Job ID = 14168047 SRX = SRX7175235 Genome = dm3 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... Read 22425039 spots for SRR10485675/SRR10485675.sra Written 22425039 spots for SRR10485675/SRR10485675.sra fastq に変換しました。 bowtie でマッピング中... Your job 14168833 ("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: 00:30:23 22425039 reads; of these: 22425039 (100.00%) were paired; of these: 6752447 (30.11%) aligned concordantly 0 times 12760504 (56.90%) aligned concordantly exactly 1 time 2912088 (12.99%) aligned concordantly >1 times ---- 6752447 pairs aligned concordantly 0 times; of these: 224815 (3.33%) aligned discordantly 1 time ---- 6527632 pairs aligned 0 times concordantly or discordantly; of these: 13055264 mates make up the pairs; of these: 12138687 (92.98%) aligned 0 times 596065 (4.57%) aligned exactly 1 time 320512 (2.46%) aligned >1 times 72.93% overall alignment rate Time searching: 00:30:23 Overall time: 00:30:23 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 16 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] 1292254 / 15836809 = 0.0816 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 15:23:10: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX7175235/SRX7175235.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX7175235/SRX7175235.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX7175235/SRX7175235.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX7175235/SRX7175235.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 15:23:10: #1 read tag files... INFO @ Fri, 10 Dec 2021 15:23:10: #1 read treatment tags... INFO @ Fri, 10 Dec 2021 15:23:16: 1000000 INFO @ Fri, 10 Dec 2021 15:23:22: 2000000 INFO @ Fri, 10 Dec 2021 15:23:28: 3000000 INFO @ Fri, 10 Dec 2021 15:23:34: 4000000 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 15:23:40: 5000000 INFO @ Fri, 10 Dec 2021 15:23:41: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX7175235/SRX7175235.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX7175235/SRX7175235.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX7175235/SRX7175235.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX7175235/SRX7175235.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 15:23:41: #1 read tag files... INFO @ Fri, 10 Dec 2021 15:23:41: #1 read treatment tags... INFO @ Fri, 10 Dec 2021 15:23:48: 6000000 INFO @ Fri, 10 Dec 2021 15:23:48: 1000000 INFO @ Fri, 10 Dec 2021 15:23:55: 7000000 INFO @ Fri, 10 Dec 2021 15:23:55: 2000000 INFO @ Fri, 10 Dec 2021 15:24:02: 8000000 INFO @ Fri, 10 Dec 2021 15:24:03: 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 15:24:10: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX7175235/SRX7175235.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX7175235/SRX7175235.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX7175235/SRX7175235.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX7175235/SRX7175235.