Job ID = 14168658 SRX = ERX3978871 Genome = dm3 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... Read 40160241 spots for ERR3975940/ERR3975940.sra Written 40160241 spots for ERR3975940/ERR3975940.sra fastq に変換しました。 bowtie でマッピング中... Your job 14169891 ("srTdm6") has been submitted Time loading reference: 00:00:00 Time loading forward index: 00:00:01 Time loading mirror index: 00:00:00 Multiseed full-index search: 01:53:37 40160241 reads; of these: 40160241 (100.00%) were paired; of these: 5570467 (13.87%) aligned concordantly 0 times 25321587 (63.05%) aligned concordantly exactly 1 time 9268187 (23.08%) aligned concordantly >1 times ---- 5570467 pairs aligned concordantly 0 times; of these: 767699 (13.78%) aligned discordantly 1 time ---- 4802768 pairs aligned 0 times concordantly or discordantly; of these: 9605536 mates make up the pairs; of these: 5854798 (60.95%) aligned 0 times 1819955 (18.95%) aligned exactly 1 time 1930783 (20.10%) aligned >1 times 92.71% overall alignment rate Time searching: 01:53:38 Overall time: 01:53:38 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 32 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] 21871450 / 35198550 = 0.6214 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 21:28:02: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/ERX3978871/ERX3978871.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/ERX3978871/ERX3978871.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/ERX3978871/ERX3978871.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/ERX3978871/ERX3978871.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 21:28:02: #1 read tag files... INFO @ Fri, 10 Dec 2021 21:28:02: #1 read treatment tags... INFO @ Fri, 10 Dec 2021 21:28:08: 1000000 INFO @ Fri, 10 Dec 2021 21:28:13: 2000000 INFO @ Fri, 10 Dec 2021 21:28:18: 3000000 INFO @ Fri, 10 Dec 2021 21:28:24: 4000000 INFO @ Fri, 10 Dec 2021 21:28:29: 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 21:28:32: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/ERX3978871/ERX3978871.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/ERX3978871/ERX3978871.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/ERX3978871/ERX3978871.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/ERX3978871/ERX3978871.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 21:28:32: #1 read tag files... INFO @ Fri, 10 Dec 2021 21:28:32: #1 read treatment tags... INFO @ Fri, 10 Dec 2021 21:28:35: 6000000 INFO @ Fri, 10 Dec 2021 21:28:38: 1000000 INFO @ Fri, 10 Dec 2021 21:28:41: 7000000 INFO @ Fri, 10 Dec 2021 21:28:44: 2000000 INFO @ Fri, 10 Dec 2021 21:28:48: 8000000 INFO @ Fri, 10 Dec 2021 21:28:50: 3000000 INFO @ Fri, 10 Dec 2021 21:28:54: 9000000 INFO @ Fri, 10 Dec 2021 21:28:56: 4000000 INFO @ Fri, 10 Dec 2021 21:29:00: 10000000 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 21:29:02: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/ERX3978871/ERX3978871.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/ERX3978871/ERX3978871.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/ERX3978871/ERX3978871.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/ERX3978871/ERX3978871.