Job ID = 14172386 SRX = SRX9281774 Genome = dm3 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... Read 1545512 spots for SRR12813305/SRR12813305.sra Written 1545512 spots for SRR12813305/SRR12813305.sra Read 1534615 spots for SRR12813306/SRR12813306.sra Written 1534615 spots for SRR12813306/SRR12813306.sra Read 1572204 spots for SRR12813307/SRR12813307.sra Written 1572204 spots for SRR12813307/SRR12813307.sra Read 1554379 spots for SRR12813308/SRR12813308.sra Written 1554379 spots for SRR12813308/SRR12813308.sra fastq に変換しました。 bowtie でマッピング中... Your job 14172810 ("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: 00:00:50 6206710 reads; of these: 6206710 (100.00%) were paired; of these: 6035868 (97.25%) aligned concordantly 0 times 125239 (2.02%) aligned concordantly exactly 1 time 45603 (0.73%) aligned concordantly >1 times ---- 6035868 pairs aligned concordantly 0 times; of these: 148 (0.00%) aligned discordantly 1 time ---- 6035720 pairs aligned 0 times concordantly or discordantly; of these: 12071440 mates make up the pairs; of these: 12039034 (99.73%) aligned 0 times 10299 (0.09%) aligned exactly 1 time 22107 (0.18%) aligned >1 times 3.02% overall alignment rate Time searching: 00:00:50 Overall time: 00:00:50 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] 3315 / 170876 = 0.0194 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 15:16:16: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX9281774/SRX9281774.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX9281774/SRX9281774.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX9281774/SRX9281774.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX9281774/SRX9281774.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 15:16:16: #1 read tag files... INFO @ Sat, 11 Dec 2021 15:16:16: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 15:16:18: #1 tag size is determined as 39 bps INFO @ Sat, 11 Dec 2021 15:16:18: #1 tag size = 39 INFO @ Sat, 11 Dec 2021 15:16:18: #1 total tags in treatment: 167528 INFO @ Sat, 11 Dec 2021 15:16:18: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 15:16:18: #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 15:16:18: #1 tags after filtering in treatment: 166406 INFO @ Sat, 11 Dec 2021 15:16:18: #1 Redundant rate of treatment: 0.01 INFO @ Sat, 11 Dec 2021 15:16:18: #1 finished! INFO @ Sat, 11 Dec 2021 15:16:18: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 15:16:18: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 15:16:19: #2 number of paired peaks: 1939 INFO @ Sat, 11 Dec 2021 15:16:19: start model_add_line... INFO @ Sat, 11 Dec 2021 15:16:19: start X-correlation... INFO @ Sat, 11 Dec 2021 15:16:19: end of X-cor INFO @ Sat, 11 Dec 2021 15:16:19: #2 finished! INFO @ Sat, 11 Dec 2021 15:16:19: #2 predicted fragment length is 288 bps INFO @ Sat, 11 Dec 2021 15:16:19: #2 alternative fragment length(s) may be 288 bps INFO @ Sat, 11 Dec 2021 15:16:19: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX9281774/SRX9281774.05_model.r INFO @ Sat, 11 Dec 2021 15:16:19: #3 Call peaks... INFO @ Sat, 11 Dec 2021 15:16:19: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Dec 2021 15:16:19: #3 Call peaks for each chromosome... INFO @ Sat, 11 Dec 2021 15:16:19: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX9281774/SRX9281774.05_peaks.xls INFO @ Sat, 11 Dec 2021 15:16:19: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX9281774/SRX9281774.05_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 15:16:19: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX9281774/SRX9281774.05_summits.bed INFO @ Sat, 11 Dec 2021 15:16:19: Done! pass1 - making usageList (4 chroms): 0 millis pass2 - checking and writing primary data (38 records, 4 fields): 2 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 15:16:46: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX9281774/SRX9281774.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX9281774/SRX9281774.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX9281774/SRX9281774.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX9281774/SRX9281774.