Job ID = 14172421 SRX = SRX7628883 Genome = dm3 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... Read 17298204 spots for SRR10963245/SRR10963245.sra Written 17298204 spots for SRR10963245/SRR10963245.sra fastq に変換しました。 bowtie でマッピング中... Your job 14172924 ("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: 00:18:16 17298204 reads; of these: 17298204 (100.00%) were paired; of these: 6725457 (38.88%) aligned concordantly 0 times 7872331 (45.51%) aligned concordantly exactly 1 time 2700416 (15.61%) aligned concordantly >1 times ---- 6725457 pairs aligned concordantly 0 times; of these: 92193 (1.37%) aligned discordantly 1 time ---- 6633264 pairs aligned 0 times concordantly or discordantly; of these: 13266528 mates make up the pairs; of these: 12658829 (95.42%) aligned 0 times 302557 (2.28%) aligned exactly 1 time 305142 (2.30%) aligned >1 times 63.41% overall alignment rate Time searching: 00:18:16 Overall time: 00:18:16 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 12 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] 693563 / 10660229 = 0.0651 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 15:45:36: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX7628883/SRX7628883.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX7628883/SRX7628883.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX7628883/SRX7628883.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX7628883/SRX7628883.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 15:45:36: #1 read tag files... INFO @ Sat, 11 Dec 2021 15:45:36: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 15:45:41: 1000000 INFO @ Sat, 11 Dec 2021 15:45:46: 2000000 INFO @ Sat, 11 Dec 2021 15:45:51: 3000000 INFO @ Sat, 11 Dec 2021 15:45:56: 4000000 INFO @ Sat, 11 Dec 2021 15:46:00: 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 15:46:05: 6000000 INFO @ Sat, 11 Dec 2021 15:46:06: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX7628883/SRX7628883.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX7628883/SRX7628883.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX7628883/SRX7628883.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX7628883/SRX7628883.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 15:46:06: #1 read tag files... INFO @ Sat, 11 Dec 2021 15:46:06: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 15:46:11: 7000000 INFO @ Sat, 11 Dec 2021 15:46:13: 1000000 INFO @ Sat, 11 Dec 2021 15:46:17: 8000000 INFO @ Sat, 11 Dec 2021 15:46:20: 2000000 INFO @ Sat, 11 Dec 2021 15:46:24: 9000000 INFO @ Sat, 11 Dec 2021 15:46:27: 3000000 INFO @ Sat, 11 Dec 2021 15:46:30: 10000000 INFO @ Sat, 11 Dec 2021 15:46:34: 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 @ Sat, 11 Dec 2021 15:46:36: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX7628883/SRX7628883.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX7628883/SRX7628883.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX7628883/SRX7628883.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX7628883/SRX7628883.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 15:46:36: #1 read tag files... INFO @ Sat, 11 Dec 2021 15:46:36: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 15:46:36: 11000000 INFO @ Sat, 11 Dec 2021 15:46:41: 5000000 INFO @ Sat, 11 Dec 2021 15:46:42: 12000000 INFO @ Sat, 11 Dec 2021 15:46:43: 1000000 INFO @ Sat, 11 Dec 2021 15:46:48: 6000000 INFO @ Sat, 11 Dec 2021 15:46:49: 13000000 INFO @ Sat, 11 Dec 2021 15:46:50: 2000000 INFO @ Sat, 11 Dec 2021 15:46:55: 14000000 INFO @ Sat, 11 Dec 2021 15:46:55: 7000000 INFO @ Sat, 11 Dec 2021 15:46:57: 3000000 INFO @ Sat, 11 Dec 2021 15:47:01: 15000000 INFO @ Sat, 