Job ID = 14171445 SRX = SRX9555292 Genome = dm3 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... Read 10659953 spots for SRR13110739/SRR13110739.sra Written 10659953 spots for SRR13110739/SRR13110739.sra Read 10570819 spots for SRR13110740/SRR13110740.sra Written 10570819 spots for SRR13110740/SRR13110740.sra Read 10660943 spots for SRR13110741/SRR13110741.sra Written 10660943 spots for SRR13110741/SRR13110741.sra Read 10581695 spots for SRR13110742/SRR13110742.sra Written 10581695 spots for SRR13110742/SRR13110742.sra fastq に変換しました。 bowtie でマッピング中... Your job 14171960 ("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: 00:07:09 42473410 reads; of these: 42473410 (100.00%) were paired; of these: 40681703 (95.78%) aligned concordantly 0 times 1364878 (3.21%) aligned concordantly exactly 1 time 426829 (1.00%) aligned concordantly >1 times ---- 40681703 pairs aligned concordantly 0 times; of these: 4754 (0.01%) aligned discordantly 1 time ---- 40676949 pairs aligned 0 times concordantly or discordantly; of these: 81353898 mates make up the pairs; of these: 81077681 (99.66%) aligned 0 times 108714 (0.13%) aligned exactly 1 time 167503 (0.21%) aligned >1 times 4.55% overall alignment rate Time searching: 00:07:09 Overall time: 00:07:09 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] 87458 / 1795448 = 0.0487 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 11:52:21: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX9555292/SRX9555292.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX9555292/SRX9555292.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX9555292/SRX9555292.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX9555292/SRX9555292.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 11:52:21: #1 read tag files... INFO @ Sat, 11 Dec 2021 11:52:21: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 11:52:26: 1000000 INFO @ Sat, 11 Dec 2021 11:52:31: 2000000 INFO @ Sat, 11 Dec 2021 11:52:36: 3000000 INFO @ Sat, 11 Dec 2021 11:52:39: #1 tag size is determined as 39 bps INFO @ Sat, 11 Dec 2021 11:52:39: #1 tag size = 39 INFO @ Sat, 11 Dec 2021 11:52:39: #1 total tags in treatment: 1704324 INFO @ Sat, 11 Dec 2021 11:52:39: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 11:52:39: #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 11:52:40: #1 tags after filtering in treatment: 1473588 INFO @ Sat, 11 Dec 2021 11:52:40: #1 Redundant rate of treatment: 0.14 INFO @ Sat, 11 Dec 2021 11:52:40: #1 finished! INFO @ Sat, 11 Dec 2021 11:52:40: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 11:52:40: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 11:52:40: #2 number of paired peaks: 7683 INFO @ Sat, 11 Dec 2021 11:52:40: start model_add_line... INFO @ Sat, 11 Dec 2021 11:52:40: start X-correlation... INFO @ Sat, 11 Dec 2021 11:52:40: end of X-cor INFO @ Sat, 11 Dec 2021 11:52:40: #2 finished! INFO @ Sat, 11 Dec 2021 11:52:40: #2 predicted fragment length is 174 bps INFO @ Sat, 11 Dec 2021 11:52:40: #2 alternative fragment length(s) may be 174 bps INFO @ Sat, 11 Dec 2021 11:52:40: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX9555292/SRX9555292.05_model.r INFO @ Sat, 11 Dec 2021 11:52:40: #3 Call peaks... INFO @ Sat, 11 Dec 2021 11:52:40: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Dec 2021 11:52:43: #3 Call peaks for each chromosome... INFO @ Sat, 11 Dec 2021 11:52:45: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX9555292/SRX9555292.05_peaks.xls INFO @ Sat, 11 Dec 2021 11:52:45: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX9555292/SRX9555292.05_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 11:52:45: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX9555292/SRX9555292.05_summits.bed INFO @ Sat, 11 Dec 2021 11:52:45: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (3995 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 11:52:51: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX9555292/SRX9555292.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX9555292/SRX9555292.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX9555292/SRX9555292.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX9555292/SRX9555292.