Job ID = 14167259 SRX = SRX8076962 Genome = dm3 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... Read 16593676 spots for SRR11504834/SRR11504834.sra Written 16593676 spots for SRR11504834/SRR11504834.sra fastq に変換しました。 bowtie でマッピング中... Your job 14167889 ("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: 00:11:08 16593676 reads; of these: 16593676 (100.00%) were paired; of these: 8924721 (53.78%) aligned concordantly 0 times 6810173 (41.04%) aligned concordantly exactly 1 time 858782 (5.18%) aligned concordantly >1 times ---- 8924721 pairs aligned concordantly 0 times; of these: 1113989 (12.48%) aligned discordantly 1 time ---- 7810732 pairs aligned 0 times concordantly or discordantly; of these: 15621464 mates make up the pairs; of these: 14556590 (93.18%) aligned 0 times 739363 (4.73%) aligned exactly 1 time 325511 (2.08%) aligned >1 times 56.14% overall alignment rate Time searching: 00:11:08 Overall time: 00:11:08 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 8 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] 1357539 / 8780466 = 0.1546 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 11:37:26: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX8076962/SRX8076962.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX8076962/SRX8076962.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX8076962/SRX8076962.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX8076962/SRX8076962.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 11:37:26: #1 read tag files... INFO @ Fri, 10 Dec 2021 11:37:26: #1 read treatment tags... INFO @ Fri, 10 Dec 2021 11:37:31: 1000000 INFO @ Fri, 10 Dec 2021 11:37:36: 2000000 INFO @ Fri, 10 Dec 2021 11:37:41: 3000000 INFO @ Fri, 10 Dec 2021 11:37:46: 4000000 INFO @ Fri, 10 Dec 2021 11:37:50: 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 11:37:55: 6000000 INFO @ Fri, 10 Dec 2021 11:37:56: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX8076962/SRX8076962.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX8076962/SRX8076962.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX8076962/SRX8076962.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX8076962/SRX8076962.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 11:37:56: #1 read tag files... INFO @ Fri, 10 Dec 2021 11:37:56: #1 read treatment tags... INFO @ Fri, 10 Dec 2021 11:38:01: 7000000 INFO @ Fri, 10 Dec 2021 11:38:02: 1000000 INFO @ Fri, 10 Dec 2021 11:38:06: 8000000 INFO @ Fri, 10 Dec 2021 11:38:07: 2000000 INFO @ Fri, 10 Dec 2021 11:38:12: 9000000 INFO @ Fri, 10 Dec 2021 11:38:13: 3000000 INFO @ Fri, 10 Dec 2021 11:38:17: 10000000 INFO @ Fri, 10 Dec 2021 11:38:19: 4000000 INFO @ Fri, 10 Dec 2021 11:38:23: 11000000 INFO @ Fri, 10 Dec 2021 11:38:24: 5000000 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 11:38:26: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX8076962/SRX8076962.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX8076962/SRX8076962.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX8076962/SRX8076962.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX8076962/SRX8076962.