Job ID = 14168138 SRX = SRX7175244 Genome = dm3 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... Read 15213485 spots for SRR10485684/SRR10485684.sra Written 15213485 spots for SRR10485684/SRR10485684.sra fastq に変換しました。 bowtie でマッピング中... Your job 14169004 ("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: 00:26:59 15213485 reads; of these: 15213485 (100.00%) were paired; of these: 1055599 (6.94%) aligned concordantly 0 times 10356730 (68.08%) aligned concordantly exactly 1 time 3801156 (24.99%) aligned concordantly >1 times ---- 1055599 pairs aligned concordantly 0 times; of these: 277623 (26.30%) aligned discordantly 1 time ---- 777976 pairs aligned 0 times concordantly or discordantly; of these: 1555952 mates make up the pairs; of these: 703341 (45.20%) aligned 0 times 485311 (31.19%) aligned exactly 1 time 367300 (23.61%) aligned >1 times 97.69% overall alignment rate Time searching: 00:26:59 Overall time: 00:26:59 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 16 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] 498712 / 14223444 = 0.0351 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 16:14:06: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX7175244/SRX7175244.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX7175244/SRX7175244.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX7175244/SRX7175244.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX7175244/SRX7175244.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 16:14:06: #1 read tag files... INFO @ Fri, 10 Dec 2021 16:14:06: #1 read treatment tags... INFO @ Fri, 10 Dec 2021 16:14:13: 1000000 INFO @ Fri, 10 Dec 2021 16:14:20: 2000000 INFO @ Fri, 10 Dec 2021 16:14:27: 3000000 INFO @ Fri, 10 Dec 2021 16:14:34: 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 16:14:37: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX7175244/SRX7175244.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX7175244/SRX7175244.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX7175244/SRX7175244.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX7175244/SRX7175244.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 16:14:37: #1 read tag files... INFO @ Fri, 10 Dec 2021 16:14:37: #1 read treatment tags... INFO @ Fri, 10 Dec 2021 16:14:41: 5000000 INFO @ Fri, 10 Dec 2021 16:14:45: 1000000 INFO @ Fri, 10 Dec 2021 16:14:49: 6000000 INFO @ Fri, 10 Dec 2021 16:14:53: 2000000 INFO @ Fri, 10 Dec 2021 16:14:57: 7000000 INFO @ Fri, 10 Dec 2021 16:15:00: 3000000 INFO @ Fri, 10 Dec 2021 16:15:04: 8000000 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 16:15:07: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX7175244/SRX7175244.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX7175244/SRX7175244.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX7175244/SRX7175244.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX7175244/SRX7175244.