Job ID = 16439449 SRX = SRX5101717 Genome = dm3 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... Read 5981626 spots for SRR8287010/SRR8287010.sra Written 5981626 spots for SRR8287010/SRR8287010.sra fastq に変換しました。 bowtie でマッピング中... Your job 16439516 ("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: 00:09:56 5981626 reads; of these: 5981626 (100.00%) were paired; of these: 573751 (9.59%) aligned concordantly 0 times 1463405 (24.47%) aligned concordantly exactly 1 time 3944470 (65.94%) aligned concordantly >1 times ---- 573751 pairs aligned concordantly 0 times; of these: 98894 (17.24%) aligned discordantly 1 time ---- 474857 pairs aligned 0 times concordantly or discordantly; of these: 949714 mates make up the pairs; of these: 222770 (23.46%) aligned 0 times 90789 (9.56%) aligned exactly 1 time 636155 (66.98%) aligned >1 times 98.14% overall alignment rate Time searching: 00:09:56 Overall time: 00:09:56 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_sort_core] merging from 8 files... [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] 4206516 / 5394669 = 0.7798 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/3.8.7/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Tue, 02 Aug 2022 15:25:44: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX5101717/SRX5101717.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX5101717/SRX5101717.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX5101717/SRX5101717.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX5101717/SRX5101717.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 @ Tue, 02 Aug 2022 15:25:44: #1 read tag files... INFO @ Tue, 02 Aug 2022 15:25:44: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 15:25:50: 1000000 INFO @ Tue, 02 Aug 2022 15:25:56: 2000000 INFO @ Tue, 02 Aug 2022 15:26:02: 3000000 INFO @ Tue, 02 Aug 2022 15:26:04: #1 tag size is determined as 72 bps INFO @ Tue, 02 Aug 2022 15:26:04: #1 tag size = 72 INFO @ Tue, 02 Aug 2022 15:26:04: #1 total tags in treatment: 1244164 INFO @ Tue, 02 Aug 2022 15:26:04: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 15:26:04: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 02 Aug 2022 15:26:04: #1 tags after filtering in treatment: 716746 INFO @ Tue, 02 Aug 2022 15:26:04: #1 Redundant rate of treatment: 0.42 INFO @ Tue, 02 Aug 2022 15:26:04: #1 finished! INFO @ Tue, 02 Aug 2022 15:26:04: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 15:26:04: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 15:26:04: #2 number of paired peaks: 6208 INFO @ Tue, 02 Aug 2022 15:26:04: start model_add_line... INFO @ Tue, 02 Aug 2022 15:26:04: start X-correlation... INFO @ Tue, 02 Aug 2022 15:26:04: end of X-cor INFO @ Tue, 02 Aug 2022 15:26:04: #2 finished! INFO @ Tue, 02 Aug 2022 15:26:04: #2 predicted fragment length is 207 bps INFO @ Tue, 02 Aug 2022 15:26:04: #2 alternative fragment length(s) may be 207 bps INFO @ Tue, 02 Aug 2022 15:26:04: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX5101717/SRX5101717.05_model.r INFO @ Tue, 02 Aug 2022 15:26:04: #3 Call peaks... INFO @ Tue, 02 Aug 2022 15:26:04: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 02 Aug 2022 15:26:06: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 15:26:07: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX5101717/SRX5101717.05_peaks.xls INFO @ Tue, 02 Aug 2022 15:26:07: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX5101717/SRX5101717.05_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 15:26:07: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX5101717/SRX5101717.05_summits.bed INFO @ Tue, 02 Aug 2022 15:26:07: Done! pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (3491 records, 4 fields): 16 millis CompletedMACS2peakCalling WARNING: Skipping mount /opt/pkg/singularity/3.8.7/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Tue, 02 Aug 2022 15:26:14: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX5101717/SRX5101717.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX5101717/SRX5101717.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX5101717/SRX5101717.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX5101717/SRX5101717.