Job ID = 14171404 SRX = SRX9711629 Genome = dm3 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... Read 17509118 spots for SRR13282244/SRR13282244.sra Written 17509118 spots for SRR13282244/SRR13282244.sra fastq に変換しました。 bowtie でマッピング中... Your job 14172033 ("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: 00:35:31 17509118 reads; of these: 17509118 (100.00%) were paired; of these: 2345659 (13.40%) aligned concordantly 0 times 11718217 (66.93%) aligned concordantly exactly 1 time 3445242 (19.68%) aligned concordantly >1 times ---- 2345659 pairs aligned concordantly 0 times; of these: 1154369 (49.21%) aligned discordantly 1 time ---- 1191290 pairs aligned 0 times concordantly or discordantly; of these: 2382580 mates make up the pairs; of these: 1165917 (48.94%) aligned 0 times 482917 (20.27%) aligned exactly 1 time 733746 (30.80%) aligned >1 times 96.67% overall alignment rate Time searching: 00:35:31 Overall time: 00:35:31 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] 941214 / 16290591 = 0.0578 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 12:20:40: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX9711629/SRX9711629.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX9711629/SRX9711629.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX9711629/SRX9711629.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX9711629/SRX9711629.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 12:20:40: #1 read tag files... INFO @ Sat, 11 Dec 2021 12:20:40: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 12:20:46: 1000000 INFO @ Sat, 11 Dec 2021 12:20:52: 2000000 INFO @ Sat, 11 Dec 2021 12:20:58: 3000000 INFO @ Sat, 11 Dec 2021 12:21:04: 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 @ Sat, 11 Dec 2021 12:21:10: 5000000 INFO @ Sat, 11 Dec 2021 12:21:10: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX9711629/SRX9711629.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX9711629/SRX9711629.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX9711629/SRX9711629.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX9711629/SRX9711629.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 12:21:10: #1 read tag files... INFO @ Sat, 11 Dec 2021 12:21:10: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 12:21:17: 6000000 INFO @ Sat, 11 Dec 2021 12:21:17: 1000000 INFO @ Sat, 11 Dec 2021 12:21:23: 7000000 INFO @ Sat, 11 Dec 2021 12:21:23: 2000000 INFO @ Sat, 11 Dec 2021 12:21:30: 8000000 INFO @ Sat, 11 Dec 2021 12:21:30: 3000000 INFO @ Sat, 11 Dec 2021 12:21:37: 9000000 INFO @ Sat, 11 Dec 2021 12:21:37: 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 12:21:40: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX9711629/SRX9711629.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX9711629/SRX9711629.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX9711629/SRX9711629.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX9711629/SRX9711629.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 12:21:40: #1 read tag files... INFO @ Sat, 11 Dec 2021 12:21:40: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 12:21:43: 10000000 INFO @ Sat, 11 Dec 2021 12:21:44: 5000000 INFO @ Sat, 11 Dec 2021 12:21:47: 1000000 INFO @ Sat, 11 Dec 2021 12:21:50: 11000000 INFO @ Sat, 11 Dec 2021 12:21:50: 6000000 INFO @ Sat, 11 Dec 2021 12:21:54: 2000000 INFO @ Sat, 11 Dec 2021 12:21:57: 12000000 INFO @ Sat, 11 Dec 2021 12:21:57: 7000000 INFO @ Sat, 11 Dec 2021 12:22:01: 3000000 INFO @ Sat, 11 Dec 2021 12:22:04: 13000000 INFO @ Sat, 11 Dec 2021 12:22:04: 8000000 INFO @ Sat, 11 Dec 2021 12:22:08: 4000000 INFO @ Sat, 11 Dec 2021 12:22:11: 14000000 INFO @ Sat, 11 Dec 2021 12:22:11: 9000000 INFO @ Sat, 11 Dec 2021 12:22:14: 5000000 INFO @ Sat, 11 Dec 2021 12:22:18: 15000000 INFO @ Sat, 11 Dec 2021 12:22:18: 10000000 INFO @ Sat, 11 Dec 2021 12:22:21: 6000000 INFO @ Sat, 11 Dec 2021 12:22:24: 16000000 INFO @ Sat, 11 Dec 2021 12:22:25: 11000000 INFO @ Sat, 11 Dec 2021 12:22:28: 7000000 INFO @ Sat, 11 Dec 2021 12:22:31: 17000000 INFO @ Sat, 11 Dec 2021 12:22:32: 12000000 INFO @ Sat, 11 Dec 2021 12:22:35: 8000000 INFO @ Sat, 11 Dec 2021 12:22:38: 18000000 INFO @ Sat, 11 Dec 2021 12:22:39: 13000000 INFO @ Sat, 11 Dec 2021 12:22:42: 9000000 INFO @ Sat, 11 Dec 2021 12:22:45: 