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 16:15:07: #1 read tag files... INFO @ Fri, 10 Dec 2021 16:15:07: #1 read treatment tags... INFO @ Fri, 10 Dec 2021 16:15:08: 4000000 INFO @ Fri, 10 Dec 2021 16:15:12: 9000000 INFO @ Fri, 10 Dec 2021 16:15:15: 1000000 INFO @ Fri, 10 Dec 2021 16:15:16: 5000000 INFO @ Fri, 10 Dec 2021 16:15:20: 10000000 INFO @ Fri, 10 Dec 2021 16:15:23: 2000000 INFO @ Fri, 10 Dec 2021 16:15:24: 6000000 INFO @ Fri, 10 Dec 2021 16:15:28: 11000000 INFO @ Fri, 10 Dec 2021 16:15:31: 3000000 INFO @ Fri, 10 Dec 2021 16:15:32: 7000000 INFO @ Fri, 10 Dec 2021 16:15:35: 12000000 INFO @ Fri, 10 Dec 2021 16:15:39: 4000000 INFO @ Fri, 10 Dec 2021 16:15:39: 8000000 INFO @ Fri, 10 Dec 2021 16:15:43: 13000000 INFO @ Fri, 10 Dec 2021 16:15:47: 5000000 INFO @ Fri, 10 Dec 2021 16:15:47: 9000000 INFO @ Fri, 10 Dec 2021 16:15:51: 14000000 INFO @ Fri, 10 Dec 2021 16:15:55: 6000000 INFO @ Fri, 10 Dec 2021 16:15:55: 10000000 INFO @ Fri, 10 Dec 2021 16:15:58: 15000000 INFO @ Fri, 10 Dec 2021 16:16:03: 11000000 INFO @ Fri, 10 Dec 2021 16:16:03: 7000000 INFO @ Fri, 10 Dec 2021 16:16:06: 16000000 INFO @ Fri, 10 Dec 2021 16:16:10: 12000000 INFO @ Fri, 10 Dec 2021 16:16:11: 8000000 INFO @ Fri, 10 Dec 2021 16:16:14: 17000000 INFO @ Fri, 10 Dec 2021 16:16:18: 13000000 INFO @ Fri, 10 Dec 2021 16:16:19: 9000000 INFO @ Fri, 10 Dec 2021 16:16:22: 18000000 INFO @ Fri, 10 Dec 2021 16:16:26: 14000000 INFO @ Fri, 10 Dec 2021 16:16:27: 10000000 INFO @ Fri, 10 Dec 2021 16:16:29: 19000000 INFO @ Fri, 10 Dec 2021 16:16:33: 15000000 INFO @ Fri, 10 Dec 2021 16:16:35: 11000000 INFO @ Fri, 10 Dec 2021 16:16:37: 20000000 INFO @ Fri, 10 Dec 2021 16:16:41: 16000000 INFO @ Fri, 10 Dec 2021 16:16:43: 12000000 INFO @ Fri, 10 Dec 2021 16:16:45: 21000000 INFO @ Fri, 10 Dec 2021 16:16:49: 17000000 INFO @ Fri, 10 Dec 2021 16:16:51: 13000000 INFO @ Fri, 10 Dec 2021 16:16:53: 22000000 INFO @ Fri, 10 Dec 2021 16:16:57: 18000000 INFO @ Fri, 10 Dec 2021 16:16:59: 14000000 INFO @ Fri, 10 Dec 2021 16:17:01: 23000000 INFO @ Fri, 10 Dec 2021 16:17:04: 19000000 INFO @ Fri, 10 Dec 2021 16:17:07: 15000000 INFO @ Fri, 10 Dec 2021 16:17:08: 24000000 INFO @ Fri, 10 Dec 2021 16:17:12: 20000000 INFO @ Fri, 10 Dec 2021 16:17:15: 16000000 INFO @ Fri, 10 Dec 2021 16:17:16: 25000000 INFO @ Fri, 10 Dec 2021 16:17:20: 21000000 INFO @ Fri, 10 Dec 2021 16:17:23: 17000000 INFO @ Fri, 10 Dec 2021 16:17:24: 26000000 INFO @ Fri, 10 Dec 2021 16:17:28: 22000000 INFO @ Fri, 10 Dec 2021 16:17:31: 18000000 INFO @ Fri, 10 Dec 2021 16:17:32: 27000000 INFO @ Fri, 10 Dec 2021 16:17:35: 23000000 INFO @ Fri, 10 Dec 2021 16:17:39: 19000000 INFO @ Fri, 10 Dec 2021 16:17:40: 28000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Fri, 10 Dec 2021 16:17:43: 24000000 INFO @ Fri, 10 Dec 2021 16:17:45: #1 tag size is determined as 50 bps INFO @ Fri, 10 Dec 2021 16:17:45: #1 tag size = 50 INFO @ Fri, 10 Dec 2021 16:17:45: #1 total tags in treatment: 13660954 INFO @ Fri, 10 Dec 2021 16:17:45: #1 user defined the maximum tags... INFO @ Fri, 10 Dec 2021 16:17:45: #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 16:17:45: #1 tags after filtering in treatment: 12962669 INFO @ Fri, 10 Dec 2021 16:17:45: #1 Redundant rate of treatment: 0.05 INFO @ Fri, 10 Dec 2021 16:17:45: #1 finished! INFO @ Fri, 10 Dec 2021 16:17:45: #2 Build Peak Model... INFO @ Fri, 10 Dec 2021 