Job ID = 14168107 SRX = ERX3978829 Genome = dm3 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... Read 35011102 spots for ERR3975898/ERR3975898.sra Written 35011102 spots for ERR3975898/ERR3975898.sra fastq に変換しました。 bowtie でマッピング中... Your job 14169160 ("srTdm6") has been submitted Time loading reference: 00:00:01 Time loading forward index: 00:00:00 Time loading mirror index: 00:00:00 Multiseed full-index search: 01:29:52 35011102 reads; of these: 35011102 (100.00%) were paired; of these: 4875485 (13.93%) aligned concordantly 0 times 22324920 (63.77%) aligned concordantly exactly 1 time 7810697 (22.31%) aligned concordantly >1 times ---- 4875485 pairs aligned concordantly 0 times; of these: 625922 (12.84%) aligned discordantly 1 time ---- 4249563 pairs aligned 0 times concordantly or discordantly; of these: 8499126 mates make up the pairs; of these: 5341206 (62.84%) aligned 0 times 1460995 (17.19%) aligned exactly 1 time 1696925 (19.97%) aligned >1 times 92.37% overall alignment rate Time searching: 01:29:53 Overall time: 01:29:53 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] 18818125 / 30638429 = 0.6142 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 17:19:43: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/ERX3978829/ERX3978829.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/ERX3978829/ERX3978829.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/ERX3978829/ERX3978829.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/ERX3978829/ERX3978829.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 17:19:43: #1 read tag files... INFO @ Fri, 10 Dec 2021 17:19:43: #1 read treatment tags... INFO @ Fri, 10 Dec 2021 17:19:50: 1000000 INFO @ Fri, 10 Dec 2021 17:19:56: 2000000 INFO @ Fri, 10 Dec 2021 17:20:02: 3000000 INFO @ Fri, 10 Dec 2021 17:20:09: 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 17:20:13: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/ERX3978829/ERX3978829.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/ERX3978829/ERX3978829.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/ERX3978829/ERX3978829.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/ERX3978829/ERX3978829.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 17:20:13: #1 read tag files... INFO @ Fri, 10 Dec 2021 17:20:13: #1 read treatment tags... INFO @ Fri, 10 Dec 2021 17:20:15: 5000000 INFO @ Fri, 10 Dec 2021 17:20:21: 1000000 INFO @ Fri, 10 Dec 2021 17:20:22: 6000000 INFO @ Fri, 10 Dec 2021 17:20:29: 2000000 INFO @ Fri, 10 Dec 2021 17:20:29: 7000000 INFO @ Fri, 10 Dec 2021 17:20:36: 8000000 INFO @ Fri, 10 Dec 2021 17:20:37: 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 17:20:43: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/ERX3978829/ERX3978829.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/ERX3978829/ERX3978829.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/ERX3978829/ERX3978829.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/ERX3978829/ERX3978829.