Job ID = 14171975 SRX = SRX7889135 Genome = dm3 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... Read 25355930 spots for SRR11283125/SRR11283125.sra Written 25355930 spots for SRR11283125/SRR11283125.sra fastq に変換しました。 bowtie でマッピング中... Your job 14172700 ("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: 01:17:35 25355930 reads; of these: 25355930 (100.00%) were paired; of these: 7878119 (31.07%) aligned concordantly 0 times 12647780 (49.88%) aligned concordantly exactly 1 time 4830031 (19.05%) aligned concordantly >1 times ---- 7878119 pairs aligned concordantly 0 times; of these: 1602205 (20.34%) aligned discordantly 1 time ---- 6275914 pairs aligned 0 times concordantly or discordantly; of these: 12551828 mates make up the pairs; of these: 9751679 (77.69%) aligned 0 times 1398221 (11.14%) aligned exactly 1 time 1401928 (11.17%) aligned >1 times 80.77% overall alignment rate Time searching: 01:17:35 Overall time: 01:17:35 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 32 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] 3075270 / 18171152 = 0.1692 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 15:18:44: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX7889135/SRX7889135.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX7889135/SRX7889135.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX7889135/SRX7889135.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX7889135/SRX7889135.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 15:18:44: #1 read tag files... INFO @ Sat, 11 Dec 2021 15:18:44: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 15:18:53: 1000000 INFO @ Sat, 11 Dec 2021 15:19:02: 2000000 INFO @ Sat, 11 Dec 2021 15:19:10: 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 @ Sat, 11 Dec 2021 15:19:14: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX7889135/SRX7889135.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX7889135/SRX7889135.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX7889135/SRX7889135.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX7889135/SRX7889135.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 15:19:14: #1 read tag files... INFO @ Sat, 11 Dec 2021 15:19:14: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 15:19:19: 4000000 INFO @ Sat, 11 Dec 2021 15:19:24: 1000000 INFO @ Sat, 11 Dec 2021 15:19:29: 5000000 INFO @ Sat, 11 Dec 2021 15:19:34: 2000000 INFO @ Sat, 11 Dec 2021 15:19:38: 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 15:19:43: 3000000 INFO @ Sat, 11 Dec 2021 15:19:44: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX7889135/SRX7889135.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX7889135/SRX7889135.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX7889135/SRX7889135.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX7889135/SRX7889135.