19000000 INFO @ Sat, 11 Dec 2021 12:22:46: 14000000 INFO @ Sat, 11 Dec 2021 12:22:49: 10000000 INFO @ Sat, 11 Dec 2021 12:22:52: 20000000 INFO @ Sat, 11 Dec 2021 12:22:52: 15000000 INFO @ Sat, 11 Dec 2021 12:22:55: 11000000 INFO @ Sat, 11 Dec 2021 12:22:59: 21000000 INFO @ Sat, 11 Dec 2021 12:22:59: 16000000 INFO @ Sat, 11 Dec 2021 12:23:02: 12000000 INFO @ Sat, 11 Dec 2021 12:23:05: 22000000 INFO @ Sat, 11 Dec 2021 12:23:06: 17000000 INFO @ Sat, 11 Dec 2021 12:23:09: 13000000 INFO @ Sat, 11 Dec 2021 12:23:12: 23000000 INFO @ Sat, 11 Dec 2021 12:23:13: 18000000 INFO @ Sat, 11 Dec 2021 12:23:16: 14000000 INFO @ Sat, 11 Dec 2021 12:23:19: 24000000 INFO @ Sat, 11 Dec 2021 12:23:20: 19000000 INFO @ Sat, 11 Dec 2021 12:23:23: 15000000 INFO @ Sat, 11 Dec 2021 12:23:26: 25000000 INFO @ Sat, 11 Dec 2021 12:23:27: 20000000 INFO @ Sat, 11 Dec 2021 12:23:30: 16000000 INFO @ Sat, 11 Dec 2021 12:23:33: 26000000 INFO @ Sat, 11 Dec 2021 12:23:34: 21000000 INFO @ Sat, 11 Dec 2021 12:23:36: 17000000 INFO @ Sat, 11 Dec 2021 12:23:40: 27000000 INFO @ Sat, 11 Dec 2021 12:23:40: 22000000 INFO @ Sat, 11 Dec 2021 12:23:43: 18000000 INFO @ Sat, 11 Dec 2021 12:23:46: 28000000 INFO @ Sat, 11 Dec 2021 12:23:47: 23000000 INFO @ Sat, 11 Dec 2021 12:23:50: 19000000 INFO @ Sat, 11 Dec 2021 12:23:53: 29000000 INFO @ Sat, 11 Dec 2021 12:23:54: 24000000 INFO @ Sat, 11 Dec 2021 12:23:57: 20000000 INFO @ Sat, 11 Dec 2021 12:24:00: 30000000 INFO @ Sat, 11 Dec 2021 12:24:01: 25000000 INFO @ Sat, 11 Dec 2021 12:24:04: 21000000 INFO @ Sat, 11 Dec 2021 12:24:07: 31000000 INFO @ Sat, 11 Dec 2021 12:24:08: 26000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 11 Dec 2021 12:24:11: 22000000 INFO @ Sat, 11 Dec 2021 12:24:14: #1 tag size is determined as 101 bps INFO @ Sat, 11 Dec 2021 12:24:14: #1 tag size = 101 INFO @ Sat, 11 Dec 2021 12:24:14: #1 total tags in treatment: 14275818 INFO @ Sat, 11 Dec 2021 12:24:14: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 12:24:14: #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 12:24:14: #1 tags after filtering in treatment: 13077678 INFO @ Sat, 11 Dec 2021 12:24:14: #1 Redundant rate of treatment: 0.08 INFO @ Sat, 11 Dec 2021 12:24:14: #1 finished! INFO @ Sat, 11 Dec 2021 12:24:14: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 12:24:14: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 12:24:15: 27000000 INFO @ Sat, 11 Dec 2021 12:24:15: #2 number of paired peaks: 104 WARNING @ Sat, 11 Dec 2021 12:24:15: Fewer paired peaks (104) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 104 pairs to build model! INFO @ Sat, 11 Dec 2021 12:24:15: start model_add_line... INFO @ Sat, 11 Dec 2021 12:24:15: start X-correlation... INFO @ Sat, 11 Dec 2021 12:24:15: end of X-cor INFO @ Sat, 11 Dec 2021 12:24:15: #2 finished! INFO @ Sat, 11 Dec 2021 12:24:15: #2 predicted fragment length is 225 bps INFO @ Sat, 11 Dec 2021 12:24:15: #2 alternative fragment length(s) may be 225 bps INFO @ Sat, 11 Dec 2021 12:24:15: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX9711629/SRX9711629.05_model.r INFO @ Sat, 11 Dec 2021 12:24:15: #3 Call peaks... INFO @ Sat, 11 Dec 2021 12:24:15: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Dec 2021 12:24:18: 23000000 INFO @ Sat, 11 Dec 2021 12:24:22: 28000000 INFO @ Sat, 11 Dec 2021 12:24:25: 24000000 INFO @ Sat, 11 Dec 2021 12:24:29: 29000000 INFO @ Sat, 11 Dec 2021 12:24:32: 25000000 INFO @ Sat, 11 Dec 2021 12:24:36: 30000000 INFO @ Sat, 11 Dec 2021 12:24:39: 26000000 INFO @ Sat, 11 Dec 2021 12:24:42: #3 Call peaks for each chromosome... INFO @ Sat, 11 Dec 2021 12:24:43: 31000000 INFO @ Sat, 11 Dec 2021 12:24:46: 27000000 INFO @ Sat, 11 Dec 2021 12:24:50: #1 tag size is determined as 101 bps INFO @ Sat, 11 Dec 2021 12:24:50: #1 tag size = 101 INFO @ Sat, 11 Dec 2021 12:24:50: #1 total tags in treatment: 14275818 INFO @ Sat, 11 Dec 2021 12:24:50: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 12:24:50: #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 12:24:50: #1 tags after filtering in treatment: 13077678 INFO @ Sat, 11 Dec 2021 12:24:50: #1 Redundant rate of treatment: 0.08 INFO @ Sat, 11 Dec 2021 12:24:50: #1 finished! INFO @ Sat, 11 Dec 2021 12:24:50: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 