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 17:20:43: #1 read tag files... INFO @ Fri, 10 Dec 2021 17:20:43: #1 read treatment tags... INFO @ Fri, 10 Dec 2021 17:20:44: 9000000 INFO @ Fri, 10 Dec 2021 17:20:46: 4000000 INFO @ Fri, 10 Dec 2021 17:20:52: 10000000 INFO @ Fri, 10 Dec 2021 17:20:52: 1000000 INFO @ Fri, 10 Dec 2021 17:20:54: 5000000 INFO @ Fri, 10 Dec 2021 17:21:00: 11000000 INFO @ Fri, 10 Dec 2021 17:21:02: 2000000 INFO @ Fri, 10 Dec 2021 17:21:03: 6000000 INFO @ Fri, 10 Dec 2021 17:21:07: 12000000 INFO @ Fri, 10 Dec 2021 17:21:11: 3000000 INFO @ Fri, 10 Dec 2021 17:21:12: 7000000 INFO @ Fri, 10 Dec 2021 17:21:15: 13000000 INFO @ Fri, 10 Dec 2021 17:21:21: 4000000 INFO @ Fri, 10 Dec 2021 17:21:21: 8000000 INFO @ Fri, 10 Dec 2021 17:21:23: 14000000 INFO @ Fri, 10 Dec 2021 17:21:29: 9000000 INFO @ Fri, 10 Dec 2021 17:21:30: 5000000 INFO @ Fri, 10 Dec 2021 17:21:32: 15000000 INFO @ Fri, 10 Dec 2021 17:21:38: 10000000 INFO @ Fri, 10 Dec 2021 17:21:39: 6000000 INFO @ Fri, 10 Dec 2021 17:21:40: 16000000 INFO @ Fri, 10 Dec 2021 17:21:46: 11000000 INFO @ Fri, 10 Dec 2021 17:21:48: 17000000 INFO @ Fri, 10 Dec 2021 17:21:48: 7000000 INFO @ Fri, 10 Dec 2021 17:21:55: 12000000 INFO @ Fri, 10 Dec 2021 17:21:56: 18000000 INFO @ Fri, 10 Dec 2021 17:21:58: 8000000 INFO @ Fri, 10 Dec 2021 17:22:04: 13000000 INFO @ Fri, 10 Dec 2021 17:22:04: 19000000 INFO @ Fri, 10 Dec 2021 17:22:07: 9000000 INFO @ Fri, 10 Dec 2021 17:22:12: 20000000 INFO @ Fri, 10 Dec 2021 17:22:12: 14000000 INFO @ Fri, 10 Dec 2021 17:22:16: 10000000 INFO @ Fri, 10 Dec 2021 17:22:20: 21000000 INFO @ Fri, 10 Dec 2021 17:22:21: 15000000 INFO @ Fri, 10 Dec 2021 17:22:26: 11000000 INFO @ Fri, 10 Dec 2021 17:22:28: 22000000 INFO @ Fri, 10 Dec 2021 17:22:29: 16000000 INFO @ Fri, 10 Dec 2021 17:22:35: 12000000 INFO @ Fri, 10 Dec 2021 17:22:37: 23000000 INFO @ Fri, 10 Dec 2021 17:22:38: 17000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Fri, 10 Dec 2021 17:22:44: 13000000 INFO @ Fri, 10 Dec 2021 17:22:45: 24000000 INFO @ Fri, 10 Dec 2021 17:22:46: 18000000 INFO @ Fri, 10 Dec 2021 17:22:53: 14000000 INFO @ Fri, 10 Dec 2021 17:22:53: 25000000 INFO @ Fri, 10 Dec 2021 17:22:55: 19000000 INFO @ Fri, 10 Dec 2021 17:23:02: 26000000 INFO @ Fri, 10 Dec 2021 17:23:02: 15000000 INFO @ Fri, 10 Dec 2021 17:23:03: 20000000 INFO @ Fri, 10 Dec 2021 17:23:10: 27000000 INFO @ Fri, 10 Dec 2021 17:23:10: #1 tag size is determined as 80 bps INFO @ Fri, 10 Dec 2021 17:23:10: #1 tag size = 80 INFO @ Fri, 10 Dec 2021 17:23:10: #1 total tags in treatment: 11718827 INFO @ Fri, 10 Dec 2021 17:23:10: #1 user defined the maximum tags... INFO @ Fri, 10 Dec 2021 17:23:10: #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 17:23:11: #1 tags after filtering in treatment: 10720795 INFO @ Fri, 10 Dec 2021 17:23:11: #1 Redundant rate of treatment: 0.09 INFO @ Fri, 10 Dec 2021 17:23:11: #1 finished! INFO @ Fri, 10 Dec 2021 17:23:11: #2 Build Peak Model... INFO @ Fri, 10 Dec 2021 17:23:11: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Dec 2021 17:23:11: #2 number of paired peaks: 857 WARNING @ Fri, 10 Dec 2021 17:23:11: Fewer paired peaks (857) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 857 pairs to build model! INFO @ Fri, 10 Dec 2021 17:23:11: