Job ID = 14171406 SRX = SRX9986171 Genome = dm3 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... Read 20408544 spots for SRR13591525/SRR13591525.sra Written 20408544 spots for SRR13591525/SRR13591525.sra fastq に変換しました。 bowtie でマッピング中... Your job 14171999 ("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: 00:24:34 20408544 reads; of these: 20408544 (100.00%) were paired; of these: 3107650 (15.23%) aligned concordantly 0 times 14414214 (70.63%) aligned concordantly exactly 1 time 2886680 (14.14%) aligned concordantly >1 times ---- 3107650 pairs aligned concordantly 0 times; of these: 955529 (30.75%) aligned discordantly 1 time ---- 2152121 pairs aligned 0 times concordantly or discordantly; of these: 4304242 mates make up the pairs; of these: 2778358 (64.55%) aligned 0 times 827872 (19.23%) aligned exactly 1 time 698012 (16.22%) aligned >1 times 93.19% overall alignment rate Time searching: 00:24:34 Overall time: 00:24:34 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] 1373805 / 18182929 = 0.0756 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 12:08:32: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX9986171/SRX9986171.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX9986171/SRX9986171.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX9986171/SRX9986171.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX9986171/SRX9986171.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 12:08:32: #1 read tag files... INFO @ Sat, 11 Dec 2021 12:08:32: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 12:08:38: 1000000 INFO @ Sat, 11 Dec 2021 12:08:43: 2000000 INFO @ Sat, 11 Dec 2021 12:08:48: 3000000 INFO @ Sat, 11 Dec 2021 12:08:54: 4000000 INFO @ Sat, 11 Dec 2021 12:08:59: 5000000 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 12:09:02: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX9986171/SRX9986171.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX9986171/SRX9986171.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX9986171/SRX9986171.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX9986171/SRX9986171.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 12:09:02: #1 read tag files... INFO @ Sat, 11 Dec 2021 12:09:02: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 12:09:04: 6000000 INFO @ Sat, 11 Dec 2021 12:09:09: 1000000 INFO @ Sat, 11 Dec 2021 12:09:11: 7000000 INFO @ Sat, 11 Dec 2021 12:09:15: 2000000 INFO @ Sat, 11 Dec 2021 12:09:17: 8000000 INFO @ Sat, 11 Dec 2021 12:09:21: 3000000 INFO @ Sat, 11 Dec 2021 12:09:23: 9000000 INFO @ Sat, 11 Dec 2021 12:09:27: 4000000 INFO @ Sat, 11 Dec 2021 12:09:29: 10000000 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 12:09:32: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX9986171/SRX9986171.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX9986171/SRX9986171.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX9986171/SRX9986171.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX9986171/SRX9986171.