Job ID = 14171426 SRX = SRX9555280 Genome = dm3 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... Read 3858056 spots for SRR13110691/SRR13110691.sra Written 3858056 spots for SRR13110691/SRR13110691.sra Read 3764719 spots for SRR13110692/SRR13110692.sra Written 3764719 spots for SRR13110692/SRR13110692.sra Read 3989447 spots for SRR13110693/SRR13110693.sra Written 3989447 spots for SRR13110693/SRR13110693.sra Read 3884062 spots for SRR13110694/SRR13110694.sra Written 3884062 spots for SRR13110694/SRR13110694.sra fastq に変換しました。 bowtie でマッピング中... Your job 14171899 ("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: 00:02:58 15496284 reads; of these: 15496284 (100.00%) were paired; of these: 15327179 (98.91%) aligned concordantly 0 times 125337 (0.81%) aligned concordantly exactly 1 time 43768 (0.28%) aligned concordantly >1 times ---- 15327179 pairs aligned concordantly 0 times; of these: 4234 (0.03%) aligned discordantly 1 time ---- 15322945 pairs aligned 0 times concordantly or discordantly; of these: 30645890 mates make up the pairs; of these: 29890305 (97.53%) aligned 0 times 360704 (1.18%) aligned exactly 1 time 394881 (1.29%) aligned >1 times 3.56% overall alignment rate Time searching: 00:02:59 Overall time: 00:02:59 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] 3887 / 170040 = 0.0229 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 11:42:19: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX9555280/SRX9555280.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX9555280/SRX9555280.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX9555280/SRX9555280.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX9555280/SRX9555280.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 11:42:19: #1 read tag files... INFO @ Sat, 11 Dec 2021 11:42:19: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 11:42:23: 1000000 INFO @ Sat, 11 Dec 2021 11:42:24: #1 tag size is determined as 39 bps INFO @ Sat, 11 Dec 2021 11:42:24: #1 tag size = 39 INFO @ Sat, 11 Dec 2021 11:42:24: #1 total tags in treatment: 165241 INFO @ Sat, 11 Dec 2021 11:42:24: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 11:42:24: #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 11:42:24: #1 tags after filtering in treatment: 163970 INFO @ Sat, 11 Dec 2021 11:42:24: #1 Redundant rate of treatment: 0.01 INFO @ Sat, 11 Dec 2021 11:42:24: #1 finished! INFO @ Sat, 11 Dec 2021 11:42:24: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 11:42:24: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 11:42:24: #2 number of paired peaks: 1862 INFO @ Sat, 11 Dec 2021 11:42:24: start model_add_line... INFO @ Sat, 11 Dec 2021 11:42:24: start X-correlation... INFO @ Sat, 11 Dec 2021 11:42:24: end of X-cor INFO @ Sat, 11 Dec 2021 11:42:24: #2 finished! INFO @ Sat, 11 Dec 2021 11:42:24: #2 predicted fragment length is 254 bps INFO @ Sat, 11 Dec 2021 11:42:24: #2 alternative fragment length(s) may be 100,254,277 bps INFO @ Sat, 11 Dec 2021 11:42:24: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX9555280/SRX9555280.05_model.r INFO @ Sat, 11 Dec 2021 11:42:24: #3 Call peaks... INFO @ Sat, 11 Dec 2021 11:42:24: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Dec 2021 11:42:24: #3 Call peaks for each chromosome... INFO @ Sat, 11 Dec 2021 11:42:24: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX9555280/SRX9555280.05_peaks.xls INFO @ Sat, 11 Dec 2021 11:42:24: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX9555280/SRX9555280.05_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 11:42:24: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX9555280/SRX9555280.05_summits.bed INFO @ Sat, 11 Dec 2021 11:42:24: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (46 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 11:42:49: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX9555280/SRX9555280.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX9555280/SRX9555280.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX9555280/SRX9555280.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX9555280/SRX9555280.