Job ID = 14168100 SRX = ERX3978825 Genome = dm3 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... Read 29717268 spots for ERR3975894/ERR3975894.sra Written 29717268 spots for ERR3975894/ERR3975894.sra fastq に変換しました。 bowtie でマッピング中... Your job 14169129 ("srTdm6") has been submitted Time loading reference: 00:00:00 Time loading forward index: 00:00:00 Time loading mirror index: 00:00:01 Multiseed full-index search: 01:23:02 29717268 reads; of these: 29717268 (100.00%) were paired; of these: 3579219 (12.04%) aligned concordantly 0 times 20484989 (68.93%) aligned concordantly exactly 1 time 5653060 (19.02%) aligned concordantly >1 times ---- 3579219 pairs aligned concordantly 0 times; of these: 627141 (17.52%) aligned discordantly 1 time ---- 2952078 pairs aligned 0 times concordantly or discordantly; of these: 5904156 mates make up the pairs; of these: 3019557 (51.14%) aligned 0 times 1422059 (24.09%) aligned exactly 1 time 1462540 (24.77%) aligned >1 times 94.92% overall alignment rate Time searching: 01:23:03 Overall time: 01:23:03 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 24 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] 16356321 / 26637014 = 0.6140 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 16:59:30: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/ERX3978825/ERX3978825.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/ERX3978825/ERX3978825.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/ERX3978825/ERX3978825.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/ERX3978825/ERX3978825.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 16:59:30: #1 read tag files... INFO @ Fri, 10 Dec 2021 16:59:30: #1 read treatment tags... INFO @ Fri, 10 Dec 2021 16:59:38: 1000000 INFO @ Fri, 10 Dec 2021 16:59:45: 2000000 INFO @ Fri, 10 Dec 2021 16:59:52: 3000000 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 16:59:59: 4000000 INFO @ Fri, 10 Dec 2021 17:00:00: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/ERX3978825/ERX3978825.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/ERX3978825/ERX3978825.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/ERX3978825/ERX3978825.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/ERX3978825/ERX3978825.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 17:00:00: #1 read tag files... INFO @ Fri, 10 Dec 2021 17:00:00: #1 read treatment tags... INFO @ Fri, 10 Dec 2021 17:00:07: 5000000 INFO @ Fri, 10 Dec 2021 17:00:09: 1000000 INFO @ Fri, 10 Dec 2021 17:00:15: 6000000 INFO @ Fri, 10 Dec 2021 17:00:18: 2000000 INFO @ Fri, 10 Dec 2021 17:00:23: 7000000 INFO @ Fri, 10 Dec 2021 17:00:27: 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 17:00:30: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/ERX3978825/ERX3978825.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/ERX3978825/ERX3978825.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/ERX3978825/ERX3978825.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/ERX3978825/ERX3978825.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 17:00:30: #1 read tag files... INFO @ Fri, 10 Dec 2021 17:00:30: #1 read treatment tags... INFO @ Fri, 10 Dec 2021 17:00:31: 8000000 INFO @ Fri, 10 Dec 2021 17:00:36: 4000000 INFO @ Fri, 10 Dec 2021 17:00:38: 1000000 INFO @ Fri, 10 Dec 2021 17:00:40: 9000000 INFO @ Fri, 10 Dec 2021 17:00:45: 5000000 INFO @ Fri, 10 Dec 2021 17:00:46: 2000000 INFO @ Fri, 10 Dec 2021 17:00:48: 10000000 INFO @ Fri, 10 Dec 2021 17:00:54: 3000000 INFO @ Fri, 10 Dec 2021 17:00:54: 6000000 INFO @ Fri, 10 Dec 2021 17:00:56: 11000000 INFO @ Fri, 10 Dec 2021 17:01:02: 4000000 INFO @ Fri, 10 Dec 2021 17:01:03: 7000000 INFO @ Fri, 10 Dec 2021 17:01:04: 12000000 INFO @ Fri, 10 Dec 2021 17:01:09: 5000000 INFO @ Fri, 10 Dec 2021 17:01:12: 13000000 INFO @ Fri, 10 Dec 2021 17:01:12: 8000000 INFO @ Fri, 10 Dec 2021 17:01:17: 6000000 INFO @ Fri, 10 Dec 2021 17:01:21: 14000000 INFO @ Fri, 10 Dec 2021 17:01:22: 9000000 INFO @ Fri, 10 Dec 2021 17:01:25: 7000000 INFO @ Fri, 10 