Job ID = 14171759 SRX = SRX10386230 Genome = dm3 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... Read 28108094 spots for SRR14009295/SRR14009295.sra Written 28108094 spots for SRR14009295/SRR14009295.sra fastq に変換しました。 bowtie でマッピング中... Your job 14172549 ("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: 01:28:23 28108094 reads; of these: 28108094 (100.00%) were paired; of these: 10762238 (38.29%) aligned concordantly 0 times 7581146 (26.97%) aligned concordantly exactly 1 time 9764710 (34.74%) aligned concordantly >1 times ---- 10762238 pairs aligned concordantly 0 times; of these: 272825 (2.54%) aligned discordantly 1 time ---- 10489413 pairs aligned 0 times concordantly or discordantly; of these: 20978826 mates make up the pairs; of these: 20239240 (96.47%) aligned 0 times 332241 (1.58%) aligned exactly 1 time 407345 (1.94%) aligned >1 times 64.00% overall alignment rate Time searching: 01:28:23 Overall time: 01:28:23 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] 7512045 / 17493483 = 0.4294 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 14:25:36: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX10386230/SRX10386230.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX10386230/SRX10386230.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX10386230/SRX10386230.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX10386230/SRX10386230.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 14:25:36: #1 read tag files... INFO @ Sat, 11 Dec 2021 14:25:36: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 14:25:45: 1000000 INFO @ Sat, 11 Dec 2021 14:25:54: 2000000 INFO @ Sat, 11 Dec 2021 14:26:03: 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 14:26:06: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX10386230/SRX10386230.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX10386230/SRX10386230.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX10386230/SRX10386230.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX10386230/SRX10386230.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 14:26:06: #1 read tag files... INFO @ Sat, 11 Dec 2021 14:26:06: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 14:26:12: 4000000 INFO @ Sat, 11 Dec 2021 14:26:16: 1000000 INFO @ Sat, 11 Dec 2021 14:26:21: 5000000 INFO @ Sat, 11 Dec 2021 14:26:28: 2000000 INFO @ Sat, 11 Dec 2021 14:26:30: 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 14:26:36: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX10386230/SRX10386230.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX10386230/SRX10386230.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX10386230/SRX10386230.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX10386230/SRX10386230.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 14:26:36: #1 read tag files... INFO @ Sat, 11 Dec 2021 14:26:36: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 14:26:39: 7000000 INFO @ Sat, 11 Dec 2021 14:26:39: 3000000 INFO @ Sat, 11 Dec 2021 14:26:47: 1000000 INFO @ Sat, 11 Dec 2021 14:26:48: 8000000 INFO @ Sat, 11 Dec 2021 14:26:51: 4000000 INFO @ Sat, 11 Dec 2021 14:26:57: 9000000 INFO @ Sat, 11 Dec 2021 14:26:59: 2000000 INFO @ Sat, 11 Dec 2021 14:27:04: 5000000 INFO @ Sat, 11 Dec 2021 14:27:06: 10000000 INFO @ Sat, 11 Dec 2021 14:27:12: 3000000 INFO @ Sat, 11 Dec 2021 14:27:16: 6000000 INFO @ Sat, 11 Dec 2021 14:27:16: 11000000 INFO @ Sat, 11 Dec 2021 14:27:24: 4000000 INFO @ Sat, 11 Dec 2021 14:27:25: 12000000 INFO @ Sat, 11 Dec 2021 14:27:27: 7000000 INFO @ Sat, 11 Dec 2021 14:27:34: 13000000 INFO @ Sat, 11 Dec 2021 14:27:36: 5000000 INFO @ Sat, 11 Dec 2021 14:27:39: 8000000 INFO @ Sat, 11 Dec 2021 14:27:43: 14000000 INFO @ Sat, 11 Dec 2021 14:27:48: 6000000 INFO @ Sat, 11 Dec 2021 14:27:51: 9000000 INFO @ Sat, 11 Dec 2021 14:27:52: 15000000 INFO @ Sat, 11 Dec 2021 14:27:59: 7000000 INFO @ Sat, 11 Dec 2021 14:28:01: 16000000 INFO @ Sat, 11 Dec 2021 14:28:03: 10000000 INFO @ Sat, 11 