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 21:29:02: #1 read tag files... INFO @ Fri, 10 Dec 2021 21:29:02: #1 read treatment tags... INFO @ Fri, 10 Dec 2021 21:29:02: 5000000 INFO @ Fri, 10 Dec 2021 21:29:06: 11000000 INFO @ Fri, 10 Dec 2021 21:29:08: 1000000 INFO @ Fri, 10 Dec 2021 21:29:08: 6000000 INFO @ Fri, 10 Dec 2021 21:29:12: 12000000 INFO @ Fri, 10 Dec 2021 21:29:14: 2000000 INFO @ Fri, 10 Dec 2021 21:29:15: 7000000 INFO @ Fri, 10 Dec 2021 21:29:18: 13000000 INFO @ Fri, 10 Dec 2021 21:29:21: 3000000 INFO @ Fri, 10 Dec 2021 21:29:21: 8000000 INFO @ Fri, 10 Dec 2021 21:29:24: 14000000 INFO @ Fri, 10 Dec 2021 21:29:27: 4000000 INFO @ Fri, 10 Dec 2021 21:29:27: 9000000 INFO @ Fri, 10 Dec 2021 21:29:30: 15000000 INFO @ Fri, 10 Dec 2021 21:29:33: 5000000 INFO @ Fri, 10 Dec 2021 21:29:33: 10000000 INFO @ Fri, 10 Dec 2021 21:29:36: 16000000 INFO @ Fri, 10 Dec 2021 21:29:39: 6000000 INFO @ Fri, 10 Dec 2021 21:29:40: 11000000 INFO @ Fri, 10 Dec 2021 21:29:43: 17000000 INFO @ Fri, 10 Dec 2021 21:29:46: 7000000 INFO @ Fri, 10 Dec 2021 21:29:46: 12000000 INFO @ Fri, 10 Dec 2021 21:29:49: 18000000 INFO @ Fri, 10 Dec 2021 21:29:52: 8000000 INFO @ Fri, 10 Dec 2021 21:29:52: 13000000 INFO @ Fri, 10 Dec 2021 21:29:55: 19000000 INFO @ Fri, 10 Dec 2021 21:29:58: 9000000 INFO @ Fri, 10 Dec 2021 21:29:58: 14000000 INFO @ Fri, 10 Dec 2021 21:30:01: 20000000 INFO @ Fri, 10 Dec 2021 21:30:04: 10000000 INFO @ Fri, 10 Dec 2021 21:30:05: 15000000 INFO @ Fri, 10 Dec 2021 21:30:07: 21000000 INFO @ Fri, 10 Dec 2021 21:30:11: 11000000 INFO @ Fri, 10 Dec 2021 21:30:11: 16000000 INFO @ Fri, 10 Dec 2021 21:30:13: 22000000 INFO @ Fri, 10 Dec 2021 21:30:17: 12000000 INFO @ Fri, 10 Dec 2021 21:30:17: 17000000 INFO @ Fri, 10 Dec 2021 21:30:20: 23000000 INFO @ Fri, 10 Dec 2021 21:30:23: 13000000 INFO @ Fri, 10 Dec 2021 21:30:23: 18000000 INFO @ Fri, 10 Dec 2021 21:30:26: 24000000 INFO @ Fri, 10 Dec 2021 21:30:29: 14000000 INFO @ Fri, 10 Dec 2021 21:30:30: 19000000 INFO @ Fri, 10 Dec 2021 21:30:32: 25000000 INFO @ Fri, 10 Dec 2021 21:30:36: 15000000 INFO @ Fri, 10 Dec 2021 21:30:36: 20000000 INFO @ Fri, 10 Dec 2021 21:30:38: 26000000 INFO @ Fri, 10 Dec 2021 21:30:42: 16000000 INFO @ Fri, 10 Dec 2021 21:30:42: 21000000 INFO @ Fri, 10 Dec 2021 21:30:45: 27000000 INFO @ Fri, 10 Dec 2021 21:30:48: 17000000 INFO @ Fri, 10 Dec 2021 21:30:49: 22000000 INFO @ Fri, 10 Dec 2021 21:30:51: 28000000 INFO @ Fri, 10 Dec 2021 21:30:54: 18000000 INFO @ Fri, 10 Dec 2021 21:30:55: 23000000 INFO @ Fri, 10 Dec 2021 21:30:57: 29000000 INFO @ Fri, 10 Dec 2021 21:31:00: 19000000 INFO @ Fri, 10 Dec 2021 21:31:01: 24000000 INFO @ Fri, 10 Dec 2021 21:31:03: 30000000 INFO @ Fri, 10 Dec 2021 21:31:07: 20000000 INFO @ Fri, 10 Dec 2021 21:31:07: #1 tag size is determined as 80 bps INFO @ Fri, 10 Dec 2021 21:31:07: #1 tag size = 80 INFO @ Fri, 10 Dec 2021 21:31:07: #1 total tags in treatment: 13216540 INFO @ Fri, 10 Dec 2021 21:31:07: #1 user defined the maximum tags... INFO @ Fri, 10 Dec 2021 21:31:07: #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 21:31:08: #1 tags after filtering in treatment: 11895303 INFO @ Fri, 10 Dec 2021 21:31:08: #1 Redundant rate of treatment: 0.10 INFO @ Fri, 10 Dec 2021 21:31:08: #1 finished! INFO @ Fri, 10 Dec 2021 21:31:08: #2 Build Peak