Job ID = 14171533 SRX = SRX10386207 Genome = dm3 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... Read 23484047 spots for SRR14009272/SRR14009272.sra Written 23484047 spots for SRR14009272/SRR14009272.sra fastq に変換しました。 bowtie でマッピング中... Your job 14172100 ("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: 00:31:07 23484047 reads; of these: 23484047 (100.00%) were paired; of these: 8414826 (35.83%) aligned concordantly 0 times 10263335 (43.70%) aligned concordantly exactly 1 time 4805886 (20.46%) aligned concordantly >1 times ---- 8414826 pairs aligned concordantly 0 times; of these: 664167 (7.89%) aligned discordantly 1 time ---- 7750659 pairs aligned 0 times concordantly or discordantly; of these: 15501318 mates make up the pairs; of these: 14193932 (91.57%) aligned 0 times 597706 (3.86%) aligned exactly 1 time 709680 (4.58%) aligned >1 times 69.78% overall alignment rate Time searching: 00:31:08 Overall time: 00:31:08 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] 3118205 / 15671053 = 0.1990 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 12:36:43: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX10386207/SRX10386207.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX10386207/SRX10386207.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX10386207/SRX10386207.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX10386207/SRX10386207.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 12:36:43: #1 read tag files... INFO @ Sat, 11 Dec 2021 12:36:43: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 12:36:48: 1000000 INFO @ Sat, 11 Dec 2021 12:36:52: 2000000 INFO @ Sat, 11 Dec 2021 12:36:57: 3000000 INFO @ Sat, 11 Dec 2021 12:37:01: 4000000 INFO @ Sat, 11 Dec 2021 12:37:05: 5000000 INFO @ Sat, 11 Dec 2021 12:37:10: 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 12:37:13: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX10386207/SRX10386207.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX10386207/SRX10386207.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX10386207/SRX10386207.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX10386207/SRX10386207.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 12:37:13: #1 read tag files... INFO @ Sat, 11 Dec 2021 12:37:13: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 12:37:14: 7000000 INFO @ Sat, 11 Dec 2021 12:37:17: 1000000 INFO @ Sat, 11 Dec 2021 12:37:19: 8000000 INFO @ Sat, 11 Dec 2021 12:37:22: 2000000 INFO @ Sat, 11 Dec 2021 12:37:23: 9000000 INFO @ Sat, 11 Dec 2021 12:37:26: 3000000 INFO @ Sat, 11 Dec 2021 12:37:28: 10000000 INFO @ Sat, 11 Dec 2021 12:37:31: 4000000 INFO @ Sat, 11 Dec 2021 12:37:32: 11000000 INFO @ Sat, 11 Dec 2021 12:37:35: 5000000 INFO @ Sat, 11 Dec 2021 12:37:37: 12000000 INFO @ Sat, 11 Dec 2021 12:37:40: 6000000 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 12:37:42: 13000000 INFO @ Sat, 11 Dec 2021 12:37:43: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX10386207/SRX10386207.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX10386207/SRX10386207.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX10386207/SRX10386207.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX10386207/SRX10386207.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 12:37:43: #1 read tag files... INFO @ Sat, 11 Dec 2021 12:37:43: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 12:37:44: 7000000 INFO @ Sat, 11 Dec 2021 12:37:46: 14000000 INFO @ Sat, 11 Dec 2021 12:37:47: 1000000 INFO @ Sat, 11 Dec 2021 12:37:49: 8000000 INFO @ Sat, 11 Dec 2021 12:37:51: 15000000 INFO @ Sat, 11 Dec 2021 12:37:52: 2000000 INFO @ Sat, 11 Dec 2021 12:37:53: 9000000 INFO @ Sat, 11 Dec 2021 12:37:55: 16000000 INFO @ Sat, 11 Dec 2021 12:37:56: 3000000 INFO @ Sat, 11 Dec 2021 12:37:58: 10000000 INFO @ Sat, 11 Dec 2021 12:38:00: 17000000 INFO @ Sat, 11 Dec 2021 12:38:01: 4000000 INFO @ Sat, 11 Dec 2021 12:38:02: 11000000 INFO @ Sat, 11 Dec 2021 12:38:04: 18000000 INFO @ Sat, 11 Dec 2021 12:38:05: 5000000 INFO @ Sat, 11 Dec 2021 12:38:07: 12000000 INFO @ Sat, 11 Dec 2021 12:38:09: 