Job ID = 14172450 SRX = SRX7628887 Genome = dm3 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... Read 16481573 spots for SRR10963249/SRR10963249.sra Written 16481573 spots for SRR10963249/SRR10963249.sra fastq に変換しました。 bowtie でマッピング中... Your job 14173000 ("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: 00:29:31 16481573 reads; of these: 16481573 (100.00%) were paired; of these: 810332 (4.92%) aligned concordantly 0 times 11029897 (66.92%) aligned concordantly exactly 1 time 4641344 (28.16%) aligned concordantly >1 times ---- 810332 pairs aligned concordantly 0 times; of these: 39226 (4.84%) aligned discordantly 1 time ---- 771106 pairs aligned 0 times concordantly or discordantly; of these: 1542212 mates make up the pairs; of these: 904547 (58.65%) aligned 0 times 376683 (24.42%) aligned exactly 1 time 260982 (16.92%) aligned >1 times 97.26% overall alignment rate Time searching: 00:29:31 Overall time: 00:29:31 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 16 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] 830431 / 15703280 = 0.0529 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 16:06:01: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX7628887/SRX7628887.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX7628887/SRX7628887.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX7628887/SRX7628887.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX7628887/SRX7628887.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 16:06:01: #1 read tag files... INFO @ Sat, 11 Dec 2021 16:06:01: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 16:06:06: 1000000 INFO @ Sat, 11 Dec 2021 16:06:11: 2000000 INFO @ Sat, 11 Dec 2021 16:06:16: 3000000 INFO @ Sat, 11 Dec 2021 16:06:21: 4000000 INFO @ Sat, 11 Dec 2021 16:06:26: 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 16:06:31: 6000000 INFO @ Sat, 11 Dec 2021 16:06:31: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX7628887/SRX7628887.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX7628887/SRX7628887.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX7628887/SRX7628887.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX7628887/SRX7628887.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 16:06:31: #1 read tag files... INFO @ Sat, 11 Dec 2021 16:06:31: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 16:06:36: 1000000 INFO @ Sat, 11 Dec 2021 16:06:36: 7000000 INFO @ Sat, 11 Dec 2021 16:06:40: 2000000 INFO @ Sat, 11 Dec 2021 16:06:41: 8000000 INFO @ Sat, 11 Dec 2021 16:06:44: 3000000 INFO @ Sat, 11 Dec 2021 16:06:46: 9000000 INFO @ Sat, 11 Dec 2021 16:06:49: 4000000 INFO @ Sat, 11 Dec 2021 16:06:51: 10000000 INFO @ Sat, 11 Dec 2021 16:06:53: 5000000 INFO @ Sat, 11 Dec 2021 16:06:56: 11000000 INFO @ Sat, 11 Dec 2021 16:06:57: 6000000 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 16:07:01: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX7628887/SRX7628887.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX7628887/SRX7628887.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX7628887/SRX7628887.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX7628887/SRX7628887.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 16:07:01: #1 read tag files... INFO @ Sat, 11 Dec 2021 16:07:01: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 16:07:01: 12000000 INFO @ Sat, 11 Dec 2021 16:07:02: 7000000 INFO @ Sat, 11 Dec 2021 16:07:05: 1000000 INFO @ Sat, 11 Dec 2021 16:07:06: 8000000 INFO @ Sat, 11 Dec 2021 16:07:06: 13000000 INFO @ Sat, 11 Dec 2021 16:07:10: 2000000 INFO @ Sat, 11 Dec 2021 16:07:10: 9000000 INFO @ Sat, 11 Dec 2021 16:07:11: 14000000 INFO @ Sat, 11 Dec 2021 16:07:14: 3000000 INFO @ Sat, 11 Dec 2021 16:07:14: 10000000 INFO @ Sat, 11 Dec 2021 16:07:16: 15000000 INFO @ Sat, 11 Dec 2021 16:07:18: 4000000 INFO @ Sat, 11 Dec 2021 16:07:19: 11000000 INFO @ Sat, 11 Dec 2021 16:07:21: 16000000 INFO @ Sat, 11 Dec 2021 16:07:22: 5000000 INFO @ Sat, 11 Dec 2021 16:07:23: 12000000 INFO @ Sat, 11 Dec 2021 16:07:26: 17000000 INFO @ Sat, 11 Dec 2021 16:07:27: 6000000 INFO @ Sat, 11 