Job ID = 14167968 SRX = ERX3978922 Genome = dm3 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... Read 30225183 spots for ERR3975991/ERR3975991.sra Written 30225183 spots for ERR3975991/ERR3975991.sra fastq に変換しました。 bowtie でマッピング中... Your job 14169067 ("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: 02:26:51 30225183 reads; of these: 30225183 (100.00%) were paired; of these: 10049431 (33.25%) aligned concordantly 0 times 14885977 (49.25%) aligned concordantly exactly 1 time 5289775 (17.50%) aligned concordantly >1 times ---- 10049431 pairs aligned concordantly 0 times; of these: 657653 (6.54%) aligned discordantly 1 time ---- 9391778 pairs aligned 0 times concordantly or discordantly; of these: 18783556 mates make up the pairs; of these: 8541433 (45.47%) aligned 0 times 5669549 (30.18%) aligned exactly 1 time 4572574 (24.34%) aligned >1 times 85.87% overall alignment rate Time searching: 02:26:51 Overall time: 02:26:51 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] 16450798 / 20541909 = 0.8008 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 16:38:49: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/ERX3978922/ERX3978922.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/ERX3978922/ERX3978922.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/ERX3978922/ERX3978922.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/ERX3978922/ERX3978922.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 16:38:49: #1 read tag files... INFO @ Fri, 10 Dec 2021 16:38:49: #1 read treatment tags... INFO @ Fri, 10 Dec 2021 16:38:54: 1000000 INFO @ Fri, 10 Dec 2021 16:39:00: 2000000 INFO @ Fri, 10 Dec 2021 16:39:05: 3000000 INFO @ Fri, 10 Dec 2021 16:39:11: 4000000 INFO @ Fri, 10 Dec 2021 16:39:17: 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 @ Fri, 10 Dec 2021 16:39:19: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/ERX3978922/ERX3978922.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/ERX3978922/ERX3978922.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/ERX3978922/ERX3978922.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/ERX3978922/ERX3978922.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 16:39:19: #1 read tag files... INFO @ Fri, 10 Dec 2021 16:39:19: #1 read treatment tags... INFO @ Fri, 10 Dec 2021 16:39:23: 6000000 INFO @ Fri, 10 Dec 2021 16:39:25: 1000000 INFO @ Fri, 10 Dec 2021 16:39:29: 7000000 INFO @ Fri, 10 Dec 2021 16:39:32: 2000000 INFO @ Fri, 10 Dec 2021 16:39:36: 8000000 INFO @ Fri, 10 Dec 2021 16:39:39: 3000000 INFO @ Fri, 10 Dec 2021 16:39:42: 9000000 INFO @ Fri, 10 Dec 2021 16:39:45: 4000000 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 16:39:49: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/ERX3978922/ERX3978922.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/ERX3978922/ERX3978922.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/ERX3978922/ERX3978922.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/ERX3978922/ERX3978922.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 16:39:49: #1 read tag files... INFO @ Fri, 10 Dec 2021 16:39:49: #1 read treatment tags... INFO @ Fri, 10 Dec 2021 16:39:49: 10000000 INFO @ Fri, 10 Dec 2021 16:39:52: 5000000 INFO @ Fri, 10 Dec 2021 16:39:56: 11000000 INFO @ Fri, 10 Dec 2021 16:39:56: 1000000 INFO @ Fri, 10 Dec 2021 16:39:59: 6000000 INFO @ Fri, 10 Dec 2021 16:40:02: 2000000 INFO @ Fri, 10 Dec 2021 16:40:02: 12000000 INFO @ Fri, 10 Dec 2021 16:40:05: 7000000 INFO @ Fri, 10 Dec 2021 16:40:09: 3000000 INFO @ Fri, 10 Dec 2021 16:40:09: 13000000 INFO @ Fri, 10 Dec 2021 16:40:12: 8000000 INFO @ Fri, 10 Dec 2021 16:40:16: 4000000 INFO @ Fri, 10 