11 Dec 2021 15:47:02: 8000000 INFO @ Sat, 11 Dec 2021 15:47:05: 4000000 INFO @ Sat, 11 Dec 2021 15:47:08: 16000000 INFO @ Sat, 11 Dec 2021 15:47:09: 9000000 INFO @ Sat, 11 Dec 2021 15:47:12: 5000000 INFO @ Sat, 11 Dec 2021 15:47:14: 17000000 INFO @ Sat, 11 Dec 2021 15:47:17: 10000000 INFO @ Sat, 11 Dec 2021 15:47:19: 6000000 INFO @ Sat, 11 Dec 2021 15:47:20: 18000000 INFO @ Sat, 11 Dec 2021 15:47:24: 11000000 INFO @ Sat, 11 Dec 2021 15:47:26: 7000000 INFO @ Sat, 11 Dec 2021 15:47:27: 19000000 INFO @ Sat, 11 Dec 2021 15:47:31: 12000000 INFO @ Sat, 11 Dec 2021 15:47:33: 20000000 INFO @ Sat, 11 Dec 2021 15:47:33: 8000000 INFO @ Sat, 11 Dec 2021 15:47:36: #1 tag size is determined as 43 bps INFO @ Sat, 11 Dec 2021 15:47:36: #1 tag size = 43 INFO @ Sat, 11 Dec 2021 15:47:36: #1 total tags in treatment: 9882859 INFO @ Sat, 11 Dec 2021 15:47:36: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 15:47:36: #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 15:47:36: #1 tags after filtering in treatment: 8549923 INFO @ Sat, 11 Dec 2021 15:47:36: #1 Redundant rate of treatment: 0.13 INFO @ Sat, 11 Dec 2021 15:47:36: #1 finished! INFO @ Sat, 11 Dec 2021 15:47:36: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 15:47:36: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 15:47:37: #2 number of paired peaks: 6595 INFO @ Sat, 11 Dec 2021 15:47:37: start model_add_line... INFO @ Sat, 11 Dec 2021 15:47:38: start X-correlation... INFO @ Sat, 11 Dec 2021 15:47:38: end of X-cor INFO @ Sat, 11 Dec 2021 15:47:38: #2 finished! INFO @ Sat, 11 Dec 2021 15:47:38: #2 predicted fragment length is 178 bps INFO @ Sat, 11 Dec 2021 15:47:38: #2 alternative fragment length(s) may be 178 bps INFO @ Sat, 11 Dec 2021 15:47:38: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX7628883/SRX7628883.05_model.r INFO @ Sat, 11 Dec 2021 15:47:38: #3 Call peaks... INFO @ Sat, 11 Dec 2021 15:47:38: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Dec 2021 15:47:38: 13000000 INFO @ Sat, 11 Dec 2021 15:47:40: 9000000 INFO @ Sat, 11 Dec 2021 15:47:45: 14000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 11 Dec 2021 15:47:47: 10000000 INFO @ Sat, 11 Dec 2021 15:47:52: 15000000 INFO @ Sat, 11 Dec 2021 15:47:54: 11000000 INFO @ Sat, 11 Dec 2021 15:47:59: 16000000 INFO @ Sat, 11 Dec 2021 15:48:01: #3 Call peaks for each chromosome... INFO @ Sat, 11 Dec 2021 15:48:01: 12000000 INFO @ Sat, 11 Dec 2021 15:48:06: 17000000 INFO @ Sat, 11 Dec 2021 15:48:09: 13000000 INFO @ Sat, 11 Dec 2021 15:48:11: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX7628883/SRX7628883.05_peaks.xls INFO @ Sat, 11 Dec 2021 15:48:11: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX7628883/SRX7628883.05_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 15:48:12: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX7628883/SRX7628883.05_summits.bed INFO @ Sat, 11 Dec 2021 15:48:12: Done! pass1 - making usageList (15 chroms): 2 millis pass2 - checking and writing primary data (8474 records, 4 fields): 18 millis CompletedMACS2peakCalling INFO @ Sat, 11 Dec 2021 15:48:13: 18000000 BigWig に変換しました。 INFO @ Sat, 11 Dec 2021 15:48:16: 14000000 INFO @ Sat, 11 Dec 2021 15:48:20: 19000000 INFO @ Sat, 11 Dec 2021 15:48:23: 15000000 INFO @ Sat, 11 Dec 2021 15:48:27: 20000000 INFO @ Sat, 11 Dec 2021 15:48:30: 16000000 INFO @ Sat, 11 Dec 2021 15:48:30: #1 tag size is determined as 43 bps INFO @ Sat, 11 Dec 2021 15:48:30: #1 tag size = 43 INFO @ Sat, 11 Dec 2021 15:48:30: #1 total tags in treatment: 9882859 INFO @ Sat, 11 Dec 2021 15:48:30: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 15:48:30: #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 