Dec 2021 17:01:29: 15000000 INFO @ Fri, 10 Dec 2021 17:01:31: 10000000 INFO @ Fri, 10 Dec 2021 17:01:33: 8000000 INFO @ Fri, 10 Dec 2021 17:01:37: 16000000 INFO @ Fri, 10 Dec 2021 17:01:40: 11000000 INFO @ Fri, 10 Dec 2021 17:01:41: 9000000 INFO @ Fri, 10 Dec 2021 17:01:46: 17000000 INFO @ Fri, 10 Dec 2021 17:01:48: 10000000 INFO @ Fri, 10 Dec 2021 17:01:49: 12000000 INFO @ Fri, 10 Dec 2021 17:01:54: 18000000 INFO @ Fri, 10 Dec 2021 17:01:56: 11000000 INFO @ Fri, 10 Dec 2021 17:01:58: 13000000 INFO @ Fri, 10 Dec 2021 17:02:02: 19000000 INFO @ Fri, 10 Dec 2021 17:02:04: 12000000 INFO @ Fri, 10 Dec 2021 17:02:07: 14000000 INFO @ Fri, 10 Dec 2021 17:02:11: 20000000 INFO @ Fri, 10 Dec 2021 17:02:12: 13000000 INFO @ Fri, 10 Dec 2021 17:02:16: 15000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Fri, 10 Dec 2021 17:02:19: 21000000 INFO @ Fri, 10 Dec 2021 17:02:20: 14000000 INFO @ Fri, 10 Dec 2021 17:02:25: 16000000 INFO @ Fri, 10 Dec 2021 17:02:28: 22000000 INFO @ Fri, 10 Dec 2021 17:02:28: 15000000 INFO @ Fri, 10 Dec 2021 17:02:34: 17000000 INFO @ Fri, 10 Dec 2021 17:02:36: 16000000 INFO @ Fri, 10 Dec 2021 17:02:36: 23000000 INFO @ Fri, 10 Dec 2021 17:02:41: #1 tag size is determined as 80 bps INFO @ Fri, 10 Dec 2021 17:02:41: #1 tag size = 80 INFO @ Fri, 10 Dec 2021 17:02:41: #1 total tags in treatment: 10141607 INFO @ Fri, 10 Dec 2021 17:02:41: #1 user defined the maximum tags... INFO @ Fri, 10 Dec 2021 17:02:41: #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 17:02:42: #1 tags after filtering in treatment: 9403724 INFO @ Fri, 10 Dec 2021 17:02:42: #1 Redundant rate of treatment: 0.07 INFO @ Fri, 10 Dec 2021 17:02:42: #1 finished! INFO @ Fri, 10 Dec 2021 17:02:42: #2 Build Peak Model... INFO @ Fri, 10 Dec 2021 17:02:42: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Dec 2021 17:02:42: #2 number of paired peaks: 722 WARNING @ Fri, 10 Dec 2021 17:02:42: Fewer paired peaks (722) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 722 pairs to build model! INFO @ Fri, 10 Dec 2021 17:02:42: start model_add_line... INFO @ Fri, 10 Dec 2021 17:02:42: start X-correlation... INFO @ Fri, 10 Dec 2021 17:02:42: end of X-cor INFO @ Fri, 10 Dec 2021 17:02:42: #2 finished! INFO @ Fri, 10 Dec 2021 17:02:42: #2 predicted fragment length is 164 bps INFO @ Fri, 10 Dec 2021 17:02:42: #2 alternative fragment length(s) may be 164 bps INFO @ Fri, 10 Dec 2021 17:02:42: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/ERX3978825/ERX3978825.05_model.r INFO @ Fri, 10 Dec 2021 17:02:42: #3 Call peaks... INFO @ Fri, 10 Dec 2021 17:02:42: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 10 Dec 2021 17:02:43: 18000000 INFO @ Fri, 10 Dec 2021 17:02:43: 17000000 INFO @ Fri, 10 Dec 2021 17:02:51: 19000000 INFO @ Fri, 10 Dec 2021 17:02:51: 18000000 BigWig に変換しました。 INFO @ Fri, 10 Dec 2021 17:02:59: 19000000 INFO @ Fri, 10 Dec 2021 17:03:00: 20000000 INFO @ Fri, 10 Dec 2021 17:03:02: #3 Call peaks for each chromosome... INFO @ Fri, 10 Dec 2021 17:03:07: 20000000 INFO @ Fri, 10 Dec 2021 17:03:08: 21000000 INFO @ Fri, 10 Dec 2021 17:03:12: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/ERX3978825/ERX3978825.05_peaks.xls INFO @ Fri, 10 Dec 2021 17:03:12: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/ERX3978825/ERX3978825.05_peaks.narrowPeak INFO @ Fri, 10 Dec 2021 17:03:12: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/ERX3978825/ERX3978825.05_summits.bed INFO @ Fri, 10 Dec 2021 17:03:13: Done! pass1 - making usageList (15 chroms): 2 millis pass2 - checking and writing primary data (7473 records, 4 fields): 8 millis CompletedMACS2peakCalling INFO @ Fri, 10 Dec 2021 17:03:15: 21000000 INFO @ Fri, 10 Dec 2021 17:03:16: 22000000 INFO @ Fri, 10 Dec 2021 17:03:22: 22000000 INFO @ Fri, 10 Dec 2021 17:03:25: 23000000 INFO @ Fri, 10 Dec 2021 17:03:30: 23000000 INFO @ Fri, 10 Dec 2021 17:03:31: #1 tag size is determined as 80 bps INFO @ Fri, 10 Dec 2021 17:03:31: #1 tag size = 80 INFO @ Fri, 10 Dec 2021 17:03:31: #1 total tags in