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 12:09:32: #1 read tag files... INFO @ Sat, 11 Dec 2021 12:09:32: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 12:09:34: 5000000 INFO @ Sat, 11 Dec 2021 12:09:36: 11000000 INFO @ Sat, 11 Dec 2021 12:09:40: 1000000 INFO @ Sat, 11 Dec 2021 12:09:41: 6000000 INFO @ Sat, 11 Dec 2021 12:09:43: 12000000 INFO @ Sat, 11 Dec 2021 12:09:48: 2000000 INFO @ Sat, 11 Dec 2021 12:09:48: 7000000 INFO @ Sat, 11 Dec 2021 12:09:50: 13000000 INFO @ Sat, 11 Dec 2021 12:09:55: 8000000 INFO @ Sat, 11 Dec 2021 12:09:55: 3000000 INFO @ Sat, 11 Dec 2021 12:09:58: 14000000 INFO @ Sat, 11 Dec 2021 12:10:02: 9000000 INFO @ Sat, 11 Dec 2021 12:10:03: 4000000 INFO @ Sat, 11 Dec 2021 12:10:05: 15000000 INFO @ Sat, 11 Dec 2021 12:10:10: 10000000 INFO @ Sat, 11 Dec 2021 12:10:11: 5000000 INFO @ Sat, 11 Dec 2021 12:10:12: 16000000 INFO @ Sat, 11 Dec 2021 12:10:17: 11000000 INFO @ Sat, 11 Dec 2021 12:10:19: 6000000 INFO @ Sat, 11 Dec 2021 12:10:19: 17000000 INFO @ Sat, 11 Dec 2021 12:10:24: 12000000 INFO @ Sat, 11 Dec 2021 12:10:26: 7000000 INFO @ Sat, 11 Dec 2021 12:10:26: 18000000 INFO @ Sat, 11 Dec 2021 12:10:31: 13000000 INFO @ Sat, 11 Dec 2021 12:10:34: 19000000 INFO @ Sat, 11 Dec 2021 12:10:34: 8000000 INFO @ Sat, 11 Dec 2021 12:10:39: 14000000 INFO @ Sat, 11 Dec 2021 12:10:41: 20000000 INFO @ Sat, 11 Dec 2021 12:10:42: 9000000 INFO @ Sat, 11 Dec 2021 12:10:46: 15000000 INFO @ Sat, 11 Dec 2021 12:10:48: 21000000 INFO @ Sat, 11 Dec 2021 12:10:49: 10000000 INFO @ Sat, 11 Dec 2021 12:10:53: 16000000 INFO @ Sat, 11 Dec 2021 12:10:55: 22000000 INFO @ Sat, 11 Dec 2021 12:10:57: 11000000 INFO @ Sat, 11 Dec 2021 12:11:00: 17000000 INFO @ Sat, 11 Dec 2021 12:11:03: 23000000 INFO @ Sat, 11 Dec 2021 12:11:05: 12000000 INFO @ Sat, 11 Dec 2021 12:11:07: 18000000 INFO @ Sat, 11 Dec 2021 12:11:10: 24000000 INFO @ Sat, 11 Dec 2021 12:11:13: 13000000 INFO @ Sat, 11 Dec 2021 12:11:14: 19000000 INFO @ Sat, 11 Dec 2021 12:11:17: 25000000 INFO @ Sat, 11 Dec 2021 12:11:20: 14000000 INFO @ Sat, 11 Dec 2021 12:11:22: 20000000 INFO @ Sat, 11 Dec 2021 12:11:24: 26000000 INFO @ Sat, 11 Dec 2021 12:11:28: 15000000 INFO @ Sat, 11 Dec 2021 12:11:29: 21000000 INFO @ Sat, 11 Dec 2021 12:11:32: 27000000 INFO @ Sat, 11 Dec 2021 12:11:36: 16000000 INFO @ Sat, 11 Dec 2021 12:11:36: 22000000 INFO @ Sat, 11 Dec 2021 12:11:39: 28000000 INFO @ Sat, 11 Dec 2021 12:11:43: 23000000 INFO @ Sat, 11 Dec 2021 12:11:44: 17000000 INFO @ Sat, 11 Dec 2021 12:11:46: 29000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 11 Dec 2021 12:11:51: 24000000 INFO @ Sat, 11 Dec 2021 12:11:51: 18000000 INFO @ Sat, 11 Dec 2021 12:11:53: 30000000 INFO @ Sat, 11 Dec 2021 12:11:58: 25000000 INFO @ Sat, 11 Dec 2021 12:11:59: 19000000 INFO @ Sat, 11 Dec 2021 12:12:00: 31000000 INFO @ Sat, 11 Dec 2021 12:12:05: 26000000 INFO @ Sat, 11 Dec 2021 12:12:07: 20000000 INFO @ Sat, 11 Dec 2021 12:12:07: 32000000 INFO @ Sat, 11 Dec 2021 12:12:12: 27000000 INFO @ Sat, 11 Dec 2021 12:12:14: 33000000 INFO @ Sat, 11 Dec 2021 12:12:14: 21000000 INFO @ Sat, 11 Dec 2021 12:12:19: 28000000 INFO @ Sat, 11 Dec 2021 12:12:22: 34000000 INFO @ Sat, 11 Dec 2021 12:12:22: 22000000 INFO @ Sat, 11 Dec 2021 12:12:26: 29000000 INFO @ Sat, 11 Dec 2021 12:12:29: 35000000 INFO @ Sat, 11 Dec 2021 12:12:30: 23000000 INFO @ Sat, 11 Dec 2021 12:12:31: #1 tag size is determined as 50 bps INFO @ Sat, 11 Dec 2021 12:12:31: #1 tag size = 50 INFO @ Sat, 11 Dec 2021 12:12:31: #1 total tags in treatment: 15944768 INFO @ Sat, 11 Dec 2021 12:12:31: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 12:12:31: #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 12:12:31: #1 tags after filtering in treatment: 12489345 INFO @ Sat, 11 Dec 2021 12:12:31: #1 Redundant rate of treatment: 0.22 INFO @ Sat, 11 Dec 2021 12:12:31: #1 finished! INFO @ Sat, 11 Dec 2021 12:12:31: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 12:12:31: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 12:12:32: #2 number of paired peaks: 574 WARNING @ Sat, 11 Dec 2021 12:12:32: 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 12:12:32: start model_add_line... INFO @ Sat, 11 Dec 2021 12:12:32: start X-correlation... INFO @ Sat, 11 Dec 2021 12:12:32: end of X-cor INFO @ Sat, 11 Dec 2021 12:12:32: #2 finished! INFO @ Sat, 11 Dec 2021 12:12:32: #2 predicted fragment length is 275 bps INFO @ Sat, 11 Dec 2021 12:12:32: #2 alternative fragment length(s) may be 2,199,225,253,275,303,334 bps INFO @ Sat, 11 Dec 2021 12:12:32: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX9986171/SRX9986171.05_model.r INFO @ Sat, 11 Dec 2021 12:12:32: #3 Call peaks... INFO @ Sat, 11 Dec 2021 12:12:32: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Dec 2021 12:12:33: 30000000 INFO @ Sat, 11 Dec 2021 12:12:38: 24000000 INFO @ Sat, 11 Dec 2021 12:12:40: 31000000 BigWig に変換しました。 INFO @ Sat, 11 Dec 2021 12:12:45: 25000000 INFO @ Sat, 11 Dec 2021 12:12:47: 32000000 INFO @ Sat, 11 Dec 2021 12:12:53: 26000000 INFO @ Sat, 11 Dec 2021 12:12:54: 33000000 INFO @ Sat, 11 Dec 2021 12:12:59: #3 Call peaks for each chromosome... INFO @ Sat, 11 Dec 2021 12:13:01: 34000000 INFO @ Sat, 11 Dec 2021 12:13:01: 27000000 INFO @ Sat, 11 Dec 2021 12:13:07: 35000000 INFO @ Sat, 11 Dec 2021 12:13:08: 28000000 INFO @ Sat, 11 Dec 2021 12:13:09: #1 tag size is determined as 50 bps INFO @ Sat, 11 Dec 2021 12:13:09: #1 tag size = 50 INFO @ Sat, 11 Dec 2021 12:13:09: #1 total tags in treatment: 15944768 INFO @ Sat, 11 Dec 2021 12:13:09: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 12:13:09: #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 12:13:10: #1 tags after filtering in treatment: 12489345 INFO @ Sat, 11 Dec 2021 12:13:10: #1 Redundant rate of treatment: 0.22 INFO @ Sat, 11 Dec 2021 12:13:10: #1 finished! INFO @ Sat, 11 Dec 2021 12:13:10: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 12:13:10: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 12:13:11: #2 number of paired peaks: 574 WARNING @ Sat, 11 Dec 2021 12:13:11: 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 12:13:11: start model_add_line... INFO @ Sat, 11 Dec 2021 12:13:11: start X-correlation... INFO @ Sat, 11 Dec 2021 12:13:11: end of X-cor INFO @ Sat, 11 Dec 2021 12:13:11: #2 finished! INFO @ Sat, 11 Dec 2021 12:13:11: #2 predicted fragment length is 275 bps INFO @ Sat, 11 Dec 2021 12:13:11: #2 alternative fragment length(s) may be 2,199,225,253,275,303,334 bps INFO @ Sat, 11 Dec 2021 12:13:11: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX9986171/SRX9986171.10_model.r INFO @ Sat, 11 Dec 2021 12:13:11: #3 Call peaks... INFO @ Sat, 11 Dec 2021 12:13:11: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Dec 2021 12:13:11: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX9986171/SRX9986171.05_peaks.xls INFO @ Sat, 11 Dec 2021 12:13:11: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX9986171/SRX9986171.05_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 