Job ID = 14171146 SRX = SRX9555318 Genome = dm3 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... Read 1231721 spots for SRR13110459/SRR13110459.sra Written 1231721 spots for SRR13110459/SRR13110459.sra Read 1215960 spots for SRR13110460/SRR13110460.sra Written 1215960 spots for SRR13110460/SRR13110460.sra Read 1243079 spots for SRR13110461/SRR13110461.sra Written 1243079 spots for SRR13110461/SRR13110461.sra Read 1225583 spots for SRR13110462/SRR13110462.sra Written 1225583 spots for SRR13110462/SRR13110462.sra fastq に変換しました。 bowtie でマッピング中... Your job 14171611 ("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: 00:00:45 4916343 reads; of these: 4916343 (100.00%) were paired; of these: 4755953 (96.74%) aligned concordantly 0 times 112382 (2.29%) aligned concordantly exactly 1 time 48008 (0.98%) aligned concordantly >1 times ---- 4755953 pairs aligned concordantly 0 times; of these: 592 (0.01%) aligned discordantly 1 time ---- 4755361 pairs aligned 0 times concordantly or discordantly; of these: 9510722 mates make up the pairs; of these: 9483314 (99.71%) aligned 0 times 9673 (0.10%) aligned exactly 1 time 17735 (0.19%) aligned >1 times 3.55% overall alignment rate Time searching: 00:00:45 Overall time: 00:00:45 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] 3670 / 160838 = 0.0228 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 10:09:27: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX9555318/SRX9555318.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX9555318/SRX9555318.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX9555318/SRX9555318.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX9555318/SRX9555318.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 10:09:27: #1 read tag files... INFO @ Sat, 11 Dec 2021 10:09:27: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 10:09:29: #1 tag size is determined as 39 bps INFO @ Sat, 11 Dec 2021 10:09:29: #1 tag size = 39 INFO @ Sat, 11 Dec 2021 10:09:29: #1 total tags in treatment: 156731 INFO @ Sat, 11 Dec 2021 10:09:29: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 10:09:29: #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 10:09:29: #1 tags after filtering in treatment: 154915 INFO @ Sat, 11 Dec 2021 10:09:29: #1 Redundant rate of treatment: 0.01 INFO @ Sat, 11 Dec 2021 10:09:29: #1 finished! INFO @ Sat, 11 Dec 2021 10:09:29: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 10:09:29: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 10:09:29: #2 number of paired peaks: 1629 INFO @ Sat, 11 Dec 2021 10:09:29: start model_add_line... INFO @ Sat, 11 Dec 2021 10:09:29: start X-correlation... INFO @ Sat, 11 Dec 2021 10:09:29: end of X-cor INFO @ Sat, 11 Dec 2021 10:09:29: #2 finished! INFO @ Sat, 11 Dec 2021 10:09:29: #2 predicted fragment length is 269 bps INFO @ Sat, 11 Dec 2021 10:09:29: #2 alternative fragment length(s) may be 211,269 bps INFO @ Sat, 11 Dec 2021 10:09:29: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX9555318/SRX9555318.05_model.r INFO @ Sat, 11 Dec 2021 10:09:29: #3 Call peaks... INFO @ Sat, 11 Dec 2021 10:09:29: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Dec 2021 10:09:29: #3 Call peaks for each chromosome... INFO @ Sat, 11 Dec 2021 10:09:30: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX9555318/SRX9555318.05_peaks.xls INFO @ Sat, 11 Dec 2021 10:09:30: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX9555318/SRX9555318.05_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 10:09:30: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX9555318/SRX9555318.05_summits.bed INFO @ Sat, 11 Dec 2021 10:09:30: Done! pass1 - making usageList (3 chroms): 1 millis pass2 - checking and writing primary data (47 records, 4 fields): 5 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 10:09:57: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX9555318/SRX9555318.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX9555318/SRX9555318.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX9555318/SRX9555318.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX9555318/SRX9555318.