19000000 INFO @ Sat, 11 Dec 2021 12:38:10: 6000000 INFO @ Sat, 11 Dec 2021 12:38:11: 13000000 INFO @ Sat, 11 Dec 2021 12:38:13: 20000000 INFO @ Sat, 11 Dec 2021 12:38:14: 7000000 INFO @ Sat, 11 Dec 2021 12:38:16: 14000000 INFO @ Sat, 11 Dec 2021 12:38:18: 21000000 INFO @ Sat, 11 Dec 2021 12:38:19: 8000000 INFO @ Sat, 11 Dec 2021 12:38:20: 15000000 INFO @ Sat, 11 Dec 2021 12:38:22: 22000000 INFO @ Sat, 11 Dec 2021 12:38:23: 9000000 INFO @ Sat, 11 Dec 2021 12:38:25: 16000000 INFO @ Sat, 11 Dec 2021 12:38:27: 23000000 INFO @ Sat, 11 Dec 2021 12:38:28: 10000000 INFO @ Sat, 11 Dec 2021 12:38:29: 17000000 INFO @ Sat, 11 Dec 2021 12:38:31: 24000000 INFO @ Sat, 11 Dec 2021 12:38:32: 11000000 INFO @ Sat, 11 Dec 2021 12:38:34: 18000000 INFO @ Sat, 11 Dec 2021 12:38:36: 25000000 INFO @ Sat, 11 Dec 2021 12:38:37: 12000000 INFO @ Sat, 11 Dec 2021 12:38:38: 19000000 INFO @ Sat, 11 Dec 2021 12:38:40: 26000000 INFO @ Sat, 11 Dec 2021 12:38:41: 13000000 INFO @ Sat, 11 Dec 2021 12:38:43: #1 tag size is determined as 50 bps INFO @ Sat, 11 Dec 2021 12:38:43: #1 tag size = 50 INFO @ Sat, 11 Dec 2021 12:38:43: #1 total tags in treatment: 12006601 INFO @ Sat, 11 Dec 2021 12:38:43: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 12:38:43: #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 12:38:43: 20000000 INFO @ Sat, 11 Dec 2021 12:38:43: #1 tags after filtering in treatment: 10235847 INFO @ Sat, 11 Dec 2021 12:38:43: #1 Redundant rate of treatment: 0.15 INFO @ Sat, 11 Dec 2021 12:38:43: #1 finished! INFO @ Sat, 11 Dec 2021 12:38:43: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 12:38:43: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 12:38:43: #2 number of paired peaks: 265 WARNING @ Sat, 11 Dec 2021 12:38:43: Fewer paired peaks (265) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 265 pairs to build model! INFO @ Sat, 11 Dec 2021 12:38:43: start model_add_line... INFO @ Sat, 11 Dec 2021 12:38:43: start X-correlation... INFO @ Sat, 11 Dec 2021 12:38:43: end of X-cor INFO @ Sat, 11 Dec 2021 12:38:43: #2 finished! INFO @ Sat, 11 Dec 2021 12:38:43: #2 predicted fragment length is 101 bps INFO @ Sat, 11 Dec 2021 12:38:43: #2 alternative fragment length(s) may be 101 bps INFO @ Sat, 11 Dec 2021 12:38:43: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX10386207/SRX10386207.05_model.r INFO @ Sat, 11 Dec 2021 12:38:44: #3 Call peaks... INFO @ Sat, 11 Dec 2021 12:38:44: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Dec 2021 12:38:46: 14000000 INFO @ Sat, 11 Dec 2021 12:38:47: 21000000 INFO @ Sat, 11 Dec 2021 12:38:50: 15000000 INFO @ Sat, 11 Dec 2021 12:38:52: 22000000 INFO @ Sat, 11 Dec 2021 12:38:55: 16000000 INFO @ Sat, 11 Dec 2021 12:38:56: 23000000 INFO @ Sat, 11 Dec 2021 12:38:59: 17000000 INFO @ Sat, 11 Dec 2021 12:39:00: 24000000 INFO @ Sat, 11 Dec 2021 12:39:03: #3 Call peaks for each chromosome... INFO @ Sat, 11 Dec 2021 12:39:04: 18000000 INFO @ Sat, 11 Dec 2021 12:39:05: 25000000 INFO @ Sat, 11 Dec 2021 12:39:08: 19000000 INFO @ Sat, 11 Dec 2021 12:39:09: 26000000 INFO @ Sat, 11 Dec 2021 12:39:12: #1 tag size is determined as 50 bps INFO @ Sat, 11 Dec 2021 12:39:12: #1 tag size = 50 INFO @ Sat, 11 Dec 2021 12:39:12: #1 total tags in treatment: 12006601 INFO @ Sat, 11 Dec 2021 12:39:12: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 12:39:12: #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 12:39:12: #1 tags after filtering in treatment: 10235847 INFO @ Sat, 11 Dec 2021 12:39:12: #1 Redundant rate of treatment: 0.15 INFO @ Sat, 11 Dec 2021 12:39:12: #1 finished! INFO @ Sat, 11 Dec 2021 12:39:12: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 12:39:12: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 12:39:13: 20000000 INFO @ Sat, 11 Dec 2021 12:39:13: #2 number of paired peaks: 265 WARNING @ Sat, 11 Dec 2021 12:39:13: Fewer paired peaks (265) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 265 pairs to build model! INFO @ Sat, 11 Dec 2021 12:39:13: start model_add_line... INFO @ Sat, 11 Dec 2021 12:39:13: start X-correlation... INFO @ Sat, 11 Dec 2021 12:39:13: end of X-cor INFO @ Sat, 11 Dec 2021 12:39:13: #2 finished! INFO @ Sat, 11 Dec 2021 12:39:13: #2 predicted fragment length is 101 bps INFO @ Sat, 11 Dec 2021 12:39:13: #2 alternative fragment length(s) may be 101 bps INFO @ Sat, 11 Dec 2021 12:39:13: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX10386207/SRX10386207.10_model.r INFO @ Sat, 11 Dec 2021 12:39:13: #3 Call peaks... INFO @ Sat, 11 Dec 2021 12:39:13: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Dec 2021 12:39:13: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX10386207/SRX10386207.05_peaks.xls INFO @ Sat, 11 Dec 2021 12:39:13: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX10386207/SRX10386207.05_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 12:39:13: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX10386207/SRX10386207.05_summits.bed INFO @ Sat, 11 Dec 2021 12:39:13: Done! pass1 - making usageList (13 chroms): 1 millis pass2 - checking and writing primary data (1544 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Sat, 11 Dec 2021 12:39:17: 21000000 INFO @ Sat, 11 Dec 2021 12:39:21: 22000000 INFO @ Sat, 11 Dec 2021 12:39:25: 23000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 11 Dec 2021 12:39:30: 24000000 INFO @ Sat, 11 Dec 2021 12:39:33: #3 Call peaks for each chromosome... INFO @ Sat, 11 Dec 2021 12:39:34: 25000000 INFO @ Sat, 11 Dec 2021 12:39:38: 26000000 INFO @ Sat, 11 Dec 2021 12:39:41: #1 tag size is determined as 50 bps INFO @ Sat, 11 Dec 2021 12:39:41: #1 tag size = 50 INFO @ Sat, 11 Dec 2021 12:39:41: #1 total tags in treatment: 12006601 INFO @ Sat, 11 Dec 2021 12:39:41: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 12:39:41: #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 12:39:41: #1 tags after filtering in treatment: 10235847 INFO @ Sat, 11 Dec 2021 12:39:41: #1 Redundant rate of treatment: 0.15 INFO @ Sat, 11 Dec 2021 12:39:41: #1 finished! INFO @ Sat, 11 Dec 2021 12:39:41: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 12:39:41: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 12:39:42: #2 number of paired peaks: 265 WARNING @ Sat, 11 Dec 2021 12:39:42: Fewer paired peaks (265) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 265 pairs to build model! INFO @ Sat, 11 Dec 2021 12:39:42: start model_add_line... INFO @ Sat, 11 Dec 2021 12:39:42: start X-correlation... INFO @ Sat, 11 Dec 2021 12:39:42: end of X-cor INFO @ Sat, 11 Dec 2021 12:39:42: #2 finished! INFO @ Sat, 11 Dec 2021 12:39:42: #2 predicted fragment length is 101 bps INFO @ Sat, 11 Dec 2021 12:39:42: #2 alternative fragment length(s) may be 101 bps INFO @ Sat, 11 Dec 2021 12:39:42: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX10386207/SRX10386207.20_model.r INFO @ Sat, 11 Dec 2021 12:39:42: #3 Call peaks... INFO @ Sat, 11 Dec 2021 12:39:42: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Dec 2021 12:39:42: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX10386207/SRX10386207.10_peaks.xls INFO @ Sat, 11 Dec 2021 12:39:42: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX10386207/SRX10386207.10_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 12:39:42: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX10386207/SRX10386207.10_summits.bed INFO @ Sat, 11 Dec 2021 12:39:42: Done! pass1 - making usageList (13 chroms): 1 millis pass2 - checking and writing primary data (1008 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Sat, 11 Dec 2021 12:40:02: #3 Call peaks for each chromosome... INFO @ Sat, 11 Dec 2021 12:40:11: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX10386207/SRX10386207.20_peaks.xls INFO @ Sat, 11 Dec 2021 12:40:11: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX10386207/SRX10386207.20_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 12:40:11: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX10386207/SRX10386207.20_summits.bed INFO @ Sat, 11 Dec 2021 12:40:11: Done! BigWig に変換しました。 pass1 - making usageList (9 chroms): 0 millis pass2 - checking and writing primary data (652 records, 4 fields): 2 millis CompletedMACS2peakCalling