Job ID = 14171699 SRX = SRX10386223 Genome = dm3 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... Read 26181065 spots for SRR14009288/SRR14009288.sra Written 26181065 spots for SRR14009288/SRR14009288.sra fastq に変換しました。 bowtie でマッピング中... Your job 14172297 ("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: 00:41:22 26181065 reads; of these: 26181065 (100.00%) were paired; of these: 5271937 (20.14%) aligned concordantly 0 times 14915839 (56.97%) aligned concordantly exactly 1 time 5993289 (22.89%) aligned concordantly >1 times ---- 5271937 pairs aligned concordantly 0 times; of these: 574397 (10.90%) aligned discordantly 1 time ---- 4697540 pairs aligned 0 times concordantly or discordantly; of these: 9395080 mates make up the pairs; of these: 8206711 (87.35%) aligned 0 times 596725 (6.35%) aligned exactly 1 time 591644 (6.30%) aligned >1 times 84.33% overall alignment rate Time searching: 00:41:23 Overall time: 00:41:23 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] 6266820 / 21453234 = 0.2921 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 @ Sat, 11 Dec 2021 13:22:56: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX10386223/SRX10386223.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX10386223/SRX10386223.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX10386223/SRX10386223.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX10386223/SRX10386223.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 @ Sat, 11 Dec 2021 13:22:56: #1 read tag files... INFO @ Sat, 11 Dec 2021 13:22:56: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 13:23:00: 1000000 INFO @ Sat, 11 Dec 2021 13:23:05: 2000000 INFO @ Sat, 11 Dec 2021 13:23:10: 3000000 INFO @ Sat, 11 Dec 2021 13:23:14: 4000000 INFO @ Sat, 11 Dec 2021 13:23:19: 5000000 INFO @ Sat, 11 Dec 2021 13:23:24: 6000000 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 @ Sat, 11 Dec 2021 13:23:26: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX10386223/SRX10386223.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX10386223/SRX10386223.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX10386223/SRX10386223.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX10386223/SRX10386223.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 @ Sat, 11 Dec 2021 13:23:26: #1 read tag files... INFO @ Sat, 11 Dec 2021 13:23:26: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 13:23:29: 7000000 INFO @ Sat, 11 Dec 2021 13:23:32: 1000000 INFO @ Sat, 11 Dec 2021 13:23:34: 8000000 INFO @ Sat, 11 Dec 2021 13:23:38: 2000000 INFO @ Sat, 11 Dec 2021 13:23:39: 9000000 INFO @ Sat, 11 Dec 2021 13:23:44: 3000000 INFO @ Sat, 11 Dec 2021 13:23:44: 10000000 INFO @ Sat, 11 Dec 2021 13:23:50: 11000000 INFO @ Sat, 11 Dec 2021 13:23:50: 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 @ Sat, 11 Dec 2021 13:23:55: 12000000 INFO @ Sat, 11 Dec 2021 13:23:56: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX10386223/SRX10386223.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX10386223/SRX10386223.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX10386223/SRX10386223.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX10386223/SRX10386223.