Job ID = 14171388 SRX = SRX9555262 Genome = dm3 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... Read 8158365 spots for SRR13110402/SRR13110402.sra Written 8158365 spots for SRR13110402/SRR13110402.sra Read 8193569 spots for SRR13110403/SRR13110403.sra Written 8193569 spots for SRR13110403/SRR13110403.sra Read 8349661 spots for SRR13110404/SRR13110404.sra Written 8349661 spots for SRR13110404/SRR13110404.sra Read 8298243 spots for SRR13110405/SRR13110405.sra Written 8298243 spots for SRR13110405/SRR13110405.sra fastq に変換しました。 bowtie でマッピング中... Your job 14171882 ("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: 00:04:35 32999838 reads; of these: 32999838 (100.00%) were paired; of these: 32105531 (97.29%) aligned concordantly 0 times 725963 (2.20%) aligned concordantly exactly 1 time 168344 (0.51%) aligned concordantly >1 times ---- 32105531 pairs aligned concordantly 0 times; of these: 3000 (0.01%) aligned discordantly 1 time ---- 32102531 pairs aligned 0 times concordantly or discordantly; of these: 64205062 mates make up the pairs; of these: 63999579 (99.68%) aligned 0 times 71704 (0.11%) aligned exactly 1 time 133779 (0.21%) aligned >1 times 3.03% overall alignment rate Time searching: 00:04:35 Overall time: 00:04:35 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] 24686 / 896478 = 0.0275 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 11:39:04: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX9555262/SRX9555262.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX9555262/SRX9555262.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX9555262/SRX9555262.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX9555262/SRX9555262.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 11:39:04: #1 read tag files... INFO @ Sat, 11 Dec 2021 11:39:04: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 11:39:10: 1000000 INFO @ Sat, 11 Dec 2021 11:39:15: #1 tag size is determined as 39 bps INFO @ Sat, 11 Dec 2021 11:39:15: #1 tag size = 39 INFO @ Sat, 11 Dec 2021 11:39:15: #1 total tags in treatment: 869701 INFO @ Sat, 11 Dec 2021 11:39:15: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 11:39:15: #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 11:39:15: #1 tags after filtering in treatment: 848070 INFO @ Sat, 11 Dec 2021 11:39:15: #1 Redundant rate of treatment: 0.02 INFO @ Sat, 11 Dec 2021 11:39:15: #1 finished! INFO @ Sat, 11 Dec 2021 11:39:15: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 11:39:15: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 11:39:15: #2 number of paired peaks: 1619 INFO @ Sat, 11 Dec 2021 11:39:15: start model_add_line... INFO @ Sat, 11 Dec 2021 11:39:15: start X-correlation... INFO @ Sat, 11 Dec 2021 11:39:15: end of X-cor INFO @ Sat, 11 Dec 2021 11:39:15: #2 finished! INFO @ Sat, 11 Dec 2021 11:39:15: #2 predicted fragment length is 153 bps INFO @ Sat, 11 Dec 2021 11:39:15: #2 alternative fragment length(s) may be 153 bps INFO @ Sat, 11 Dec 2021 11:39:15: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX9555262/SRX9555262.05_model.r INFO @ Sat, 11 Dec 2021 11:39:15: #3 Call peaks... INFO @ Sat, 11 Dec 2021 11:39:15: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Dec 2021 11:39:17: #3 Call peaks for each chromosome... INFO @ Sat, 11 Dec 2021 11:39:18: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX9555262/SRX9555262.05_peaks.xls INFO @ Sat, 11 Dec 2021 11:39:18: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX9555262/SRX9555262.05_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 11:39:18: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX9555262/SRX9555262.05_summits.bed INFO @ Sat, 11 Dec 2021 11:39:18: Done! pass1 - making usageList (11 chroms): 1 millis pass2 - checking and writing primary data (270 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 @ Sat, 11 Dec 2021 11:39:34: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX9555262/SRX9555262.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX9555262/SRX9555262.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX9555262/SRX9555262.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX9555262/SRX9555262.