Job ID = 14172250 SRX = SRX9281750 Genome = dm3 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... Read 4854753 spots for SRR12813479/SRR12813479.sra Written 4854753 spots for SRR12813479/SRR12813479.sra Read 4870576 spots for SRR12813480/SRR12813480.sra Written 4870576 spots for SRR12813480/SRR12813480.sra Read 5005475 spots for SRR12813481/SRR12813481.sra Written 5005475 spots for SRR12813481/SRR12813481.sra Read 4534017 spots for SRR12813482/SRR12813482.sra Written 4534017 spots for SRR12813482/SRR12813482.sra fastq に変換しました。 bowtie でマッピング中... Your job 14172705 ("srTdm6") has been submitted Time loading reference: 00:00:00 Time loading forward index: 00:00:00 Time loading mirror index: 00:00:00 Multiseed full-index search: 00:04:02 19264821 reads; of these: 19264821 (100.00%) were paired; of these: 16642625 (86.39%) aligned concordantly 0 times 2418609 (12.55%) aligned concordantly exactly 1 time 203587 (1.06%) aligned concordantly >1 times ---- 16642625 pairs aligned concordantly 0 times; of these: 16097 (0.10%) aligned discordantly 1 time ---- 16626528 pairs aligned 0 times concordantly or discordantly; of these: 33253056 mates make up the pairs; of these: 32931440 (99.03%) aligned 0 times 169907 (0.51%) aligned exactly 1 time 151709 (0.46%) aligned >1 times 14.53% overall alignment rate Time searching: 00:04:02 Overall time: 00:04:02 マッピングが完了しました。 samtools でBAM に変換中... [samopen] SAM header is present: 15 sequences. [bam_rmdup_core] processing reference chr2L... [bam_rmdup_core] processing reference chr2LHet... [bam_rmdup_core] processing reference chr2R... [bam_rmdup_core] processing reference chr2RHet... [bam_rmdup_core] processing reference chr3L... [bam_rmdup_core] processing reference chr3LHet... [bam_rmdup_core] processing reference chr3R... [bam_rmdup_core] processing reference chr3RHet... [bam_rmdup_core] processing reference chr4... [bam_rmdup_core] processing reference chrM... [bam_rmdup_core] processing reference chrU... [bam_rmdup_core] processing reference chrUextra... [bam_rmdup_core] processing reference chrX... [bam_rmdup_core] processing reference chrXHet... [bam_rmdup_core] processing reference chrYHet... [bam_rmdup_core] 421416 / 2632619 = 0.1601 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/3.8.3/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Sat, 11 Dec 2021 15:00:18: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX9281750/SRX9281750.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX9281750/SRX9281750.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX9281750/SRX9281750.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX9281750/SRX9281750.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 @ Sat, 11 Dec 2021 15:00:18: #1 read tag files... INFO @ Sat, 11 Dec 2021 15:00:18: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 15:00:23: 1000000 INFO @ Sat, 11 Dec 2021 15:00:28: 2000000 INFO @ Sat, 11 Dec 2021 15:00:33: 3000000 INFO @ Sat, 11 Dec 2021 15:00:38: 4000000 INFO @ Sat, 11 Dec 2021 15:00:42: #1 tag size is determined as 39 bps INFO @ Sat, 11 Dec 2021 15:00:42: #1 tag size = 39 INFO @ Sat, 11 Dec 2021 15:00:42: #1 total tags in treatment: 2200994 INFO @ Sat, 11 Dec 2021 15:00:42: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 15:00:42: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 11 Dec 2021 15:00:42: #1 tags after filtering in treatment: 1340123 INFO @ Sat, 11 Dec 2021 15:00:42: #1 Redundant rate of treatment: 0.39 INFO @ Sat, 11 Dec 2021 15:00:42: #1 finished! INFO @ Sat, 11 Dec 2021 15:00:42: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 15:00:42: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 15:00:42: #2 number of paired peaks: 10423 INFO @ Sat, 11 Dec 2021 15:00:42: start model_add_line... INFO @ Sat, 11 Dec 2021 15:00:42: start X-correlation... INFO @ Sat, 11 Dec 2021 15:00:42: end of X-cor INFO @ Sat, 11 Dec 2021 15:00:42: #2 finished! INFO @ Sat, 11 Dec 2021 15:00:42: #2 predicted fragment length is 156 bps INFO @ Sat, 11 Dec 2021 15:00:42: #2 alternative fragment length(s) may be 1,156 bps INFO @ Sat, 11 Dec 2021 15:00:42: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX9281750/SRX9281750.05_model.r INFO @ Sat, 11 Dec 2021 15:00:42: #3 Call peaks... INFO @ Sat, 11 Dec 2021 15:00:42: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Dec 2021 15:00:45: #3 Call peaks for each chromosome... WARNING: Skipping mount /opt/pkg/singularity/3.8.3/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Sat, 11 Dec 2021 15:00:47: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX9281750/SRX9281750.05_peaks.xls INFO @ Sat, 11 Dec 2021 15:00:47: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX9281750/SRX9281750.05_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 15:00:47: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX9281750/SRX9281750.05_summits.bed INFO @ Sat, 11 Dec 2021 15:00:47: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (7377 records, 4 fields): 9 millis CompletedMACS2peakCalling INFO @ Sat, 11 Dec 2021 15:00:48: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX9281750/SRX9281750.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX9281750/SRX9281750.