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 15:24:10: #1 read tag files... INFO @ Fri, 10 Dec 2021 15:24:10: #1 read treatment tags... INFO @ Fri, 10 Dec 2021 15:24:10: 9000000 INFO @ Fri, 10 Dec 2021 15:24:10: 4000000 INFO @ Fri, 10 Dec 2021 15:24:17: 1000000 INFO @ Fri, 10 Dec 2021 15:24:17: 10000000 INFO @ Fri, 10 Dec 2021 15:24:18: 5000000 INFO @ Fri, 10 Dec 2021 15:24:25: 2000000 INFO @ Fri, 10 Dec 2021 15:24:25: 11000000 INFO @ Fri, 10 Dec 2021 15:24:25: 6000000 INFO @ Fri, 10 Dec 2021 15:24:32: 3000000 INFO @ Fri, 10 Dec 2021 15:24:32: 12000000 INFO @ Fri, 10 Dec 2021 15:24:33: 7000000 INFO @ Fri, 10 Dec 2021 15:24:40: 4000000 INFO @ Fri, 10 Dec 2021 15:24:40: 13000000 INFO @ Fri, 10 Dec 2021 15:24:40: 8000000 INFO @ Fri, 10 Dec 2021 15:24:47: 5000000 INFO @ Fri, 10 Dec 2021 15:24:48: 14000000 INFO @ Fri, 10 Dec 2021 15:24:48: 9000000 INFO @ Fri, 10 Dec 2021 15:24:55: 6000000 INFO @ Fri, 10 Dec 2021 15:24:55: 15000000 INFO @ Fri, 10 Dec 2021 15:24:56: 10000000 INFO @ Fri, 10 Dec 2021 15:25:02: 7000000 INFO @ Fri, 10 Dec 2021 15:25:03: 16000000 INFO @ Fri, 10 Dec 2021 15:25:03: 11000000 INFO @ Fri, 10 Dec 2021 15:25:10: 8000000 INFO @ Fri, 10 Dec 2021 15:25:10: 17000000 INFO @ Fri, 10 Dec 2021 15:25:11: 12000000 INFO @ Fri, 10 Dec 2021 15:25:17: 9000000 INFO @ Fri, 10 Dec 2021 15:25:18: 18000000 INFO @ Fri, 10 Dec 2021 15:25:18: 13000000 INFO @ Fri, 10 Dec 2021 15:25:25: 10000000 INFO @ Fri, 10 Dec 2021 15:25:26: 19000000 INFO @ Fri, 10 Dec 2021 15:25:26: 14000000 INFO @ Fri, 10 Dec 2021 15:25:32: 11000000 INFO @ Fri, 10 Dec 2021 15:25:33: 20000000 INFO @ Fri, 10 Dec 2021 15:25:33: 15000000 INFO @ Fri, 10 Dec 2021 15:25:40: 12000000 INFO @ Fri, 10 Dec 2021 15:25:41: 21000000 INFO @ Fri, 10 Dec 2021 15:25:41: 16000000 INFO @ Fri, 10 Dec 2021 15:25:47: 13000000 INFO @ Fri, 10 Dec 2021 15:25:48: 17000000 INFO @ Fri, 10 Dec 2021 15:25:48: 22000000 INFO @ Fri, 10 Dec 2021 15:25:55: 14000000 INFO @ Fri, 10 Dec 2021 15:25:56: 18000000 INFO @ Fri, 10 Dec 2021 15:25:56: 23000000 INFO @ Fri, 10 Dec 2021 15:26:02: 15000000 INFO @ Fri, 10 Dec 2021 15:26:03: 19000000 INFO @ Fri, 10 Dec 2021 15:26:03: 24000000 INFO @ Fri, 10 Dec 2021 15:26:10: 16000000 INFO @ Fri, 10 Dec 2021 15:26:11: 20000000 INFO @ Fri, 10 Dec 2021 15:26:11: 25000000 INFO @ Fri, 10 Dec 2021 15:26:17: 17000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Fri, 10 Dec 2021 15:26:18: 21000000 INFO @ Fri, 10 Dec 2021 15:26:19: 26000000 INFO @ Fri, 10 Dec 2021 15:26:25: 18000000 INFO @ Fri, 10 Dec 2021 15:26:26: 22000000 INFO @ Fri, 10 Dec 2021 15:26:26: 27000000 INFO @ Fri, 10 Dec 2021 15:26:32: 19000000 INFO @ Fri, 10 Dec 2021 15:26:33: 23000000 INFO @ Fri, 10 Dec 2021 15:26:34: 28000000 INFO @ Fri, 10 Dec 2021 15:26:40: 20000000 INFO @ Fri, 10 Dec 2021 15:26:41: 24000000 INFO @ Fri, 10 Dec 2021 15:26:42: 29000000 INFO @ Fri, 10 Dec 2021 15:26:47: 21000000 INFO @ Fri, 10 Dec 2021 15:26:49: 25000000 INFO @ Fri, 10 Dec 2021 15:26:49: 30000000 INFO @ Fri, 10 Dec 2021 15:26:50: #1 tag size is determined as 75 bps INFO @ Fri, 10 Dec 2021 15:26:50: #1 tag size = 75 INFO @ Fri, 10 Dec 2021 15:26:50: #1 total tags in treatment: 14386127 INFO @ Fri, 10 Dec 2021 15:26:50: #1 user defined the maximum