Job ID = 14168357 SRX = SRX11078124 Genome = dm3 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... 2021-12-10T09:03:18 prefetch.2.10.7: 1) Downloading 'SRR14743552'... 2021-12-10T09:03:18 prefetch.2.10.7: Downloading via HTTPS... 2021-12-10T09:03:59 prefetch.2.10.7: HTTPS download succeed 2021-12-10T09:03:59 prefetch.2.10.7: 1) 'SRR14743552' was downloaded successfully 2021-12-10T09:03:59 prefetch.2.10.7: 'SRR14743552' has 0 unresolved dependencies Read 22686194 spots for SRR14743552/SRR14743552.sra Written 22686194 spots for SRR14743552/SRR14743552.sra fastq に変換しました。 bowtie でマッピング中... Your job 14169548 ("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: 00:09:24 22686194 reads; of these: 22686194 (100.00%) were paired; of these: 17087718 (75.32%) aligned concordantly 0 times 4326453 (19.07%) aligned concordantly exactly 1 time 1272023 (5.61%) aligned concordantly >1 times ---- 17087718 pairs aligned concordantly 0 times; of these: 12892 (0.08%) aligned discordantly 1 time ---- 17074826 pairs aligned 0 times concordantly or discordantly; of these: 34149652 mates make up the pairs; of these: 33804019 (98.99%) aligned 0 times 193933 (0.57%) aligned exactly 1 time 151700 (0.44%) aligned >1 times 25.50% overall alignment rate Time searching: 00:09:24 Overall time: 00:09:24 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_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] 371556 / 5606688 = 0.0663 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 @ Fri, 10 Dec 2021 18:18:00: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX11078124/SRX11078124.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX11078124/SRX11078124.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX11078124/SRX11078124.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX11078124/SRX11078124.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 @ Fri, 10 Dec 2021 18:18:00: #1 read tag files... INFO @ Fri, 10 Dec 2021 18:18:00: #1 read treatment tags... INFO @ Fri, 10 Dec 2021 18:18:05: 1000000 INFO @ Fri, 10 Dec 2021 18:18:10: 2000000 INFO @ Fri, 10 Dec 2021 18:18:15: 3000000 INFO @ Fri, 10 Dec 2021 18:18:20: 4000000 INFO @ Fri, 10 Dec 2021 18:18:24: 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 @ Fri, 10 Dec 2021 18:18:29: 6000000 INFO @ Fri, 10 Dec 2021 18:18:30: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX11078124/SRX11078124.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX11078124/SRX11078124.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX11078124/SRX11078124.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX11078124/SRX11078124.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 @ Fri, 10 Dec 2021 18:18:30: #1 read tag files... INFO @ Fri, 10 Dec 2021 18:18:30: #1 read treatment tags... INFO @ Fri, 10 Dec 2021 18:18:35: 7000000 INFO @ Fri, 10 Dec 2021 18:18:36: 1000000 INFO @ Fri, 10 Dec 2021 18:18:40: 8000000 INFO @ Fri, 10 Dec 2021 18:18:42: 2000000 INFO @ Fri, 10 Dec 2021 18:18:45: 9000000 INFO @ Fri, 10 Dec 2021 18:18:47: 3000000 INFO @ Fri, 10 Dec 2021 18:18:51: 10000000 INFO @ Fri, 10 Dec 2021 18:18:52: 4000000 INFO @ Fri, 10 Dec 2021 18:18:55: #1 tag size is determined as 40 bps INFO @ Fri, 10 Dec 2021 18:18:55: #1 tag size = 40 INFO @ Fri, 10 Dec 2021 18:18:55: #1 total tags in treatment: 5227153 INFO @ Fri, 10 Dec 2021 18:18:55: #1 user defined the maximum tags... INFO @ Fri, 10 Dec 2021 18:18:55: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 10 Dec 2021 18:18:56: #1 tags after filtering in treatment: 4825068 INFO @ Fri, 10 Dec 2021 