Job ID = 14171451 SRX = SRX9555297 Genome = dm3 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... Read 2810040 spots for SRR13110759/SRR13110759.sra Written 2810040 spots for SRR13110759/SRR13110759.sra Read 2788546 spots for SRR13110760/SRR13110760.sra Written 2788546 spots for SRR13110760/SRR13110760.sra Read 2828638 spots for SRR13110761/SRR13110761.sra Written 2828638 spots for SRR13110761/SRR13110761.sra Read 2799752 spots for SRR13110762/SRR13110762.sra Written 2799752 spots for SRR13110762/SRR13110762.sra fastq に変換しました。 bowtie でマッピング中... Your job 14171929 ("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: 00:02:06 11226976 reads; of these: 11226976 (100.00%) were paired; of these: 10033358 (89.37%) aligned concordantly 0 times 1065560 (9.49%) aligned concordantly exactly 1 time 128058 (1.14%) aligned concordantly >1 times ---- 10033358 pairs aligned concordantly 0 times; of these: 2751 (0.03%) aligned discordantly 1 time ---- 10030607 pairs aligned 0 times concordantly or discordantly; of these: 20061214 mates make up the pairs; of these: 19991932 (99.65%) aligned 0 times 34099 (0.17%) aligned exactly 1 time 35183 (0.18%) aligned >1 times 10.96% overall alignment rate Time searching: 00:02:07 Overall time: 00:02:07 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] 107486 / 1195880 = 0.0899 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 11:46:13: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX9555297/SRX9555297.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX9555297/SRX9555297.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX9555297/SRX9555297.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX9555297/SRX9555297.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 11:46:13: #1 read tag files... INFO @ Sat, 11 Dec 2021 11:46:13: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 11:46:17: 1000000 INFO @ Sat, 11 Dec 2021 11:46:23: 2000000 INFO @ Sat, 11 Dec 2021 11:46:24: #1 tag size is determined as 40 bps INFO @ Sat, 11 Dec 2021 11:46:24: #1 tag size = 40 INFO @ Sat, 11 Dec 2021 11:46:24: #1 total tags in treatment: 1086166 INFO @ Sat, 11 Dec 2021 11:46:24: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 11:46:24: #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 11:46:24: #1 tags after filtering in treatment: 826405 INFO @ Sat, 11 Dec 2021 11:46:24: #1 Redundant rate of treatment: 0.24 INFO @ Sat, 11 Dec 2021 11:46:24: #1 finished! INFO @ Sat, 11 Dec 2021 11:46:24: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 11:46:24: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 11:46:24: #2 number of paired peaks: 10328 INFO @ Sat, 11 Dec 2021 11:46:24: start model_add_line... INFO @ Sat, 11 Dec 2021 11:46:24: start X-correlation... INFO @ Sat, 11 Dec 2021 11:46:24: end of X-cor INFO @ Sat, 11 Dec 2021 11:46:24: #2 finished! INFO @ Sat, 11 Dec 2021 11:46:24: #2 predicted fragment length is 155 bps INFO @ Sat, 11 Dec 2021 11:46:24: #2 alternative fragment length(s) may be 155,228,315 bps INFO @ Sat, 11 Dec 2021 11:46:24: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX9555297/SRX9555297.05_model.r INFO @ Sat, 11 Dec 2021 11:46:24: #3 Call peaks... INFO @ Sat, 11 Dec 2021 11:46:24: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Dec 2021 11:46:26: #3 Call peaks for each chromosome... INFO @ Sat, 11 Dec 2021 11:46:27: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX9555297/SRX9555297.05_peaks.xls INFO @ Sat, 11 Dec 2021 11:46:27: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX9555297/SRX9555297.05_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 11:46:27: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX9555297/SRX9555297.05_summits.bed INFO @ Sat, 11 Dec 2021 11:46:27: Done! pass1 - making usageList (14 chroms): 2 millis pass2 - checking and writing primary data (6306 records, 4 fields): 7 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 11:46:43: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX9555297/SRX9555297.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX9555297/SRX9555297.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX9555297/SRX9555297.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX9555297/SRX9555297.