start model_add_line... INFO @ Fri, 10 Dec 2021 17:23:11: start X-correlation... INFO @ Fri, 10 Dec 2021 17:23:11: end of X-cor INFO @ Fri, 10 Dec 2021 17:23:11: #2 finished! INFO @ Fri, 10 Dec 2021 17:23:11: #2 predicted fragment length is 176 bps INFO @ Fri, 10 Dec 2021 17:23:11: #2 alternative fragment length(s) may be 176 bps INFO @ Fri, 10 Dec 2021 17:23:11: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/ERX3978829/ERX3978829.05_model.r INFO @ Fri, 10 Dec 2021 17:23:11: #3 Call peaks... INFO @ Fri, 10 Dec 2021 17:23:11: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 10 Dec 2021 17:23:12: 21000000 INFO @ Fri, 10 Dec 2021 17:23:12: 16000000 INFO @ Fri, 10 Dec 2021 17:23:20: 22000000 INFO @ Fri, 10 Dec 2021 17:23:21: 17000000 BigWig に変換しました。 INFO @ Fri, 10 Dec 2021 17:23:28: 23000000 INFO @ Fri, 10 Dec 2021 17:23:30: 18000000 INFO @ Fri, 10 Dec 2021 17:23:35: #3 Call peaks for each chromosome... INFO @ Fri, 10 Dec 2021 17:23:36: 24000000 INFO @ Fri, 10 Dec 2021 17:23:40: 19000000 INFO @ Fri, 10 Dec 2021 17:23:44: 25000000 INFO @ Fri, 10 Dec 2021 17:23:47: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/ERX3978829/ERX3978829.05_peaks.xls INFO @ Fri, 10 Dec 2021 17:23:47: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/ERX3978829/ERX3978829.05_peaks.narrowPeak INFO @ Fri, 10 Dec 2021 17:23:47: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/ERX3978829/ERX3978829.05_summits.bed INFO @ Fri, 10 Dec 2021 17:23:47: Done! pass1 - making usageList (15 chroms): 2 millis pass2 - checking and writing primary data (9845 records, 4 fields): 11 millis CompletedMACS2peakCalling INFO @ Fri, 10 Dec 2021 17:23:49: 20000000 INFO @ Fri, 10 Dec 2021 17:23:52: 26000000 INFO @ Fri, 10 Dec 2021 17:23:58: 21000000 INFO @ Fri, 10 Dec 2021 17:24:00: 27000000 INFO @ Fri, 10 Dec 2021 17:24:00: #1 tag size is determined as 80 bps INFO @ Fri, 10 Dec 2021 17:24:00: #1 tag size = 80 INFO @ Fri, 10 Dec 2021 17:24:00: #1 total tags in treatment: 11718827 INFO @ Fri, 10 Dec 2021 17:24:00: #1 user defined the maximum tags... INFO @ Fri, 10 Dec 2021 17:24:00: #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 17:24:00: #1 tags after filtering in treatment: 10720795 INFO @ Fri, 10 Dec 2021 17:24:00: #1 Redundant rate of treatment: 0.09 INFO @ Fri, 10 Dec 2021 17:24:00: #1 finished! INFO @ Fri, 10 Dec 2021 17:24:00: #2 Build Peak Model... INFO @ Fri, 10 Dec 2021 17:24:00: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Dec 2021 17:24:01: #2 number of paired peaks: 857 WARNING @ Fri, 10 Dec 2021 17:24:01: Fewer paired peaks (857) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 857 pairs to build model! INFO @ Fri, 10 Dec 2021 17:24:01: start model_add_line... INFO @ Fri, 10 Dec 2021 17:24:01: start X-correlation... INFO @ Fri, 10 Dec 2021 17:24:01: end of X-cor INFO @ Fri, 10 Dec 2021 17:24:01: #2 finished! INFO @ Fri, 10 Dec 2021 17:24:01: #2 predicted fragment length is 176 bps INFO @ Fri, 10 Dec 2021 17:24:01: #2 alternative fragment length(s) may be 176 bps INFO @ Fri, 10 Dec 2021 17:24:01: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/ERX3978829/ERX3978829.10_model.r