treatment: 10141607 INFO @ Fri, 10 Dec 2021 17:03:31: #1 user defined the maximum tags... INFO @ Fri, 10 Dec 2021 17:03:31: #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 17:03:31: #1 tags after filtering in treatment: 9403724 INFO @ Fri, 10 Dec 2021 17:03:31: #1 Redundant rate of treatment: 0.07 INFO @ Fri, 10 Dec 2021 17:03:31: #1 finished! INFO @ Fri, 10 Dec 2021 17:03:31: #2 Build Peak Model... INFO @ Fri, 10 Dec 2021 17:03:31: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Dec 2021 17:03:32: #2 number of paired peaks: 722 WARNING @ Fri, 10 Dec 2021 17:03:32: Fewer paired peaks (722) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 722 pairs to build model! INFO @ Fri, 10 Dec 2021 17:03:32: start model_add_line... INFO @ Fri, 10 Dec 2021 17:03:32: start X-correlation... INFO @ Fri, 10 Dec 2021 17:03:32: end of X-cor INFO @ Fri, 10 Dec 2021 17:03:32: #2 finished! INFO @ Fri, 10 Dec 2021 17:03:32: #2 predicted fragment length is 164 bps INFO @ Fri, 10 Dec 2021 17:03:32: #2 alternative fragment length(s) may be 164 bps INFO @ Fri, 10 Dec 2021 17:03:32: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/ERX3978825/ERX3978825.10_model.r INFO @ Fri, 10 Dec 2021 17:03:32: #3 Call peaks... INFO @ Fri, 10 Dec 2021 17:03:32: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 10 Dec 2021 17:03:35: #1 tag size is determined as 80 bps INFO @ Fri, 10 Dec 2021 17:03:35: #1 tag size = 80 INFO @ Fri, 10 Dec 2021 17:03:35: #1 total tags in treatment: 10141607 INFO @ Fri, 10 Dec 2021 17:03:35: #1 user defined the maximum tags... INFO @ Fri, 10 Dec 2021 17:03:35: #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 17:03:35: #1 tags after filtering in treatment: 9403724 INFO @ Fri, 10 Dec 2021 17:03:35: #1 Redundant rate of treatment: 0.07 INFO @ Fri, 10 Dec 2021 17:03:35: #1 finished! INFO @ Fri, 10 Dec 2021 17:03:35: #2 Build Peak Model... INFO @ Fri, 10 Dec 2021 17:03:35: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Dec 2021 17:03:36: #2 number of paired peaks: 722 WARNING @ Fri, 10 Dec 2021 17:03:36: Fewer paired peaks (722) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 722 pairs to build model! INFO @ Fri, 10 Dec 2021 17:03:36: start model_add_line... INFO @ Fri, 10 Dec 2021 17:03:36: start X-correlation... INFO @ Fri, 10 Dec 2021 17:03:36: end of X-cor INFO @ Fri, 10 Dec 2021 17:03:36: #2 finished! INFO @ Fri, 10 Dec 2021 17:03:36: #2 predicted fragment length is 164 bps INFO @ Fri, 10 Dec 2021 17:03:36: #2 alternative fragment length(s) may be 164 bps INFO @ Fri, 10 Dec 2021 17:03:36: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/ERX3978825/ERX3978825.20_model.r INFO @ Fri, 10 Dec 2021 17:03:36: #3 Call peaks... INFO @ Fri, 10 Dec 2021 17:03:36: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 10 Dec 2021 17:03:52: #3 Call peaks for each chromosome... INFO @ Fri, 10 Dec 2021 17:03:55: #3 Call peaks for each chromosome... INFO @ Fri, 10 Dec 2021 17:04:01: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/ERX3978825/ERX3978825.10_peaks.xls INFO @ Fri, 10 Dec 2021 17:04:01: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/ERX3978825/ERX3978825.10_peaks.narrowPeak INFO @ Fri, 10 Dec 2021 17:04:01: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/ERX3978825/ERX3978825.10_summits.bed INFO @ Fri, 10 Dec 2021 17:04:01: Done! pass1 - making usageList (15 chroms): 2 millis pass2 - checking and writing primary data (3600 records, 4 fields): 4 millis CompletedMACS2peakCalling INFO @ Fri, 10 Dec 2021 17:04:05: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/ERX3978825/ERX3978825.20_peaks.xls INFO @ Fri, 10 Dec 2021 17:04:05: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/ERX3978825/ERX3978825.20_peaks.narrowPeak INFO @ Fri, 10 Dec 2021 17:04:05: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/ERX3978825/ERX3978825.20_summits.bed INFO @ Fri, 10 Dec 2021 17:04:05: Done! pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (1365 records, 4 fields): 3 millis CompletedMACS2peakCalling