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 @ Sat, 11 Dec 2021 13:23:56: #1 read tag files... INFO @ Sat, 11 Dec 2021 13:23:56: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 13:23:56: 5000000 INFO @ Sat, 11 Dec 2021 13:24:00: 13000000 INFO @ Sat, 11 Dec 2021 13:24:02: 1000000 INFO @ Sat, 11 Dec 2021 13:24:03: 6000000 INFO @ Sat, 11 Dec 2021 13:24:06: 14000000 INFO @ Sat, 11 Dec 2021 13:24:08: 2000000 INFO @ Sat, 11 Dec 2021 13:24:09: 7000000 INFO @ Sat, 11 Dec 2021 13:24:11: 15000000 INFO @ Sat, 11 Dec 2021 13:24:14: 3000000 INFO @ Sat, 11 Dec 2021 13:24:15: 8000000 INFO @ Sat, 11 Dec 2021 13:24:16: 16000000 INFO @ Sat, 11 Dec 2021 13:24:21: 4000000 INFO @ Sat, 11 Dec 2021 13:24:21: 9000000 INFO @ Sat, 11 Dec 2021 13:24:22: 17000000 INFO @ Sat, 11 Dec 2021 13:24:27: 5000000 INFO @ Sat, 11 Dec 2021 13:24:27: 18000000 INFO @ Sat, 11 Dec 2021 13:24:27: 10000000 INFO @ Sat, 11 Dec 2021 13:24:33: 19000000 INFO @ Sat, 11 Dec 2021 13:24:33: 6000000 INFO @ Sat, 11 Dec 2021 13:24:33: 11000000 INFO @ Sat, 11 Dec 2021 13:24:38: 20000000 INFO @ Sat, 11 Dec 2021 13:24:39: 12000000 INFO @ Sat, 11 Dec 2021 13:24:39: 7000000 INFO @ Sat, 11 Dec 2021 13:24:43: 21000000 INFO @ Sat, 11 Dec 2021 13:24:45: 13000000 INFO @ Sat, 11 Dec 2021 13:24:46: 8000000 INFO @ Sat, 11 Dec 2021 13:24:49: 22000000 INFO @ Sat, 11 Dec 2021 13:24:51: 14000000 INFO @ Sat, 11 Dec 2021 13:24:52: 9000000 INFO @ Sat, 11 Dec 2021 13:24:54: 23000000 INFO @ Sat, 11 Dec 2021 13:24:57: 15000000 INFO @ Sat, 11 Dec 2021 13:24:58: 10000000 INFO @ Sat, 11 Dec 2021 13:25:00: 24000000 INFO @ Sat, 11 Dec 2021 13:25:03: 16000000 INFO @ Sat, 11 Dec 2021 13:25:04: 11000000 INFO @ Sat, 11 Dec 2021 13:25:05: 25000000 INFO @ Sat, 11 Dec 2021 13:25:10: 17000000 INFO @ Sat, 11 Dec 2021 13:25:10: 12000000 INFO @ Sat, 11 Dec 2021 13:25:11: 26000000 INFO @ Sat, 11 Dec 2021 13:25:16: 18000000 INFO @ Sat, 11 Dec 2021 13:25:16: 13000000 INFO @ Sat, 11 Dec 2021 13:25:17: 27000000 INFO @ Sat, 11 Dec 2021 13:25:22: 19000000 INFO @ Sat, 11 Dec 2021 13:25:22: 28000000 INFO @ Sat, 11 Dec 2021 13:25:22: 14000000 INFO @ Sat, 11 Dec 2021 13:25:28: 29000000 INFO @ Sat, 11 Dec 2021 13:25:28: 20000000 INFO @ Sat, 11 Dec 2021 13:25:28: 15000000 INFO @ Sat, 11 Dec 2021 13:25:33: 30000000 INFO @ Sat, 11 Dec 2021 13:25:34: 21000000 INFO @ Sat, 11 Dec 2021 13:25:35: 16000000 INFO @ Sat, 11 Dec 2021 13:25:38: 31000000 INFO @ Sat, 11 Dec 2021 13:25:41: 22000000 INFO @ Sat, 11 Dec 2021 13:25:41: 17000000 INFO @ Sat, 11 Dec 2021 13:25:42: #1 tag size is determined as 50 bps INFO @ Sat, 11 Dec 2021 13:25:42: #1 tag size = 50 INFO @ Sat, 11 Dec 2021 13:25:42: #1 total tags in treatment: 14735465 INFO @ Sat, 11 Dec 2021 13:25:42: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 13:25:42: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 11 Dec 2021 13:25:42: #1 tags after filtering in treatment: 12400116 INFO @ Sat, 11 Dec 2021 13:25:42: #1 Redundant rate of treatment: 0.16 INFO @ Sat, 11 Dec 2021 13:25:42: #1 finished! INFO @ Sat, 11 Dec 2021 13:25:42: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 13:25:42: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 13:25:43: #2 number of paired peaks: 198 WARNING @ Sat, 11 Dec 2021 13:25:43: Fewer paired peaks (198) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 198 