12:13:11: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX9986171/SRX9986171.05_summits.bed INFO @ Sat, 11 Dec 2021 12:13:11: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (1956 records, 4 fields): 4 millis CompletedMACS2peakCalling INFO @ Sat, 11 Dec 2021 12:13:15: 29000000 INFO @ Sat, 11 Dec 2021 12:13:22: 30000000 INFO @ Sat, 11 Dec 2021 12:13:29: 31000000 INFO @ Sat, 11 Dec 2021 12:13:36: 32000000 INFO @ Sat, 11 Dec 2021 12:13:38: #3 Call peaks for each chromosome... INFO @ Sat, 11 Dec 2021 12:13:42: 33000000 INFO @ Sat, 11 Dec 2021 12:13:49: 34000000 INFO @ Sat, 11 Dec 2021 12:13:50: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX9986171/SRX9986171.10_peaks.xls INFO @ Sat, 11 Dec 2021 12:13:50: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX9986171/SRX9986171.10_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 12:13:50: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX9986171/SRX9986171.10_summits.bed INFO @ Sat, 11 Dec 2021 12:13:50: Done! pass1 - making usageList (13 chroms): 1 millis pass2 - checking and writing primary data (899 records, 4 fields): 5 millis CompletedMACS2peakCalling INFO @ Sat, 11 Dec 2021 12:13:56: 35000000 INFO @ Sat, 11 Dec 2021 12:13:58: #1 tag size is determined as 50 bps INFO @ Sat, 11 Dec 2021 12:13:58: #1 tag size = 50 INFO @ Sat, 11 Dec 2021 12:13:58: #1 total tags in treatment: 15944768 INFO @ Sat, 11 Dec 2021 12:13:58: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 12:13:58: #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 12:13:58: #1 tags after filtering in treatment: 12489345 INFO @ Sat, 11 Dec 2021 12:13:58: #1 Redundant rate of treatment: 0.22 INFO @ Sat, 11 Dec 2021 12:13:58: #1 finished! INFO @ Sat, 11 Dec 2021 12:13:58: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 12:13:58: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 12:13:59: #2 number of paired peaks: 574 WARNING @ Sat, 11 Dec 2021 12:13:59: 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 12:13:59: start model_add_line... INFO @ Sat, 11 Dec 2021 12:13:59: start X-correlation... INFO @ Sat, 11 Dec 2021 12:13:59: end of X-cor INFO @ Sat, 11 Dec 2021 12:13:59: #2 finished! INFO @ Sat, 11 Dec 2021 12:13:59: #2 predicted fragment length is 275 bps INFO @ Sat, 11 Dec 2021 12:13:59: #2 alternative fragment length(s) may be 2,199,225,253,275,303,334 bps INFO @ Sat, 11 Dec 2021 12:13:59: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX9986171/SRX9986171.20_model.r INFO @ Sat, 11 Dec 2021 12:13:59: #3 Call peaks... INFO @ Sat, 11 Dec 2021 12:13:59: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Dec 2021 12:14:25: #3 Call peaks for each chromosome... INFO @ Sat, 11 Dec 2021 12:14:37: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX9986171/SRX9986171.20_peaks.xls INFO @ Sat, 11 Dec 2021 12:14:37: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX9986171/SRX9986171.20_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 12:14:37: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX9986171/SRX9986171.20_summits.bed INFO @ Sat, 11 Dec 2021 12:14:37: Done! pass1 - making usageList (11 chroms): 1 millis pass2 - checking and writing primary data (298 records, 4 fields): 2 millis CompletedMACS2peakCalling