Job ID = 14168033 SRX = ERX3978930 Genome = dm3 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... Read 40345631 spots for ERR3976000/ERR3976000.sra Written 40345631 spots for ERR3976000/ERR3976000.sra fastq に変換しました。 bowtie でマッピング中... Your job 14169181 ("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: 02:30:04 40345631 reads; of these: 40345631 (100.00%) were paired; of these: 14030524 (34.78%) aligned concordantly 0 times 20333426 (50.40%) aligned concordantly exactly 1 time 5981681 (14.83%) aligned concordantly >1 times ---- 14030524 pairs aligned concordantly 0 times; of these: 903453 (6.44%) aligned discordantly 1 time ---- 13127071 pairs aligned 0 times concordantly or discordantly; of these: 26254142 mates make up the pairs; of these: 12895504 (49.12%) aligned 0 times 8424918 (32.09%) aligned exactly 1 time 4933720 (18.79%) aligned >1 times 84.02% overall alignment rate Time searching: 02:30:04 Overall time: 02:30:04 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 28 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] 20221010 / 26905032 = 0.7516 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 @ Fri, 10 Dec 2021 17:25:29: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/ERX3978930/ERX3978930.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/ERX3978930/ERX3978930.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/ERX3978930/ERX3978930.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/ERX3978930/ERX3978930.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 @ Fri, 10 Dec 2021 17:25:29: #1 read tag files... INFO @ Fri, 10 Dec 2021 17:25:29: #1 read treatment tags... INFO @ Fri, 10 Dec 2021 17:25:37: 1000000 INFO @ Fri, 10 Dec 2021 17:25:45: 2000000 INFO @ Fri, 10 Dec 2021 17:25:53: 3000000 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 @ Fri, 10 Dec 2021 17:25:59: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/ERX3978930/ERX3978930.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/ERX3978930/ERX3978930.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/ERX3978930/ERX3978930.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/ERX3978930/ERX3978930.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 @ Fri, 10 Dec 2021 17:25:59: #1 read tag files... INFO @ Fri, 10 Dec 2021 17:25:59: #1 read treatment tags... INFO @ Fri, 10 Dec 2021 17:26:01: 4000000 INFO @ Fri, 10 Dec 2021 17:26:07: 1000000 INFO @ Fri, 10 Dec 2021 17:26:11: 5000000 INFO @ Fri, 10 Dec 2021 17:26:15: 2000000 INFO @ Fri, 10 Dec 2021 17:26:20: 6000000 INFO @ Fri, 10 Dec 2021 17:26:24: 3000000 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 @ Fri, 10 Dec 2021 17:26:29: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/ERX3978930/ERX3978930.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/ERX3978930/ERX3978930.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/ERX3978930/ERX3978930.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/ERX3978930/ERX3978930.