Job ID = 6458319 SRX = SRX5011069 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T12:15:34 prefetch.2.10.7: 1) Downloading 'SRR8191518'... 2020-06-21T12:15:34 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T12:18:17 prefetch.2.10.7: HTTPS download succeed 2020-06-21T12:18:17 prefetch.2.10.7: 1) 'SRR8191518' was downloaded successfully 2020-06-21T12:18:17 prefetch.2.10.7: 'SRR8191518' has 0 unresolved dependencies Read 33839220 spots for SRR8191518/SRR8191518.sra Written 33839220 spots for SRR8191518/SRR8191518.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: 00:06:33 33839220 reads; of these: 33839220 (100.00%) were unpaired; of these: 11539736 (34.10%) aligned 0 times 17252871 (50.98%) aligned exactly 1 time 5046613 (14.91%) aligned >1 times 65.90% overall alignment rate Time searching: 00:06:33 Overall time: 00:06:33 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] 14960272 / 22299484 = 0.6709 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 21:29:50: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX5011069/SRX5011069.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX5011069/SRX5011069.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX5011069/SRX5011069.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX5011069/SRX5011069.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 21:29:50: #1 read tag files... INFO @ Sun, 21 Jun 2020 21:29:50: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 21:29:56: 1000000 INFO @ Sun, 21 Jun 2020 21:30:01: 2000000 INFO @ Sun, 21 Jun 2020 21:30:06: 3000000 INFO @ Sun, 21 Jun 2020 21:30:12: 4000000 INFO @ Sun, 21 Jun 2020 21:30:17: 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 21:30:20: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX5011069/SRX5011069.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX5011069/SRX5011069.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX5011069/SRX5011069.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX5011069/SRX5011069.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 21:30:20: #1 read tag files... INFO @ Sun, 21 Jun 2020 21:30:20: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 21:30:23: 6000000 INFO @ Sun, 21 Jun 2020 21:30:26: 1000000 INFO @ Sun, 21 Jun 2020 21:30:28: 7000000 INFO @ Sun, 21 Jun 2020 21:30:31: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 21:30:31: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 21:30:31: #1 total tags in treatment: 7339212 INFO @ Sun, 21 Jun 2020 21:30:31: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 21:30:31: #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 21:30:31: #1 tags after filtering in treatment: 7339123 INFO @ Sun, 21 Jun 2020 21:30:31: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 21:30:31: #1 finished! INFO @ Sun, 21 Jun 2020 21:30:31: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 21:30:31: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 21:30:32: #2 number of paired peaks: 2919 INFO @ Sun, 21 Jun 2020 21:30:32: start model_add_line... INFO @ Sun, 21 Jun 2020 21:30:32: start X-correlation... INFO @ Sun, 21 Jun 2020 21:30:32: end of X-cor INFO @ Sun, 21 Jun 2020 21:30:32: #2 finished! INFO @ Sun, 21 Jun 2020 21:30:32: #2 predicted fragment length is 165 bps INFO @ Sun, 21 Jun 2020 21:30:32: #2 alternative fragment length(s) may be 165 bps INFO @ Sun, 21 Jun 2020 21:30:32: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX5011069/SRX5011069.05_model.r INFO @ Sun, 21 Jun 2020 21:30:32: #3 Call peaks... INFO @ Sun, 21 Jun 2020 21:30:32: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 21:30:32: 2000000 INFO @ Sun, 21 Jun 2020 21:30:38: 3000000 INFO @ Sun, 21 Jun 2020 21:30:44: 4000000 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 21:30:50: 5000000 INFO @ Sun, 21 Jun 2020 21:30:50: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 21:30:50: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX5011069/SRX5011069.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX5011069/SRX5011069.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX5011069/SRX5011069.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX5011069/SRX5011069.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 21:30:50: #1 read tag files... INFO @ Sun, 21 Jun 2020 21:30:50: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 21:30:57: 6000000 INFO @ Sun, 21 Jun 2020 21:30:57: 1000000 INFO @ Sun, 21 Jun 2020 21:30:59: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX5011069/SRX5011069.05_peaks.xls INFO @ Sun, 21 Jun 2020 21:30:59: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX5011069/SRX5011069.