Dec 2021 14:28:10: 17000000 INFO @ Sat, 11 Dec 2021 14:28:11: 8000000 INFO @ Sat, 11 Dec 2021 14:28:15: 11000000 INFO @ Sat, 11 Dec 2021 14:28:19: 18000000 INFO @ Sat, 11 Dec 2021 14:28:23: 9000000 INFO @ Sat, 11 Dec 2021 14:28:26: 12000000 INFO @ Sat, 11 Dec 2021 14:28:28: 19000000 INFO @ Sat, 11 Dec 2021 14:28:34: 10000000 INFO @ Sat, 11 Dec 2021 14:28:37: 20000000 INFO @ Sat, 11 Dec 2021 14:28:38: 13000000 INFO @ Sat, 11 Dec 2021 14:28:46: #1 tag size is determined as 50 bps INFO @ Sat, 11 Dec 2021 14:28:46: #1 tag size = 50 INFO @ Sat, 11 Dec 2021 14:28:46: #1 total tags in treatment: 9897887 INFO @ Sat, 11 Dec 2021 14:28:46: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 14:28:46: #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 14:28:46: #1 tags after filtering in treatment: 7101047 INFO @ Sat, 11 Dec 2021 14:28:46: #1 Redundant rate of treatment: 0.28 INFO @ Sat, 11 Dec 2021 14:28:46: #1 finished! INFO @ Sat, 11 Dec 2021 14:28:46: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 14:28:46: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 14:28:46: 11000000 INFO @ Sat, 11 Dec 2021 14:28:47: #2 number of paired peaks: 1081 INFO @ Sat, 11 Dec 2021 14:28:47: start model_add_line... INFO @ Sat, 11 Dec 2021 14:28:47: start X-correlation... INFO @ Sat, 11 Dec 2021 14:28:47: end of X-cor INFO @ Sat, 11 Dec 2021 14:28:47: #2 finished! INFO @ Sat, 11 Dec 2021 14:28:47: #2 predicted fragment length is 88 bps INFO @ Sat, 11 Dec 2021 14:28:47: #2 alternative fragment length(s) may be 88 bps INFO @ Sat, 11 Dec 2021 14:28:47: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX10386230/SRX10386230.05_model.r WARNING @ Sat, 11 Dec 2021 14:28:47: #2 Since the d (88) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 11 Dec 2021 14:28:47: #2 You may need to consider one of the other alternative d(s): 88 WARNING @ Sat, 11 Dec 2021 14:28:47: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sat, 11 Dec 2021 14:28:47: #3 Call peaks... INFO @ Sat, 11 Dec 2021 14:28:47: #3 Pre-compute pvalue-qvalue table... BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 11 Dec 2021 14:28:49: 14000000 INFO @ Sat, 11 Dec 2021 14:28:57: 12000000 INFO @ Sat, 11 Dec 2021 14:29:00: 15000000 INFO @ Sat, 11 Dec 2021 14:29:09: #3 Call peaks for each chromosome... INFO @ Sat, 11 Dec 2021 14:29:09: 13000000 INFO @ Sat, 11 Dec 2021 14:29:12: 16000000 INFO @ Sat, 11 Dec 2021 14:29:19: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX10386230/SRX10386230.05_peaks.xls INFO @ Sat, 11 Dec 2021 14:29:19: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX10386230/SRX10386230.05_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 14:29:19: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX10386230/SRX10386230.05_summits.bed INFO @ Sat, 11 Dec 2021 14:29:19: Done! pass1 - making usageList (14 chroms): 2 millis pass2 - checking and writing primary data (2973 records, 4 fields): 12 millis CompletedMACS2peakCalling INFO @ Sat, 11 Dec 2021 14:29:20: 14000000 INFO @ Sat, 11 Dec 2021 14:29:23: 17000000 INFO @ Sat, 11 Dec 2021 14:29:31: 15000000 BigWig に変換しました。 INFO @ Sat, 11 Dec 2021 14:29:34: 18000000 INFO @ Sat, 11 Dec 2021 14:29:42: 16000000 INFO @ Sat, 11 Dec 2021 14:29:45: 19000000 INFO @ Sat, 11 Dec 2021 14:29:54: 17000000 INFO @ Sat, 11 Dec 2021 14:29:56: 20000000 INFO @ Sat, 11 Dec 2021 14:30:05: 18000000 INFO @ Sat, 11 Dec 2021 14:30:07: #1 tag size is determined as 50 bps INFO @ Sat, 11 Dec 2021 14:30:07: #1 tag size = 50 INFO @ Sat, 11 Dec 2021 14:30:07: #1 total tags in treatment: 9897887 INFO @ Sat, 11 Dec 2021 14:30:07: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 14:30:07: #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 14:30:07: #1 tags after filtering in treatment: 7101047 INFO @ Sat, 11 Dec 2021 14:30:07: #1 Redundant rate of treatment: 0.28 INFO @ Sat, 11 Dec 2021 14:30:07: #1 finished! INFO @ Sat, 11 Dec 2021 14:30:07: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 