Job ID = 14171635 SRX = SRX10386212 Genome = dm3 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... Read 49357 spots for SRR14009277/SRR14009277.sra Written 49357 spots for SRR14009277/SRR14009277.sra fastq に変換しました。 bowtie でマッピング中... Your job 14172044 ("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: 00:00:08 49357 reads; of these: 49357 (100.00%) were paired; of these: 6796 (13.77%) aligned concordantly 0 times 29143 (59.05%) aligned concordantly exactly 1 time 13418 (27.19%) aligned concordantly >1 times ---- 6796 pairs aligned concordantly 0 times; of these: 861 (12.67%) aligned discordantly 1 time ---- 5935 pairs aligned 0 times concordantly or discordantly; of these: 11870 mates make up the pairs; of these: 10008 (84.31%) aligned 0 times 1006 (8.48%) aligned exactly 1 time 856 (7.21%) aligned >1 times 89.86% overall alignment rate Time searching: 00:00:08 Overall time: 00:00:08 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] 70 / 43290 = 0.0016 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 12:14:08: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX10386212/SRX10386212.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX10386212/SRX10386212.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX10386212/SRX10386212.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX10386212/SRX10386212.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 12:14:08: #1 read tag files... INFO @ Sat, 11 Dec 2021 12:14:08: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 12:14:08: #1 tag size is determined as 50 bps INFO @ Sat, 11 Dec 2021 12:14:08: #1 tag size = 50 INFO @ Sat, 11 Dec 2021 12:14:08: #1 total tags in treatment: 42491 INFO @ Sat, 11 Dec 2021 12:14:08: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 12:14:08: #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 12:14:08: #1 tags after filtering in treatment: 42221 INFO @ Sat, 11 Dec 2021 12:14:08: #1 Redundant rate of treatment: 0.01 INFO @ Sat, 11 Dec 2021 12:14:08: #1 finished! INFO @ Sat, 11 Dec 2021 12:14:08: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 12:14:08: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 12:14:08: #2 number of paired peaks: 1250 INFO @ Sat, 11 Dec 2021 12:14:08: start model_add_line... INFO @ Sat, 11 Dec 2021 12:14:08: start X-correlation... INFO @ Sat, 11 Dec 2021 12:14:08: end of X-cor INFO @ Sat, 11 Dec 2021 12:14:08: #2 finished! INFO @ Sat, 11 Dec 2021 12:14:08: #2 predicted fragment length is 299 bps INFO @ Sat, 11 Dec 2021 12:14:08: #2 alternative fragment length(s) may be 299 bps INFO @ Sat, 11 Dec 2021 12:14:08: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX10386212/SRX10386212.05_model.r INFO @ Sat, 11 Dec 2021 12:14:08: #3 Call peaks... INFO @ Sat, 11 Dec 2021 12:14:08: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Dec 2021 12:14:08: #3 Call peaks for each chromosome... INFO @ Sat, 11 Dec 2021 12:14:09: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX10386212/SRX10386212.05_peaks.xls INFO @ Sat, 11 Dec 2021 12:14:09: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX10386212/SRX10386212.05_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 12:14:09: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX10386212/SRX10386212.05_summits.bed INFO @ Sat, 11 Dec 2021 12:14:09: Done! pass1 - making usageList (4 chroms): 1 millis pass2 - checking and writing primary data (30 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 12:14:38: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX10386212/SRX10386212.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX10386212/SRX10386212.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX10386212/SRX10386212.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX10386212/SRX10386212.