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 11:52:51: #1 read tag files... INFO @ Sat, 11 Dec 2021 11:52:51: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 11:52:56: 1000000 INFO @ Sat, 11 Dec 2021 11:53:00: 2000000 INFO @ Sat, 11 Dec 2021 11:53:05: 3000000 INFO @ Sat, 11 Dec 2021 11:53:08: #1 tag size is determined as 39 bps INFO @ Sat, 11 Dec 2021 11:53:08: #1 tag size = 39 INFO @ Sat, 11 Dec 2021 11:53:08: #1 total tags in treatment: 1704324 INFO @ Sat, 11 Dec 2021 11:53:08: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 11:53:08: #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 11:53:08: #1 tags after filtering in treatment: 1473588 INFO @ Sat, 11 Dec 2021 11:53:08: #1 Redundant rate of treatment: 0.14 INFO @ Sat, 11 Dec 2021 11:53:08: #1 finished! INFO @ Sat, 11 Dec 2021 11:53:08: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 11:53:08: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 11:53:08: #2 number of paired peaks: 7683 INFO @ Sat, 11 Dec 2021 11:53:08: start model_add_line... INFO @ Sat, 11 Dec 2021 11:53:08: start X-correlation... INFO @ Sat, 11 Dec 2021 11:53:08: end of X-cor INFO @ Sat, 11 Dec 2021 11:53:08: #2 finished! INFO @ Sat, 11 Dec 2021 11:53:08: #2 predicted fragment length is 174 bps INFO @ Sat, 11 Dec 2021 11:53:08: #2 alternative fragment length(s) may be 174 bps INFO @ Sat, 11 Dec 2021 11:53:08: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX9555292/SRX9555292.10_model.r INFO @ Sat, 11 Dec 2021 11:53:08: #3 Call peaks... INFO @ Sat, 11 Dec 2021 11:53:08: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Dec 2021 11:53:11: #3 Call peaks for each chromosome... INFO @ Sat, 11 Dec 2021 11:53:13: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX9555292/SRX9555292.10_peaks.xls INFO @ Sat, 11 Dec 2021 11:53:13: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX9555292/SRX9555292.10_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 11:53:13: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX9555292/SRX9555292.10_summits.bed INFO @ Sat, 11 Dec 2021 11:53:13: Done! pass1 - making usageList (13 chroms): 1 millis pass2 - checking and writing primary data (1534 records, 4 fields): 3 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 11:53:21: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX9555292/SRX9555292.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX9555292/SRX9555292.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX9555292/SRX9555292.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX9555292/SRX9555292.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 11:53:21: #1 read tag files... INFO @ Sat, 11 Dec 2021 11:53:21: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 11:53:26: 1000000 INFO @ Sat, 11 Dec 2021 11:53:31: 2000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 11 Dec 2021 11:53:35: 3000000 INFO @ Sat, 11 Dec 2021 11:53:39: #1 tag size is determined as 39 bps INFO @ Sat, 11 Dec 2021 11:53:39: #1 tag size = 39 INFO @ Sat, 11 Dec 2021 11:53:39: #1 total tags in treatment: 1704324 INFO @ Sat, 11 Dec 2021 11:53:39: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 11:53:39: #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 11:53:39: #1 tags after filtering in treatment: 1473588 INFO @ Sat, 11 Dec 2021 11:53:39: #1 Redundant rate of treatment: 0.14 INFO @ Sat, 11 Dec 2021 11:53:39: #1 finished! INFO @ Sat, 11 Dec 2021 11:53:39: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 11:53:39: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 11:53:39: #2 number of paired peaks: 7683 INFO @ Sat, 11 Dec 2021 11:53:39: start model_add_line... INFO @ Sat, 11 Dec 2021 11:53:39: start X-correlation... INFO @ Sat, 11 Dec 2021 11:53:39: end of X-cor INFO @ Sat, 11 Dec 2021 11:53:39: #2 finished! INFO @ Sat, 11 Dec 2021 11:53:39: #2 predicted fragment length is 174 bps INFO @ Sat, 11 Dec 2021 11:53:39: #2 alternative fragment length(s) may be 174 bps INFO @ Sat, 11 Dec 2021 11:53:39: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX9555292/SRX9555292.20_model.r INFO @ Sat, 11 Dec 2021 11:53:39: #3 Call peaks... INFO @ Sat, 11 Dec 2021 11:53:39: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Sat, 11 Dec 2021 11:53:42: #3 Call peaks for each chromosome... INFO @ Sat, 11 Dec 2021 11:53:44: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX9555292/SRX9555292.20_peaks.xls INFO @ Sat, 11 Dec 2021 11:53:44: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX9555292/SRX9555292.20_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 11:53:44: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX9555292/SRX9555292.20_summits.bed INFO @ Sat, 11 Dec 2021 11:53:44: Done! pass1 - making usageList (13 chroms): 1 millis pass2 - checking and writing primary data (414 records, 4 fields): 1 millis CompletedMACS2peakCalling