Job ID = 14172031 SRX = SRX10089743 Genome = dm3 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... Read 34721185 spots for SRR13700630/SRR13700630.sra Written 34721185 spots for SRR13700630/SRR13700630.sra fastq に変換しました。 bowtie でマッピング中... Your job 14172573 ("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: 00:32:43 34721185 reads; of these: 34721185 (100.00%) were paired; of these: 2122243 (6.11%) aligned concordantly 0 times 27728821 (79.86%) aligned concordantly exactly 1 time 4870121 (14.03%) aligned concordantly >1 times ---- 2122243 pairs aligned concordantly 0 times; of these: 360825 (17.00%) aligned discordantly 1 time ---- 1761418 pairs aligned 0 times concordantly or discordantly; of these: 3522836 mates make up the pairs; of these: 2658477 (75.46%) aligned 0 times 628706 (17.85%) aligned exactly 1 time 235653 (6.69%) aligned >1 times 96.17% overall alignment rate Time searching: 00:32:43 Overall time: 00:32:43 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 24 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] 11683013 / 32399702 = 0.3606 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 14:35:46: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX10089743/SRX10089743.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX10089743/SRX10089743.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX10089743/SRX10089743.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX10089743/SRX10089743.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 14:35:46: #1 read tag files... INFO @ Sat, 11 Dec 2021 14:35:46: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 14:35:52: 1000000 INFO @ Sat, 11 Dec 2021 14:35:57: 2000000 INFO @ Sat, 11 Dec 2021 14:36:02: 3000000 INFO @ Sat, 11 Dec 2021 14:36:07: 4000000 INFO @ Sat, 11 Dec 2021 14:36:12: 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 14:36:16: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX10089743/SRX10089743.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX10089743/SRX10089743.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX10089743/SRX10089743.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX10089743/SRX10089743.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 14:36:16: #1 read tag files... INFO @ Sat, 11 Dec 2021 14:36:16: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 14:36:18: 6000000 INFO @ Sat, 11 Dec 2021 14:36:23: 1000000 INFO @ Sat, 11 Dec 2021 14:36:24: 7000000 INFO @ Sat, 11 Dec 2021 14:36:29: 2000000 INFO @ Sat, 11 Dec 2021 14:36:30: 8000000 INFO @ Sat, 11 Dec 2021 14:36:35: 3000000 INFO @ Sat, 11 Dec 2021 14:36:36: 9000000 INFO @ Sat, 11 Dec 2021 14:36:41: 4000000 INFO @ Sat, 11 Dec 2021 14:36:42: 10000000 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 14:36:46: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX10089743/SRX10089743.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX10089743/SRX10089743.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX10089743/SRX10089743.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX10089743/SRX10089743.