020 21:10:07: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 21:10:07: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 21:10:07: #2 number of paired peaks: 6158 INFO @ Sun, 21 Jun 2020 21:10:07: start model_add_line... INFO @ Sun, 21 Jun 2020 21:10:07: start X-correlation... INFO @ Sun, 21 Jun 2020 21:10:07: end of X-cor INFO @ Sun, 21 Jun 2020 21:10:07: #2 finished! INFO @ Sun, 21 Jun 2020 21:10:07: #2 predicted fragment length is 178 bps INFO @ Sun, 21 Jun 2020 21:10:07: #2 alternative fragment length(s) may be 178 bps INFO @ Sun, 21 Jun 2020 21:10:07: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX4798851/SRX4798851.20_model.r INFO @ Sun, 21 Jun 2020 21:10:07: #3 Call peaks... INFO @ Sun, 21 Jun 2020 21:10:07: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 21:10:19: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 21:10:24: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX4798851/SRX4798851.20_peaks.xls INFO @ Sun, 21 Jun 2020 21:10:24: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX4798851/SRX4798851.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 21:10:24: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX4798851/SRX4798851.20_summits.bed INFO @ Sun, 21 Jun 2020 21:10:24: Done! pass1 - making usageList (16 chroms): 1 millis pass2 - checking and writing primary data (3818 records, 4 fields): 5 millis CompletedMACS2peakCalling