pairs to build model! INFO @ Sat, 11 Dec 2021 13:25:43: start model_add_line... INFO @ Sat, 11 Dec 2021 13:25:43: start X-correlation... INFO @ Sat, 11 Dec 2021 13:25:43: end of X-cor INFO @ Sat, 11 Dec 2021 13:25:43: #2 finished! INFO @ Sat, 11 Dec 2021 13:25:43: #2 predicted fragment length is 116 bps INFO @ Sat, 11 Dec 2021 13:25:43: #2 alternative fragment length(s) may be 116 bps INFO @ Sat, 11 Dec 2021 13:25:43: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX10386223/SRX10386223.05_model.r INFO @ Sat, 11 Dec 2021 13:25:43: #3 Call peaks... INFO @ Sat, 11 Dec 2021 13:25:43: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Dec 2021 13:25:47: 23000000 INFO @ Sat, 11 Dec 2021 13:25:47: 18000000 INFO @ Sat, 11 Dec 2021 13:25:53: 24000000 INFO @ Sat, 11 Dec 2021 13:25:54: 19000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 11 Dec 2021 13:25:59: 25000000 INFO @ Sat, 11 Dec 2021 13:26:00: 20000000 INFO @ Sat, 11 Dec 2021 13:26:06: 26000000 INFO @ Sat, 11 Dec 2021 13:26:06: #3 Call peaks for each chromosome... INFO @ Sat, 11 Dec 2021 13:26:06: 21000000 INFO @ Sat, 11 Dec 2021 13:26:11: 27000000 INFO @ Sat, 11 Dec 2021 13:26:12: 22000000 INFO @ Sat, 11 Dec 2021 13:26:18: 28000000 INFO @ Sat, 11 Dec 2021 13:26:18: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX10386223/SRX10386223.05_peaks.xls INFO @ Sat, 11 Dec 2021 13:26:18: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX10386223/SRX10386223.05_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 13:26:18: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX10386223/SRX10386223.05_summits.bed INFO @ Sat, 11 Dec 2021 13:26:18: Done! pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (1753 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Sat, 11 Dec 2021 13:26:19: 23000000 INFO @ Sat, 11 Dec 2021 13:26:24: 29000000 INFO @ Sat, 11 Dec 2021 13:26:25: 24000000 INFO @ Sat, 11 Dec 2021 13:26:30: 30000000 INFO @ Sat, 11 Dec 2021 13:26:32: 25000000 INFO @ Sat, 11 Dec 2021 13:26:36: 31000000 INFO @ Sat, 11 Dec 2021 13:26:38: 26000000 INFO @ Sat, 11 Dec 2021 13:26:40: #1 tag size is determined as 50 bps INFO @ Sat, 11 Dec 2021 13:26:40: #1 tag size = 50 INFO @ Sat, 11 Dec 2021 13:26:40: #1 total tags in treatment: 14735465 INFO @ Sat, 11 Dec 2021 13:26:40: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 13:26:40: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 11 Dec 2021 13:26:40: #1 tags after filtering in treatment: 12400116 INFO @ Sat, 11 Dec 2021 13:26:40: #1 Redundant rate of treatment: 0.16 INFO @ Sat, 11 Dec 2021 13:26:40: #1 finished! INFO @ Sat, 11 Dec 2021 13:26:40: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 13:26:40: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 13:26:41: #2 number of paired peaks: 198 WARNING @ Sat, 11 Dec 2021 13:26:41: Fewer paired peaks (198) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 198 pairs to build model! INFO @ Sat, 11 Dec 2021 13:26:41: start model_add_line... INFO @ Sat, 11 Dec 2021 13:26:41: start X-correlation... INFO @ Sat, 11 Dec 2021 13:26:41: end of X-cor INFO @ Sat, 11 Dec 2021 13:26:41: #2 finished! INFO @ Sat, 11 Dec 2021 13:26:41: #2 predicted fragment length is 116 bps INFO @ Sat, 11 Dec 2021 13:26:41: #2 alternative fragment length(s) may be 116 bps INFO @ Sat, 11 Dec 2021 13:26:41: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX10386223/SRX10386223.10_model.r INFO @ Sat, 11 Dec 2021 13:26:41: #3 Call peaks... INFO @ Sat, 11 Dec 2021 13:26:41: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Dec 2021 13:26:43: 27000000 INFO @ Sat, 11 Dec 2021 13:26:49: 28000000 INFO @ Sat, 11 Dec 2021 13:26:56: 29000000 BigWig に変換しました。 