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 14:36:46: #1 read tag files... INFO @ Sat, 11 Dec 2021 14:36:46: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 14:36:47: 5000000 INFO @ Sat, 11 Dec 2021 14:36:48: 11000000 INFO @ Sat, 11 Dec 2021 14:36:52: 1000000 INFO @ Sat, 11 Dec 2021 14:36:54: 6000000 INFO @ Sat, 11 Dec 2021 14:36:54: 12000000 INFO @ Sat, 11 Dec 2021 14:36:58: 2000000 INFO @ Sat, 11 Dec 2021 14:37:00: 7000000 INFO @ Sat, 11 Dec 2021 14:37:00: 13000000 INFO @ Sat, 11 Dec 2021 14:37:04: 3000000 INFO @ Sat, 11 Dec 2021 14:37:06: 8000000 INFO @ Sat, 11 Dec 2021 14:37:06: 14000000 INFO @ Sat, 11 Dec 2021 14:37:11: 4000000 INFO @ Sat, 11 Dec 2021 14:37:12: 9000000 INFO @ Sat, 11 Dec 2021 14:37:12: 15000000 INFO @ Sat, 11 Dec 2021 14:37:17: 5000000 INFO @ Sat, 11 Dec 2021 14:37:18: 10000000 INFO @ Sat, 11 Dec 2021 14:37:18: 16000000 INFO @ Sat, 11 Dec 2021 14:37:23: 6000000 INFO @ Sat, 11 Dec 2021 14:37:24: 11000000 INFO @ Sat, 11 Dec 2021 14:37:25: 17000000 INFO @ Sat, 11 Dec 2021 14:37:29: 7000000 INFO @ Sat, 11 Dec 2021 14:37:30: 12000000 INFO @ Sat, 11 Dec 2021 14:37:31: 18000000 INFO @ Sat, 11 Dec 2021 14:37:35: 8000000 INFO @ Sat, 11 Dec 2021 14:37:36: 13000000 INFO @ Sat, 11 Dec 2021 14:37:37: 19000000 INFO @ Sat, 11 Dec 2021 14:37:41: 9000000 INFO @ Sat, 11 Dec 2021 14:37:42: 14000000 INFO @ Sat, 11 Dec 2021 14:37:42: 20000000 INFO @ Sat, 11 Dec 2021 14:37:47: 10000000 INFO @ Sat, 11 Dec 2021 14:37:48: 15000000 INFO @ Sat, 11 Dec 2021 14:37:48: 21000000 INFO @ Sat, 11 Dec 2021 14:37:53: 11000000 INFO @ Sat, 11 Dec 2021 14:37:54: 16000000 INFO @ Sat, 11 Dec 2021 14:37:55: 22000000 INFO @ Sat, 11 Dec 2021 14:37:59: 12000000 INFO @ Sat, 11 Dec 2021 14:38:01: 17000000 INFO @ Sat, 11 Dec 2021 14:38:01: 23000000 INFO @ Sat, 11 Dec 2021 14:38:05: 13000000 INFO @ Sat, 11 Dec 2021 14:38:07: 18000000 INFO @ Sat, 11 Dec 2021 14:38:07: 24000000 INFO @ Sat, 11 Dec 2021 14:38:11: 14000000 INFO @ Sat, 11 Dec 2021 14:38:13: 19000000 INFO @ Sat, 11 Dec 2021 14:38:13: 25000000 INFO @ Sat, 11 Dec 2021 14:38:17: 15000000 INFO @ Sat, 11 Dec 2021 14:38:19: 20000000 INFO @ Sat, 11 Dec 2021 14:38:19: 26000000 INFO @ Sat, 11 Dec 2021 14:38:24: 16000000 INFO @ Sat, 11 Dec 2021 14:38:25: 21000000 INFO @ Sat, 11 Dec 2021 14:38:25: 27000000 INFO @ Sat, 11 Dec 2021 14:38:30: 17000000 INFO @ Sat, 11 Dec 2021 14:38:31: 22000000 INFO @ Sat, 11 Dec 2021 14:38:31: 28000000 INFO @ Sat, 11 Dec 2021 14:38:36: 18000000 INFO @ Sat, 11 Dec 2021 14:38:37: 23000000 INFO @ Sat, 11 Dec 2021 14:38:37: 29000000 INFO @ Sat, 11 Dec 2021 14:38:41: 19000000 INFO @ Sat, 11 Dec 2021 14:38:43: 24000000 INFO @ Sat, 11 Dec 2021 14:38:43: 30000000 INFO @ Sat, 11 Dec 2021 14:38:47: 20000000 INFO @ Sat, 11 Dec 2021 14:38:49: 25000000 INFO @ Sat, 11 Dec 2021 14:38:49: 31000000 INFO @ Sat, 11 Dec 2021 14:38:54: 21000000 INFO @ Sat, 11 Dec 2021 14:38:55: 26000000 INFO @ Sat, 11 Dec 2021 14:38:55: 32000000 INFO @ Sat, 11 Dec 2021 14:39:00: 22000000 INFO @ Sat, 11 Dec 2021 14:39:01: 27000000 INFO @ Sat, 11 Dec 2021 14:39:01: 33000000 INFO @ Sat, 11 Dec 2021 14:39:06: 23000000 INFO @ Sat, 11 Dec 2021 14:39:07: 28000000 INFO @ Sat, 11 Dec 2021 14:39:07: 34000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 11 Dec 2021 14:39:12: 24000000 INFO @ Sat, 11 Dec 2021 14:39:13: 29000000 INFO @ Sat, 11 Dec 2021 14:39:13: 35000000 INFO @ Sat, 11 Dec 2021 14:39:18: 25000000 INFO @ Sat, 11 Dec 2021 14:39:19: 30000000 INFO @ Sat, 11 Dec 2021 14:39:20: 36000000 INFO @ Sat, 11 Dec 2021 14:39:24: 26000000 INFO @ Sat, 11 Dec 2021 14:39:25: 31000000 INFO @ Sat, 11 Dec 2021 14:39:26: 37000000 INFO @ Sat, 11 Dec 2021 14:39:30: 27000000 INFO @ Sat, 11 Dec 2021 14:39:31: 32000000 INFO @ Sat, 11 Dec 2021 14:39:32: 38000000 INFO @ Sat, 11 Dec 2021 14:39:36: 28000000 INFO @ Sat, 11 Dec 2021 14:39:37: 33000000 INFO @ Sat, 11 Dec 2021 14:39:37: 39000000 INFO @ Sat, 11 Dec 2021 14:39:42: 29000000 INFO @ Sat, 11 Dec 2021 14:39:43: 34000000 INFO @ Sat, 11 Dec 2021 