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 15:19:44: #1 read tag files... INFO @ Sat, 11 Dec 2021 15:19:44: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 15:19:48: 7000000 INFO @ Sat, 11 Dec 2021 15:19:54: 4000000 INFO @ Sat, 11 Dec 2021 15:19:56: 1000000 INFO @ Sat, 11 Dec 2021 15:19:59: 8000000 INFO @ Sat, 11 Dec 2021 15:20:05: 5000000 INFO @ Sat, 11 Dec 2021 15:20:07: 2000000 INFO @ Sat, 11 Dec 2021 15:20:10: 9000000 INFO @ Sat, 11 Dec 2021 15:20:16: 6000000 INFO @ Sat, 11 Dec 2021 15:20:18: 3000000 INFO @ Sat, 11 Dec 2021 15:20:20: 10000000 INFO @ Sat, 11 Dec 2021 15:20:26: 7000000 INFO @ Sat, 11 Dec 2021 15:20:28: 4000000 INFO @ Sat, 11 Dec 2021 15:20:31: 11000000 INFO @ Sat, 11 Dec 2021 15:20:37: 8000000 INFO @ Sat, 11 Dec 2021 15:20:39: 5000000 INFO @ Sat, 11 Dec 2021 15:20:41: 12000000 INFO @ Sat, 11 Dec 2021 15:20:47: 9000000 INFO @ Sat, 11 Dec 2021 15:20:49: 6000000 INFO @ Sat, 11 Dec 2021 15:20:51: 13000000 INFO @ Sat, 11 Dec 2021 15:20:57: 10000000 INFO @ Sat, 11 Dec 2021 15:20:59: 7000000 INFO @ Sat, 11 Dec 2021 15:21:02: 14000000 INFO @ Sat, 11 Dec 2021 15:21:07: 11000000 INFO @ Sat, 11 Dec 2021 15:21:10: 8000000 INFO @ Sat, 11 Dec 2021 15:21:12: 15000000 INFO @ Sat, 11 Dec 2021 15:21:17: 12000000 INFO @ Sat, 11 Dec 2021 15:21:20: 9000000 INFO @ Sat, 11 Dec 2021 15:21:22: 16000000 INFO @ Sat, 11 Dec 2021 15:21:27: 13000000 INFO @ Sat, 11 Dec 2021 15:21:30: 10000000 INFO @ Sat, 11 Dec 2021 15:21:32: 17000000 INFO @ Sat, 11 Dec 2021 15:21:37: 14000000 INFO @ Sat, 11 Dec 2021 15:21:40: 11000000 INFO @ Sat, 11 Dec 2021 15:21:42: 18000000 INFO @ Sat, 11 Dec 2021 15:21:47: 15000000 INFO @ Sat, 11 Dec 2021 15:21:51: 12000000 INFO @ Sat, 11 Dec 2021 15:21:52: 19000000 INFO @ Sat, 11 Dec 2021 15:21:57: 16000000 INFO @ Sat, 11 Dec 2021 15:22:01: 13000000 INFO @ Sat, 11 Dec 2021 15:22:02: 20000000 INFO @ Sat, 11 Dec 2021 15:22:07: 17000000 INFO @ Sat, 11 Dec 2021 15:22:11: 14000000 INFO @ Sat, 11 Dec 2021 15:22:12: 21000000 INFO @ Sat, 11 Dec 2021 15:22:17: 18000000 INFO @ Sat, 11 Dec 2021 15:22:21: 15000000 INFO @ Sat, 11 Dec 2021 15:22:22: 22000000 INFO @ Sat, 11 Dec 2021 15:22:27: 19000000 INFO @ Sat, 11 Dec 2021 15:22:31: 16000000 INFO @ Sat, 11 Dec 2021 15:22:31: 23000000 INFO @ Sat, 11 Dec 2021 15:22:37: 20000000 INFO @ Sat, 11 Dec 2021 15:22:41: 17000000 INFO @ Sat, 11 Dec 2021 15:22:41: 24000000 INFO @ Sat, 11 Dec 2021 15:22:46: 21000000 INFO @ Sat, 11 Dec 2021 15:22:51: 18000000 INFO @ Sat, 11 Dec 2021 15:22:52: 25000000 INFO @ Sat, 11 Dec 2021 15:22:56: 22000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 11 Dec 2021 15:23:01: 19000000 INFO @ Sat, 11 Dec 2021 15:23:02: 26000000 INFO @ Sat, 11 Dec 2021 15:23:06: 23000000 INFO @ Sat, 11 Dec 2021 15:23:11: 20000000 INFO @ Sat, 11 Dec 2021 15:23:11: 27000000 INFO @ Sat, 11 Dec 2021 15:23:16: 24000000 INFO @ Sat, 11 Dec 2021 15:23:21: 21000000 INFO @ Sat, 11 Dec 2021 15:23:21: 28000000 INFO @ Sat, 11 Dec 2021 15:23:26: 25000000 INFO @ Sat, 11 Dec 2021 15:23:31: 29000000 INFO @ Sat, 11 Dec 2021 15:23:31: 22000000 INFO @ Sat, 11 Dec 2021 15:23:37: 26000000 INFO @ Sat, 11 Dec 2021 15:23:41: 30000000 INFO @ Sat, 11 Dec 2021 15:23:42: 23000000 INFO @ Sat, 11 Dec 2021 15:23:47: 27000000 INFO @ Sat, 11 Dec 2021 15:23:51: 31000000 INFO @ Sat, 11 Dec 2021 15:23:52: 24000000 INFO @ Sat, 11 Dec 2021 15:23:58: 28000000 INFO @ Sat, 11 Dec 2021 15:24:01: 32000000 BigWig に変換しました。 