INFO @ Sat, 11 Dec 2021 13:27:01: 30000000 INFO @ Sat, 11 Dec 2021 13:27:05: #3 Call peaks for each chromosome... INFO @ Sat, 11 Dec 2021 13:27:07: 31000000 INFO @ Sat, 11 Dec 2021 13:27:11: #1 tag size is determined as 50 bps INFO @ Sat, 11 Dec 2021 13:27:11: #1 tag size = 50 INFO @ Sat, 11 Dec 2021 13:27:11: #1 total tags in treatment: 14735465 INFO @ Sat, 11 Dec 2021 13:27:11: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 13:27:11: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 11 Dec 2021 13:27:11: #1 tags after filtering in treatment: 12400116 INFO @ Sat, 11 Dec 2021 13:27:11: #1 Redundant rate of treatment: 0.16 INFO @ Sat, 11 Dec 2021 13:27:11: #1 finished! INFO @ Sat, 11 Dec 2021 13:27:11: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 13:27:11: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 13:27:12: #2 number of paired peaks: 198 WARNING @ Sat, 11 Dec 2021 13:27:12: Fewer paired peaks (198) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 198 pairs to build model! INFO @ Sat, 11 Dec 2021 13:27:12: start model_add_line... INFO @ Sat, 11 Dec 2021 13:27:12: start X-correlation... INFO @ Sat, 11 Dec 2021 13:27:12: end of X-cor INFO @ Sat, 11 Dec 2021 13:27:12: #2 finished! INFO @ Sat, 11 Dec 2021 13:27:12: #2 predicted fragment length is 116 bps INFO @ Sat, 11 Dec 2021 13:27:12: #2 alternative fragment length(s) may be 116 bps INFO @ Sat, 11 Dec 2021 13:27:12: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX10386223/SRX10386223.20_model.r INFO @ Sat, 11 Dec 2021 13:27:12: #3 Call peaks... INFO @ Sat, 11 Dec 2021 13:27:12: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Dec 2021 13:27:17: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX10386223/SRX10386223.10_peaks.xls INFO @ Sat, 11 Dec 2021 13:27:17: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX10386223/SRX10386223.10_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 13:27:17: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX10386223/SRX10386223.10_summits.bed INFO @ Sat, 11 Dec 2021 13:27:17: Done! pass1 - making usageList (14 chroms): 0 millis pass2 - checking and writing primary data (1054 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Sat, 11 Dec 2021 13:27:35: #3 Call peaks for each chromosome... INFO @ Sat, 11 Dec 2021 13:27:47: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX10386223/SRX10386223.20_peaks.xls INFO @ Sat, 11 Dec 2021 13:27:47: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX10386223/SRX10386223.20_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 13:27:47: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX10386223/SRX10386223.20_summits.bed INFO @ Sat, 11 Dec 2021 13:27:47: Done! pass1 - making usageList (11 chroms): 0 millis pass2 - checking and writing primary data (692 records, 4 fields): 2 millis CompletedMACS2peakCalling