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 21:30:59: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX5011069/SRX5011069.05_summits.bed INFO @ Sun, 21 Jun 2020 21:30:59: Done! pass1 - making usageList (749 chroms): 2 millis pass2 - checking and writing primary data (5476 records, 4 fields): 22 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 21:31:04: 7000000 INFO @ Sun, 21 Jun 2020 21:31:04: 2000000 INFO @ Sun, 21 Jun 2020 21:31:06: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 21:31:06: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 21:31:06: #1 total tags in treatment: 7339212 INFO @ Sun, 21 Jun 2020 21:31:06: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 21:31:06: #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 21:31:06: #1 tags after filtering in treatment: 7339123 INFO @ Sun, 21 Jun 2020 21:31:06: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 21:31:06: #1 finished! INFO @ Sun, 21 Jun 2020 21:31:06: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 21:31:06: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 21:31:07: #2 number of paired peaks: 2919 INFO @ Sun, 21 Jun 2020 21:31:07: start model_add_line... INFO @ Sun, 21 Jun 2020 21:31:07: start X-correlation... INFO @ Sun, 21 Jun 2020 21:31:07: end of X-cor INFO @ Sun, 21 Jun 2020 21:31:07: #2 finished! INFO @ Sun, 21 Jun 2020 21:31:07: #2 predicted fragment length is 165 bps INFO @ Sun, 21 Jun 2020 21:31:07: #2 alternative fragment length(s) may be 165 bps INFO @ Sun, 21 Jun 2020 21:31:07: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX5011069/SRX5011069.10_model.r INFO @ Sun, 21 Jun 2020 21:31:07: #3 Call peaks... INFO @ Sun, 21 Jun 2020 21:31:07: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 21:31:10: 3000000 INFO @ Sun, 21 Jun 2020 21:31:16: 4000000 INFO @ Sun, 21 Jun 2020 21:31:22: 5000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 21:31:26: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 21:31:28: 6000000 INFO @ Sun, 21 Jun 2020 21:31:34: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX5011069/SRX5011069.10_peaks.xls INFO @ Sun, 21 Jun 2020 21:31:34: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX5011069/SRX5011069.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 21:31:34: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX5011069/SRX5011069.10_summits.bed INFO @ Sun, 21 Jun 2020 21:31:34: Done! INFO @ Sun, 21 Jun 2020 21:31:35: 7000000 pass1 - making usageList (645 chroms): 1 millis pass2 - checking and writing primary data (3246 records, 4 fields): 19 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 21:31:37: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 21:31:37: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 21:31:37: #1 total tags in treatment: 7339212 INFO @ Sun, 21 Jun 2020 21:31:37: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 21:31:37: #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 21:31:37: #1 tags after filtering in treatment: 7339123 INFO @ Sun, 21 Jun 2020 21:31:37: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 21:31:37: #1 finished! INFO @ Sun, 21 Jun 2020 21:31:37: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 21:31:37: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 21:31:38: #2 number of paired peaks: 2919 INFO @ Sun, 21 Jun 2020 21:31:38: start model_add_line... INFO @ Sun, 21 Jun 2020 21:31:38: start X-correlation... INFO @ Sun, 21 Jun 2020 21:31:38: end of X-cor INFO @ Sun, 21 Jun 2020 21:31:38: #2 finished! INFO @ Sun, 21 Jun 2020 21:31:38: #2 predicted fragment length is 165 bps INFO @ Sun, 21 Jun 2020 21:31:38: #2 alternative fragment length(s) may be 165 bps INFO @ Sun, 21 Jun 2020 21:31:38: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX5011069/SRX5011069.20_model.r INFO @ Sun, 21 Jun 2020 21:31:38: #3 Call peaks... INFO @ Sun, 21 Jun 2020 21:31:38: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 21:31:56: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 21:32:04: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX5011069/SRX5011069.20_peaks.xls INFO @ Sun, 21 Jun 2020 21:32:04: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX5011069/SRX5011069.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 21:32:04: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX5011069/SRX5011069.20_summits.bed INFO @ Sun, 21 Jun 2020 21:32:04: Done! pass1 - making usageList (413 chroms): 1 millis pass2 - checking and writing primary data (1356 records, 4 fields): 162 millis CompletedMACS2peakCalling