Job ID = 14168115 SRX = ERX3978943 Genome = dm3 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... Read 22409331 spots for ERR3976013/ERR3976013.sra Written 22409331 spots for ERR3976013/ERR3976013.sra fastq に変換しました。 bowtie でマッピング中... Your job 14169105 ("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: 01:07:11 22409331 reads; of these: 22409331 (100.00%) were paired; of these: 3355041 (14.97%) aligned concordantly 0 times 14917266 (66.57%) aligned concordantly exactly 1 time 4137024 (18.46%) aligned concordantly >1 times ---- 3355041 pairs aligned concordantly 0 times; of these: 574598 (17.13%) aligned discordantly 1 time ---- 2780443 pairs aligned 0 times concordantly or discordantly; of these: 5560886 mates make up the pairs; of these: 2502755 (45.01%) aligned 0 times 1561529 (28.08%) aligned exactly 1 time 1496602 (26.91%) aligned >1 times 94.42% overall alignment rate Time searching: 01:07:11 Overall time: 01:07:11 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 20 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] 10980646 / 19468097 = 0.5640 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 16:46:45: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/ERX3978943/ERX3978943.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/ERX3978943/ERX3978943.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/ERX3978943/ERX3978943.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/ERX3978943/ERX3978943.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 16:46:45: #1 read tag files... INFO @ Fri, 10 Dec 2021 16:46:45: #1 read treatment tags... INFO @ Fri, 10 Dec 2021 16:46:51: 1000000 INFO @ Fri, 10 Dec 2021 16:46:56: 2000000 INFO @ Fri, 10 Dec 2021 16:47:02: 3000000 INFO @ Fri, 10 Dec 2021 16:47:08: 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 16:47:13: 5000000 INFO @ Fri, 10 Dec 2021 16:47:15: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/ERX3978943/ERX3978943.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/ERX3978943/ERX3978943.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/ERX3978943/ERX3978943.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/ERX3978943/ERX3978943.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 16:47:15: #1 read tag files... INFO @ Fri, 10 Dec 2021 16:47:15: #1 read treatment tags... INFO @ Fri, 10 Dec 2021 16:47:19: 6000000 INFO @ Fri, 10 Dec 2021 16:47:22: 1000000 INFO @ Fri, 10 Dec 2021 16:47:26: 7000000 INFO @ Fri, 10 Dec 2021 16:47:28: 2000000 INFO @ Fri, 10 Dec 2021 16:47:32: 8000000 INFO @ Fri, 10 Dec 2021 16:47:35: 3000000 INFO @ Fri, 10 Dec 2021 16:47:38: 9000000 INFO @ Fri, 10 Dec 2021 16:47:41: 4000000 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 16:47:45: 10000000 INFO @ Fri, 10 Dec 2021 16:47:45: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/ERX3978943/ERX3978943.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/ERX3978943/ERX3978943.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/ERX3978943/ERX3978943.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/ERX3978943/ERX3978943.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 16:47:45: #1 read tag files... INFO @ Fri, 10 Dec 2021 16:47:45: #1 read treatment tags... INFO @ Fri, 10 Dec 2021 16:47:48: 5000000 INFO @ Fri, 10 Dec 2021 16:47:52: 11000000 INFO @ Fri, 10 Dec 2021 16:47:53: 1000000 INFO @ Fri, 10 Dec 2021 16:47:55: 6000000 INFO @ Fri, 10 Dec 2021 16:47:59: 12000000 INFO @ Fri, 10 Dec 2021 16:48:01: 2000000 INFO @ Fri, 10 Dec 2021 16:48:02: 7000000 INFO @ Fri, 10 Dec 2021 16:48:06: 13000000 INFO @ Fri, 10 Dec 2021 16:48:09: 8000000 INFO @ Fri, 10 Dec 2021 16:48:09: 3000000 INFO @ Fri, 10 Dec 2021 16:48:13: 14000000 INFO @ Fri, 10 Dec 2021 16:48:16: 9000000 INFO @ Fri, 10 Dec 2021 16:48:17: 4000000 INFO @ Fri, 10 Dec 2021 16:48:21: 15000000 INFO @ Fri, 