Dec 2021 16:40:16: 14000000 INFO @ Fri, 10 Dec 2021 16:40:18: 9000000 INFO @ Fri, 10 Dec 2021 16:40:22: 5000000 INFO @ Fri, 10 Dec 2021 16:40:23: 15000000 INFO @ Fri, 10 Dec 2021 16:40:25: 10000000 INFO @ Fri, 10 Dec 2021 16:40:29: 6000000 INFO @ Fri, 10 Dec 2021 16:40:30: 16000000 INFO @ Fri, 10 Dec 2021 16:40:32: 11000000 INFO @ Fri, 10 Dec 2021 16:40:35: 7000000 INFO @ Fri, 10 Dec 2021 16:40:36: 17000000 INFO @ Fri, 10 Dec 2021 16:40:39: 12000000 INFO @ Fri, 10 Dec 2021 16:40:42: 8000000 INFO @ Fri, 10 Dec 2021 16:40:43: 18000000 INFO @ Fri, 10 Dec 2021 16:40:45: 13000000 INFO @ Fri, 10 Dec 2021 16:40:49: 9000000 INFO @ Fri, 10 Dec 2021 16:40:50: 19000000 INFO @ Fri, 10 Dec 2021 16:40:50: #1 tag size is determined as 80 bps INFO @ Fri, 10 Dec 2021 16:40:50: #1 tag size = 80 INFO @ Fri, 10 Dec 2021 16:40:50: #1 total tags in treatment: 4089534 INFO @ Fri, 10 Dec 2021 16:40:50: #1 user defined the maximum tags... INFO @ Fri, 10 Dec 2021 16:40:50: #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 16:40:50: #1 tags after filtering in treatment: 3421265 INFO @ Fri, 10 Dec 2021 16:40:50: #1 Redundant rate of treatment: 0.16 INFO @ Fri, 10 Dec 2021 16:40:50: #1 finished! INFO @ Fri, 10 Dec 2021 16:40:50: #2 Build Peak Model... INFO @ Fri, 10 Dec 2021 16:40:50: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Dec 2021 16:40:50: #2 number of paired peaks: 3558 INFO @ Fri, 10 Dec 2021 16:40:50: start model_add_line... INFO @ Fri, 10 Dec 2021 16:40:50: start X-correlation... INFO @ Fri, 10 Dec 2021 16:40:50: end of X-cor INFO @ Fri, 10 Dec 2021 16:40:50: #2 finished! INFO @ Fri, 10 Dec 2021 16:40:50: #2 predicted fragment length is 162 bps INFO @ Fri, 10 Dec 2021 16:40:50: #2 alternative fragment length(s) may be 162 bps INFO @ Fri, 10 Dec 2021 16:40:50: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/ERX3978922/ERX3978922.05_model.r INFO @ Fri, 10 Dec 2021 16:40:50: #3 Call peaks... INFO @ Fri, 10 Dec 2021 16:40:50: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 10 Dec 2021 16:40:52: 14000000 INFO @ Fri, 10 Dec 2021 16:40:55: 10000000 INFO @ Fri, 10 Dec 2021 16:40:58: #3 Call peaks for each chromosome... INFO @ Fri, 10 Dec 2021 16:40:59: 15000000 INFO @ Fri, 10 Dec 2021 16:41:02: 11000000 INFO @ Fri, 10 Dec 2021 16:41:02: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/ERX3978922/ERX3978922.05_peaks.xls INFO @ Fri, 10 Dec 2021 16:41:02: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/ERX3978922/ERX3978922.05_peaks.narrowPeak INFO @ Fri, 10 Dec 2021 16:41:02: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/ERX3978922/ERX3978922.05_summits.bed INFO @ Fri, 10 Dec 2021 16:41:02: Done! BedGraph に変換しました。 BigWig に変換中... pass1 - making usageList (15 chroms): 2 millis pass2 - checking and writing primary data (9146 records, 4 fields): 9 millis CompletedMACS2peakCalling INFO @ Fri, 10 Dec 2021 16:41:06: 16000000 INFO @ Fri, 10 Dec 2021 16:41:08: 12000000 INFO @ Fri, 10 Dec 2021 16:41:12: 17000000 INFO @ Fri, 10 Dec 2021 16:41:15: 13000000 INFO @ Fri, 10 Dec 2021 16:41:19: 18000000 INFO @ Fri, 10 Dec 2021 16:41:22: 14000000 BigWig に変換しました。 