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 12:14:38: #1 read tag files... INFO @ Sat, 11 Dec 2021 12:14:38: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 12:14:38: #1 tag size is determined as 50 bps INFO @ Sat, 11 Dec 2021 12:14:38: #1 tag size = 50 INFO @ Sat, 11 Dec 2021 12:14:38: #1 total tags in treatment: 42491 INFO @ Sat, 11 Dec 2021 12:14:38: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 12:14:38: #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 12:14:38: #1 tags after filtering in treatment: 42221 INFO @ Sat, 11 Dec 2021 12:14:38: #1 Redundant rate of treatment: 0.01 INFO @ Sat, 11 Dec 2021 12:14:38: #1 finished! INFO @ Sat, 11 Dec 2021 12:14:38: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 12:14:38: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 12:14:38: #2 number of paired peaks: 1250 INFO @ Sat, 11 Dec 2021 12:14:38: start model_add_line... INFO @ Sat, 11 Dec 2021 12:14:38: start X-correlation... INFO @ Sat, 11 Dec 2021 12:14:38: end of X-cor INFO @ Sat, 11 Dec 2021 12:14:38: #2 finished! INFO @ Sat, 11 Dec 2021 12:14:38: #2 predicted fragment length is 299 bps INFO @ Sat, 11 Dec 2021 12:14:38: #2 alternative fragment length(s) may be 299 bps INFO @ Sat, 11 Dec 2021 12:14:38: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX10386212/SRX10386212.10_model.r INFO @ Sat, 11 Dec 2021 12:14:38: #3 Call peaks... INFO @ Sat, 11 Dec 2021 12:14:38: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Dec 2021 12:14:39: #3 Call peaks for each chromosome... INFO @ Sat, 11 Dec 2021 12:14:39: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX10386212/SRX10386212.10_peaks.xls INFO @ Sat, 11 Dec 2021 12:14:39: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX10386212/SRX10386212.10_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 12:14:39: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX10386212/SRX10386212.10_summits.bed INFO @ Sat, 11 Dec 2021 12:14:39: Done! pass1 - making usageList (1 chroms): 1 millis pass2 - checking and writing primary data (7 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... BigWig に変換しました。 INFO @ Sat, 11 Dec 2021 12:15:08: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX10386212/SRX10386212.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX10386212/SRX10386212.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX10386212/SRX10386212.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX10386212/SRX10386212.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 12:15:08: #1 read tag files... INFO @ Sat, 11 Dec 2021 12:15:08: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 12:15:08: #1 tag size is determined as 50 bps INFO @ Sat, 11 Dec 2021 12:15:08: #1 tag size = 50 INFO @ Sat, 11 Dec 2021 12:15:08: #1 total tags in treatment: 42491 INFO @ Sat, 11 Dec 2021 12:15:08: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 12:15:08: #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 12:15:08: #1 tags after filtering in treatment: 42221 INFO @ Sat, 11 Dec 2021 12:15:08: #1 Redundant rate of treatment: 0.01 INFO @ Sat, 11 Dec 2021 12:15:08: #1 finished! INFO @ Sat, 11 Dec 2021 12:15:08: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 12:15:08: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 12:15:08: #2 number of paired peaks: 1250 INFO @ Sat, 11 Dec 2021 12:15:08: start model_add_line... INFO @ Sat, 11 Dec 2021 12:15:08: start X-correlation... INFO @ Sat, 11 Dec 2021 12:15:08: end of X-cor INFO @ Sat, 11 Dec 2021 12:15:08: #2 finished! INFO @ Sat, 11 Dec 2021 12:15:08: #2 predicted fragment length is 299 bps INFO @ Sat, 11 Dec 2021 12:15:08: #2 alternative fragment length(s) may be 299 bps INFO @ Sat, 11 Dec 2021 12:15:08: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX10386212/SRX10386212.20_model.r INFO @ Sat, 11 Dec 2021 12:15:08: #3 Call peaks... INFO @ Sat, 11 Dec 2021 12:15:08: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Dec 2021 12:15:09: #3 Call peaks for each chromosome... INFO @ Sat, 11 Dec 2021 12:15:09: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX10386212/SRX10386212.20_peaks.xls INFO @ Sat, 11 Dec 2021 12:15:09: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX10386212/SRX10386212.20_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 12:15:09: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX10386212/SRX10386212.20_summits.bed INFO @ Sat, 11 Dec 2021 12:15:09: Done! pass1 - making usageList (1 chroms): 1 millis pass2 - checking and writing primary data (2 records, 4 fields): 1 millis CompletedMACS2peakCalling