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 11:46:43: #1 read tag files... INFO @ Sat, 11 Dec 2021 11:46:43: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 11:46:48: 1000000 INFO @ Sat, 11 Dec 2021 11:46:53: 2000000 INFO @ Sat, 11 Dec 2021 11:46:54: #1 tag size is determined as 40 bps INFO @ Sat, 11 Dec 2021 11:46:54: #1 tag size = 40 INFO @ Sat, 11 Dec 2021 11:46:54: #1 total tags in treatment: 1086166 INFO @ Sat, 11 Dec 2021 11:46:54: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 11:46:54: #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 11:46:54: #1 tags after filtering in treatment: 826405 INFO @ Sat, 11 Dec 2021 11:46:54: #1 Redundant rate of treatment: 0.24 INFO @ Sat, 11 Dec 2021 11:46:54: #1 finished! INFO @ Sat, 11 Dec 2021 11:46:54: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 11:46:54: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 11:46:54: #2 number of paired peaks: 10328 INFO @ Sat, 11 Dec 2021 11:46:54: start model_add_line... INFO @ Sat, 11 Dec 2021 11:46:54: start X-correlation... INFO @ Sat, 11 Dec 2021 11:46:54: end of X-cor INFO @ Sat, 11 Dec 2021 11:46:54: #2 finished! INFO @ Sat, 11 Dec 2021 11:46:54: #2 predicted fragment length is 155 bps INFO @ Sat, 11 Dec 2021 11:46:54: #2 alternative fragment length(s) may be 155,228,315 bps INFO @ Sat, 11 Dec 2021 11:46:54: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX9555297/SRX9555297.10_model.r INFO @ Sat, 11 Dec 2021 11:46:54: #3 Call peaks... INFO @ Sat, 11 Dec 2021 11:46:54: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Dec 2021 11:46:56: #3 Call peaks for each chromosome... INFO @ Sat, 11 Dec 2021 11:46:57: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX9555297/SRX9555297.10_peaks.xls INFO @ Sat, 11 Dec 2021 11:46:57: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX9555297/SRX9555297.10_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 11:46:57: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX9555297/SRX9555297.10_summits.bed INFO @ Sat, 11 Dec 2021 11:46:57: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (3297 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 11:47:13: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX9555297/SRX9555297.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX9555297/SRX9555297.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX9555297/SRX9555297.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX9555297/SRX9555297.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 11:47:13: #1 read tag files... INFO @ Sat, 11 Dec 2021 11:47:13: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 11:47:18: 1000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 11 Dec 2021 11:47:23: 2000000 INFO @ Sat, 11 Dec 2021 11:47:24: #1 tag size is determined as 40 bps INFO @ Sat, 11 Dec 2021 11:47:24: #1 tag size = 40 INFO @ Sat, 11 Dec 2021 11:47:24: #1 total tags in treatment: 1086166 INFO @ Sat, 11 Dec 2021 11:47:24: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 11:47:24: #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 11:47:24: #1 tags after filtering in treatment: 826405 INFO @ Sat, 11 Dec 2021 11:47:24: #1 Redundant rate of treatment: 0.24 INFO @ Sat, 11 Dec 2021 11:47:24: #1 finished! INFO @ Sat, 11 Dec 2021 11:47:24: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 11:47:24: #2 looking for paired plus/minus strand peaks... BigWig に変換しました。 INFO @ Sat, 11 Dec 2021 11:47:24: #2 number of paired peaks: 10328 INFO @ Sat, 11 Dec 2021 11:47:24: start model_add_line... INFO @ Sat, 11 Dec 2021 11:47:24: start X-correlation... INFO @ Sat, 11 Dec 2021 11:47:24: end of X-cor INFO @ Sat, 11 Dec 2021 11:47:24: #2 finished! INFO @ Sat, 11 Dec 2021 11:47:24: #2 predicted fragment length is 155 bps INFO @ Sat, 11 Dec 2021 11:47:24: #2 alternative fragment length(s) may be 155,228,315 bps INFO @ Sat, 11 Dec 2021 11:47:24: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX9555297/SRX9555297.20_model.r INFO @ Sat, 11 Dec 2021 11:47:24: #3 Call peaks... INFO @ Sat, 11 Dec 2021 11:47:24: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Dec 2021 11:47:26: #3 Call peaks for each chromosome... INFO @ Sat, 11 Dec 2021 11:47:27: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX9555297/SRX9555297.20_peaks.xls INFO @ Sat, 11 Dec 2021 11:47:27: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX9555297/SRX9555297.20_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 11:47:27: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX9555297/SRX9555297.20_summits.bed INFO @ Sat, 11 Dec 2021 11:47:27: Done! pass1 - making usageList (13 chroms): 0 millis pass2 - checking and writing primary data (616 records, 4 fields): 2 millis CompletedMACS2peakCalling