INFO @ Sat, 11 Dec 2021 15:24:03: 25000000 INFO @ Sat, 11 Dec 2021 15:24:08: 29000000 INFO @ Sat, 11 Dec 2021 15:24:12: 33000000 INFO @ Sat, 11 Dec 2021 15:24:13: 26000000 INFO @ Sat, 11 Dec 2021 15:24:18: 30000000 INFO @ Sat, 11 Dec 2021 15:24:22: 34000000 INFO @ Sat, 11 Dec 2021 15:24:24: 27000000 INFO @ Sat, 11 Dec 2021 15:24:28: 31000000 INFO @ Sat, 11 Dec 2021 15:24:30: #1 tag size is determined as 122 bps INFO @ Sat, 11 Dec 2021 15:24:30: #1 tag size = 122 INFO @ Sat, 11 Dec 2021 15:24:30: #1 total tags in treatment: 14590089 INFO @ Sat, 11 Dec 2021 15:24:30: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 15:24:30: #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 15:24:30: #1 tags after filtering in treatment: 13343287 INFO @ Sat, 11 Dec 2021 15:24:30: #1 Redundant rate of treatment: 0.09 INFO @ Sat, 11 Dec 2021 15:24:30: #1 finished! INFO @ Sat, 11 Dec 2021 15:24:30: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 15:24:30: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 15:24:31: #2 number of paired peaks: 574 WARNING @ Sat, 11 Dec 2021 15:24:31: Fewer paired peaks (574) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 574 pairs to build model! INFO @ Sat, 11 Dec 2021 15:24:31: start model_add_line... INFO @ Sat, 11 Dec 2021 15:24:31: start X-correlation... INFO @ Sat, 11 Dec 2021 15:24:31: end of X-cor INFO @ Sat, 11 Dec 2021 15:24:31: #2 finished! INFO @ Sat, 11 Dec 2021 15:24:31: #2 predicted fragment length is 262 bps INFO @ Sat, 11 Dec 2021 15:24:31: #2 alternative fragment length(s) may be 262 bps INFO @ Sat, 11 Dec 2021 15:24:31: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX7889135/SRX7889135.05_model.r INFO @ Sat, 11 Dec 2021 15:24:31: #3 Call peaks... INFO @ Sat, 11 Dec 2021 15:24:31: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Dec 2021 15:24:34: 28000000 INFO @ Sat, 11 Dec 2021 15:24:38: 32000000 INFO @ Sat, 11 Dec 2021 15:24:44: 29000000 INFO @ Sat, 11 Dec 2021 15:24:48: 33000000 INFO @ Sat, 11 Dec 2021 15:24:53: 30000000 INFO @ Sat, 11 Dec 2021 15:24:58: 34000000 INFO @ Sat, 11 Dec 2021 15:24:59: #3 Call peaks for each chromosome... INFO @ Sat, 11 Dec 2021 15:25:03: 31000000 INFO @ Sat, 11 Dec 2021 15:25:06: #1 tag size is determined as 122 bps INFO @ Sat, 11 Dec 2021 15:25:06: #1 tag size = 122 INFO @ Sat, 11 Dec 2021 15:25:06: #1 total tags in treatment: 14590089 INFO @ Sat, 11 Dec 2021 15:25:06: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 15:25:06: #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 15:25:06: #1 tags after filtering in treatment: 13343287 INFO @ Sat, 11 Dec 2021 15:25:06: #1 Redundant rate of treatment: 0.09 INFO @ Sat, 11 Dec 2021 15:25:06: #1 finished! INFO @ Sat, 11 Dec 2021 15:25:06: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 15:25:06: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 15:25:07: #2 number of paired peaks: 574 WARNING @ Sat, 11 Dec 2021 15:25:07: Fewer paired peaks (574) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 574 pairs to build model! INFO @ Sat, 11 Dec 2021 15:25:07: start model_add_line... INFO @ Sat, 11 Dec 2021 15:25:07: start X-correlation... INFO @ Sat, 11 Dec 2021 15:25:07: end of X-cor INFO @ Sat, 11 Dec 2021 15:25:07: #2 finished! INFO @ Sat, 11 Dec 2021 15:25:07: #2 predicted fragment length is 262 bps INFO @ Sat, 11 Dec 2021 15:25:07: #2 alternative fragment length(s) may be 262 bps INFO @ Sat, 11 Dec 2021 15:25:07: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX7889135/SRX7889135.10_model.r INFO @ Sat, 11 Dec 2021 15:25:07: #3 Call peaks... INFO @ Sat, 11 Dec 2021 15:25:07: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Dec 2021 15:25:12: 32000000 INFO @ Sat, 11 Dec 2021 