INFO @ Fri, 10 Dec 2021 16:41:25: 19000000 INFO @ Fri, 10 Dec 2021 16:41:26: #1 tag size is determined as 80 bps INFO @ Fri, 10 Dec 2021 16:41:26: #1 tag size = 80 INFO @ Fri, 10 Dec 2021 16:41:26: #1 total tags in treatment: 4089534 INFO @ Fri, 10 Dec 2021 16:41:26: #1 user defined the maximum tags... INFO @ Fri, 10 Dec 2021 16:41:26: #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 16:41:26: #1 tags after filtering in treatment: 3421265 INFO @ Fri, 10 Dec 2021 16:41:26: #1 Redundant rate of treatment: 0.16 INFO @ Fri, 10 Dec 2021 16:41:26: #1 finished! INFO @ Fri, 10 Dec 2021 16:41:26: #2 Build Peak Model... INFO @ Fri, 10 Dec 2021 16:41:26: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Dec 2021 16:41:26: #2 number of paired peaks: 3558 INFO @ Fri, 10 Dec 2021 16:41:26: start model_add_line... INFO @ Fri, 10 Dec 2021 16:41:26: start X-correlation... INFO @ Fri, 10 Dec 2021 16:41:26: end of X-cor INFO @ Fri, 10 Dec 2021 16:41:26: #2 finished! INFO @ Fri, 10 Dec 2021 16:41:26: #2 predicted fragment length is 162 bps INFO @ Fri, 10 Dec 2021 16:41:26: #2 alternative fragment length(s) may be 162 bps INFO @ Fri, 10 Dec 2021 16:41:26: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/ERX3978922/ERX3978922.10_model.r INFO @ Fri, 10 Dec 2021 16:41:26: #3 Call peaks... INFO @ Fri, 10 Dec 2021 16:41:26: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 10 Dec 2021 16:41:28: 15000000 INFO @ Fri, 10 Dec 2021 16:41:34: #3 Call peaks for each chromosome... INFO @ Fri, 10 Dec 2021 16:41:35: 16000000 INFO @ Fri, 10 Dec 2021 16:41:38: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/ERX3978922/ERX3978922.10_peaks.xls INFO @ Fri, 10 Dec 2021 16:41:38: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/ERX3978922/ERX3978922.10_peaks.narrowPeak INFO @ Fri, 10 Dec 2021 16:41:38: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/ERX3978922/ERX3978922.10_summits.bed INFO @ Fri, 10 Dec 2021 16:41:38: Done! pass1 - making usageList (14 chroms): 2 millis pass2 - checking and writing primary data (5028 records, 4 fields): 8 millis CompletedMACS2peakCalling INFO @ Fri, 10 Dec 2021 16:41:41: 17000000 INFO @ Fri, 10 Dec 2021 16:41:47: 18000000 INFO @ Fri, 10 Dec 2021 16:41:53: 19000000 INFO @ Fri, 10 Dec 2021 16:41:53: #1 tag size is determined as 80 bps INFO @ Fri, 10 Dec 2021 16:41:53: #1 tag size = 80 INFO @ Fri, 10 Dec 2021 16:41:53: #1 total tags in treatment: 4089534 INFO @ Fri, 10 Dec 2021 16:41:53: #1 user defined the maximum tags... INFO @ Fri, 10 Dec 2021 16:41:53: #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 16:41:53: #1 tags after filtering in treatment: 3421265 INFO @ Fri, 10 Dec 2021 16:41:53: #1 Redundant rate of treatment: 0.16 INFO @ Fri, 10 Dec 2021 16:41:53: #1 finished! INFO @ Fri, 10 Dec 2021 16:41:53: #2 Build Peak Model... INFO @ Fri, 10 Dec 2021 16:41:53: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Dec 2021 16:41:53: #2 number of paired peaks: 3558 INFO @ Fri, 10 Dec 2021 16:41:53: start model_add_line... INFO @ Fri, 10 Dec 2021 16:41:53: start X-correlation... INFO @ Fri, 10 Dec 2021 16:41:53: end of X-cor INFO @ Fri, 10 Dec 2021 16:41:53: #2 finished! INFO @ Fri, 10 Dec 2021 16:41:53: #2 predicted fragment length is 162 bps INFO @ Fri, 10 Dec 2021 16:41:53: #2 alternative fragment length(s) may be 162 bps INFO @ Fri, 10 Dec 2021 16:41:53: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/ERX3978922/ERX3978922.20_model.r INFO @ Fri, 10 Dec 2021 16:41:54: #3 Call peaks... INFO @ Fri, 10 Dec 2021 16:41:54: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 10 Dec 2021 16:42:02: #3 Call peaks for each chromosome... INFO @ Fri, 10 Dec 2021 16:42:05: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/ERX3978922/ERX3978922.20_peaks.xls INFO @ Fri, 10 Dec 2021 16:42:05: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/ERX3978922/ERX3978922.20_peaks.narrowPeak INFO @ Fri, 10 Dec 2021 16:42:06: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/ERX3978922/ERX3978922.20_summits.bed INFO @ Fri, 10 Dec 2021 16:42:06: Done! pass1 - making usageList (13 chroms): 1 millis pass2 - checking and writing primary data (1455 records, 4 fields): 4 millis CompletedMACS2peakCalling