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 11:38:26: #1 read tag files... INFO @ Fri, 10 Dec 2021 11:38:26: #1 read treatment tags... INFO @ Fri, 10 Dec 2021 11:38:29: 12000000 INFO @ Fri, 10 Dec 2021 11:38:30: 6000000 INFO @ Fri, 10 Dec 2021 11:38:32: 1000000 INFO @ Fri, 10 Dec 2021 11:38:34: 13000000 INFO @ Fri, 10 Dec 2021 11:38:35: 7000000 INFO @ Fri, 10 Dec 2021 11:38:37: 2000000 INFO @ Fri, 10 Dec 2021 11:38:40: 14000000 INFO @ Fri, 10 Dec 2021 11:38:41: 8000000 INFO @ Fri, 10 Dec 2021 11:38:43: 3000000 INFO @ Fri, 10 Dec 2021 11:38:46: 15000000 INFO @ Fri, 10 Dec 2021 11:38:47: 9000000 INFO @ Fri, 10 Dec 2021 11:38:49: 4000000 INFO @ Fri, 10 Dec 2021 11:38:51: #1 tag size is determined as 43 bps INFO @ Fri, 10 Dec 2021 11:38:51: #1 tag size = 43 INFO @ Fri, 10 Dec 2021 11:38:51: #1 total tags in treatment: 6440615 INFO @ Fri, 10 Dec 2021 11:38:51: #1 user defined the maximum tags... INFO @ Fri, 10 Dec 2021 11:38:51: #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 11:38:51: #1 tags after filtering in treatment: 6088819 INFO @ Fri, 10 Dec 2021 11:38:51: #1 Redundant rate of treatment: 0.05 INFO @ Fri, 10 Dec 2021 11:38:51: #1 finished! INFO @ Fri, 10 Dec 2021 11:38:51: #2 Build Peak Model... INFO @ Fri, 10 Dec 2021 11:38:51: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Dec 2021 11:38:52: #2 number of paired peaks: 7692 INFO @ Fri, 10 Dec 2021 11:38:52: start model_add_line... INFO @ Fri, 10 Dec 2021 11:38:52: start X-correlation... INFO @ Fri, 10 Dec 2021 11:38:52: end of X-cor INFO @ Fri, 10 Dec 2021 11:38:52: #2 finished! INFO @ Fri, 10 Dec 2021 11:38:52: #2 predicted fragment length is 264 bps INFO @ Fri, 10 Dec 2021 11:38:52: #2 alternative fragment length(s) may be 4,264 bps INFO @ Fri, 10 Dec 2021 11:38:52: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX8076962/SRX8076962.05_model.r INFO @ Fri, 10 Dec 2021 11:38:52: #3 Call peaks... INFO @ Fri, 10 Dec 2021 11:38:52: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 10 Dec 2021 11:38:52: 10000000 INFO @ Fri, 10 Dec 2021 11:38:54: 5000000 INFO @ Fri, 10 Dec 2021 11:38:58: 11000000 INFO @ Fri, 10 Dec 2021 11:39:00: 6000000 INFO @ Fri, 10 Dec 2021 11:39:03: 12000000 INFO @ Fri, 10 Dec 2021 11:39:05: 7000000 INFO @ Fri, 10 Dec 2021 11:39:07: #3 Call peaks for each chromosome... INFO @ Fri, 10 Dec 2021 11:39:09: 13000000 INFO @ Fri, 10 Dec 2021 11:39:11: 8000000 INFO @ Fri, 10 Dec 2021 11:39:13: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX8076962/SRX8076962.05_peaks.xls INFO @ Fri, 10 Dec 2021 11:39:13: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX8076962/SRX8076962.05_peaks.narrowPeak INFO @ Fri, 10 Dec 2021 11:39:13: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX8076962/SRX8076962.05_summits.bed INFO @ Fri, 10 Dec 2021 11:39:13: Done! pass1 - making usageList (12 chroms): 1 millis pass2 - checking and writing primary data (682 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Fri, 10 Dec 2021 11:39:15: 14000000 INFO @ Fri, 10 Dec 2021 11:39:17: 9000000 INFO @ Fri, 10 Dec 2021 11:39:20: 15000000 INFO @ Fri, 10 Dec 2021 11:39:22: 10000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Fri, 10 Dec 2021 11:39:26: #1 tag size is determined as 43 bps INFO @ Fri, 10 Dec 2021 11:39:26: #1 tag size = 43 INFO @ Fri, 10 Dec 2021 11:39:26: #1 total tags in treatment: 6440615 INFO @ Fri, 10 Dec 2021 11:39:26: #1 user defined the maximum tags... INFO @ Fri, 10 Dec 2021 11:39:26: #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 11:39:26: #1 tags after filtering in treatment: 6088819 INFO @ Fri, 10 Dec 2021 11:39:26: #1 Redundant rate of treatment: 0.05 INFO @ Fri, 10 Dec 2021 11:39:26: #1 finished! INFO @ Fri, 10 Dec 2021 11:39:26: #2 Build Peak Model... INFO @ Fri, 10 Dec 2021 11:39:26: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Dec 