16:17:45: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Dec 2021 16:17:46: #2 number of paired peaks: 103 WARNING @ Fri, 10 Dec 2021 16:17:46: Fewer paired peaks (103) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 103 pairs to build model! INFO @ Fri, 10 Dec 2021 16:17:46: start model_add_line... INFO @ Fri, 10 Dec 2021 16:17:46: start X-correlation... INFO @ Fri, 10 Dec 2021 16:17:46: end of X-cor INFO @ Fri, 10 Dec 2021 16:17:46: #2 finished! INFO @ Fri, 10 Dec 2021 16:17:46: #2 predicted fragment length is 149 bps INFO @ Fri, 10 Dec 2021 16:17:46: #2 alternative fragment length(s) may be 139,149 bps INFO @ Fri, 10 Dec 2021 16:17:46: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX7175244/SRX7175244.05_model.r INFO @ Fri, 10 Dec 2021 16:17:46: #3 Call peaks... INFO @ Fri, 10 Dec 2021 16:17:46: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 10 Dec 2021 16:17:47: 20000000 INFO @ Fri, 10 Dec 2021 16:17:51: 25000000 INFO @ Fri, 10 Dec 2021 16:17:55: 21000000 INFO @ Fri, 10 Dec 2021 16:17:58: 26000000 INFO @ Fri, 10 Dec 2021 16:18:02: 22000000 INFO @ Fri, 10 Dec 2021 16:18:05: 27000000 INFO @ Fri, 10 Dec 2021 16:18:10: 23000000 INFO @ Fri, 10 Dec 2021 16:18:12: #3 Call peaks for each chromosome... INFO @ Fri, 10 Dec 2021 16:18:12: 28000000 INFO @ Fri, 10 Dec 2021 16:18:17: #1 tag size is determined as 50 bps INFO @ Fri, 10 Dec 2021 16:18:17: #1 tag size = 50 INFO @ Fri, 10 Dec 2021 16:18:17: #1 total tags in treatment: 13660954 INFO @ Fri, 10 Dec 2021 16:18:17: #1 user defined the maximum tags... INFO @ Fri, 10 Dec 2021 16:18:17: #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 16:18:17: 24000000 INFO @ Fri, 10 Dec 2021 16:18:18: #1 tags after filtering in treatment: 12962669 INFO @ Fri, 10 Dec 2021 16:18:18: #1 Redundant rate of treatment: 0.05 INFO @ Fri, 10 Dec 2021 16:18:18: #1 finished! INFO @ Fri, 10 Dec 2021 16:18:18: #2 Build Peak Model... INFO @ Fri, 10 Dec 2021 16:18:18: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Dec 2021 16:18:19: #2 number of paired peaks: 103 WARNING @ Fri, 10 Dec 2021 16:18:19: Fewer paired peaks (103) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 103 pairs to build model! INFO @ Fri, 10 Dec 2021 16:18:19: start model_add_line... INFO @ Fri, 10 Dec 2021 16:18:19: start X-correlation... INFO @ Fri, 10 Dec 2021 16:18:19: end of X-cor INFO @ Fri, 10 Dec 2021 16:18:19: #2 finished! INFO @ Fri, 10 Dec 2021 16:18:19: #2 predicted fragment length is 149 bps INFO @ Fri, 10 Dec 2021 16:18:19: #2 alternative fragment length(s) may be 139,149 bps INFO @ Fri, 10 Dec 2021 16:18:19: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX7175244/SRX7175244.10_model.r INFO @ Fri, 10 Dec 2021 16:18:19: #3 Call peaks... INFO @ Fri, 10 Dec 2021 16:18:19: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 10 Dec 2021 16:18:24: 25000000 INFO @ Fri, 10 Dec 2021 16:18:25: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX7175244/SRX7175244.05_peaks.xls INFO @ Fri, 10 Dec 2021 16:18:25: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX7175244/SRX7175244.05_peaks.narrowPeak INFO @ Fri, 10 Dec 2021 