18:18:56: #1 Redundant rate of treatment: 0.08 INFO @ Fri, 10 Dec 2021 18:18:56: #1 finished! INFO @ Fri, 10 Dec 2021 18:18:56: #2 Build Peak Model... INFO @ Fri, 10 Dec 2021 18:18:56: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Dec 2021 18:18:56: #2 number of paired peaks: 596 WARNING @ Fri, 10 Dec 2021 18:18:56: Fewer paired peaks (596) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 596 pairs to build model! INFO @ Fri, 10 Dec 2021 18:18:56: start model_add_line... INFO @ Fri, 10 Dec 2021 18:18:56: start X-correlation... INFO @ Fri, 10 Dec 2021 18:18:56: end of X-cor INFO @ Fri, 10 Dec 2021 18:18:56: #2 finished! INFO @ Fri, 10 Dec 2021 18:18:56: #2 predicted fragment length is 110 bps INFO @ Fri, 10 Dec 2021 18:18:56: #2 alternative fragment length(s) may be 4,110,131 bps INFO @ Fri, 10 Dec 2021 18:18:56: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX11078124/SRX11078124.05_model.r INFO @ Fri, 10 Dec 2021 18:18:56: #3 Call peaks... INFO @ Fri, 10 Dec 2021 18:18:56: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 10 Dec 2021 18:18:58: 5000000 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 @ Fri, 10 Dec 2021 18:19:00: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX11078124/SRX11078124.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX11078124/SRX11078124.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX11078124/SRX11078124.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX11078124/SRX11078124.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 @ Fri, 10 Dec 2021 18:19:00: #1 read tag files... INFO @ Fri, 10 Dec 2021 18:19:00: #1 read treatment tags... INFO @ Fri, 10 Dec 2021 18:19:03: 6000000 INFO @ Fri, 10 Dec 2021 18:19:06: 1000000 INFO @ Fri, 10 Dec 2021 18:19:06: #3 Call peaks for each chromosome... INFO @ Fri, 10 Dec 2021 18:19:09: 7000000 INFO @ Fri, 10 Dec 2021 18:19:11: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX11078124/SRX11078124.05_peaks.xls INFO @ Fri, 10 Dec 2021 18:19:11: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX11078124/SRX11078124.05_peaks.narrowPeak INFO @ Fri, 10 Dec 2021 18:19:11: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX11078124/SRX11078124.05_summits.bed INFO @ Fri, 10 Dec 2021 18:19:11: Done! pass1 - making usageList (13 chroms): 0 millis pass2 - checking and writing primary data (459 records, 4 fields): 14 millis CompletedMACS2peakCalling INFO @ Fri, 10 Dec 2021 18:19:12: 2000000 INFO @ Fri, 10 Dec 2021 18:19:15: 8000000 INFO @ Fri, 10 Dec 2021 18:19:17: 3000000 INFO @ Fri, 10 Dec 2021 18:19:20: 9000000 INFO @ Fri, 10 Dec 2021 18:19:23: 4000000 INFO @ Fri, 10 Dec 2021 18:19:26: 10000000 INFO @ Fri, 10 Dec 2021 18:19:29: 5000000 INFO @ Fri, 10 Dec 2021 18:19:31: #1 tag size is determined as 40 bps INFO @ Fri, 10 Dec 2021 18:19:31: #1 tag size = 40 INFO @ Fri, 10 Dec 2021 18:19:31: #1 total tags in treatment: 5227153 INFO @ Fri, 10 Dec 2021 18:19:31: #1 user defined the maximum tags... INFO @ Fri, 10 Dec 2021 18:19:31: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 10 Dec 2021 18:19:31: #1 tags after filtering in treatment: 4825068 INFO @ Fri, 10 Dec 2021 18:19:31: #1 Redundant rate of treatment: 0.08 INFO @ Fri, 10 Dec 2021 18:19:31: #1 finished! INFO @ Fri, 10 Dec 2021 18:19:31: #2 Build Peak Model... INFO @ Fri, 10 Dec 2021 18:19:31: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Dec 2021 18:19:31: #2 number of paired peaks: 596 WARNING @ Fri, 10 Dec 2021 18:19:31: Fewer paired peaks (596) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 596 pairs to build model! INFO @ Fri, 10 Dec 2021 18:19:31: start model_add_line... INFO @ Fri, 10 Dec 2021 18:19:31: start X-correlation... INFO @ Fri, 10 Dec 2021 18:19:31: end of X-cor INFO @ Fri, 10 Dec 2021 18:19:31: #2 finished! INFO @ Fri, 10 Dec 2021 18:19:31: #2 predicted fragment length is 110 bps INFO @ Fri, 10 Dec 2021 18:19:31: #2 alternative fragment length(s) may be 4,110,131 bps INFO @ Fri, 10 Dec 2021 18:19:31: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX11078124/SRX11078124.10_model.r INFO @ Fri, 10 Dec 2021 18:19:31: #3 Call peaks... INFO @ Fri, 10 Dec 2021 18:19:31: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 10 Dec 2021 18:19:34: 6000000 INFO @ Fri, 10 Dec 2021 18:19:39: 7000000 INFO @ Fri, 10 Dec 2021 18:19:41: #3 Call peaks for each chromosome... BedGraph に変換しました。 BigWig に変換中... INFO @ Fri, 10 Dec 2021 18:19:45: 8000000 INFO @ Fri, 10 Dec 2021 18:19:46: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX11078124/SRX11078124.10_peaks.xls INFO @ Fri, 10 Dec 2021 18:19:46: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX11078124/SRX11078124.10_peaks.narrowPeak INFO @ Fri, 10 Dec 2021 18:19:46: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX11078124/SRX11078124.10_summits.bed INFO @ Fri, 10 Dec 2021 18:19:46: Done! pass1 - making usageList (9 chroms): 0 millis pass2 - checking and writing primary data (236 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Fri, 10 Dec 2021 18:19:50: 9000000 INFO @ Fri, 10 Dec 2021 18:19:55: 10000000 INFO @ Fri, 10 Dec 2021 18:19:59: #1 tag size is determined as 40 bps INFO @ Fri, 10 Dec 2021 18:19:59: #1 tag size = 40 INFO @ Fri, 10 Dec 2021 18:19:59: #1 total tags in treatment: 5227153 INFO @ Fri, 10 Dec 2021 18:19:59: #1 user defined the maximum tags... INFO @ Fri, 10 Dec 2021 18:19:59: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 10 Dec 2021 18:19:59: #1 tags after filtering in treatment: 4825068 INFO @ Fri, 10 Dec 2021 18:19:59: #1 Redundant rate of treatment: 0.08 INFO @ Fri, 10 Dec 2021 18:19:59: #1 finished! INFO @ Fri, 10 Dec 2021 18:19:59: #2 Build Peak Model... INFO @ Fri, 10 Dec 2021 18:19:59: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Dec 2021 18:19:59: #2 number of paired peaks: 596 WARNING @ Fri, 10 Dec 2021 18:19:59: Fewer paired peaks (596) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 596 pairs to build model! INFO @ Fri, 10 Dec 2021 18:19:59: start model_add_line... INFO @ Fri, 10 Dec 2021 18:19:59: start X-correlation... INFO @ Fri, 10 Dec 2021 18:19:59: end of X-cor INFO @ Fri, 10 Dec 2021 18:19:59: #2 finished! INFO @ Fri, 10 Dec 2021 18:19:59: #2 predicted fragment length is 110 bps INFO @ Fri, 10 Dec 2021 18:19:59: #2 alternative fragment length(s) may be 4,110,131 bps INFO @ Fri, 10 Dec 2021 18:19:59: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX11078124/SRX11078124.20_model.r INFO @ Fri, 10 Dec 2021 18:19:59: #3 Call peaks... INFO @ Fri, 10 Dec 2021 18:19:59: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Fri, 10 Dec 2021 18:20:09: #3 Call peaks for each chromosome... INFO @ Fri, 10 Dec 2021 18:20:14: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX11078124/SRX11078124.20_peaks.xls INFO @ Fri, 10 Dec 2021 18:20:14: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX11078124/SRX11078124.20_peaks.narrowPeak INFO @ Fri, 10 Dec 2021 18:20:14: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX11078124/SRX11078124.20_summits.bed INFO @ Fri, 10 Dec 2021 18:20:14: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (109 records, 4 fields): 2 millis CompletedMACS2peakCalling