Model... INFO @ Fri, 10 Dec 2021 21:31:08: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Dec 2021 21:31:08: 25000000 INFO @ Fri, 10 Dec 2021 21:31:09: #2 number of paired peaks: 938 WARNING @ Fri, 10 Dec 2021 21:31:09: Fewer paired peaks (938) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 938 pairs to build model! INFO @ Fri, 10 Dec 2021 21:31:09: start model_add_line... INFO @ Fri, 10 Dec 2021 21:31:09: start X-correlation... INFO @ Fri, 10 Dec 2021 21:31:09: end of X-cor INFO @ Fri, 10 Dec 2021 21:31:09: #2 finished! INFO @ Fri, 10 Dec 2021 21:31:09: #2 predicted fragment length is 161 bps INFO @ Fri, 10 Dec 2021 21:31:09: #2 alternative fragment length(s) may be 161 bps INFO @ Fri, 10 Dec 2021 21:31:09: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/ERX3978871/ERX3978871.05_model.r INFO @ Fri, 10 Dec 2021 21:31:09: #3 Call peaks... INFO @ Fri, 10 Dec 2021 21:31:09: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 10 Dec 2021 21:31:13: 21000000 INFO @ Fri, 10 Dec 2021 21:31:14: 26000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Fri, 10 Dec 2021 21:31:19: 22000000 INFO @ Fri, 10 Dec 2021 21:31:20: 27000000 INFO @ Fri, 10 Dec 2021 21:31:25: 23000000 INFO @ Fri, 10 Dec 2021 21:31:26: 28000000 INFO @ Fri, 10 Dec 2021 21:31:31: 24000000 INFO @ Fri, 10 Dec 2021 21:31:32: 29000000 INFO @ Fri, 10 Dec 2021 21:31:33: #3 Call peaks for each chromosome... INFO @ Fri, 10 Dec 2021 21:31:37: 25000000 INFO @ Fri, 10 Dec 2021 21:31:38: 30000000 INFO @ Fri, 10 Dec 2021 21:31:42: #1 tag size is determined as 80 bps INFO @ Fri, 10 Dec 2021 21:31:42: #1 tag size = 80 INFO @ Fri, 10 Dec 2021 21:31:42: #1 total tags in treatment: 13216540 INFO @ Fri, 10 Dec 2021 21:31:42: #1 user defined the maximum tags... INFO @ Fri, 10 Dec 2021 21:31:42: #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 21:31:42: #1 tags after filtering in treatment: 11895303 INFO @ Fri, 10 Dec 2021 21:31:42: #1 Redundant rate of treatment: 0.10 INFO @ Fri, 10 Dec 2021 21:31:42: #1 finished! INFO @ Fri, 10 Dec 2021 21:31:42: #2 Build Peak Model... INFO @ Fri, 10 Dec 2021 21:31:42: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Dec 2021 21:31:43: 26000000 INFO @ Fri, 10 Dec 2021 21:31:43: #2 number of paired peaks: 938 WARNING @ Fri, 10 Dec 2021 21:31:43: Fewer paired peaks (938) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 938 pairs to build model! INFO @ Fri, 10 Dec 2021 21:31:43: start model_add_line... INFO @ Fri, 10 Dec 2021 21:31:43: start X-correlation... INFO @ Fri, 10 Dec 2021 21:31:43: end of X-cor INFO @ Fri, 10 Dec 2021 21:31:43: #2 finished! INFO @ Fri, 10 Dec 2021 21:31:43: #2 predicted fragment length is 161 bps INFO @ Fri, 10 Dec 2021 21:31:43: #2 alternative fragment length(s) may be 161 bps INFO @ Fri, 10 Dec 2021 21:31:43: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/ERX3978871/ERX3978871.10_model.r INFO @ Fri, 10 Dec 2021 21:31:43: #3 Call peaks... INFO @ Fri, 10 Dec 2021 21:31:43: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 10 Dec 2021 21:31:46: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/ERX3978871/ERX3978871.05_peaks.xls INFO @ Fri, 10 Dec 2021 21:31:46: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/ERX3978871/ERX3978871.05_peaks.narrowPeak