Job ID = 14168363 SRX = SRX11078127 Genome = dm3 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... 2021-12-10T09:07:50 prefetch.2.10.7: 1) Downloading 'SRR14743555'... 2021-12-10T09:07:50 prefetch.2.10.7: Downloading via HTTPS... 2021-12-10T09:08:03 prefetch.2.10.7: HTTPS download succeed 2021-12-10T09:08:03 prefetch.2.10.7: 'SRR14743555' is valid 2021-12-10T09:08:03 prefetch.2.10.7: 1) 'SRR14743555' was downloaded successfully 2021-12-10T09:08:03 prefetch.2.10.7: 'SRR14743555' has 0 unresolved dependencies Read 6956216 spots for SRR14743555/SRR14743555.sra Written 6956216 spots for SRR14743555/SRR14743555.sra fastq に変換しました。 bowtie でマッピング中... Your job 14169527 ("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: 00:01:07 6956216 reads; of these: 6956216 (100.00%) were paired; of these: 6697000 (96.27%) aligned concordantly 0 times 192334 (2.76%) aligned concordantly exactly 1 time 66882 (0.96%) aligned concordantly >1 times ---- 6697000 pairs aligned concordantly 0 times; of these: 273 (0.00%) aligned discordantly 1 time ---- 6696727 pairs aligned 0 times concordantly or discordantly; of these: 13393454 mates make up the pairs; of these: 13345850 (99.64%) aligned 0 times 13752 (0.10%) aligned exactly 1 time 33852 (0.25%) aligned >1 times 4.07% overall alignment rate Time searching: 00:01:07 Overall time: 00:01:07 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] 5882 / 259310 = 0.0227 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 @ Fri, 10 Dec 2021 18:10:22: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX11078127/SRX11078127.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX11078127/SRX11078127.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX11078127/SRX11078127.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX11078127/SRX11078127.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 @ Fri, 10 Dec 2021 18:10:22: #1 read tag files... INFO @ Fri, 10 Dec 2021 18:10:22: #1 read treatment tags... INFO @ Fri, 10 Dec 2021 18:10:25: #1 tag size is determined as 40 bps INFO @ Fri, 10 Dec 2021 18:10:25: #1 tag size = 40 INFO @ Fri, 10 Dec 2021 18:10:25: #1 total tags in treatment: 253342 INFO @ Fri, 10 Dec 2021 18:10:25: #1 user defined the maximum tags... INFO @ Fri, 10 Dec 2021 18:10:25: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 10 Dec 2021 18:10:25: #1 tags after filtering in treatment: 250887 INFO @ Fri, 10 Dec 2021 18:10:25: #1 Redundant rate of treatment: 0.01 INFO @ Fri, 10 Dec 2021 18:10:25: #1 finished! INFO @ Fri, 10 Dec 2021 18:10:25: #2 Build Peak Model... INFO @ Fri, 10 Dec 2021 18:10:25: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Dec 2021 18:10:25: #2 number of paired peaks: 1094 INFO @ Fri, 10 Dec 2021 18:10:25: start model_add_line... INFO @ Fri, 10 Dec 2021 18:10:25: start X-correlation... INFO @ Fri, 10 Dec 2021 18:10:25: end of X-cor INFO @ Fri, 10 Dec 2021 18:10:25: #2 finished! INFO @ Fri, 10 Dec 2021 18:10:25: #2 predicted fragment length is 98 bps INFO @ Fri, 10 Dec 2021 18:10:25: #2 alternative fragment length(s) may be 98 bps INFO @ Fri, 10 Dec 2021 18:10:25: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX11078127/SRX11078127.05_model.r INFO @ Fri, 10 Dec 2021 18:10:25: #3 Call peaks... INFO @ Fri, 10 Dec 2021 18:10:25: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 10 Dec 2021 18:10:26: #3 Call peaks for each chromosome... INFO @ Fri, 10 Dec 2021 18:10:26: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX11078127/SRX11078127.05_peaks.xls INFO @ Fri, 10 Dec 2021 18:10:26: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX11078127/SRX11078127.05_peaks.narrowPeak INFO @ Fri, 10 Dec 2021 18:10:26: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX11078127/SRX11078127.05_summits.bed INFO @ Fri, 10 Dec 2021 18:10:26: Done! pass1 - making usageList (3 chroms): 1 millis pass2 - checking and writing primary data (53 records, 4 fields): 1 millis CompletedMACS2peakCalling 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 @ Fri, 10 Dec 2021 18:10:52: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX11078127/SRX11078127.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX11078127/SRX11078127.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX11078127/SRX11078127.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX11078127/SRX11078127.