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 @ Fri, 10 Dec 2021 17:26:29: #1 read tag files... INFO @ Fri, 10 Dec 2021 17:26:29: #1 read treatment tags... INFO @ Fri, 10 Dec 2021 17:26:29: 7000000 INFO @ Fri, 10 Dec 2021 17:26:32: 4000000 INFO @ Fri, 10 Dec 2021 17:26:38: 8000000 INFO @ Fri, 10 Dec 2021 17:26:38: 1000000 INFO @ Fri, 10 Dec 2021 17:26:41: 5000000 INFO @ Fri, 10 Dec 2021 17:26:47: 9000000 INFO @ Fri, 10 Dec 2021 17:26:47: 2000000 INFO @ Fri, 10 Dec 2021 17:26:50: 6000000 INFO @ Fri, 10 Dec 2021 17:26:56: 10000000 INFO @ Fri, 10 Dec 2021 17:26:57: 3000000 INFO @ Fri, 10 Dec 2021 17:26:58: 7000000 INFO @ Fri, 10 Dec 2021 17:27:06: 11000000 INFO @ Fri, 10 Dec 2021 17:27:06: 4000000 INFO @ Fri, 10 Dec 2021 17:27:07: 8000000 INFO @ Fri, 10 Dec 2021 17:27:15: 12000000 INFO @ Fri, 10 Dec 2021 17:27:15: 9000000 INFO @ Fri, 10 Dec 2021 17:27:15: 5000000 INFO @ Fri, 10 Dec 2021 17:27:24: 10000000 INFO @ Fri, 10 Dec 2021 17:27:25: 13000000 INFO @ Fri, 10 Dec 2021 17:27:25: 6000000 INFO @ Fri, 10 Dec 2021 17:27:32: 11000000 INFO @ Fri, 10 Dec 2021 17:27:34: 7000000 INFO @ Fri, 10 Dec 2021 17:27:34: 14000000 INFO @ Fri, 10 Dec 2021 17:27:41: 12000000 INFO @ Fri, 10 Dec 2021 17:27:43: 8000000 INFO @ Fri, 10 Dec 2021 17:27:43: 15000000 INFO @ Fri, 10 Dec 2021 17:27:50: 13000000 INFO @ Fri, 10 Dec 2021 17:27:53: 9000000 INFO @ Fri, 10 Dec 2021 17:27:53: 16000000 INFO @ Fri, 10 Dec 2021 17:27:58: 14000000 INFO @ Fri, 10 Dec 2021 17:28:02: 10000000 INFO @ Fri, 10 Dec 2021 17:28:03: 17000000 INFO @ Fri, 10 Dec 2021 17:28:07: 15000000 INFO @ Fri, 10 Dec 2021 17:28:11: 11000000 INFO @ Fri, 10 Dec 2021 17:28:12: 18000000 INFO @ Fri, 10 Dec 2021 17:28:15: 16000000 INFO @ Fri, 10 Dec 2021 17:28:20: 12000000 INFO @ Fri, 10 Dec 2021 17:28:22: 19000000 INFO @ Fri, 10 Dec 2021 17:28:24: 17000000 INFO @ Fri, 10 Dec 2021 17:28:30: 13000000 INFO @ Fri, 10 Dec 2021 17:28:32: 20000000 INFO @ Fri, 10 Dec 2021 17:28:33: 18000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Fri, 10 Dec 2021 17:28:39: 14000000 INFO @ Fri, 10 Dec 2021 17:28:42: 21000000 INFO @ Fri, 10 Dec 2021 17:28:42: 19000000 INFO @ Fri, 10 Dec 2021 17:28:48: 15000000 INFO @ Fri, 10 Dec 2021 17:28:51: 20000000 INFO @ Fri, 10 Dec 2021 17:28:51: 22000000 INFO @ Fri, 10 Dec 2021 17:28:57: 16000000 INFO @ Fri, 10 Dec 2021 17:29:00: 21000000 INFO @ Fri, 10 Dec 2021 17:29:01: 23000000 INFO @ Fri, 10 Dec 2021 17:29:07: 17000000 INFO @ Fri, 10 Dec 2021 17:29:09: 22000000 BigWig に変換しました。 INFO @ Fri, 10 Dec 2021 17:29:11: 24000000 INFO @ Fri, 10 Dec 2021 17:29:16: 18000000 INFO @ Fri, 10 Dec 2021 17:29:18: 23000000 INFO @ Fri, 10 Dec 2021 17:29:21: 25000000 INFO @ Fri, 10 Dec 2021 17:29:26: 19000000 INFO @ Fri, 10 Dec 2021 17:29:27: 24000000 INFO @ Fri, 10 Dec 2021 17:29:30: 26000000 INFO @ Fri, 10 Dec 2021 17:29:35: 20000000 INFO @ Fri, 10 Dec 2021 17:29:36: 25000000 INFO @ Fri, 10 Dec 2021 17:29:39: 27000000 INFO @ Fri, 10 Dec 2021 17:29:43: #1 tag size is determined as 80 bps INFO @ Fri, 10 Dec 2021 17:29:43: #1 tag size = 80 INFO @ Fri, 10 Dec 2021 17:29:43: #1 total tags in treatment: 