14:39:43: 40000000 INFO @ Sat, 11 Dec 2021 14:39:48: 30000000 INFO @ Sat, 11 Dec 2021 14:39:49: 35000000 INFO @ Sat, 11 Dec 2021 14:39:49: 41000000 INFO @ Sat, 11 Dec 2021 14:39:54: 31000000 INFO @ Sat, 11 Dec 2021 14:39:55: 36000000 INFO @ Sat, 11 Dec 2021 14:39:55: 42000000 INFO @ Sat, 11 Dec 2021 14:40:00: 32000000 INFO @ Sat, 11 Dec 2021 14:40:01: 43000000 INFO @ Sat, 11 Dec 2021 14:40:01: 37000000 INFO @ Sat, 11 Dec 2021 14:40:04: #1 tag size is determined as 40 bps INFO @ Sat, 11 Dec 2021 14:40:04: #1 tag size = 40 INFO @ Sat, 11 Dec 2021 14:40:04: #1 total tags in treatment: 20940030 INFO @ Sat, 11 Dec 2021 14:40:04: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 14:40:04: #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 14:40:04: #1 tags after filtering in treatment: 13653175 INFO @ Sat, 11 Dec 2021 14:40:04: #1 Redundant rate of treatment: 0.35 INFO @ Sat, 11 Dec 2021 14:40:04: #1 finished! INFO @ Sat, 11 Dec 2021 14:40:04: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 14:40:04: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 14:40:05: #2 number of paired peaks: 1660 INFO @ Sat, 11 Dec 2021 14:40:05: start model_add_line... BigWig に変換しました。 INFO @ Sat, 11 Dec 2021 14:40:05: start X-correlation... INFO @ Sat, 11 Dec 2021 14:40:05: end of X-cor INFO @ Sat, 11 Dec 2021 14:40:05: #2 finished! INFO @ Sat, 11 Dec 2021 14:40:05: #2 predicted fragment length is 97 bps INFO @ Sat, 11 Dec 2021 14:40:05: #2 alternative fragment length(s) may be 97 bps INFO @ Sat, 11 Dec 2021 14:40:05: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX10089743/SRX10089743.05_model.r INFO @ Sat, 11 Dec 2021 14:40:05: #3 Call peaks... INFO @ Sat, 11 Dec 2021 14:40:05: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Dec 2021 14:40:05: 33000000 INFO @ Sat, 11 Dec 2021 14:40:07: 38000000 INFO @ Sat, 11 Dec 2021 14:40:11: 34000000 INFO @ Sat, 11 Dec 2021 14:40:13: 39000000 INFO @ Sat, 11 Dec 2021 14:40:17: 35000000 INFO @ Sat, 11 Dec 2021 14:40:18: 40000000 INFO @ Sat, 11 Dec 2021 14:40:23: 36000000 INFO @ Sat, 11 Dec 2021 14:40:24: 41000000 INFO @ Sat, 11 Dec 2021 14:40:29: 37000000 INFO @ Sat, 11 Dec 2021 14:40:30: 42000000 INFO @ Sat, 11 Dec 2021 14:40:32: #3 Call peaks for each chromosome... INFO @ Sat, 11 Dec 2021 14:40:35: 38000000 INFO @ Sat, 11 Dec 2021 14:40:35: 43000000 INFO @ Sat, 11 Dec 2021 14:40:38: #1 tag size is determined as 40 bps INFO @ Sat, 11 Dec 2021 14:40:38: #1 tag size = 40 INFO @ Sat, 11 Dec 2021 14:40:38: #1 total tags in treatment: 20940030 INFO @ Sat, 11 Dec 2021 14:40:38: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 14:40:38: #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 14:40:38: #1 tags after filtering in treatment: 13653175 INFO @ Sat, 11 Dec 2021 14:40:38: #1 Redundant rate of treatment: 0.35 INFO @ Sat, 11 Dec 2021 14:40:38: #1 finished! INFO @ Sat, 11 Dec 2021 14:40:38: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 14:40:38: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 14:40:39: #2 number of paired peaks: 1660 INFO @ Sat, 11 Dec 2021 14:40:39: start model_add_line... INFO @ Sat, 11 Dec 2021 14:40:40: start X-correlation... INFO @ Sat, 11 Dec 2021 14:40:40: end of X-cor INFO @ Sat, 11 Dec 2021 14:40:40: #2 finished! INFO @ Sat, 11 Dec 2021 14:40:40: #2 predicted fragment length is 97 bps INFO @ Sat, 11 Dec 2021 14:40:40: #2 alternative fragment length(s) may be 97 bps INFO @ Sat, 11 Dec 2021 14:40:40: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX10089743/SRX10089743.10_model.r