10 Dec 2021 16:48:23: 10000000 INFO @ Fri, 10 Dec 2021 16:48:25: 5000000 INFO @ Fri, 10 Dec 2021 16:48:28: 16000000 INFO @ Fri, 10 Dec 2021 16:48:31: 11000000 INFO @ Fri, 10 Dec 2021 16:48:33: 6000000 INFO @ Fri, 10 Dec 2021 16:48:37: 17000000 INFO @ Fri, 10 Dec 2021 16:48:38: 12000000 INFO @ Fri, 10 Dec 2021 16:48:41: 7000000 INFO @ Fri, 10 Dec 2021 16:48:45: 13000000 INFO @ Fri, 10 Dec 2021 16:48:45: 18000000 INFO @ Fri, 10 Dec 2021 16:48:49: 8000000 INFO @ Fri, 10 Dec 2021 16:48:52: 14000000 INFO @ Fri, 10 Dec 2021 16:48:53: 19000000 INFO @ Fri, 10 Dec 2021 16:48:57: 9000000 INFO @ Fri, 10 Dec 2021 16:48:59: 15000000 INFO @ Fri, 10 Dec 2021 16:49:00: 20000000 INFO @ Fri, 10 Dec 2021 16:49:03: #1 tag size is determined as 75 bps INFO @ Fri, 10 Dec 2021 16:49:03: #1 tag size = 75 INFO @ Fri, 10 Dec 2021 16:49:03: #1 total tags in treatment: 8350251 INFO @ Fri, 10 Dec 2021 16:49:03: #1 user defined the maximum tags... INFO @ Fri, 10 Dec 2021 16:49:03: #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 16:49:03: #1 tags after filtering in treatment: 7842627 INFO @ Fri, 10 Dec 2021 16:49:03: #1 Redundant rate of treatment: 0.06 INFO @ Fri, 10 Dec 2021 16:49:03: #1 finished! INFO @ Fri, 10 Dec 2021 16:49:03: #2 Build Peak Model... INFO @ Fri, 10 Dec 2021 16:49:03: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Dec 2021 16:49:03: #2 number of paired peaks: 385 WARNING @ Fri, 10 Dec 2021 16:49:03: Fewer paired peaks (385) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 385 pairs to build model! INFO @ Fri, 10 Dec 2021 16:49:03: start model_add_line... INFO @ Fri, 10 Dec 2021 16:49:03: start X-correlation... INFO @ Fri, 10 Dec 2021 16:49:03: end of X-cor INFO @ Fri, 10 Dec 2021 16:49:03: #2 finished! INFO @ Fri, 10 Dec 2021 16:49:03: #2 predicted fragment length is 151 bps INFO @ Fri, 10 Dec 2021 16:49:03: #2 alternative fragment length(s) may be 151 bps INFO @ Fri, 10 Dec 2021 16:49:03: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/ERX3978943/ERX3978943.05_model.r INFO @ Fri, 10 Dec 2021 16:49:03: #3 Call peaks... INFO @ Fri, 10 Dec 2021 16:49:03: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 10 Dec 2021 16:49:05: 10000000 INFO @ Fri, 10 Dec 2021 16:49:07: 16000000 INFO @ Fri, 10 Dec 2021 16:49:13: 11000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Fri, 10 Dec 2021 16:49:15: 17000000 INFO @ Fri, 10 Dec 2021 16:49:20: #3 Call peaks for each chromosome... INFO @ Fri, 10 Dec 2021 16:49:21: 12000000 INFO @ Fri, 10 Dec 2021 16:49:24: 18000000 INFO @ Fri, 10 Dec 2021 16:49:28: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/ERX3978943/ERX3978943.05_peaks.xls INFO @ Fri, 10 Dec 2021 16:49:28: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/ERX3978943/ERX3978943.05_peaks.narrowPeak INFO @ Fri, 10 Dec 2021 16:49:28: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/ERX3978943/ERX3978943.05_summits.bed INFO @ Fri, 10 Dec 2021 16:49:28: Done! pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (4293 records, 4 fields): 6 millis CompletedMACS2peakCalling INFO @ Fri, 10 Dec 2021 16:49:29: 13000000 INFO @ Fri, 10 Dec 2021 16:49:32: 19000000 INFO @ Fri, 10 Dec 2021 16:49:36: 14000000 INFO @ Fri, 10 Dec 2021 16:49:39: 20000000 INFO @ Fri, 10 Dec 2021 16:49:41: #1 tag size is determined as 75 bps INFO @ Fri, 10 Dec 2021 16:49:41: #1 tag size = 75 INFO @ Fri, 10 Dec 2021 16:49:41: #1 total tags in treatment: 8350251 INFO @ Fri, 10 Dec 2021 16:49:41: #1 user defined the maximum tags... INFO @ Fri, 10 Dec 2021 16:49:41: #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 16:49:41: #1 tags after filtering in treatment: 7842627 INFO @ Fri, 10 Dec 2021 16:49:41: #1 Redundant rate of treatment: 0.06 INFO @ Fri, 10 Dec 2021 16:49:41: #1 finished! INFO @ Fri, 10 Dec 2021 16:49:41: #2 Build Peak Model... INFO @ Fri, 10 