Job ID = 14171449 SRX = SRX9555295 Genome = dm3 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... Read 7639196 spots for SRR13110751/SRR13110751.sra Written 7639196 spots for SRR13110751/SRR13110751.sra Read 7571002 spots for SRR13110752/SRR13110752.sra Written 7571002 spots for SRR13110752/SRR13110752.sra Read 7680374 spots for SRR13110753/SRR13110753.sra Written 7680374 spots for SRR13110753/SRR13110753.sra Read 7607840 spots for SRR13110754/SRR13110754.sra Written 7607840 spots for SRR13110754/SRR13110754.sra fastq に変換しました。 bowtie でマッピング中... Your job 14171946 ("srTdm6") has been submitted Time loading reference: 00:00:00 Time loading forward index: 00:00:01 Time loading mirror index: 00:00:00 Multiseed full-index search: 00:04:45 30498412 reads; of these: 30498412 (100.00%) were paired; of these: 29514633 (96.77%) aligned concordantly 0 times 766499 (2.51%) aligned concordantly exactly 1 time 217280 (0.71%) aligned concordantly >1 times ---- 29514633 pairs aligned concordantly 0 times; of these: 2678 (0.01%) aligned discordantly 1 time ---- 29511955 pairs aligned 0 times concordantly or discordantly; of these: 59023910 mates make up the pairs; of these: 58845289 (99.70%) aligned 0 times 64366 (0.11%) aligned exactly 1 time 114255 (0.19%) aligned >1 times 3.53% overall alignment rate Time searching: 00:04:46 Overall time: 00:04:46 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] 41770 / 985873 = 0.0424 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 11:49:30: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX9555295/SRX9555295.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX9555295/SRX9555295.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX9555295/SRX9555295.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX9555295/SRX9555295.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 11:49:30: #1 read tag files... INFO @ Sat, 11 Dec 2021 11:49:30: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 11:49:35: 1000000 INFO @ Sat, 11 Dec 2021 11:49:40: 2000000 INFO @ Sat, 11 Dec 2021 11:49:41: #1 tag size is determined as 39 bps INFO @ Sat, 11 Dec 2021 11:49:41: #1 tag size = 39 INFO @ Sat, 11 Dec 2021 11:49:41: #1 total tags in treatment: 942051 INFO @ Sat, 11 Dec 2021 11:49:41: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 11:49:41: #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 11:49:41: #1 tags after filtering in treatment: 847275 INFO @ Sat, 11 Dec 2021 11:49:41: #1 Redundant rate of treatment: 0.10 INFO @ Sat, 11 Dec 2021 11:49:41: #1 finished! INFO @ Sat, 11 Dec 2021 11:49:41: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 11:49:41: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 11:49:41: #2 number of paired peaks: 7349 INFO @ Sat, 11 Dec 2021 11:49:41: start model_add_line... INFO @ Sat, 11 Dec 2021 11:49:41: start X-correlation... INFO @ Sat, 11 Dec 2021 11:49:41: end of X-cor INFO @ Sat, 11 Dec 2021 11:49:41: #2 finished! INFO @ Sat, 11 Dec 2021 11:49:41: #2 predicted fragment length is 158 bps INFO @ Sat, 11 Dec 2021 11:49:41: #2 alternative fragment length(s) may be 158 bps INFO @ Sat, 11 Dec 2021 11:49:41: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX9555295/SRX9555295.05_model.r INFO @ Sat, 11 Dec 2021 11:49:41: #3 Call peaks... INFO @ Sat, 11 Dec 2021 11:49:41: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Dec 2021 11:49:43: #3 Call peaks for each chromosome... INFO @ Sat, 11 Dec 2021 11:49:44: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX9555295/SRX9555295.05_peaks.xls INFO @ Sat, 11 Dec 2021 11:49:44: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX9555295/SRX9555295.05_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 11:49:44: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX9555295/SRX9555295.05_summits.bed INFO @ Sat, 11 Dec 2021 11:49:44: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (2505 records, 4 fields): 4 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 @ Sat, 11 Dec 2021 11:50:00: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX9555295/SRX9555295.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX9555295/SRX9555295.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX9555295/SRX9555295.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX9555295/SRX9555295.