15:25:12: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX7889135/SRX7889135.05_peaks.xls INFO @ Sat, 11 Dec 2021 15:25:12: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX7889135/SRX7889135.05_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 15:25:12: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX7889135/SRX7889135.05_summits.bed INFO @ Sat, 11 Dec 2021 15:25:12: Done! pass1 - making usageList (15 chroms): 2 millis pass2 - checking and writing primary data (6122 records, 4 fields): 6 millis CompletedMACS2peakCalling INFO @ Sat, 11 Dec 2021 15:25:20: 33000000 INFO @ Sat, 11 Dec 2021 15:25:29: 34000000 INFO @ Sat, 11 Dec 2021 15:25:33: #3 Call peaks for each chromosome... INFO @ Sat, 11 Dec 2021 15:25:35: #1 tag size is determined as 122 bps INFO @ Sat, 11 Dec 2021 15:25:35: #1 tag size = 122 INFO @ Sat, 11 Dec 2021 15:25:35: #1 total tags in treatment: 14590089 INFO @ Sat, 11 Dec 2021 15:25:35: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 15:25:35: #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 15:25:36: #1 tags after filtering in treatment: 13343287 INFO @ Sat, 11 Dec 2021 15:25:36: #1 Redundant rate of treatment: 0.09 INFO @ Sat, 11 Dec 2021 15:25:36: #1 finished! INFO @ Sat, 11 Dec 2021 15:25:36: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 15:25:36: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 15:25:36: #2 number of paired peaks: 574 WARNING @ Sat, 11 Dec 2021 15:25:36: Fewer paired peaks (574) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 574 pairs to build model! INFO @ Sat, 11 Dec 2021 15:25:36: start model_add_line... INFO @ Sat, 11 Dec 2021 15:25:37: start X-correlation... INFO @ Sat, 11 Dec 2021 15:25:37: end of X-cor INFO @ Sat, 11 Dec 2021 15:25:37: #2 finished! INFO @ Sat, 11 Dec 2021 15:25:37: #2 predicted fragment length is 262 bps INFO @ Sat, 11 Dec 2021 15:25:37: #2 alternative fragment length(s) may be 262 bps INFO @ Sat, 11 Dec 2021 15:25:37: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX7889135/SRX7889135.20_model.r INFO @ Sat, 11 Dec 2021 15:25:37: #3 Call peaks... INFO @ Sat, 11 Dec 2021 15:25:37: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Dec 2021 15:25:47: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX7889135/SRX7889135.10_peaks.xls INFO @ Sat, 11 Dec 2021 15:25:47: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX7889135/SRX7889135.10_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 15:25:47: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX7889135/SRX7889135.10_summits.bed INFO @ Sat, 11 Dec 2021 15:25:47: Done! pass1 - making usageList (15 chroms): 2 millis pass2 - checking and writing primary data (3977 records, 4 fields): 5 millis CompletedMACS2peakCalling INFO @ Sat, 11 Dec 2021 15:26:04: #3 Call peaks for each chromosome... INFO @ Sat, 11 Dec 2021 15:26:18: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX7889135/SRX7889135.20_peaks.xls INFO @ Sat, 11 Dec 2021 15:26:18: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX7889135/SRX7889135.20_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 15:26:18: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX7889135/SRX7889135.20_summits.bed INFO @ Sat, 11 Dec 2021 15:26:18: Done! pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (2140 records, 4 fields): 4 millis CompletedMACS2peakCalling