15:48:31: #1 tags after filtering in treatment: 8549923 INFO @ Sat, 11 Dec 2021 15:48:31: #1 Redundant rate of treatment: 0.13 INFO @ Sat, 11 Dec 2021 15:48:31: #1 finished! INFO @ Sat, 11 Dec 2021 15:48:31: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 15:48:31: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 15:48:32: #2 number of paired peaks: 6595 INFO @ Sat, 11 Dec 2021 15:48:32: start model_add_line... INFO @ Sat, 11 Dec 2021 15:48:32: start X-correlation... INFO @ Sat, 11 Dec 2021 15:48:32: end of X-cor INFO @ Sat, 11 Dec 2021 15:48:32: #2 finished! INFO @ Sat, 11 Dec 2021 15:48:32: #2 predicted fragment length is 178 bps INFO @ Sat, 11 Dec 2021 15:48:32: #2 alternative fragment length(s) may be 178 bps INFO @ Sat, 11 Dec 2021 15:48:32: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX7628883/SRX7628883.10_model.r INFO @ Sat, 11 Dec 2021 15:48:32: #3 Call peaks... INFO @ Sat, 11 Dec 2021 15:48:32: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Dec 2021 15:48:36: 17000000 INFO @ Sat, 11 Dec 2021 15:48:43: 18000000 INFO @ Sat, 11 Dec 2021 15:48:50: 19000000 INFO @ Sat, 11 Dec 2021 15:48:55: #3 Call peaks for each chromosome... INFO @ Sat, 11 Dec 2021 15:48:56: 20000000 INFO @ Sat, 11 Dec 2021 15:49:00: #1 tag size is determined as 43 bps INFO @ Sat, 11 Dec 2021 15:49:00: #1 tag size = 43 INFO @ Sat, 11 Dec 2021 15:49:00: #1 total tags in treatment: 9882859 INFO @ Sat, 11 Dec 2021 15:49:00: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 15:49:00: #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 15:49:00: #1 tags after filtering in treatment: 8549923 INFO @ Sat, 11 Dec 2021 15:49:00: #1 Redundant rate of treatment: 0.13 INFO @ Sat, 11 Dec 2021 15:49:00: #1 finished! INFO @ Sat, 11 Dec 2021 15:49:00: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 15:49:00: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 15:49:01: #2 number of paired peaks: 6595 INFO @ Sat, 11 Dec 2021 15:49:01: start model_add_line... INFO @ Sat, 11 Dec 2021 15:49:01: start X-correlation... INFO @ Sat, 11 Dec 2021 15:49:01: end of X-cor INFO @ Sat, 11 Dec 2021 15:49:01: #2 finished! INFO @ Sat, 11 Dec 2021 15:49:01: #2 predicted fragment length is 178 bps INFO @ Sat, 11 Dec 2021 15:49:01: #2 alternative fragment length(s) may be 178 bps INFO @ Sat, 11 Dec 2021 15:49:01: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX7628883/SRX7628883.20_model.r INFO @ Sat, 11 Dec 2021 15:49:01: #3 Call peaks... INFO @ Sat, 11 Dec 2021 15:49:01: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Dec 2021 15:49:05: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX7628883/SRX7628883.10_peaks.xls INFO @ Sat, 11 Dec 2021 15:49:06: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX7628883/SRX7628883.10_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 15:49:06: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX7628883/SRX7628883.10_summits.bed INFO @ Sat, 11 Dec 2021 15:49:06: Done! pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (5594 records, 4 fields): 7 millis CompletedMACS2peakCalling INFO @ Sat, 11 Dec 2021 15:49:24: #3 Call peaks for each chromosome... INFO @ Sat, 11 Dec 2021 15:49:34: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX7628883/SRX7628883.20_peaks.xls INFO @ Sat, 11 Dec 2021 15:49:34: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX7628883/SRX7628883.20_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 15:49:34: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX7628883/SRX7628883.20_summits.bed INFO @ Sat, 11 Dec 2021 15:49:34: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (3051 records, 4 fields): 4 millis CompletedMACS2peakCalling