Dec 2021 16:07:27: 13000000 INFO @ Sat, 11 Dec 2021 16:07:31: 7000000 INFO @ Sat, 11 Dec 2021 16:07:31: 18000000 INFO @ Sat, 11 Dec 2021 16:07:32: 14000000 INFO @ Sat, 11 Dec 2021 16:07:35: 8000000 INFO @ Sat, 11 Dec 2021 16:07:36: 15000000 INFO @ Sat, 11 Dec 2021 16:07:36: 19000000 INFO @ Sat, 11 Dec 2021 16:07:40: 9000000 INFO @ Sat, 11 Dec 2021 16:07:40: 16000000 INFO @ Sat, 11 Dec 2021 16:07:42: 20000000 INFO @ Sat, 11 Dec 2021 16:07:44: 10000000 INFO @ Sat, 11 Dec 2021 16:07:44: 17000000 INFO @ Sat, 11 Dec 2021 16:07:47: 21000000 INFO @ Sat, 11 Dec 2021 16:07:49: 11000000 INFO @ Sat, 11 Dec 2021 16:07:49: 18000000 INFO @ Sat, 11 Dec 2021 16:07:52: 22000000 INFO @ Sat, 11 Dec 2021 16:07:53: 12000000 INFO @ Sat, 11 Dec 2021 16:07:53: 19000000 INFO @ Sat, 11 Dec 2021 16:07:57: 23000000 INFO @ Sat, 11 Dec 2021 16:07:57: 13000000 INFO @ Sat, 11 Dec 2021 16:07:57: 20000000 INFO @ Sat, 11 Dec 2021 16:08:02: 21000000 INFO @ Sat, 11 Dec 2021 16:08:02: 14000000 INFO @ Sat, 11 Dec 2021 16:08:02: 24000000 INFO @ Sat, 11 Dec 2021 16:08:06: 22000000 INFO @ Sat, 11 Dec 2021 16:08:06: 15000000 INFO @ Sat, 11 Dec 2021 16:08:07: 25000000 INFO @ Sat, 11 Dec 2021 16:08:10: 23000000 INFO @ Sat, 11 Dec 2021 16:08:10: 16000000 INFO @ Sat, 11 Dec 2021 16:08:12: 26000000 INFO @ Sat, 11 Dec 2021 16:08:14: 24000000 INFO @ Sat, 11 Dec 2021 16:08:14: 17000000 INFO @ Sat, 11 Dec 2021 16:08:17: 27000000 INFO @ Sat, 11 Dec 2021 16:08:18: 25000000 INFO @ Sat, 11 Dec 2021 16:08:19: 18000000 INFO @ Sat, 11 Dec 2021 16:08:22: 28000000 INFO @ Sat, 11 Dec 2021 16:08:22: 26000000 INFO @ Sat, 11 Dec 2021 16:08:23: 19000000 INFO @ Sat, 11 Dec 2021 16:08:27: 27000000 INFO @ Sat, 11 Dec 2021 16:08:27: 20000000 INFO @ Sat, 11 Dec 2021 16:08:27: 29000000 INFO @ Sat, 11 Dec 2021 16:08:31: 28000000 INFO @ Sat, 11 Dec 2021 16:08:32: 21000000 INFO @ Sat, 11 Dec 2021 16:08:32: 30000000 INFO @ Sat, 11 Dec 2021 16:08:34: #1 tag size is determined as 42 bps INFO @ Sat, 11 Dec 2021 16:08:34: #1 tag size = 42 INFO @ Sat, 11 Dec 2021 16:08:34: #1 total tags in treatment: 14841735 INFO @ Sat, 11 Dec 2021 16:08:34: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 16:08:34: #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 16:08:35: #1 tags after filtering in treatment: 13840069 INFO @ Sat, 11 Dec 2021 16:08:35: #1 Redundant rate of treatment: 0.07 INFO @ Sat, 11 Dec 2021 16:08:35: #1 finished! INFO @ Sat, 11 Dec 2021 16:08:35: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 16:08:35: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 16:08:35: 29000000 INFO @ Sat, 11 Dec 2021 16:08:36: #2 number of paired peaks: 1060 INFO @ Sat, 11 Dec 2021 16:08:36: start model_add_line... INFO @ Sat, 11 Dec 2021 16:08:36: start X-correlation... INFO @ Sat, 11 Dec 2021 16:08:36: end of X-cor INFO @ Sat, 11 Dec 2021 16:08:36: #2 finished! INFO @ Sat, 11 Dec 2021 16:08:36: #2 predicted fragment length is 139 bps INFO @ Sat, 11 Dec 2021 16:08:36: #2 alternative fragment length(s) may be 4,139 bps INFO @ Sat, 11 Dec 2021 16:08:36: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX7628887/SRX7628887.05_model.r INFO @ Sat, 11 Dec 2021 16:08:36: #3 Call peaks... INFO @ Sat, 11 Dec 2021 16:08:36: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Dec 2021 16:08:37: 22000000 INFO @ Sat, 11 Dec 2021 16:08:39: 30000000 INFO @ Sat, 11 Dec 2021 16:08:41: #1 tag size is determined as 42 bps INFO @ Sat, 11 Dec 2021 16:08:41: #1 tag size = 42 INFO @ Sat, 11 Dec 2021 16:08:41: #1 total tags in treatment: 14841735 INFO @ Sat, 11 Dec 2021 16:08:41: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 16:08:41: #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 16:08:41: #1 tags after filtering in treatment: 13840069 INFO @ Sat, 11 Dec 2021 16:08:41: #1 Redundant rate of treatment: 0.07 INFO @ Sat, 11 Dec 2021 16:08:41: #1 finished! INFO @ Sat, 11 Dec 2021 16:08:41: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 16:08:41: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 16:08:41: 23000000 INFO @ Sat, 11 Dec 2021 16:08:42: #2 number of paired peaks: 1060 