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 11:42:49: #1 read tag files... INFO @ Sat, 11 Dec 2021 11:42:49: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 11:42:54: 1000000 INFO @ Sat, 11 Dec 2021 11:42:55: #1 tag size is determined as 39 bps INFO @ Sat, 11 Dec 2021 11:42:55: #1 tag size = 39 INFO @ Sat, 11 Dec 2021 11:42:55: #1 total tags in treatment: 165241 INFO @ Sat, 11 Dec 2021 11:42:55: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 11:42:55: #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 11:42:55: #1 tags after filtering in treatment: 163970 INFO @ Sat, 11 Dec 2021 11:42:55: #1 Redundant rate of treatment: 0.01 INFO @ Sat, 11 Dec 2021 11:42:55: #1 finished! INFO @ Sat, 11 Dec 2021 11:42:55: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 11:42:55: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 11:42:55: #2 number of paired peaks: 1862 INFO @ Sat, 11 Dec 2021 11:42:55: start model_add_line... INFO @ Sat, 11 Dec 2021 11:42:55: start X-correlation... INFO @ Sat, 11 Dec 2021 11:42:55: end of X-cor INFO @ Sat, 11 Dec 2021 11:42:55: #2 finished! INFO @ Sat, 11 Dec 2021 11:42:55: #2 predicted fragment length is 254 bps INFO @ Sat, 11 Dec 2021 11:42:55: #2 alternative fragment length(s) may be 100,254,277 bps INFO @ Sat, 11 Dec 2021 11:42:55: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX9555280/SRX9555280.10_model.r INFO @ Sat, 11 Dec 2021 11:42:55: #3 Call peaks... INFO @ Sat, 11 Dec 2021 11:42:55: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Dec 2021 11:42:55: #3 Call peaks for each chromosome... INFO @ Sat, 11 Dec 2021 11:42:56: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX9555280/SRX9555280.10_peaks.xls INFO @ Sat, 11 Dec 2021 11:42:56: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX9555280/SRX9555280.10_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 11:42:56: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX9555280/SRX9555280.10_summits.bed INFO @ Sat, 11 Dec 2021 11:42:56: Done! pass1 - making usageList (2 chroms): 1 millis pass2 - checking and writing primary data (18 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 @ Sat, 11 Dec 2021 11:43:19: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX9555280/SRX9555280.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX9555280/SRX9555280.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX9555280/SRX9555280.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX9555280/SRX9555280.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 11:43:19: #1 read tag files... INFO @ Sat, 11 Dec 2021 11:43:19: #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 @ Sat, 11 Dec 2021 11:43:24: 1000000 INFO @ Sat, 11 Dec 2021 11:43:25: #1 tag size is determined as 39 bps INFO @ Sat, 11 Dec 2021 11:43:25: #1 tag size = 39 INFO @ Sat, 11 Dec 2021 11:43:25: #1 total tags in treatment: 165241 INFO @ Sat, 11 Dec 2021 11:43:25: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 11:43:25: #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 11:43:25: #1 tags after filtering in treatment: 163970 INFO @ Sat, 11 Dec 2021 11:43:25: #1 Redundant rate of treatment: 0.01 INFO @ Sat, 11 Dec 2021 11:43:25: #1 finished! INFO @ Sat, 11 Dec 2021 11:43:25: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 11:43:25: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 11:43:25: #2 number of paired peaks: 1862 INFO @ Sat, 11 Dec 2021 11:43:25: start model_add_line... INFO @ Sat, 11 Dec 2021 11:43:25: start X-correlation... INFO @ Sat, 11 Dec 2021 11:43:25: end of X-cor INFO @ Sat, 11 Dec 2021 11:43:25: #2 finished! INFO @ Sat, 11 Dec 2021 11:43:25: #2 predicted fragment length is 254 bps INFO @ Sat, 11 Dec 2021 11:43:25: #2 alternative fragment length(s) may be 100,254,277 bps INFO @ Sat, 11 Dec 2021 11:43:25: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX9555280/SRX9555280.20_model.r INFO @ Sat, 11 Dec 2021 11:43:25: #3 Call peaks... INFO @ Sat, 11 Dec 2021 11:43:25: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Dec 2021 11:43:25: #3 Call peaks for each chromosome... INFO @ Sat, 11 Dec 2021 11:43:25: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX9555280/SRX9555280.20_peaks.xls INFO @ Sat, 11 Dec 2021 11:43:25: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX9555280/SRX9555280.20_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 11:43:25: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX9555280/SRX9555280.20_summits.bed INFO @ Sat, 11 Dec 2021 11:43:25: Done! pass1 - making usageList (1 chroms): 1 millis pass2 - checking and writing primary data (3 records, 4 fields): 1 millis CompletedMACS2peakCalling