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 15:16:46: #1 read tag files... INFO @ Sat, 11 Dec 2021 15:16:46: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 15:16:48: #1 tag size is determined as 39 bps INFO @ Sat, 11 Dec 2021 15:16:48: #1 tag size = 39 INFO @ Sat, 11 Dec 2021 15:16:48: #1 total tags in treatment: 167528 INFO @ Sat, 11 Dec 2021 15:16:48: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 15:16:48: #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 15:16:48: #1 tags after filtering in treatment: 166406 INFO @ Sat, 11 Dec 2021 15:16:48: #1 Redundant rate of treatment: 0.01 INFO @ Sat, 11 Dec 2021 15:16:48: #1 finished! INFO @ Sat, 11 Dec 2021 15:16:48: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 15:16:48: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 15:16:49: #2 number of paired peaks: 1939 INFO @ Sat, 11 Dec 2021 15:16:49: start model_add_line... INFO @ Sat, 11 Dec 2021 15:16:49: start X-correlation... INFO @ Sat, 11 Dec 2021 15:16:49: end of X-cor INFO @ Sat, 11 Dec 2021 15:16:49: #2 finished! INFO @ Sat, 11 Dec 2021 15:16:49: #2 predicted fragment length is 288 bps INFO @ Sat, 11 Dec 2021 15:16:49: #2 alternative fragment length(s) may be 288 bps INFO @ Sat, 11 Dec 2021 15:16:49: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX9281774/SRX9281774.10_model.r INFO @ Sat, 11 Dec 2021 15:16:49: #3 Call peaks... INFO @ Sat, 11 Dec 2021 15:16:49: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Dec 2021 15:16:49: #3 Call peaks for each chromosome... INFO @ Sat, 11 Dec 2021 15:16:49: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX9281774/SRX9281774.10_peaks.xls INFO @ Sat, 11 Dec 2021 15:16:49: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX9281774/SRX9281774.10_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 15:16:49: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX9281774/SRX9281774.10_summits.bed INFO @ Sat, 11 Dec 2021 15:16:49: Done! pass1 - making usageList (3 chroms): 1 millis pass2 - checking and writing primary data (16 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 BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 11 Dec 2021 15:17:16: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX9281774/SRX9281774.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX9281774/SRX9281774.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX9281774/SRX9281774.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX9281774/SRX9281774.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 15:17:16: #1 read tag files... INFO @ Sat, 11 Dec 2021 15:17:16: #1 read treatment tags... BigWig に変換しました。 INFO @ Sat, 11 Dec 2021 15:17:18: #1 tag size is determined as 39 bps INFO @ Sat, 11 Dec 2021 15:17:18: #1 tag size = 39 INFO @ Sat, 11 Dec 2021 15:17:18: #1 total tags in treatment: 167528 INFO @ Sat, 11 Dec 2021 15:17:18: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 15:17:18: #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 15:17:18: #1 tags after filtering in treatment: 166406 INFO @ Sat, 11 Dec 2021 15:17:18: #1 Redundant rate of treatment: 0.01 INFO @ Sat, 11 Dec 2021 15:17:18: #1 finished! INFO @ Sat, 11 Dec 2021 15:17:18: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 15:17:18: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 15:17:19: #2 number of paired peaks: 1939 INFO @ Sat, 11 Dec 2021 15:17:19: start model_add_line... INFO @ Sat, 11 Dec 2021 15:17:19: start X-correlation... INFO @ Sat, 11 Dec 2021 15:17:19: end of X-cor INFO @ Sat, 11 Dec 2021 15:17:19: #2 finished! INFO @ Sat, 11 Dec 2021 15:17:19: #2 predicted fragment length is 288 bps INFO @ Sat, 11 Dec 2021 15:17:19: #2 alternative fragment length(s) may be 288 bps INFO @ Sat, 11 Dec 2021 15:17:19: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX9281774/SRX9281774.20_model.r INFO @ Sat, 11 Dec 2021 15:17:19: #3 Call peaks... INFO @ Sat, 11 Dec 2021 15:17:19: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Dec 2021 15:17:19: #3 Call peaks for each chromosome... INFO @ Sat, 11 Dec 2021 15:17:19: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX9281774/SRX9281774.20_peaks.xls INFO @ Sat, 11 Dec 2021 15:17:19: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX9281774/SRX9281774.20_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 15:17:19: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX9281774/SRX9281774.20_summits.bed INFO @ Sat, 11 Dec 2021 15:17:19: Done! pass1 - making usageList (2 chroms): 0 millis pass2 - checking and writing primary data (5 records, 4 fields): 2 millis CompletedMACS2peakCalling