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX9281750/SRX9281750.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX9281750/SRX9281750.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 @ Sat, 11 Dec 2021 15:00:48: #1 read tag files... INFO @ Sat, 11 Dec 2021 15:00:48: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 15:00:53: 1000000 INFO @ Sat, 11 Dec 2021 15:00:58: 2000000 INFO @ Sat, 11 Dec 2021 15:01:03: 3000000 INFO @ Sat, 11 Dec 2021 15:01:08: 4000000 INFO @ Sat, 11 Dec 2021 15:01:12: #1 tag size is determined as 39 bps INFO @ Sat, 11 Dec 2021 15:01:12: #1 tag size = 39 INFO @ Sat, 11 Dec 2021 15:01:12: #1 total tags in treatment: 2200994 INFO @ Sat, 11 Dec 2021 15:01:12: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 15:01:12: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 11 Dec 2021 15:01:12: #1 tags after filtering in treatment: 1340123 INFO @ Sat, 11 Dec 2021 15:01:12: #1 Redundant rate of treatment: 0.39 INFO @ Sat, 11 Dec 2021 15:01:12: #1 finished! INFO @ Sat, 11 Dec 2021 15:01:12: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 15:01:12: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 15:01:12: #2 number of paired peaks: 10423 INFO @ Sat, 11 Dec 2021 15:01:12: start model_add_line... INFO @ Sat, 11 Dec 2021 15:01:12: start X-correlation... INFO @ Sat, 11 Dec 2021 15:01:12: end of X-cor INFO @ Sat, 11 Dec 2021 15:01:12: #2 finished! INFO @ Sat, 11 Dec 2021 15:01:12: #2 predicted fragment length is 156 bps INFO @ Sat, 11 Dec 2021 15:01:12: #2 alternative fragment length(s) may be 1,156 bps INFO @ Sat, 11 Dec 2021 15:01:12: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX9281750/SRX9281750.10_model.r INFO @ Sat, 11 Dec 2021 15:01:12: #3 Call peaks... INFO @ Sat, 11 Dec 2021 15:01:12: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Dec 2021 15:01:15: #3 Call peaks for each chromosome... BedGraph に変換中... WARNING: Skipping mount /opt/pkg/singularity/3.8.3/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Sat, 11 Dec 2021 15:01:17: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX9281750/SRX9281750.10_peaks.xls INFO @ Sat, 11 Dec 2021 15:01:17: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX9281750/SRX9281750.10_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 15:01:17: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX9281750/SRX9281750.10_summits.bed INFO @ Sat, 11 Dec 2021 15:01:17: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (5960 records, 4 fields): 7 millis CompletedMACS2peakCalling INFO @ Sat, 11 Dec 2021 15:01:18: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX9281750/SRX9281750.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX9281750/SRX9281750.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX9281750/SRX9281750.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX9281750/SRX9281750.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 @ Sat, 11 Dec 2021 15:01:18: #1 read tag files... INFO @ Sat, 11 Dec 2021 15:01:18: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 15:01:23: 1000000 INFO @ Sat, 11 Dec 2021 15:01:28: 2000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 11 Dec 2021 15:01:33: 3000000 BigWig に変換しました。 INFO @ Sat, 11 Dec 2021 15:01:39: 4000000 INFO @ Sat, 11 Dec 2021 15:01:42: #1 tag size is determined as 39 bps INFO @ Sat, 11 Dec 2021 15:01:42: #1 tag size = 39 INFO @ Sat, 11 Dec 2021 15:01:42: #1 total tags in treatment: 2200994 INFO @ Sat, 11 Dec 2021 15:01:42: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 15:01:42: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 11 Dec 2021 15:01:42: #1 tags after filtering in treatment: 1340123 INFO @ Sat, 11 Dec 2021 15:01:42: #1 Redundant rate of treatment: 0.39 INFO @ Sat, 11 Dec 2021 15:01:42: #1 finished! INFO @ Sat, 11 Dec 2021 15:01:42: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 15:01:42: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 15:01:43: #2 number of paired peaks: 10423 INFO @ Sat, 11 Dec 2021 15:01:43: start model_add_line... INFO @ Sat, 11 Dec 2021 15:01:43: start X-correlation... INFO @ Sat, 11 Dec 2021 15:01:43: end of X-cor INFO @ Sat, 11 Dec 2021 15:01:43: #2 finished! INFO @ Sat, 11 Dec 2021 15:01:43: #2 predicted fragment length is 156 bps INFO @ Sat, 11 Dec 2021 15:01:43: #2 alternative fragment length(s) may be 1,156 bps INFO @ Sat, 11 Dec 2021 15:01:43: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX9281750/SRX9281750.20_model.r INFO @ Sat, 11 Dec 2021 15:01:43: #3 Call peaks... INFO @ Sat, 11 Dec 2021 15:01:43: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Dec 2021 15:01:46: #3 Call peaks for each chromosome... INFO @ Sat, 11 Dec 2021 15:01:47: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX9281750/SRX9281750.20_peaks.xls INFO @ Sat, 11 Dec 2021 15:01:47: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX9281750/SRX9281750.20_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 15:01:47: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX9281750/SRX9281750.20_summits.bed INFO @ Sat, 11 Dec 2021 15:01:47: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (3069 records, 4 fields): 5 millis CompletedMACS2peakCalling