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 @ Tue, 02 Aug 2022 15:26:14: #1 read tag files... INFO @ Tue, 02 Aug 2022 15:26:14: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 15:26:19: 1000000 INFO @ Tue, 02 Aug 2022 15:26:25: 2000000 INFO @ Tue, 02 Aug 2022 15:26:31: 3000000 INFO @ Tue, 02 Aug 2022 15:26:33: #1 tag size is determined as 72 bps INFO @ Tue, 02 Aug 2022 15:26:33: #1 tag size = 72 INFO @ Tue, 02 Aug 2022 15:26:33: #1 total tags in treatment: 1244164 INFO @ Tue, 02 Aug 2022 15:26:33: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 15:26:33: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 02 Aug 2022 15:26:33: #1 tags after filtering in treatment: 716746 INFO @ Tue, 02 Aug 2022 15:26:33: #1 Redundant rate of treatment: 0.42 INFO @ Tue, 02 Aug 2022 15:26:33: #1 finished! INFO @ Tue, 02 Aug 2022 15:26:33: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 15:26:33: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 15:26:34: #2 number of paired peaks: 6208 INFO @ Tue, 02 Aug 2022 15:26:34: start model_add_line... INFO @ Tue, 02 Aug 2022 15:26:34: start X-correlation... INFO @ Tue, 02 Aug 2022 15:26:34: end of X-cor INFO @ Tue, 02 Aug 2022 15:26:34: #2 finished! INFO @ Tue, 02 Aug 2022 15:26:34: #2 predicted fragment length is 207 bps INFO @ Tue, 02 Aug 2022 15:26:34: #2 alternative fragment length(s) may be 207 bps INFO @ Tue, 02 Aug 2022 15:26:34: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX5101717/SRX5101717.10_model.r INFO @ Tue, 02 Aug 2022 15:26:34: #3 Call peaks... INFO @ Tue, 02 Aug 2022 15:26:34: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 02 Aug 2022 15:26:36: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 15:26:37: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX5101717/SRX5101717.10_peaks.xls INFO @ Tue, 02 Aug 2022 15:26:37: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX5101717/SRX5101717.10_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 15:26:37: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX5101717/SRX5101717.10_summits.bed INFO @ Tue, 02 Aug 2022 15:26:37: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (1554 records, 4 fields): 18 millis CompletedMACS2peakCalling BedGraph に変換中... WARNING: Skipping mount /opt/pkg/singularity/3.8.7/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Tue, 02 Aug 2022 15:26:44: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX5101717/SRX5101717.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX5101717/SRX5101717.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX5101717/SRX5101717.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX5101717/SRX5101717.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 @ Tue, 02 Aug 2022 15:26:44: #1 read tag files... INFO @ Tue, 02 Aug 2022 15:26:44: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 15:26:50: 1000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 02 Aug 2022 15:26:55: 2000000 BigWig に変換しました。 INFO @ Tue, 02 Aug 2022 15:27:01: 3000000 INFO @ Tue, 02 Aug 2022 15:27:03: #1 tag size is determined as 72 bps INFO @ Tue, 02 Aug 2022 15:27:03: #1 tag size = 72 INFO @ Tue, 02 Aug 2022 15:27:03: #1 total tags in treatment: 1244164 INFO @ Tue, 02 Aug 2022 15:27:03: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 15:27:03: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 02 Aug 2022 15:27:03: #1 tags after filtering in treatment: 716746 INFO @ Tue, 02 Aug 2022 15:27:03: #1 Redundant rate of treatment: 0.42 INFO @ Tue, 02 Aug 2022 15:27:03: #1 finished! INFO @ Tue, 02 Aug 2022 15:27:03: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 15:27:03: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 15:27:03: #2 number of paired peaks: 6208 INFO @ Tue, 02 Aug 2022 15:27:03: start model_add_line... INFO @ Tue, 02 Aug 2022 15:27:03: start X-correlation... INFO @ Tue, 02 Aug 2022 15:27:03: end of X-cor INFO @ Tue, 02 Aug 2022 15:27:03: #2 finished! INFO @ Tue, 02 Aug 2022 15:27:03: #2 predicted fragment length is 207 bps INFO @ Tue, 02 Aug 2022 15:27:03: #2 alternative fragment length(s) may be 207 bps INFO @ Tue, 02 Aug 2022 15:27:03: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX5101717/SRX5101717.20_model.r INFO @ Tue, 02 Aug 2022 15:27:03: #3 Call peaks... INFO @ Tue, 02 Aug 2022 15:27:03: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 02 Aug 2022 15:27:05: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 15:27:06: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX5101717/SRX5101717.20_peaks.xls INFO @ Tue, 02 Aug 2022 15:27:06: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX5101717/SRX5101717.20_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 15:27:06: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX5101717/SRX5101717.20_summits.bed INFO @ Tue, 02 Aug 2022 15:27:06: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (478 records, 4 fields): 14 millis CompletedMACS2peakCalling