6598061 INFO @ Fri, 10 Dec 2021 17:29:43: #1 user defined the maximum tags... INFO @ Fri, 10 Dec 2021 17:29:43: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 10 Dec 2021 17:29:43: #1 tags after filtering in treatment: 5967763 INFO @ Fri, 10 Dec 2021 17:29:43: #1 Redundant rate of treatment: 0.10 INFO @ Fri, 10 Dec 2021 17:29:43: #1 finished! INFO @ Fri, 10 Dec 2021 17:29:43: #2 Build Peak Model... INFO @ Fri, 10 Dec 2021 17:29:43: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Dec 2021 17:29:43: #2 number of paired peaks: 1582 INFO @ Fri, 10 Dec 2021 17:29:43: start model_add_line... INFO @ Fri, 10 Dec 2021 17:29:43: start X-correlation... INFO @ Fri, 10 Dec 2021 17:29:43: end of X-cor INFO @ Fri, 10 Dec 2021 17:29:43: #2 finished! INFO @ Fri, 10 Dec 2021 17:29:43: #2 predicted fragment length is 162 bps INFO @ Fri, 10 Dec 2021 17:29:43: #2 alternative fragment length(s) may be 162 bps INFO @ Fri, 10 Dec 2021 17:29:43: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/ERX3978930/ERX3978930.05_model.r INFO @ Fri, 10 Dec 2021 17:29:43: #3 Call peaks... INFO @ Fri, 10 Dec 2021 17:29:43: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 10 Dec 2021 17:29:44: 26000000 INFO @ Fri, 10 Dec 2021 17:29:45: 21000000 INFO @ Fri, 10 Dec 2021 17:29:53: 27000000 INFO @ Fri, 10 Dec 2021 17:29:54: 22000000 INFO @ Fri, 10 Dec 2021 17:29:56: #1 tag size is determined as 80 bps INFO @ Fri, 10 Dec 2021 17:29:56: #1 tag size = 80 INFO @ Fri, 10 Dec 2021 17:29:56: #1 total tags in treatment: 6598061 INFO @ Fri, 10 Dec 2021 17:29:56: #1 user defined the maximum tags... INFO @ Fri, 10 Dec 2021 17:29:56: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 10 Dec 2021 17:29:56: #1 tags after filtering in treatment: 5967763 INFO @ Fri, 10 Dec 2021 17:29:56: #1 Redundant rate of treatment: 0.10 INFO @ Fri, 10 Dec 2021 17:29:56: #1 finished! INFO @ Fri, 10 Dec 2021 17:29:56: #2 Build Peak Model... INFO @ Fri, 10 Dec 2021 17:29:56: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Dec 2021 17:29:56: #2 number of paired peaks: 1582 INFO @ Fri, 10 Dec 2021 17:29:56: start model_add_line... INFO @ Fri, 10 Dec 2021 17:29:56: start X-correlation... INFO @ Fri, 10 Dec 2021 17:29:56: end of X-cor INFO @ Fri, 10 Dec 2021 17:29:56: #2 finished! INFO @ Fri, 10 Dec 2021 17:29:56: #2 predicted fragment length is 162 bps INFO @ Fri, 10 Dec 2021 17:29:56: #2 alternative fragment length(s) may be 162 bps INFO @ Fri, 10 Dec 2021 17:29:56: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/ERX3978930/ERX3978930.10_model.r INFO @ Fri, 10 Dec 2021 17:29:56: #3 Call peaks... INFO @ Fri, 10 Dec 2021 17:29:56: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 10 Dec 2021 17:29:59: #3 Call peaks for each chromosome... INFO @ Fri, 10 Dec 2021 17:30:03: 23000000 INFO @ Fri, 10 Dec 2021 17:30:08: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/ERX3978930/ERX3978930.05_peaks.xls INFO @ Fri, 10 Dec 2021 17:30:08: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/ERX3978930/ERX3978930.05_peaks.narrowPeak