2021 11:39:27: #2 number of paired peaks: 7692 INFO @ Fri, 10 Dec 2021 11:39:27: start model_add_line... INFO @ Fri, 10 Dec 2021 11:39:27: start X-correlation... INFO @ Fri, 10 Dec 2021 11:39:27: end of X-cor INFO @ Fri, 10 Dec 2021 11:39:27: #2 finished! INFO @ Fri, 10 Dec 2021 11:39:27: #2 predicted fragment length is 264 bps INFO @ Fri, 10 Dec 2021 11:39:27: #2 alternative fragment length(s) may be 4,264 bps INFO @ Fri, 10 Dec 2021 11:39:27: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX8076962/SRX8076962.10_model.r INFO @ Fri, 10 Dec 2021 11:39:27: #3 Call peaks... INFO @ Fri, 10 Dec 2021 11:39:27: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 10 Dec 2021 11:39:28: 11000000 INFO @ Fri, 10 Dec 2021 11:39:33: 12000000 INFO @ Fri, 10 Dec 2021 11:39:38: 13000000 INFO @ Fri, 10 Dec 2021 11:39:43: #3 Call peaks for each chromosome... INFO @ Fri, 10 Dec 2021 11:39:43: 14000000 INFO @ Fri, 10 Dec 2021 11:39:48: 15000000 INFO @ Fri, 10 Dec 2021 11:39:49: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX8076962/SRX8076962.10_peaks.xls INFO @ Fri, 10 Dec 2021 11:39:49: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX8076962/SRX8076962.10_peaks.narrowPeak INFO @ Fri, 10 Dec 2021 11:39:49: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX8076962/SRX8076962.10_summits.bed INFO @ Fri, 10 Dec 2021 11:39:49: Done! pass1 - making usageList (9 chroms): 0 millis pass2 - checking and writing primary data (247 records, 4 fields): 2 millis CompletedMACS2peakCalling BigWig に変換しました。 INFO @ Fri, 10 Dec 2021 11:39:52: #1 tag size is determined as 43 bps INFO @ Fri, 10 Dec 2021 11:39:52: #1 tag size = 43 INFO @ Fri, 10 Dec 2021 11:39:52: #1 total tags in treatment: 6440615 INFO @ Fri, 10 Dec 2021 11:39:52: #1 user defined the maximum tags... INFO @ Fri, 10 Dec 2021 11:39:52: #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 11:39:52: #1 tags after filtering in treatment: 6088819 INFO @ Fri, 10 Dec 2021 11:39:52: #1 Redundant rate of treatment: 0.05 INFO @ Fri, 10 Dec 2021 11:39:52: #1 finished! INFO @ Fri, 10 Dec 2021 11:39:52: #2 Build Peak Model... INFO @ Fri, 10 Dec 2021 11:39:52: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Dec 2021 11:39:53: #2 number of paired peaks: 7692 INFO @ Fri, 10 Dec 2021 11:39:53: start model_add_line... INFO @ Fri, 10 Dec 2021 11:39:53: start X-correlation... INFO @ Fri, 10 Dec 2021 11:39:53: end of X-cor INFO @ Fri, 10 Dec 2021 11:39:53: #2 finished! INFO @ Fri, 10 Dec 2021 11:39:53: #2 predicted fragment length is 264 bps INFO @ Fri, 10 Dec 2021 11:39:53: #2 alternative fragment length(s) may be 4,264 bps INFO @ Fri, 10 Dec 2021 11:39:53: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX8076962/SRX8076962.20_model.r INFO @ Fri, 10 Dec 2021 11:39:53: #3 Call peaks... INFO @ Fri, 10 Dec 2021 11:39:53: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 10 Dec 2021 11:40:08: #3 Call peaks for each chromosome... INFO @ Fri, 10 Dec 2021 11:40:15: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX8076962/SRX8076962.20_peaks.xls INFO @ Fri, 10 Dec 2021 11:40:15: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX8076962/SRX8076962.20_peaks.narrowPeak INFO @ Fri, 10 Dec 2021 11:40:15: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX8076962/SRX8076962.20_summits.bed INFO @ Fri, 10 Dec 2021 11:40:15: Done! pass1 - making usageList (9 chroms): 0 millis pass2 - checking and writing primary data (93 records, 4 fields): 2 millis CompletedMACS2peakCalling