INFO @ Fri, 10 Dec 2021 17:24:01: #3 Call peaks... INFO @ Fri, 10 Dec 2021 17:24:01: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 10 Dec 2021 17:24:07: 22000000 INFO @ Fri, 10 Dec 2021 17:24:16: 23000000 INFO @ Fri, 10 Dec 2021 17:24:25: 24000000 INFO @ Fri, 10 Dec 2021 17:24:25: #3 Call peaks for each chromosome... INFO @ Fri, 10 Dec 2021 17:24:33: 25000000 INFO @ Fri, 10 Dec 2021 17:24:37: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/ERX3978829/ERX3978829.10_peaks.xls INFO @ Fri, 10 Dec 2021 17:24:37: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/ERX3978829/ERX3978829.10_peaks.narrowPeak INFO @ Fri, 10 Dec 2021 17:24:37: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/ERX3978829/ERX3978829.10_summits.bed INFO @ Fri, 10 Dec 2021 17:24:37: Done! pass1 - making usageList (15 chroms): 2 millis pass2 - checking and writing primary data (5097 records, 4 fields): 6 millis CompletedMACS2peakCalling INFO @ Fri, 10 Dec 2021 17:24:42: 26000000 INFO @ Fri, 10 Dec 2021 17:24:50: 27000000 INFO @ Fri, 10 Dec 2021 17:24:50: #1 tag size is determined as 80 bps INFO @ Fri, 10 Dec 2021 17:24:50: #1 tag size = 80 INFO @ Fri, 10 Dec 2021 17:24:50: #1 total tags in treatment: 11718827 INFO @ Fri, 10 Dec 2021 17:24:50: #1 user defined the maximum tags... INFO @ Fri, 10 Dec 2021 17:24:50: #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 17:24:50: #1 tags after filtering in treatment: 10720795 INFO @ Fri, 10 Dec 2021 17:24:50: #1 Redundant rate of treatment: 0.09 INFO @ Fri, 10 Dec 2021 17:24:50: #1 finished! INFO @ Fri, 10 Dec 2021 17:24:50: #2 Build Peak Model... INFO @ Fri, 10 Dec 2021 17:24:50: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Dec 2021 17:24:51: #2 number of paired peaks: 857 WARNING @ Fri, 10 Dec 2021 17:24:51: Fewer paired peaks (857) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 857 pairs to build model! INFO @ Fri, 10 Dec 2021 17:24:51: start model_add_line... INFO @ Fri, 10 Dec 2021 17:24:51: start X-correlation... INFO @ Fri, 10 Dec 2021 17:24:51: end of X-cor INFO @ Fri, 10 Dec 2021 17:24:51: #2 finished! INFO @ Fri, 10 Dec 2021 17:24:51: #2 predicted fragment length is 176 bps INFO @ Fri, 10 Dec 2021 17:24:51: #2 alternative fragment length(s) may be 176 bps INFO @ Fri, 10 Dec 2021 17:24:51: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/ERX3978829/ERX3978829.20_model.r INFO @ Fri, 10 Dec 2021 17:24:51: #3 Call peaks... INFO @ Fri, 10 Dec 2021 17:24:51: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 10 Dec 2021 17:25:16: #3 Call peaks for each chromosome... INFO @ Fri, 10 Dec 2021 17:25:29: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/ERX3978829/ERX3978829.20_peaks.xls INFO @ Fri, 10 Dec 2021 17:25:29: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/ERX3978829/ERX3978829.20_peaks.narrowPeak INFO @ Fri, 10 Dec 2021 17:25:29: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/ERX3978829/ERX3978829.20_summits.bed INFO @ Fri, 10 Dec 2021 17:25:29: Done! pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (2132 records, 4 fields): 4 millis CompletedMACS2peakCalling