Job ID = 14168666 SRX = ERX3978875 Genome = dm3 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... Read 31327034 spots for ERR3975944/ERR3975944.sra Written 31327034 spots for ERR3975944/ERR3975944.sra fastq に変換しました。 bowtie でマッピング中... Your job 14169869 ("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: 01:31:19 31327034 reads; of these: 31327034 (100.00%) were paired; of these: 3774490 (12.05%) aligned concordantly 0 times 22089757 (70.51%) aligned concordantly exactly 1 time 5462787 (17.44%) aligned concordantly >1 times ---- 3774490 pairs aligned concordantly 0 times; of these: 878142 (23.27%) aligned discordantly 1 time ---- 2896348 pairs aligned 0 times concordantly or discordantly; of these: 5792696 mates make up the pairs; of these: 2578915 (44.52%) aligned 0 times 1615936 (27.90%) aligned exactly 1 time 1597845 (27.58%) aligned >1 times 95.88% overall alignment rate Time searching: 01:31:20 Overall time: 01:31:20 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] 20873832 / 28330976 = 0.7368 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 21:02:23: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/ERX3978875/ERX3978875.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/ERX3978875/ERX3978875.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/ERX3978875/ERX3978875.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/ERX3978875/ERX3978875.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 21:02:23: #1 read tag files... INFO @ Fri, 10 Dec 2021 21:02:23: #1 read treatment tags... INFO @ Fri, 10 Dec 2021 21:02:28: 1000000 INFO @ Fri, 10 Dec 2021 21:02:32: 2000000 INFO @ Fri, 10 Dec 2021 21:02:37: 3000000 INFO @ Fri, 10 Dec 2021 21:02:42: 4000000 INFO @ Fri, 10 Dec 2021 21:02:46: 5000000 INFO @ Fri, 10 Dec 2021 21:02:51: 6000000 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 21:02:53: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/ERX3978875/ERX3978875.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/ERX3978875/ERX3978875.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/ERX3978875/ERX3978875.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/ERX3978875/ERX3978875.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 21:02:53: #1 read tag files... INFO @ Fri, 10 Dec 2021 21:02:53: #1 read treatment tags... INFO @ Fri, 10 Dec 2021 21:02:56: 7000000 INFO @ Fri, 10 Dec 2021 21:02:59: 1000000 INFO @ Fri, 10 Dec 2021 21:03:00: 8000000 INFO @ Fri, 10 Dec 2021 21:03:04: 2000000 INFO @ Fri, 10 Dec 2021 21:03:05: 9000000 INFO @ Fri, 10 Dec 2021 21:03:10: 10000000 INFO @ Fri, 10 Dec 2021 21:03:10: 3000000 INFO @ Fri, 10 Dec 2021 21:03:15: 11000000 INFO @ Fri, 10 Dec 2021 21:03:16: 4000000 INFO @ Fri, 10 Dec 2021 21:03:19: 12000000 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 21:03:22: 5000000 INFO @ Fri, 10 Dec 2021 21:03:23: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/ERX3978875/ERX3978875.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/ERX3978875/ERX3978875.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/ERX3978875/ERX3978875.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/ERX3978875/ERX3978875.