tags... INFO @ Fri, 10 Dec 2021 15:26:50: #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 15:26:50: #1 tags after filtering in treatment: 13292141 INFO @ Fri, 10 Dec 2021 15:26:50: #1 Redundant rate of treatment: 0.08 INFO @ Fri, 10 Dec 2021 15:26:50: #1 finished! INFO @ Fri, 10 Dec 2021 15:26:50: #2 Build Peak Model... INFO @ Fri, 10 Dec 2021 15:26:50: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Dec 2021 15:26:51: #2 number of paired peaks: 1837 INFO @ Fri, 10 Dec 2021 15:26:51: start model_add_line... INFO @ Fri, 10 Dec 2021 15:26:51: start X-correlation... INFO @ Fri, 10 Dec 2021 15:26:51: end of X-cor INFO @ Fri, 10 Dec 2021 15:26:51: #2 finished! INFO @ Fri, 10 Dec 2021 15:26:51: #2 predicted fragment length is 212 bps INFO @ Fri, 10 Dec 2021 15:26:51: #2 alternative fragment length(s) may be 212 bps INFO @ Fri, 10 Dec 2021 15:26:51: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX7175235/SRX7175235.05_model.r INFO @ Fri, 10 Dec 2021 15:26:51: #3 Call peaks... INFO @ Fri, 10 Dec 2021 15:26:51: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 10 Dec 2021 15:26:54: 22000000 INFO @ Fri, 10 Dec 2021 15:26:56: 26000000 INFO @ Fri, 10 Dec 2021 15:27:02: 23000000 INFO @ Fri, 10 Dec 2021 15:27:04: 27000000 INFO @ Fri, 10 Dec 2021 15:27:09: 24000000 INFO @ Fri, 10 Dec 2021 15:27:11: 28000000 BigWig に変換しました。 INFO @ Fri, 10 Dec 2021 15:27:17: 25000000 INFO @ Fri, 10 Dec 2021 15:27:18: 29000000 INFO @ Fri, 10 Dec 2021 15:27:21: #3 Call peaks for each chromosome... INFO @ Fri, 10 Dec 2021 15:27:25: 26000000 INFO @ Fri, 10 Dec 2021 15:27:26: 30000000 INFO @ Fri, 10 Dec 2021 15:27:27: #1 tag size is determined as 75 bps INFO @ Fri, 10 Dec 2021 15:27:27: #1 tag size = 75 INFO @ Fri, 10 Dec 2021 15:27:27: #1 total tags in treatment: 14386127 INFO @ Fri, 10 Dec 2021 15:27:27: #1 user defined the maximum tags... INFO @ Fri, 10 Dec 2021 15:27:27: #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 15:27:27: #1 tags after filtering in treatment: 13292141 INFO @ Fri, 10 Dec 2021 15:27:27: #1 Redundant rate of treatment: 0.08 INFO @ Fri, 10 Dec 2021 15:27:27: #1 finished! INFO @ Fri, 10 Dec 2021 15:27:27: #2 Build Peak Model... INFO @ Fri, 10 Dec 2021 15:27:27: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Dec 2021 15:27:28: #2 number of paired peaks: 1837 INFO @ Fri, 10 Dec 2021 15:27:28: start model_add_line... INFO @ Fri, 10 Dec 2021 15:27:28: start X-correlation... INFO @ Fri, 10 Dec 2021 15:27:28: end of X-cor INFO @ Fri, 10 Dec 2021 15:27:28: #2 finished! INFO @ Fri, 10 Dec 2021 15:27:28: #2 predicted fragment length is 212 bps INFO @ Fri, 10 Dec 2021 15:27:28: #2 alternative fragment length(s) may be 212 bps INFO @ Fri, 10 Dec 2021 15:27:28: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX7175235/SRX7175235.10_model.r INFO @ Fri, 10 Dec 2021 15:27:28: #3 Call peaks... INFO @ Fri, 10 Dec 2021 15:27:28: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 10 Dec 2021 15:27:31: 27000000 INFO @ Fri, 10 Dec 2021 15:27:36: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX7175235/SRX7175235.05_peaks.xls