Job ID = 14172258 SRX = SRX9281757 Genome = dm3 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... Read 5069586 spots for SRR12813507/SRR12813507.sra Written 5069586 spots for SRR12813507/SRR12813507.sra Read 5068648 spots for SRR12813508/SRR12813508.sra Written 5068648 spots for SRR12813508/SRR12813508.sra Read 5187103 spots for SRR12813509/SRR12813509.sra Written 5187103 spots for SRR12813509/SRR12813509.sra Read 4901672 spots for SRR12813510/SRR12813510.sra Written 4901672 spots for SRR12813510/SRR12813510.sra fastq に変換しました。 bowtie でマッピング中... Your job 14172728 ("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: 00:05:48 20227009 reads; of these: 20227009 (100.00%) were paired; of these: 16511743 (81.63%) aligned concordantly 0 times 3363267 (16.63%) aligned concordantly exactly 1 time 351999 (1.74%) aligned concordantly >1 times ---- 16511743 pairs aligned concordantly 0 times; of these: 24940 (0.15%) aligned discordantly 1 time ---- 16486803 pairs aligned 0 times concordantly or discordantly; of these: 32973606 mates make up the pairs; of these: 32322113 (98.02%) aligned 0 times 361119 (1.10%) aligned exactly 1 time 290374 (0.88%) aligned >1 times 20.10% overall alignment rate Time searching: 00:05:48 Overall time: 00:05:48 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] 750919 / 3721978 = 0.2018 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 15:04:32: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX9281757/SRX9281757.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX9281757/SRX9281757.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX9281757/SRX9281757.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX9281757/SRX9281757.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 15:04:32: #1 read tag files... INFO @ Sat, 11 Dec 2021 15:04:32: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 15:04:37: 1000000 INFO @ Sat, 11 Dec 2021 15:04:42: 2000000 INFO @ Sat, 11 Dec 2021 15:04:46: 3000000 INFO @ Sat, 11 Dec 2021 15:04:51: 4000000 INFO @ Sat, 11 Dec 2021 15:04:56: 5000000 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 15:05:01: 6000000 INFO @ Sat, 11 Dec 2021 15:05:02: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX9281757/SRX9281757.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX9281757/SRX9281757.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX9281757/SRX9281757.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX9281757/SRX9281757.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 15:05:02: #1 read tag files... INFO @ Sat, 11 Dec 2021 15:05:02: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 15:05:05: #1 tag size is determined as 39 bps INFO @ Sat, 11 Dec 2021 15:05:05: #1 tag size = 39 INFO @ Sat, 11 Dec 2021 15:05:05: #1 total tags in treatment: 2964517 INFO @ Sat, 11 Dec 2021 15:05:05: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 15:05:05: #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 15:05:05: #1 tags after filtering in treatment: 1847324 INFO @ Sat, 11 Dec 2021 15:05:05: #1 Redundant rate of treatment: 0.38 INFO @ Sat, 11 Dec 2021 15:05:05: #1 finished! INFO @ Sat, 11 Dec 2021 15:05:05: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 15:05:05: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 15:05:05: #2 number of paired peaks: 11126 INFO @ Sat, 11 Dec 2021 15:05:05: start model_add_line... INFO @ Sat, 11 Dec 2021 15:05:05: start X-correlation... INFO @ Sat, 11 Dec 2021 15:05:05: end of X-cor INFO @ Sat, 11 Dec 2021 15:05:05: #2 finished! INFO @ Sat, 11 Dec 2021 15:05:05: #2 predicted fragment length is 147 bps INFO @ Sat, 11 Dec 2021 15:05:05: #2 alternative fragment length(s) may be 147,307 bps INFO @ Sat, 11 Dec 2021 15:05:05: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX9281757/SRX9281757.05_model.r INFO @ Sat, 11 Dec 2021 15:05:05: #3 Call peaks... INFO @ Sat, 11 Dec 2021 15:05:05: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Dec 2021 15:05:09: 1000000 INFO @ Sat, 11 Dec 2021 15:05:09: #3 Call peaks for each chromosome... INFO @ Sat, 11 Dec 2021 15:05:11: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX9281757/SRX9281757.05_peaks.xls INFO @ Sat, 11 Dec 2021 15:05:11: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX9281757/SRX9281757.05_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 15:05:12: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX9281757/SRX9281757.05_summits.bed INFO @ Sat, 11 Dec 2021 15:05:12: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (8406 records, 4 fields): 9 millis CompletedMACS2peakCalling INFO @ Sat, 11 Dec 2021 15:05:14: 2000000 INFO @ Sat, 11 Dec 2021 15:05:20: 3000000 INFO @ Sat, 11 Dec 2021 15:05:26: 4000000 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 15:05:31: 5000000 INFO @ Sat, 11 Dec 2021 15:05:32: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX9281757/SRX9281757.