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 11:39:34: #1 read tag files... INFO @ Sat, 11 Dec 2021 11:39:34: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 11:39:39: 1000000 INFO @ Sat, 11 Dec 2021 11:39:43: #1 tag size is determined as 39 bps INFO @ Sat, 11 Dec 2021 11:39:43: #1 tag size = 39 INFO @ Sat, 11 Dec 2021 11:39:43: #1 total tags in treatment: 869701 INFO @ Sat, 11 Dec 2021 11:39:43: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 11:39:43: #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 11:39:43: #1 tags after filtering in treatment: 848070 INFO @ Sat, 11 Dec 2021 11:39:43: #1 Redundant rate of treatment: 0.02 INFO @ Sat, 11 Dec 2021 11:39:43: #1 finished! INFO @ Sat, 11 Dec 2021 11:39:43: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 11:39:43: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 11:39:43: #2 number of paired peaks: 1619 INFO @ Sat, 11 Dec 2021 11:39:43: start model_add_line... INFO @ Sat, 11 Dec 2021 11:39:43: start X-correlation... INFO @ Sat, 11 Dec 2021 11:39:43: end of X-cor INFO @ Sat, 11 Dec 2021 11:39:43: #2 finished! INFO @ Sat, 11 Dec 2021 11:39:43: #2 predicted fragment length is 153 bps INFO @ Sat, 11 Dec 2021 11:39:43: #2 alternative fragment length(s) may be 153 bps INFO @ Sat, 11 Dec 2021 11:39:43: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX9555262/SRX9555262.10_model.r INFO @ Sat, 11 Dec 2021 11:39:43: #3 Call peaks... INFO @ Sat, 11 Dec 2021 11:39:43: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Dec 2021 11:39:45: #3 Call peaks for each chromosome... INFO @ Sat, 11 Dec 2021 11:39:46: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX9555262/SRX9555262.10_peaks.xls INFO @ Sat, 11 Dec 2021 11:39:46: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX9555262/SRX9555262.10_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 11:39:46: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX9555262/SRX9555262.10_summits.bed INFO @ Sat, 11 Dec 2021 11:39:46: Done! pass1 - making usageList (9 chroms): 0 millis pass2 - checking and writing primary data (124 records, 4 fields): 2 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 11:40:04: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX9555262/SRX9555262.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX9555262/SRX9555262.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX9555262/SRX9555262.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX9555262/SRX9555262.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 11:40:04: #1 read tag files... INFO @ Sat, 11 Dec 2021 11:40:04: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 11:40:09: 1000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 11 Dec 2021 11:40:14: #1 tag size is determined as 39 bps INFO @ Sat, 11 Dec 2021 11:40:14: #1 tag size = 39 INFO @ Sat, 11 Dec 2021 11:40:14: #1 total tags in treatment: 869701 INFO @ Sat, 11 Dec 2021 11:40:14: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 11:40:14: #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 11:40:14: #1 tags after filtering in treatment: 848070 INFO @ Sat, 11 Dec 2021 11:40:14: #1 Redundant rate of treatment: 0.02 INFO @ Sat, 11 Dec 2021 11:40:14: #1 finished! INFO @ Sat, 11 Dec 2021 11:40:14: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 11:40:14: #2 looking for paired plus/minus strand peaks... BigWig に変換しました。 INFO @ Sat, 11 Dec 2021 11:40:14: #2 number of paired peaks: 1619 INFO @ Sat, 11 Dec 2021 11:40:14: start model_add_line... INFO @ Sat, 11 Dec 2021 11:40:14: start X-correlation... INFO @ Sat, 11 Dec 2021 11:40:14: end of X-cor INFO @ Sat, 11 Dec 2021 11:40:14: #2 finished! INFO @ Sat, 11 Dec 2021 11:40:14: #2 predicted fragment length is 153 bps INFO @ Sat, 11 Dec 2021 11:40:14: #2 alternative fragment length(s) may be 153 bps INFO @ Sat, 11 Dec 2021 11:40:14: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX9555262/SRX9555262.20_model.r INFO @ Sat, 11 Dec 2021 11:40:15: #3 Call peaks... INFO @ Sat, 11 Dec 2021 11:40:15: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Dec 2021 11:40:16: #3 Call peaks for each chromosome... INFO @ Sat, 11 Dec 2021 11:40:17: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX9555262/SRX9555262.20_peaks.xls INFO @ Sat, 11 Dec 2021 11:40:17: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX9555262/SRX9555262.20_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 11:40:17: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX9555262/SRX9555262.20_summits.bed INFO @ Sat, 11 Dec 2021 11:40:17: Done! pass1 - making usageList (3 chroms): 1 millis pass2 - checking and writing primary data (34 records, 4 fields): 0 millis CompletedMACS2peakCalling