INFO @ Fri, 10 Dec 2021 15:27:36: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX7175235/SRX7175235.05_peaks.narrowPeak INFO @ Fri, 10 Dec 2021 15:27:36: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX7175235/SRX7175235.05_summits.bed INFO @ Fri, 10 Dec 2021 15:27:36: Done! pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (6354 records, 4 fields): 19 millis CompletedMACS2peakCalling INFO @ Fri, 10 Dec 2021 15:27:38: 28000000 INFO @ Fri, 10 Dec 2021 15:27:44: 29000000 INFO @ Fri, 10 Dec 2021 15:27:50: 30000000 INFO @ Fri, 10 Dec 2021 15:27:51: #1 tag size is determined as 75 bps INFO @ Fri, 10 Dec 2021 15:27:51: #1 tag size = 75 INFO @ Fri, 10 Dec 2021 15:27:51: #1 total tags in treatment: 14386127 INFO @ Fri, 10 Dec 2021 15:27:51: #1 user defined the maximum tags... INFO @ Fri, 10 Dec 2021 15:27:51: #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 15:27:51: #1 tags after filtering in treatment: 13292141 INFO @ Fri, 10 Dec 2021 15:27:51: #1 Redundant rate of treatment: 0.08 INFO @ Fri, 10 Dec 2021 15:27:51: #1 finished! INFO @ Fri, 10 Dec 2021 15:27:51: #2 Build Peak Model... INFO @ Fri, 10 Dec 2021 15:27:51: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Dec 2021 15:27:52: #2 number of paired peaks: 1837 INFO @ Fri, 10 Dec 2021 15:27:52: start model_add_line... INFO @ Fri, 10 Dec 2021 15:27:52: start X-correlation... INFO @ Fri, 10 Dec 2021 15:27:52: end of X-cor INFO @ Fri, 10 Dec 2021 15:27:52: #2 finished! INFO @ Fri, 10 Dec 2021 15:27:52: #2 predicted fragment length is 212 bps INFO @ Fri, 10 Dec 2021 15:27:52: #2 alternative fragment length(s) may be 212 bps INFO @ Fri, 10 Dec 2021 15:27:52: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX7175235/SRX7175235.20_model.r INFO @ Fri, 10 Dec 2021 15:27:52: #3 Call peaks... INFO @ Fri, 10 Dec 2021 15:27:52: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 10 Dec 2021 15:27:58: #3 Call peaks for each chromosome... INFO @ Fri, 10 Dec 2021 15:28:12: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX7175235/SRX7175235.10_peaks.xls INFO @ Fri, 10 Dec 2021 15:28:12: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX7175235/SRX7175235.10_peaks.narrowPeak INFO @ Fri, 10 Dec 2021 15:28:12: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX7175235/SRX7175235.10_summits.bed INFO @ Fri, 10 Dec 2021 15:28:13: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (4797 records, 4 fields): 6 millis CompletedMACS2peakCalling INFO @ Fri, 10 Dec 2021 15:28:23: #3 Call peaks for each chromosome... INFO @ Fri, 10 Dec 2021 15:28:37: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX7175235/SRX7175235.20_peaks.xls INFO @ Fri, 10 Dec 2021 15:28:37: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX7175235/SRX7175235.20_peaks.narrowPeak INFO @ Fri, 10 Dec 2021 15:28:37: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX7175235/SRX7175235.20_summits.bed INFO @ Fri, 10 Dec 2021 15:28:37: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (3103 records, 4 fields): 5 millis CompletedMACS2peakCalling