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX9281757/SRX9281757.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX9281757/SRX9281757.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX9281757/SRX9281757.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 15:05:32: #1 read tag files... INFO @ Sat, 11 Dec 2021 15:05:32: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 15:05:37: 6000000 INFO @ Sat, 11 Dec 2021 15:05:38: 1000000 INFO @ Sat, 11 Dec 2021 15:05:40: #1 tag size is determined as 39 bps INFO @ Sat, 11 Dec 2021 15:05:40: #1 tag size = 39 INFO @ Sat, 11 Dec 2021 15:05:40: #1 total tags in treatment: 2964517 INFO @ Sat, 11 Dec 2021 15:05:40: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 15:05:40: #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 15:05:40: #1 tags after filtering in treatment: 1847324 INFO @ Sat, 11 Dec 2021 15:05:40: #1 Redundant rate of treatment: 0.38 INFO @ Sat, 11 Dec 2021 15:05:40: #1 finished! INFO @ Sat, 11 Dec 2021 15:05:40: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 15:05:40: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 15:05:41: #2 number of paired peaks: 11126 INFO @ Sat, 11 Dec 2021 15:05:41: start model_add_line... INFO @ Sat, 11 Dec 2021 15:05:41: start X-correlation... INFO @ Sat, 11 Dec 2021 15:05:41: end of X-cor INFO @ Sat, 11 Dec 2021 15:05:41: #2 finished! INFO @ Sat, 11 Dec 2021 15:05:41: #2 predicted fragment length is 147 bps INFO @ Sat, 11 Dec 2021 15:05:41: #2 alternative fragment length(s) may be 147,307 bps INFO @ Sat, 11 Dec 2021 15:05:41: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX9281757/SRX9281757.10_model.r INFO @ Sat, 11 Dec 2021 15:05:41: #3 Call peaks... INFO @ Sat, 11 Dec 2021 15:05:41: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Dec 2021 15:05:43: 2000000 INFO @ Sat, 11 Dec 2021 15:05:45: #3 Call peaks for each chromosome... INFO @ Sat, 11 Dec 2021 15:05:47: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX9281757/SRX9281757.10_peaks.xls INFO @ Sat, 11 Dec 2021 15:05:47: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX9281757/SRX9281757.10_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 15:05:47: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX9281757/SRX9281757.10_summits.bed INFO @ Sat, 11 Dec 2021 15:05:47: Done! pass1 - making usageList (14 chroms): 2 millis pass2 - checking and writing primary data (6343 records, 4 fields): 7 millis CompletedMACS2peakCalling INFO @ Sat, 11 Dec 2021 15:05:49: 3000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 11 Dec 2021 15:05:54: 4000000 BigWig に変換しました。 INFO @ Sat, 11 Dec 2021 15:05:59: 5000000 INFO @ Sat, 11 Dec 2021 15:06:04: 6000000 INFO @ Sat, 11 Dec 2021 15:06:07: #1 tag size is determined as 39 bps INFO @ Sat, 11 Dec 2021 15:06:07: #1 tag size = 39 INFO @ Sat, 11 Dec 2021 15:06:07: #1 total tags in treatment: 2964517 INFO @ Sat, 11 Dec 2021 15:06:07: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 15:06:07: #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 15:06:07: #1 tags after filtering in treatment: 1847324 INFO @ Sat, 11 Dec 2021 15:06:07: #1 Redundant rate of treatment: 0.38 INFO @ Sat, 11 Dec 2021 15:06:07: #1 finished! INFO @ Sat, 11 Dec 2021 15:06:07: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 15:06:07: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 15:06:08: #2 number of paired peaks: 11126 INFO @ Sat, 11 Dec 2021 15:06:08: start model_add_line... INFO @ Sat, 11 Dec 2021 15:06:08: start X-correlation... INFO @ Sat, 11 Dec 2021 15:06:08: end of X-cor INFO @ Sat, 11 Dec 2021 15:06:08: #2 finished! INFO @ Sat, 11 Dec 2021 15:06:08: #2 predicted fragment length is 147 bps INFO @ Sat, 11 Dec 2021 15:06:08: #2 alternative fragment length(s) may be 147,307 bps INFO @ Sat, 11 Dec 2021 15:06:08: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX9281757/SRX9281757.20_model.r INFO @ Sat, 11 Dec 2021 15:06:08: #3 Call peaks... INFO @ Sat, 11 Dec 2021 15:06:08: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Dec 2021 15:06:12: #3 Call peaks for each chromosome... INFO @ Sat, 11 Dec 2021 15:06:14: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX9281757/SRX9281757.20_peaks.xls INFO @ Sat, 11 Dec 2021 15:06:14: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX9281757/SRX9281757.20_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 15:06:14: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX9281757/SRX9281757.20_summits.bed INFO @ Sat, 11 Dec 2021 15:06:14: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (2906 records, 4 fields): 4 millis CompletedMACS2peakCalling