INFO @ Fri, 10 Dec 2021 21:31:46: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/ERX3978871/ERX3978871.05_summits.bed INFO @ Fri, 10 Dec 2021 21:31:46: Done! pass1 - making usageList (15 chroms): 2 millis pass2 - checking and writing primary data (10245 records, 4 fields): 29 millis CompletedMACS2peakCalling INFO @ Fri, 10 Dec 2021 21:31:49: 27000000 INFO @ Fri, 10 Dec 2021 21:31:54: 28000000 INFO @ Fri, 10 Dec 2021 21:32:00: 29000000 INFO @ Fri, 10 Dec 2021 21:32:05: 30000000 INFO @ Fri, 10 Dec 2021 21:32:08: #3 Call peaks for each chromosome... BigWig に変換しました。 INFO @ Fri, 10 Dec 2021 21:32:09: #1 tag size is determined as 80 bps INFO @ Fri, 10 Dec 2021 21:32:09: #1 tag size = 80 INFO @ Fri, 10 Dec 2021 21:32:09: #1 total tags in treatment: 13216540 INFO @ Fri, 10 Dec 2021 21:32:09: #1 user defined the maximum tags... INFO @ Fri, 10 Dec 2021 21:32:09: #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 21:32:09: #1 tags after filtering in treatment: 11895303 INFO @ Fri, 10 Dec 2021 21:32:09: #1 Redundant rate of treatment: 0.10 INFO @ Fri, 10 Dec 2021 21:32:09: #1 finished! INFO @ Fri, 10 Dec 2021 21:32:09: #2 Build Peak Model... INFO @ Fri, 10 Dec 2021 21:32:09: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Dec 2021 21:32:10: #2 number of paired peaks: 938 WARNING @ Fri, 10 Dec 2021 21:32:10: Fewer paired peaks (938) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 938 pairs to build model! INFO @ Fri, 10 Dec 2021 21:32:10: start model_add_line... INFO @ Fri, 10 Dec 2021 21:32:10: start X-correlation... INFO @ Fri, 10 Dec 2021 21:32:10: end of X-cor INFO @ Fri, 10 Dec 2021 21:32:10: #2 finished! INFO @ Fri, 10 Dec 2021 21:32:10: #2 predicted fragment length is 161 bps INFO @ Fri, 10 Dec 2021 21:32:10: #2 alternative fragment length(s) may be 161 bps INFO @ Fri, 10 Dec 2021 21:32:10: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/ERX3978871/ERX3978871.20_model.r INFO @ Fri, 10 Dec 2021 21:32:10: #3 Call peaks... INFO @ Fri, 10 Dec 2021 21:32:10: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 10 Dec 2021 21:32:21: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/ERX3978871/ERX3978871.10_peaks.xls INFO @ Fri, 10 Dec 2021 21:32:21: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/ERX3978871/ERX3978871.10_peaks.narrowPeak INFO @ Fri, 10 Dec 2021 21:32:21: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/ERX3978871/ERX3978871.10_summits.bed INFO @ Fri, 10 Dec 2021 21:32:21: Done! pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (5557 records, 4 fields): 7 millis CompletedMACS2peakCalling INFO @ Fri, 10 Dec 2021 21:32:35: #3 Call peaks for each chromosome... INFO @ Fri, 10 Dec 2021 21:32:47: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/ERX3978871/ERX3978871.20_peaks.xls INFO @ Fri, 10 Dec 2021 21:32:47: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/ERX3978871/ERX3978871.20_peaks.narrowPeak INFO @ Fri, 10 Dec 2021 21:32:47: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/ERX3978871/ERX3978871.20_summits.bed INFO @ Fri, 10 Dec 2021 21:32:47: Done! pass1 - making usageList (15 chroms): 0 millis pass2 - checking and writing primary data (2430 records, 4 fields): 5 millis CompletedMACS2peakCalling