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 10:09:57: #1 read tag files... INFO @ Sat, 11 Dec 2021 10:09:57: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 10:09:59: #1 tag size is determined as 39 bps INFO @ Sat, 11 Dec 2021 10:09:59: #1 tag size = 39 INFO @ Sat, 11 Dec 2021 10:09:59: #1 total tags in treatment: 156731 INFO @ Sat, 11 Dec 2021 10:09:59: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 10:09:59: #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 10:09:59: #1 tags after filtering in treatment: 154915 INFO @ Sat, 11 Dec 2021 10:09:59: #1 Redundant rate of treatment: 0.01 INFO @ Sat, 11 Dec 2021 10:09:59: #1 finished! INFO @ Sat, 11 Dec 2021 10:09:59: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 10:09:59: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 10:09:59: #2 number of paired peaks: 1629 INFO @ Sat, 11 Dec 2021 10:09:59: start model_add_line... INFO @ Sat, 11 Dec 2021 10:09:59: start X-correlation... INFO @ Sat, 11 Dec 2021 10:09:59: end of X-cor INFO @ Sat, 11 Dec 2021 10:09:59: #2 finished! INFO @ Sat, 11 Dec 2021 10:09:59: #2 predicted fragment length is 269 bps INFO @ Sat, 11 Dec 2021 10:09:59: #2 alternative fragment length(s) may be 211,269 bps INFO @ Sat, 11 Dec 2021 10:09:59: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX9555318/SRX9555318.10_model.r INFO @ Sat, 11 Dec 2021 10:09:59: #3 Call peaks... INFO @ Sat, 11 Dec 2021 10:09:59: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Dec 2021 10:09:59: #3 Call peaks for each chromosome... INFO @ Sat, 11 Dec 2021 10:09:59: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX9555318/SRX9555318.10_peaks.xls INFO @ Sat, 11 Dec 2021 10:09:59: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX9555318/SRX9555318.10_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 10:09:59: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX9555318/SRX9555318.10_summits.bed INFO @ Sat, 11 Dec 2021 10:09:59: Done! pass1 - making usageList (3 chroms): 0 millis pass2 - checking and writing primary data (32 records, 4 fields): 5 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 10:10:27: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX9555318/SRX9555318.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX9555318/SRX9555318.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX9555318/SRX9555318.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX9555318/SRX9555318.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 10:10:27: #1 read tag files... INFO @ Sat, 11 Dec 2021 10:10:27: #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 10:10:29: #1 tag size is determined as 39 bps INFO @ Sat, 11 Dec 2021 10:10:29: #1 tag size = 39 INFO @ Sat, 11 Dec 2021 10:10:29: #1 total tags in treatment: 156731 INFO @ Sat, 11 Dec 2021 10:10:29: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 10:10:29: #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 10:10:29: #1 tags after filtering in treatment: 154915 INFO @ Sat, 11 Dec 2021 10:10:29: #1 Redundant rate of treatment: 0.01 INFO @ Sat, 11 Dec 2021 10:10:29: #1 finished! INFO @ Sat, 11 Dec 2021 10:10:29: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 10:10:29: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 10:10:29: #2 number of paired peaks: 1629 INFO @ Sat, 11 Dec 2021 10:10:29: start model_add_line... INFO @ Sat, 11 Dec 2021 10:10:29: start X-correlation... INFO @ Sat, 11 Dec 2021 10:10:29: end of X-cor INFO @ Sat, 11 Dec 2021 10:10:29: #2 finished! INFO @ Sat, 11 Dec 2021 10:10:29: #2 predicted fragment length is 269 bps INFO @ Sat, 11 Dec 2021 10:10:29: #2 alternative fragment length(s) may be 211,269 bps INFO @ Sat, 11 Dec 2021 10:10:29: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX9555318/SRX9555318.20_model.r INFO @ Sat, 11 Dec 2021 10:10:29: #3 Call peaks... INFO @ Sat, 11 Dec 2021 10:10:29: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Dec 2021 10:10:29: #3 Call peaks for each chromosome... INFO @ Sat, 11 Dec 2021 10:10:30: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX9555318/SRX9555318.20_peaks.xls INFO @ Sat, 11 Dec 2021 10:10:30: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX9555318/SRX9555318.20_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 10:10:30: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX9555318/SRX9555318.20_summits.bed INFO @ Sat, 11 Dec 2021 10:10:30: Done! pass1 - making usageList (3 chroms): 1 millis pass2 - checking and writing primary data (12 records, 4 fields): 1 millis CompletedMACS2peakCalling