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 21:03:23: #1 read tag files... INFO @ Fri, 10 Dec 2021 21:03:23: #1 read treatment tags... INFO @ Fri, 10 Dec 2021 21:03:24: 13000000 INFO @ Fri, 10 Dec 2021 21:03:28: 6000000 INFO @ Fri, 10 Dec 2021 21:03:28: 1000000 INFO @ Fri, 10 Dec 2021 21:03:29: 14000000 INFO @ Fri, 10 Dec 2021 21:03:33: 2000000 INFO @ Fri, 10 Dec 2021 21:03:33: 7000000 INFO @ Fri, 10 Dec 2021 21:03:34: 15000000 INFO @ Fri, 10 Dec 2021 21:03:37: 3000000 INFO @ Fri, 10 Dec 2021 21:03:39: 16000000 INFO @ Fri, 10 Dec 2021 21:03:39: 8000000 INFO @ Fri, 10 Dec 2021 21:03:42: 4000000 INFO @ Fri, 10 Dec 2021 21:03:44: 17000000 INFO @ Fri, 10 Dec 2021 21:03:45: 9000000 INFO @ Fri, 10 Dec 2021 21:03:47: 5000000 INFO @ Fri, 10 Dec 2021 21:03:49: 18000000 INFO @ Fri, 10 Dec 2021 21:03:50: #1 tag size is determined as 80 bps INFO @ Fri, 10 Dec 2021 21:03:50: #1 tag size = 80 INFO @ Fri, 10 Dec 2021 21:03:50: #1 total tags in treatment: 7205078 INFO @ Fri, 10 Dec 2021 21:03:50: #1 user defined the maximum tags... INFO @ Fri, 10 Dec 2021 21:03:50: #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 21:03:50: #1 tags after filtering in treatment: 6520550 INFO @ Fri, 10 Dec 2021 21:03:50: #1 Redundant rate of treatment: 0.10 INFO @ Fri, 10 Dec 2021 21:03:50: #1 finished! INFO @ Fri, 10 Dec 2021 21:03:50: #2 Build Peak Model... INFO @ Fri, 10 Dec 2021 21:03:50: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Dec 2021 21:03:51: 10000000 INFO @ Fri, 10 Dec 2021 21:03:51: #2 number of paired peaks: 1318 INFO @ Fri, 10 Dec 2021 21:03:51: start model_add_line... INFO @ Fri, 10 Dec 2021 21:03:51: start X-correlation... INFO @ Fri, 10 Dec 2021 21:03:51: end of X-cor INFO @ Fri, 10 Dec 2021 21:03:51: #2 finished! INFO @ Fri, 10 Dec 2021 21:03:51: #2 predicted fragment length is 162 bps INFO @ Fri, 10 Dec 2021 21:03:51: #2 alternative fragment length(s) may be 162 bps INFO @ Fri, 10 Dec 2021 21:03:51: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/ERX3978875/ERX3978875.05_model.r INFO @ Fri, 10 Dec 2021 21:03:51: #3 Call peaks... INFO @ Fri, 10 Dec 2021 21:03:51: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 10 Dec 2021 21:03:52: 6000000 INFO @ Fri, 10 Dec 2021 21:03:56: 11000000 INFO @ Fri, 10 Dec 2021 21:03:57: 7000000 INFO @ Fri, 10 Dec 2021 21:04:01: 8000000 INFO @ Fri, 10 Dec 2021 21:04:02: 12000000 INFO @ Fri, 10 Dec 2021 21:04:05: #3 Call peaks for each chromosome... INFO @ Fri, 10 Dec 2021 21:04:06: 9000000 INFO @ Fri, 10 Dec 2021 21:04:08: 13000000 INFO @ Fri, 10 Dec 2021 21:04:11: 10000000 INFO @ Fri, 10 Dec 2021 21:04:12: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/ERX3978875/ERX3978875.05_peaks.xls INFO @ Fri, 10 Dec 2021 21:04:12: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/ERX3978875/ERX3978875.05_peaks.narrowPeak INFO @ Fri, 10 Dec 2021 21:04:13: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/ERX3978875/ERX3978875.05_summits.bed INFO @ Fri, 10 Dec 2021 21:04:13: Done! pass1 - making usageList (15 chroms): 2 millis pass2 - checking and writing primary data (7144 records, 4 fields): 8 millis CompletedMACS2peakCalling INFO @ Fri, 10 Dec 2021 21:04:14: 14000000 INFO @ Fri, 10 Dec 2021 21:04:16: 11000000 INFO @ Fri, 10 Dec 2021 21:04:20: 15000000 INFO @ Fri, 10 Dec 2021 21:04:21: 12000000 INFO @ Fri, 10 Dec 2021 21:04:25: 16000000 INFO @ Fri, 10 Dec 2021 21:04:26: 13000000 INFO @ Fri, 10 Dec 2021 21:04:31: 14000000 INFO @ Fri, 10 Dec 2021 21:04:31: 17000000 INFO @ Fri, 10 Dec 2021 21:04:35: 15000000 INFO @ Fri, 10 Dec 2021 21:04:37: 18000000 INFO @ Fri, 10 Dec 2021 21:04:39: #1 tag size is determined as 80 bps INFO @ Fri, 10 Dec 2021 21:04:39: #1 tag size = 80 INFO @ Fri, 10 Dec 2021 21:04:39: #1 total tags in treatment: 7205078 INFO @ Fri, 10 Dec 2021 21:04:39: #1 user defined the maximum tags... INFO @ Fri, 10 Dec 2021 21:04:39: #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 21:04:39: #1 tags after filtering in treatment: 6520550 INFO @ Fri, 10 Dec 2021 21:04:39: #1 Redundant rate of