16:18:25: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX7175244/SRX7175244.05_summits.bed INFO @ Fri, 10 Dec 2021 16:18:25: Done! pass1 - making usageList (14 chroms): 3 millis pass2 - checking and writing primary data (1382 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Fri, 10 Dec 2021 16:18:31: 26000000 INFO @ Fri, 10 Dec 2021 16:18:37: 27000000 INFO @ Fri, 10 Dec 2021 16:18:44: 28000000 INFO @ Fri, 10 Dec 2021 16:18:49: #1 tag size is determined as 50 bps INFO @ Fri, 10 Dec 2021 16:18:49: #1 tag size = 50 INFO @ Fri, 10 Dec 2021 16:18:49: #1 total tags in treatment: 13660954 INFO @ Fri, 10 Dec 2021 16:18:49: #1 user defined the maximum tags... INFO @ Fri, 10 Dec 2021 16:18:49: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) BigWig に変換しました。 INFO @ Fri, 10 Dec 2021 16:18:49: #1 tags after filtering in treatment: 12962669 INFO @ Fri, 10 Dec 2021 16:18:49: #1 Redundant rate of treatment: 0.05 INFO @ Fri, 10 Dec 2021 16:18:49: #1 finished! INFO @ Fri, 10 Dec 2021 16:18:49: #2 Build Peak Model... INFO @ Fri, 10 Dec 2021 16:18:49: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Dec 2021 16:18:49: #3 Call peaks for each chromosome... INFO @ Fri, 10 Dec 2021 16:18:50: #2 number of paired peaks: 103 WARNING @ Fri, 10 Dec 2021 16:18:50: Fewer paired peaks (103) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 103 pairs to build model! INFO @ Fri, 10 Dec 2021 16:18:50: start model_add_line... INFO @ Fri, 10 Dec 2021 16:18:50: start X-correlation... INFO @ Fri, 10 Dec 2021 16:18:50: end of X-cor INFO @ Fri, 10 Dec 2021 16:18:50: #2 finished! INFO @ Fri, 10 Dec 2021 16:18:50: #2 predicted fragment length is 149 bps INFO @ Fri, 10 Dec 2021 16:18:50: #2 alternative fragment length(s) may be 139,149 bps INFO @ Fri, 10 Dec 2021 16:18:50: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX7175244/SRX7175244.20_model.r INFO @ Fri, 10 Dec 2021 16:18:50: #3 Call peaks... INFO @ Fri, 10 Dec 2021 16:18:50: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 10 Dec 2021 16:19:04: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX7175244/SRX7175244.10_peaks.xls INFO @ Fri, 10 Dec 2021 16:19:04: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX7175244/SRX7175244.10_peaks.narrowPeak INFO @ Fri, 10 Dec 2021 16:19:04: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX7175244/SRX7175244.10_summits.bed INFO @ Fri, 10 Dec 2021 16:19:04: Done! pass1 - making usageList (13 chroms): 1 millis pass2 - checking and writing primary data (812 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Fri, 10 Dec 2021 16:19:20: #3 Call peaks for each chromosome... INFO @ Fri, 10 Dec 2021 16:19:35: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX7175244/SRX7175244.20_peaks.xls INFO @ Fri, 10 Dec 2021 16:19:35: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX7175244/SRX7175244.20_peaks.narrowPeak INFO @ Fri, 10 Dec 2021 16:19:35: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX7175244/SRX7175244.20_summits.bed INFO @ Fri, 10 Dec 2021 16:19:35: Done! pass1 - making usageList (10 chroms): 1 millis pass2 - checking and writing primary data (424 records, 4 fields): 1 millis CompletedMACS2peakCalling