INFO @ Sat, 11 Dec 2021 14:40:40: #3 Call peaks... INFO @ Sat, 11 Dec 2021 14:40:40: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Dec 2021 14:40:40: 39000000 INFO @ Sat, 11 Dec 2021 14:40:45: 40000000 INFO @ Sat, 11 Dec 2021 14:40:45: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX10089743/SRX10089743.05_peaks.xls INFO @ Sat, 11 Dec 2021 14:40:46: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX10089743/SRX10089743.05_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 14:40:46: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX10089743/SRX10089743.05_summits.bed INFO @ Sat, 11 Dec 2021 14:40:46: Done! pass1 - making usageList (15 chroms): 3 millis pass2 - checking and writing primary data (15294 records, 4 fields): 14 millis CompletedMACS2peakCalling INFO @ Sat, 11 Dec 2021 14:40:50: 41000000 INFO @ Sat, 11 Dec 2021 14:40:55: 42000000 INFO @ Sat, 11 Dec 2021 14:41:00: 43000000 INFO @ Sat, 11 Dec 2021 14:41:02: #1 tag size is determined as 40 bps INFO @ Sat, 11 Dec 2021 14:41:02: #1 tag size = 40 INFO @ Sat, 11 Dec 2021 14:41:02: #1 total tags in treatment: 20940030 INFO @ Sat, 11 Dec 2021 14:41:02: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 14:41:02: #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 14:41:03: #1 tags after filtering in treatment: 13653175 INFO @ Sat, 11 Dec 2021 14:41:03: #1 Redundant rate of treatment: 0.35 INFO @ Sat, 11 Dec 2021 14:41:03: #1 finished! INFO @ Sat, 11 Dec 2021 14:41:03: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 14:41:03: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 14:41:04: #2 number of paired peaks: 1660 INFO @ Sat, 11 Dec 2021 14:41:04: start model_add_line... INFO @ Sat, 11 Dec 2021 14:41:04: start X-correlation... INFO @ Sat, 11 Dec 2021 14:41:04: end of X-cor INFO @ Sat, 11 Dec 2021 14:41:04: #2 finished! INFO @ Sat, 11 Dec 2021 14:41:04: #2 predicted fragment length is 97 bps INFO @ Sat, 11 Dec 2021 14:41:04: #2 alternative fragment length(s) may be 97 bps INFO @ Sat, 11 Dec 2021 14:41:04: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX10089743/SRX10089743.20_model.r INFO @ Sat, 11 Dec 2021 14:41:04: #3 Call peaks... INFO @ Sat, 11 Dec 2021 14:41:04: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Dec 2021 14:41:06: #3 Call peaks for each chromosome... INFO @ Sat, 11 Dec 2021 14:41:20: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX10089743/SRX10089743.10_peaks.xls INFO @ Sat, 11 Dec 2021 14:41:20: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX10089743/SRX10089743.10_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 14:41:20: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX10089743/SRX10089743.10_summits.bed INFO @ Sat, 11 Dec 2021 14:41:20: Done! pass1 - making usageList (15 chroms): 2 millis pass2 - checking and writing primary data (9186 records, 4 fields): 9 millis CompletedMACS2peakCalling INFO @ Sat, 11 Dec 2021 14:41:30: #3 Call peaks for each chromosome... INFO @ Sat, 11 Dec 2021 14:41:43: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX10089743/SRX10089743.20_peaks.xls INFO @ Sat, 11 Dec 2021 14:41:43: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX10089743/SRX10089743.20_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 14:41:43: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX10089743/SRX10089743.20_summits.bed INFO @ Sat, 11 Dec 2021 14:41:43: Done! pass1 - making usageList (13 chroms): 1 millis pass2 - checking and writing primary data (3761 records, 4 fields): 5 millis CompletedMACS2peakCalling