treatment: 0.10 INFO @ Fri, 10 Dec 2021 21:04:39: #1 finished! INFO @ Fri, 10 Dec 2021 21:04:39: #2 Build Peak Model... INFO @ Fri, 10 Dec 2021 21:04:39: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Dec 2021 21:04:40: #2 number of paired peaks: 1318 INFO @ Fri, 10 Dec 2021 21:04:40: start model_add_line... INFO @ Fri, 10 Dec 2021 21:04:40: start X-correlation... INFO @ Fri, 10 Dec 2021 21:04:40: end of X-cor INFO @ Fri, 10 Dec 2021 21:04:40: #2 finished! INFO @ Fri, 10 Dec 2021 21:04:40: #2 predicted fragment length is 162 bps INFO @ Fri, 10 Dec 2021 21:04:40: #2 alternative fragment length(s) may be 162 bps INFO @ Fri, 10 Dec 2021 21:04:40: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/ERX3978875/ERX3978875.10_model.r INFO @ Fri, 10 Dec 2021 21:04:40: #3 Call peaks... INFO @ Fri, 10 Dec 2021 21:04:40: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 10 Dec 2021 21:04:40: 16000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Fri, 10 Dec 2021 21:04:45: 17000000 INFO @ Fri, 10 Dec 2021 21:04:50: 18000000 INFO @ Fri, 10 Dec 2021 21:04:51: #1 tag size is determined as 80 bps INFO @ Fri, 10 Dec 2021 21:04:51: #1 tag size = 80 INFO @ Fri, 10 Dec 2021 21:04:51: #1 total tags in treatment: 7205078 INFO @ Fri, 10 Dec 2021 21:04:51: #1 user defined the maximum tags... INFO @ Fri, 10 Dec 2021 21:04:51: #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 21:04:51: #1 tags after filtering in treatment: 6520550 INFO @ Fri, 10 Dec 2021 21:04:51: #1 Redundant rate of treatment: 0.10 INFO @ Fri, 10 Dec 2021 21:04:51: #1 finished! INFO @ Fri, 10 Dec 2021 21:04:51: #2 Build Peak Model... INFO @ Fri, 10 Dec 2021 21:04:51: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Dec 2021 21:04:52: #2 number of paired peaks: 1318 INFO @ Fri, 10 Dec 2021 21:04:52: start model_add_line... INFO @ Fri, 10 Dec 2021 21:04:52: start X-correlation... INFO @ Fri, 10 Dec 2021 21:04:52: end of X-cor INFO @ Fri, 10 Dec 2021 21:04:52: #2 finished! INFO @ Fri, 10 Dec 2021 21:04:52: #2 predicted fragment length is 162 bps INFO @ Fri, 10 Dec 2021 21:04:52: #2 alternative fragment length(s) may be 162 bps INFO @ Fri, 10 Dec 2021 21:04:52: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/ERX3978875/ERX3978875.20_model.r INFO @ Fri, 10 Dec 2021 21:04:52: #3 Call peaks... INFO @ Fri, 10 Dec 2021 21:04:52: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 10 Dec 2021 21:04:54: #3 Call peaks for each chromosome... INFO @ Fri, 10 Dec 2021 21:05:01: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/ERX3978875/ERX3978875.10_peaks.xls INFO @ Fri, 10 Dec 2021 21:05:01: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/ERX3978875/ERX3978875.10_peaks.narrowPeak INFO @ Fri, 10 Dec 2021 21:05:02: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/ERX3978875/ERX3978875.10_summits.bed INFO @ Fri, 10 Dec 2021 21:05:02: Done! pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (3389 records, 4 fields): 5 millis CompletedMACS2peakCalling INFO @ Fri, 10 Dec 2021 21:05:06: #3 Call peaks for each chromosome... BigWig に変換しました。 INFO @ Fri, 10 Dec 2021 21:05:13: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/ERX3978875/ERX3978875.20_peaks.xls INFO @ Fri, 10 Dec 2021 21:05:13: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/ERX3978875/ERX3978875.20_peaks.narrowPeak INFO @ Fri, 10 Dec 2021 21:05:13: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/ERX3978875/ERX3978875.20_summits.bed INFO @ Fri, 10 Dec 2021 21:05:13: Done! pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (1304 records, 4 fields): 3 millis CompletedMACS2peakCalling