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 11:50:00: #1 read tag files... INFO @ Sat, 11 Dec 2021 11:50:00: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 11:50:05: 1000000 INFO @ Sat, 11 Dec 2021 11:50:09: 2000000 INFO @ Sat, 11 Dec 2021 11:50:10: #1 tag size is determined as 39 bps INFO @ Sat, 11 Dec 2021 11:50:10: #1 tag size = 39 INFO @ Sat, 11 Dec 2021 11:50:10: #1 total tags in treatment: 942051 INFO @ Sat, 11 Dec 2021 11:50:10: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 11:50:10: #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 11:50:10: #1 tags after filtering in treatment: 847275 INFO @ Sat, 11 Dec 2021 11:50:10: #1 Redundant rate of treatment: 0.10 INFO @ Sat, 11 Dec 2021 11:50:10: #1 finished! INFO @ Sat, 11 Dec 2021 11:50:10: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 11:50:10: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 11:50:10: #2 number of paired peaks: 7349 INFO @ Sat, 11 Dec 2021 11:50:10: start model_add_line... INFO @ Sat, 11 Dec 2021 11:50:10: start X-correlation... INFO @ Sat, 11 Dec 2021 11:50:10: end of X-cor INFO @ Sat, 11 Dec 2021 11:50:10: #2 finished! INFO @ Sat, 11 Dec 2021 11:50:10: #2 predicted fragment length is 158 bps INFO @ Sat, 11 Dec 2021 11:50:10: #2 alternative fragment length(s) may be 158 bps INFO @ Sat, 11 Dec 2021 11:50:10: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX9555295/SRX9555295.10_model.r INFO @ Sat, 11 Dec 2021 11:50:10: #3 Call peaks... INFO @ Sat, 11 Dec 2021 11:50:10: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Dec 2021 11:50:12: #3 Call peaks for each chromosome... INFO @ Sat, 11 Dec 2021 11:50:13: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX9555295/SRX9555295.10_peaks.xls INFO @ Sat, 11 Dec 2021 11:50:13: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX9555295/SRX9555295.10_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 11:50:13: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX9555295/SRX9555295.10_summits.bed INFO @ Sat, 11 Dec 2021 11:50:13: Done! pass1 - making usageList (13 chroms): 0 millis pass2 - checking and writing primary data (843 records, 4 fields): 3 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 @ Sat, 11 Dec 2021 11:50:30: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX9555295/SRX9555295.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX9555295/SRX9555295.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX9555295/SRX9555295.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX9555295/SRX9555295.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 11:50:30: #1 read tag files... INFO @ Sat, 11 Dec 2021 11:50:30: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 11:50:35: 1000000 BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。 INFO @ Sat, 11 Dec 2021 11:50:41: 2000000 INFO @ Sat, 11 Dec 2021 11:50:41: #1 tag size is determined as 39 bps INFO @ Sat, 11 Dec 2021 11:50:41: #1 tag size = 39 INFO @ Sat, 11 Dec 2021 11:50:41: #1 total tags in treatment: 942051 INFO @ Sat, 11 Dec 2021 11:50:41: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 11:50:41: #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 11:50:41: #1 tags after filtering in treatment: 847275 INFO @ Sat, 11 Dec 2021 11:50:41: #1 Redundant rate of treatment: 0.10 INFO @ Sat, 11 Dec 2021 11:50:41: #1 finished! INFO @ Sat, 11 Dec 2021 11:50:41: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 11:50:41: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 11:50:41: #2 number of paired peaks: 7349 INFO @ Sat, 11 Dec 2021 11:50:41: start model_add_line... INFO @ Sat, 11 Dec 2021 11:50:41: start X-correlation... INFO @ Sat, 11 Dec 2021 11:50:41: end of X-cor INFO @ Sat, 11 Dec 2021 11:50:41: #2 finished! INFO @ Sat, 11 Dec 2021 11:50:41: #2 predicted fragment length is 158 bps INFO @ Sat, 11 Dec 2021 11:50:41: #2 alternative fragment length(s) may be 158 bps INFO @ Sat, 11 Dec 2021 11:50:41: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX9555295/SRX9555295.20_model.r INFO @ Sat, 11 Dec 2021 11:50:41: #3 Call peaks... INFO @ Sat, 11 Dec 2021 11:50:41: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Dec 2021 11:50:43: #3 Call peaks for each chromosome... INFO @ Sat, 11 Dec 2021 11:50:44: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX9555295/SRX9555295.20_peaks.xls INFO @ Sat, 11 Dec 2021 11:50:44: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX9555295/SRX9555295.20_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 11:50:44: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX9555295/SRX9555295.20_summits.bed INFO @ Sat, 11 Dec 2021 11:50:44: Done! pass1 - making usageList (13 chroms): 1 millis pass2 - checking and writing primary data (228 records, 4 fields): 1 millis CompletedMACS2peakCalling