14:30:07: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 14:30:08: #2 number of paired peaks: 1081 INFO @ Sat, 11 Dec 2021 14:30:08: start model_add_line... INFO @ Sat, 11 Dec 2021 14:30:08: start X-correlation... INFO @ Sat, 11 Dec 2021 14:30:08: end of X-cor INFO @ Sat, 11 Dec 2021 14:30:08: #2 finished! INFO @ Sat, 11 Dec 2021 14:30:08: #2 predicted fragment length is 88 bps INFO @ Sat, 11 Dec 2021 14:30:08: #2 alternative fragment length(s) may be 88 bps INFO @ Sat, 11 Dec 2021 14:30:08: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX10386230/SRX10386230.10_model.r WARNING @ Sat, 11 Dec 2021 14:30:08: #2 Since the d (88) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 11 Dec 2021 14:30:08: #2 You may need to consider one of the other alternative d(s): 88 WARNING @ Sat, 11 Dec 2021 14:30:08: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sat, 11 Dec 2021 14:30:08: #3 Call peaks... INFO @ Sat, 11 Dec 2021 14:30:08: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Dec 2021 14:30:15: 19000000 INFO @ Sat, 11 Dec 2021 14:30:25: 20000000 INFO @ Sat, 11 Dec 2021 14:30:31: #3 Call peaks for each chromosome... INFO @ Sat, 11 Dec 2021 14:30:34: #1 tag size is determined as 50 bps INFO @ Sat, 11 Dec 2021 14:30:34: #1 tag size = 50 INFO @ Sat, 11 Dec 2021 14:30:34: #1 total tags in treatment: 9897887 INFO @ Sat, 11 Dec 2021 14:30:34: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 14:30:34: #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 14:30:34: #1 tags after filtering in treatment: 7101047 INFO @ Sat, 11 Dec 2021 14:30:34: #1 Redundant rate of treatment: 0.28 INFO @ Sat, 11 Dec 2021 14:30:34: #1 finished! INFO @ Sat, 11 Dec 2021 14:30:34: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 14:30:34: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 14:30:35: #2 number of paired peaks: 1081 INFO @ Sat, 11 Dec 2021 14:30:35: start model_add_line... INFO @ Sat, 11 Dec 2021 14:30:35: start X-correlation... INFO @ Sat, 11 Dec 2021 14:30:35: end of X-cor INFO @ Sat, 11 Dec 2021 14:30:35: #2 finished! INFO @ Sat, 11 Dec 2021 14:30:35: #2 predicted fragment length is 88 bps INFO @ Sat, 11 Dec 2021 14:30:35: #2 alternative fragment length(s) may be 88 bps INFO @ Sat, 11 Dec 2021 14:30:35: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX10386230/SRX10386230.20_model.r WARNING @ Sat, 11 Dec 2021 14:30:35: #2 Since the d (88) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 11 Dec 2021 14:30:35: #2 You may need to consider one of the other alternative d(s): 88 WARNING @ Sat, 11 Dec 2021 14:30:35: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sat, 11 Dec 2021 14:30:35: #3 Call peaks... INFO @ Sat, 11 Dec 2021 14:30:35: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Dec 2021 14:30:42: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX10386230/SRX10386230.10_peaks.xls INFO @ Sat, 11 Dec 2021 14:30:42: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX10386230/SRX10386230.10_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 14:30:42: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX10386230/SRX10386230.10_summits.bed INFO @ Sat, 11 Dec 2021 14:30:42: Done! pass1 - making usageList (12 chroms): 2 millis pass2 - checking and writing primary data (1699 records, 4 fields): 4 millis CompletedMACS2peakCalling INFO @ Sat, 11 Dec 2021 14:30:58: #3 Call peaks for each chromosome... INFO @ Sat, 11 Dec 2021 14:31:09: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX10386230/SRX10386230.20_peaks.xls INFO @ Sat, 11 Dec 2021 14:31:09: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX10386230/SRX10386230.20_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 14:31:09: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX10386230/SRX10386230.20_summits.bed INFO @ Sat, 11 Dec 2021 14:31:09: Done! pass1 - making usageList (11 chroms): 1 millis pass2 - checking and writing primary data (1005 records, 4 fields): 5 millis CompletedMACS2peakCalling