Dec 2021 16:49:41: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Dec 2021 16:49:42: #2 number of paired peaks: 385 WARNING @ Fri, 10 Dec 2021 16:49:42: Fewer paired peaks (385) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 385 pairs to build model! INFO @ Fri, 10 Dec 2021 16:49:42: start model_add_line... INFO @ Fri, 10 Dec 2021 16:49:42: start X-correlation... INFO @ Fri, 10 Dec 2021 16:49:42: end of X-cor INFO @ Fri, 10 Dec 2021 16:49:42: #2 finished! INFO @ Fri, 10 Dec 2021 16:49:42: #2 predicted fragment length is 151 bps INFO @ Fri, 10 Dec 2021 16:49:42: #2 alternative fragment length(s) may be 151 bps INFO @ Fri, 10 Dec 2021 16:49:42: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/ERX3978943/ERX3978943.10_model.r INFO @ Fri, 10 Dec 2021 16:49:42: #3 Call peaks... INFO @ Fri, 10 Dec 2021 16:49:42: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 10 Dec 2021 16:49:44: 15000000 BigWig に変換しました。 INFO @ Fri, 10 Dec 2021 16:49:51: 16000000 INFO @ Fri, 10 Dec 2021 16:49:58: #3 Call peaks for each chromosome... INFO @ Fri, 10 Dec 2021 16:49:58: 17000000 INFO @ Fri, 10 Dec 2021 16:50:04: 18000000 INFO @ Fri, 10 Dec 2021 16:50:06: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/ERX3978943/ERX3978943.10_peaks.xls INFO @ Fri, 10 Dec 2021 16:50:06: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/ERX3978943/ERX3978943.10_peaks.narrowPeak INFO @ Fri, 10 Dec 2021 16:50:06: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/ERX3978943/ERX3978943.10_summits.bed INFO @ Fri, 10 Dec 2021 16:50:06: Done! pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (1704 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Fri, 10 Dec 2021 16:50:10: 19000000 INFO @ Fri, 10 Dec 2021 16:50:18: 20000000 INFO @ Fri, 10 Dec 2021 16:50:20: #1 tag size is determined as 75 bps INFO @ Fri, 10 Dec 2021 16:50:20: #1 tag size = 75 INFO @ Fri, 10 Dec 2021 16:50:20: #1 total tags in treatment: 8350251 INFO @ Fri, 10 Dec 2021 16:50:20: #1 user defined the maximum tags... INFO @ Fri, 10 Dec 2021 16:50:20: #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 16:50:20: #1 tags after filtering in treatment: 7842627 INFO @ Fri, 10 Dec 2021 16:50:20: #1 Redundant rate of treatment: 0.06 INFO @ Fri, 10 Dec 2021 16:50:20: #1 finished! INFO @ Fri, 10 Dec 2021 16:50:20: #2 Build Peak Model... INFO @ Fri, 10 Dec 2021 16:50:20: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Dec 2021 16:50:21: #2 number of paired peaks: 385 WARNING @ Fri, 10 Dec 2021 16:50:21: Fewer paired peaks (385) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 385 pairs to build model! INFO @ Fri, 10 Dec 2021 16:50:21: start model_add_line... INFO @ Fri, 10 Dec 2021 16:50:21: start X-correlation... INFO @ Fri, 10 Dec 2021 16:50:21: end of X-cor INFO @ Fri, 10 Dec 2021 16:50:21: #2 finished! INFO @ Fri, 10 Dec 2021 16:50:21: #2 predicted fragment length is 151 bps INFO @ Fri, 10 Dec 2021 16:50:21: #2 alternative fragment length(s) may be 151 bps INFO @ Fri, 10 Dec 2021 16:50:21: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/ERX3978943/ERX3978943.20_model.r INFO @ Fri, 10 Dec 2021 16:50:21: #3 Call peaks... INFO @ Fri, 10 Dec 2021 16:50:21: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 10 Dec 2021 16:50:37: #3 Call peaks for each chromosome... INFO @ Fri, 10 Dec 2021 16:50:45: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/ERX3978943/ERX3978943.20_peaks.xls INFO @ Fri, 10 Dec 2021 16:50:45: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/ERX3978943/ERX3978943.20_peaks.narrowPeak INFO @ Fri, 10 Dec 2021 16:50:45: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/ERX3978943/ERX3978943.20_summits.bed INFO @ Fri, 10 Dec 2021 16:50:45: Done! pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (738 records, 4 fields): 3 millis CompletedMACS2peakCalling