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 @ Fri, 10 Dec 2021 18:10:52: #1 read tag files... INFO @ Fri, 10 Dec 2021 18:10:52: #1 read treatment tags... INFO @ Fri, 10 Dec 2021 18:10:55: #1 tag size is determined as 40 bps INFO @ Fri, 10 Dec 2021 18:10:55: #1 tag size = 40 INFO @ Fri, 10 Dec 2021 18:10:55: #1 total tags in treatment: 253342 INFO @ Fri, 10 Dec 2021 18:10:55: #1 user defined the maximum tags... INFO @ Fri, 10 Dec 2021 18:10:55: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 10 Dec 2021 18:10:55: #1 tags after filtering in treatment: 250887 INFO @ Fri, 10 Dec 2021 18:10:55: #1 Redundant rate of treatment: 0.01 INFO @ Fri, 10 Dec 2021 18:10:55: #1 finished! INFO @ Fri, 10 Dec 2021 18:10:55: #2 Build Peak Model... INFO @ Fri, 10 Dec 2021 18:10:55: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Dec 2021 18:10:55: #2 number of paired peaks: 1094 INFO @ Fri, 10 Dec 2021 18:10:55: start model_add_line... INFO @ Fri, 10 Dec 2021 18:10:55: start X-correlation... INFO @ Fri, 10 Dec 2021 18:10:55: end of X-cor INFO @ Fri, 10 Dec 2021 18:10:55: #2 finished! INFO @ Fri, 10 Dec 2021 18:10:55: #2 predicted fragment length is 98 bps INFO @ Fri, 10 Dec 2021 18:10:55: #2 alternative fragment length(s) may be 98 bps INFO @ Fri, 10 Dec 2021 18:10:55: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX11078127/SRX11078127.10_model.r INFO @ Fri, 10 Dec 2021 18:10:55: #3 Call peaks... INFO @ Fri, 10 Dec 2021 18:10:55: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 10 Dec 2021 18:10:56: #3 Call peaks for each chromosome... INFO @ Fri, 10 Dec 2021 18:10:56: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX11078127/SRX11078127.10_peaks.xls INFO @ Fri, 10 Dec 2021 18:10:56: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX11078127/SRX11078127.10_peaks.narrowPeak INFO @ Fri, 10 Dec 2021 18:10:56: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX11078127/SRX11078127.10_summits.bed INFO @ Fri, 10 Dec 2021 18:10:56: Done! pass1 - making usageList (3 chroms): 1 millis pass2 - checking and writing primary data (38 records, 4 fields): 1 millis CompletedMACS2peakCalling 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 @ Fri, 10 Dec 2021 18:11:22: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX11078127/SRX11078127.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX11078127/SRX11078127.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX11078127/SRX11078127.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX11078127/SRX11078127.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 @ Fri, 10 Dec 2021 18:11:22: #1 read tag files... INFO @ Fri, 10 Dec 2021 18:11:22: #1 read treatment tags... BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。 INFO @ Fri, 10 Dec 2021 18:11:25: #1 tag size is determined as 40 bps INFO @ Fri, 10 Dec 2021 18:11:25: #1 tag size = 40 INFO @ Fri, 10 Dec 2021 18:11:25: #1 total tags in treatment: 253342 INFO @ Fri, 10 Dec 2021 18:11:25: #1 user defined the maximum tags... INFO @ Fri, 10 Dec 2021 18:11:25: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 10 Dec 2021 18:11:25: #1 tags after filtering in treatment: 250887 INFO @ Fri, 10 Dec 2021 18:11:25: #1 Redundant rate of treatment: 0.01 INFO @ Fri, 10 Dec 2021 18:11:25: #1 finished! INFO @ Fri, 10 Dec 2021 18:11:25: #2 Build Peak Model... INFO @ Fri, 10 Dec 2021 18:11:25: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Dec 2021 18:11:25: #2 number of paired peaks: 1094 INFO @ Fri, 10 Dec 2021 18:11:25: start model_add_line... INFO @ Fri, 10 Dec 2021 18:11:25: start X-correlation... INFO @ Fri, 10 Dec 2021 18:11:25: end of X-cor INFO @ Fri, 10 Dec 2021 18:11:25: #2 finished! INFO @ Fri, 10 Dec 2021 18:11:25: #2 predicted fragment length is 98 bps INFO @ Fri, 10 Dec 2021 18:11:25: #2 alternative fragment length(s) may be 98 bps INFO @ Fri, 10 Dec 2021 18:11:25: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX11078127/SRX11078127.20_model.r INFO @ Fri, 10 Dec 2021 18:11:25: #3 Call peaks... INFO @ Fri, 10 Dec 2021 18:11:25: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 10 Dec 2021 18:11:25: #3 Call peaks for each chromosome... INFO @ Fri, 10 Dec 2021 18:11:26: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX11078127/SRX11078127.20_peaks.xls INFO @ Fri, 10 Dec 2021 18:11:26: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX11078127/SRX11078127.20_peaks.narrowPeak INFO @ Fri, 10 Dec 2021 18:11:26: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX11078127/SRX11078127.20_summits.bed INFO @ Fri, 10 Dec 2021 18:11:26: Done! pass1 - making usageList (3 chroms): 1 millis pass2 - checking and writing primary data (20 records, 4 fields): 1 millis CompletedMACS2peakCalling