12:24:50: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 12:24:51: #2 number of paired peaks: 104 WARNING @ Sat, 11 Dec 2021 12:24:51: Fewer paired peaks (104) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 104 pairs to build model! INFO @ Sat, 11 Dec 2021 12:24:51: start model_add_line... INFO @ Sat, 11 Dec 2021 12:24:51: start X-correlation... INFO @ Sat, 11 Dec 2021 12:24:51: end of X-cor INFO @ Sat, 11 Dec 2021 12:24:51: #2 finished! INFO @ Sat, 11 Dec 2021 12:24:51: #2 predicted fragment length is 225 bps INFO @ Sat, 11 Dec 2021 12:24:51: #2 alternative fragment length(s) may be 225 bps INFO @ Sat, 11 Dec 2021 12:24:51: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX9711629/SRX9711629.10_model.r INFO @ Sat, 11 Dec 2021 12:24:51: #3 Call peaks... INFO @ Sat, 11 Dec 2021 12:24:51: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Dec 2021 12:24:53: 28000000 INFO @ Sat, 11 Dec 2021 12:24:55: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX9711629/SRX9711629.05_peaks.xls INFO @ Sat, 11 Dec 2021 12:24:55: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX9711629/SRX9711629.05_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 12:24:55: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX9711629/SRX9711629.05_summits.bed INFO @ Sat, 11 Dec 2021 12:24:55: Done! pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (831 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Sat, 11 Dec 2021 12:24:59: 29000000 INFO @ Sat, 11 Dec 2021 12:25:06: 30000000 BigWig に変換しました。 INFO @ Sat, 11 Dec 2021 12:25:12: 31000000 INFO @ Sat, 11 Dec 2021 12:25:18: #3 Call peaks for each chromosome... INFO @ Sat, 11 Dec 2021 12:25:18: #1 tag size is determined as 101 bps INFO @ Sat, 11 Dec 2021 12:25:18: #1 tag size = 101 INFO @ Sat, 11 Dec 2021 12:25:18: #1 total tags in treatment: 14275818 INFO @ Sat, 11 Dec 2021 12:25:18: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 12:25:18: #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 12:25:18: #1 tags after filtering in treatment: 13077678 INFO @ Sat, 11 Dec 2021 12:25:18: #1 Redundant rate of treatment: 0.08 INFO @ Sat, 11 Dec 2021 12:25:18: #1 finished! INFO @ Sat, 11 Dec 2021 12:25:18: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 12:25:18: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 12:25:19: #2 number of paired peaks: 104 WARNING @ Sat, 11 Dec 2021 12:25:19: Fewer paired peaks (104) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 104 pairs to build model! INFO @ Sat, 11 Dec 2021 12:25:19: start model_add_line... INFO @ Sat, 11 Dec 2021 12:25:19: start X-correlation... INFO @ Sat, 11 Dec 2021 12:25:19: end of X-cor INFO @ Sat, 11 Dec 2021 12:25:19: #2 finished! INFO @ Sat, 11 Dec 2021 12:25:19: #2 predicted fragment length is 225 bps INFO @ Sat, 11 Dec 2021 12:25:19: #2 alternative fragment length(s) may be 225 bps INFO @ Sat, 11 Dec 2021 12:25:19: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX9711629/SRX9711629.20_model.r INFO @ Sat, 11 Dec 2021 12:25:19: #3 Call peaks... INFO @ Sat, 11 Dec 2021 12:25:19: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Dec 2021 12:25:31: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX9711629/SRX9711629.10_peaks.xls INFO @ Sat, 11 Dec 2021 12:25:31: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX9711629/SRX9711629.10_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 12:25:31: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX9711629/SRX9711629.10_summits.bed INFO @ Sat, 11 Dec 2021 12:25:31: Done! pass1 - making usageList (13 chroms): 1 millis pass2 - checking and writing primary data (354 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Sat, 11 Dec 2021 12:25:45: #3 Call peaks for each chromosome... INFO @ Sat, 11 Dec 2021 12:25:59: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX9711629/SRX9711629.20_peaks.xls INFO @ Sat, 11 Dec 2021 12:25:59: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX9711629/SRX9711629.20_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 12:25:59: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX9711629/SRX9711629.20_summits.bed INFO @ Sat, 11 Dec 2021 12:25:59: Done! pass1 - making usageList (12 chroms): 1 millis pass2 - checking and writing primary data (137 records, 4 fields): 1 millis CompletedMACS2peakCalling