INFO @ Fri, 10 Dec 2021 17:30:08: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/ERX3978930/ERX3978930.05_summits.bed INFO @ Fri, 10 Dec 2021 17:30:08: Done! pass1 - making usageList (15 chroms): 2 millis pass2 - checking and writing primary data (8099 records, 4 fields): 10 millis CompletedMACS2peakCalling INFO @ Fri, 10 Dec 2021 17:30:12: 24000000 INFO @ Fri, 10 Dec 2021 17:30:12: #3 Call peaks for each chromosome... INFO @ Fri, 10 Dec 2021 17:30:20: 25000000 INFO @ Fri, 10 Dec 2021 17:30:21: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/ERX3978930/ERX3978930.10_peaks.xls INFO @ Fri, 10 Dec 2021 17:30:21: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/ERX3978930/ERX3978930.10_peaks.narrowPeak INFO @ Fri, 10 Dec 2021 17:30:21: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/ERX3978930/ERX3978930.10_summits.bed INFO @ Fri, 10 Dec 2021 17:30:21: Done! pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (3690 records, 4 fields): 8 millis CompletedMACS2peakCalling INFO @ Fri, 10 Dec 2021 17:30:28: 26000000 INFO @ Fri, 10 Dec 2021 17:30:36: 27000000 INFO @ Fri, 10 Dec 2021 17:30:39: #1 tag size is determined as 80 bps INFO @ Fri, 10 Dec 2021 17:30:39: #1 tag size = 80 INFO @ Fri, 10 Dec 2021 17:30:39: #1 total tags in treatment: 6598061 INFO @ Fri, 10 Dec 2021 17:30:39: #1 user defined the maximum tags... INFO @ Fri, 10 Dec 2021 17:30:39: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 10 Dec 2021 17:30:39: #1 tags after filtering in treatment: 5967763 INFO @ Fri, 10 Dec 2021 17:30:39: #1 Redundant rate of treatment: 0.10 INFO @ Fri, 10 Dec 2021 17:30:39: #1 finished! INFO @ Fri, 10 Dec 2021 17:30:39: #2 Build Peak Model... INFO @ Fri, 10 Dec 2021 17:30:39: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Dec 2021 17:30:40: #2 number of paired peaks: 1582 INFO @ Fri, 10 Dec 2021 17:30:40: start model_add_line... INFO @ Fri, 10 Dec 2021 17:30:40: start X-correlation... INFO @ Fri, 10 Dec 2021 17:30:40: end of X-cor INFO @ Fri, 10 Dec 2021 17:30:40: #2 finished! INFO @ Fri, 10 Dec 2021 17:30:40: #2 predicted fragment length is 162 bps INFO @ Fri, 10 Dec 2021 17:30:40: #2 alternative fragment length(s) may be 162 bps INFO @ Fri, 10 Dec 2021 17:30:40: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/ERX3978930/ERX3978930.20_model.r INFO @ Fri, 10 Dec 2021 17:30:40: #3 Call peaks... INFO @ Fri, 10 Dec 2021 17:30:40: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 10 Dec 2021 17:30:55: #3 Call peaks for each chromosome... INFO @ Fri, 10 Dec 2021 17:31:03: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/ERX3978930/ERX3978930.20_peaks.xls INFO @ Fri, 10 Dec 2021 17:31:03: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/ERX3978930/ERX3978930.20_peaks.narrowPeak INFO @ Fri, 10 Dec 2021 17:31:03: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/ERX3978930/ERX3978930.20_summits.bed INFO @ Fri, 10 Dec 2021 17:31:03: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (1282 records, 4 fields): 3 millis CompletedMACS2peakCalling