INFO @ Sat, 11 Dec 2021 16:08:42: start model_add_line... INFO @ Sat, 11 Dec 2021 16:08:42: start X-correlation... INFO @ Sat, 11 Dec 2021 16:08:42: end of X-cor INFO @ Sat, 11 Dec 2021 16:08:42: #2 finished! INFO @ Sat, 11 Dec 2021 16:08:42: #2 predicted fragment length is 139 bps INFO @ Sat, 11 Dec 2021 16:08:42: #2 alternative fragment length(s) may be 4,139 bps INFO @ Sat, 11 Dec 2021 16:08:42: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX7628887/SRX7628887.10_model.r INFO @ Sat, 11 Dec 2021 16:08:42: #3 Call peaks... INFO @ Sat, 11 Dec 2021 16:08:42: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Dec 2021 16:08:46: 24000000 INFO @ Sat, 11 Dec 2021 16:08:50: 25000000 INFO @ Sat, 11 Dec 2021 16:08:54: 26000000 INFO @ Sat, 11 Dec 2021 16:08:59: 27000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 11 Dec 2021 16:09:04: #3 Call peaks for each chromosome... INFO @ Sat, 11 Dec 2021 16:09:04: 28000000 INFO @ Sat, 11 Dec 2021 16:09:09: 29000000 INFO @ Sat, 11 Dec 2021 16:09:11: #3 Call peaks for each chromosome... INFO @ Sat, 11 Dec 2021 16:09:13: 30000000 INFO @ Sat, 11 Dec 2021 16:09:15: #1 tag size is determined as 42 bps INFO @ Sat, 11 Dec 2021 16:09:15: #1 tag size = 42 INFO @ Sat, 11 Dec 2021 16:09:15: #1 total tags in treatment: 14841735 INFO @ Sat, 11 Dec 2021 16:09:15: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 16:09:15: #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 16:09:15: #1 tags after filtering in treatment: 13840069 INFO @ Sat, 11 Dec 2021 16:09:15: #1 Redundant rate of treatment: 0.07 INFO @ Sat, 11 Dec 2021 16:09:15: #1 finished! INFO @ Sat, 11 Dec 2021 16:09:15: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 16:09:15: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 16:09:16: #2 number of paired peaks: 1060 INFO @ Sat, 11 Dec 2021 16:09:16: start model_add_line... INFO @ Sat, 11 Dec 2021 16:09:16: start X-correlation... INFO @ Sat, 11 Dec 2021 16:09:16: end of X-cor INFO @ Sat, 11 Dec 2021 16:09:16: #2 finished! INFO @ Sat, 11 Dec 2021 16:09:16: #2 predicted fragment length is 139 bps INFO @ Sat, 11 Dec 2021 16:09:16: #2 alternative fragment length(s) may be 4,139 bps INFO @ Sat, 11 Dec 2021 16:09:16: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX7628887/SRX7628887.20_model.r INFO @ Sat, 11 Dec 2021 16:09:16: #3 Call peaks... INFO @ Sat, 11 Dec 2021 16:09:16: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Dec 2021 16:09:17: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX7628887/SRX7628887.05_peaks.xls INFO @ Sat, 11 Dec 2021 16:09:17: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX7628887/SRX7628887.05_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 16:09:17: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX7628887/SRX7628887.05_summits.bed INFO @ Sat, 11 Dec 2021 16:09:17: Done! pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (2705 records, 4 fields): 4 millis CompletedMACS2peakCalling INFO @ Sat, 11 Dec 2021 16:09:24: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX7628887/SRX7628887.10_peaks.xls INFO @ Sat, 11 Dec 2021 16:09:24: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX7628887/SRX7628887.10_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 16:09:24: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX7628887/SRX7628887.10_summits.bed INFO @ Sat, 11 Dec 2021 16:09:24: Done! pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (1635 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Sat, 11 Dec 2021 16:09:45: #3 Call peaks for each chromosome... INFO @ Sat, 11 Dec 2021 16:09:59: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX7628887/SRX7628887.20_peaks.xls INFO @ Sat, 11 Dec 2021 16:09:59: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX7628887/SRX7628887.20_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 16:09:59: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX7628887/SRX7628887.20_summits.bed INFO @ Sat, 11 Dec 2021 16:09:59: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (803 records, 4 fields): 2 millis CompletedMACS2peakCalling BigWig に変換しました。