Job ID = 14168541 SRX = ERX3978757 Genome = dm3 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... Read 16866130 spots for ERR3975770/ERR3975770.sra Written 16866130 spots for ERR3975770/ERR3975770.sra Read 18030185 spots for ERR3975771/ERR3975771.sra Written 18030185 spots for ERR3975771/ERR3975771.sra fastq に変換しました。 bowtie でマッピング中... Your job 14169808 ("srTdm6") has been submitted Time loading reference: 00:00:00 Time loading forward index: 00:00:01 Time loading mirror index: 00:00:00 Multiseed full-index search: 00:49:17 34896315 reads; of these: 34896315 (100.00%) were paired; of these: 11880292 (34.04%) aligned concordantly 0 times 2738447 (7.85%) aligned concordantly exactly 1 time 20277576 (58.11%) aligned concordantly >1 times ---- 11880292 pairs aligned concordantly 0 times; of these: 826815 (6.96%) aligned discordantly 1 time ---- 11053477 pairs aligned 0 times concordantly or discordantly; of these: 22106954 mates make up the pairs; of these: 9880276 (44.69%) aligned 0 times 375143 (1.70%) aligned exactly 1 time 11851535 (53.61%) aligned >1 times 85.84% overall alignment rate Time searching: 00:49:18 Overall time: 00:49:18 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 44 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] 18177973 / 23607991 = 0.7700 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 20:07:32: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/ERX3978757/ERX3978757.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/ERX3978757/ERX3978757.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/ERX3978757/ERX3978757.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/ERX3978757/ERX3978757.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 20:07:32: #1 read tag files... INFO @ Fri, 10 Dec 2021 20:07:32: #1 read treatment tags... INFO @ Fri, 10 Dec 2021 20:07:40: 1000000 INFO @ Fri, 10 Dec 2021 20:07:47: 2000000 INFO @ Fri, 10 Dec 2021 20:07:54: 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 @ Fri, 10 Dec 2021 20:08:01: 4000000 INFO @ Fri, 10 Dec 2021 20:08:02: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/ERX3978757/ERX3978757.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/ERX3978757/ERX3978757.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/ERX3978757/ERX3978757.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/ERX3978757/ERX3978757.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 20:08:02: #1 read tag files... INFO @ Fri, 10 Dec 2021 20:08:02: #1 read treatment tags... INFO @ Fri, 10 Dec 2021 20:08:10: 5000000 INFO @ Fri, 10 Dec 2021 20:08:11: 1000000 INFO @ Fri, 10 Dec 2021 20:08:18: 6000000 INFO @ Fri, 10 Dec 2021 20:08:20: 2000000 INFO @ Fri, 10 Dec 2021 20:08:26: 7000000 INFO @ Fri, 10 Dec 2021 20:08:28: 3000000 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 20:08:32: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/ERX3978757/ERX3978757.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/ERX3978757/ERX3978757.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/ERX3978757/ERX3978757.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/ERX3978757/ERX3978757.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 20:08:32: #1 read tag files... INFO @ Fri, 10 Dec 2021 20:08:32: #1 read treatment tags... INFO @ Fri, 10 Dec 2021 20:08:34: 8000000 INFO @ Fri, 10 Dec 2021 20:08:37: 4000000 INFO @ Fri, 10 Dec 2021 20:08:41: 1000000 INFO @ Fri, 10 Dec 2021 20:08:42: 9000000 INFO @ Fri, 10 Dec 2021 20:08:46: 5000000 INFO @ Fri, 10 Dec 2021 20:08:50: 2000000 INFO @ Fri, 10 Dec 2021 20:08:50: 10000000 INFO @ Fri, 10 Dec 2021 20:08:55: 6000000 INFO @ Fri, 10 Dec 2021 20:08:59: 11000000 INFO @ Fri, 10 Dec 2021 20:08:59: 3000000 INFO @ Fri, 10 Dec 2021 20:09:03: 7000000 INFO @ Fri, 10 Dec 2021 20:09:07: 12000000 INFO @ Fri, 10 Dec 2021 20:09:08: 4000000 INFO @ Fri, 10 Dec 2021 20:09:11: 8000000 INFO @ Fri, 10 Dec 2021 20:09:15: 13000000 INFO @ Fri, 10 Dec 2021 20:09:16: 5000000 INFO @ Fri, 10 Dec 2021 20:09:20: 9000000 INFO @ Fri, 10 Dec 2021 20:09:23: 14000000 INFO @ Fri, 10 Dec 2021 20:09:25: 6000000 INFO @ Fri, 10 Dec 2021 20:09:28: 10000000 INFO @ Fri, 10 Dec 2021 20:09:31: 15000000 INFO @ Fri, 10 Dec 2021 20:09:33: 7000000 INFO @ Fri, 10 Dec 2021 20:09:36: 11000000 INFO @ Fri, 10 Dec 2021 20:09:39: 16000000 INFO @ Fri, 10 Dec 2021 20:09:41: 8000000 INFO @ Fri, 10 Dec 2021 20:09:44: 12000000 INFO @ Fri, 10 Dec 2021 20:09:48: 17000000 INFO @ Fri, 10 Dec 2021 20:09:50: 9000000 INFO @ Fri, 10 Dec 2021 20:09:52: 13000000 INFO @ Fri, 10 Dec 2021 20:09:56: 18000000 INFO @ Fri, 10 Dec 2021 20:09:58: 10000000 INFO @ Fri, 10 Dec 2021 20:10:01: 14000000 INFO @ Fri, 10 Dec 2021 20:10:04: 19000000 INFO @ Fri, 10 Dec 2021 20:10:06: 11000000 INFO @ Fri, 10 Dec 2021 20:10:09: 15000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Fri, 10 Dec 2021 20:10:12: 20000000 INFO @ Fri, 10 Dec 2021 20:10:14: 12000000 INFO @ Fri, 10 Dec 2021 20:10:17: 16000000 INFO @ Fri, 10 Dec 2021 20:10:20: 21000000 INFO @ Fri, 10 Dec 2021 20:10:22: 13000000 INFO @ Fri, 10 Dec 2021 20:10:25: 17000000 BigWig に変換しました。 INFO @ Fri, 10 Dec 2021 20:10:28: 22000000 INFO @ Fri, 10 Dec 2021 20:10:30: 14000000 INFO @ Fri, 10 Dec 2021 20:10:33: 18000000 INFO @ Fri, 10 Dec 2021 20:10:37: 23000000 INFO @ Fri, 10 Dec 2021 20:10:38: 15000000 INFO @ Fri, 10 Dec 2021 20:10:41: 19000000 INFO @ Fri, 10 Dec 2021 20:10:42: #1 tag size is determined as 125 bps INFO @ Fri, 10 Dec 2021 20:10:42: #1 tag size = 125 INFO @ Fri, 10 Dec 2021 20:10:42: #1 total tags in treatment: 4958667 INFO @ Fri, 10 Dec 2021 20:10:42: #1 user defined the maximum tags... INFO @ Fri, 10 Dec 2021 20:10:42: #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 20:10:42: #1 tags after filtering in treatment: 2971642 INFO @ Fri, 10 Dec 2021 20:10:42: #1 Redundant rate of treatment: 0.40 INFO @ Fri, 10 Dec 2021 20:10:42: #1 finished! INFO @ Fri, 10 Dec 2021 20:10:42: #2 Build Peak Model... INFO @ Fri, 10 Dec 2021 20:10:42: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Dec 2021 20:10:42: #2 number of paired peaks: 2846 INFO @ Fri, 10 Dec 2021 20:10:42: start model_add_line... INFO @ Fri, 10 Dec 2021 20:10:42: start X-correlation... INFO @ Fri, 10 Dec 2021 20:10:42: end of X-cor INFO @ Fri, 10 Dec 2021 20:10:42: #2 finished! INFO @ Fri, 10 Dec 2021 20:10:42: #2 predicted fragment length is 208 bps INFO @ Fri, 10 Dec 2021 20:10:42: #2 alternative fragment length(s) may be 208 bps INFO @ Fri, 10 Dec 2021 20:10:42: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/ERX3978757/ERX3978757.05_model.r WARNING @ Fri, 10 Dec 2021 20:10:42: #2 Since the d (208) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 10 Dec 2021 20:10:42: #2 You may need to consider one of the other alternative d(s): 208 WARNING @ Fri, 10 Dec 2021 20:10:42: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Fri, 10 Dec 2021 20:10:42: #3 Call peaks... INFO @ Fri, 10 Dec 2021 20:10:42: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 10 Dec 2021 20:10:47: 16000000 INFO @ Fri, 10 Dec 2021 20:10:49: 20000000 INFO @ Fri, 10 Dec 2021 20:10:49: #3 Call peaks for each chromosome... INFO @ Fri, 10 Dec 2021 20:10:52: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/ERX3978757/ERX3978757.05_peaks.xls INFO @ Fri, 10 Dec 2021 20:10:52: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/ERX3978757/ERX3978757.05_peaks.narrowPeak INFO @ Fri, 10 Dec 2021 20:10:52: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/ERX3978757/ERX3978757.05_summits.bed INFO @ Fri, 10 Dec 2021 20:10:52: Done! pass1 - making usageList (15 chroms): 2 millis pass2 - checking and writing primary data (5327 records, 4 fields): 12 millis CompletedMACS2peakCalling INFO @ Fri, 10 Dec 2021 20:10:54: 17000000 INFO @ Fri, 10 Dec 2021 20:10:57: 21000000 INFO @ Fri, 10 Dec 2021 20:11:02: 18000000 INFO @ Fri, 10 Dec 2021 20:11:05: 22000000 INFO @ Fri, 10 Dec 2021 20:11:10: 19000000 INFO @ Fri, 10 Dec 2021 20:11:14: 23000000 INFO @ Fri, 10 Dec 2021 20:11:18: 20000000 INFO @ Fri, 10 Dec 2021 20:11:18: #1 tag size is determined as 125 bps INFO @ Fri, 10 Dec 2021 20:11:18: #1 tag size = 125 INFO @ Fri, 10 Dec 2021 20:11:18: #1 total tags in treatment: 4958667 INFO @ Fri, 10 Dec 2021 20:11:18: #1 user defined the maximum tags... INFO @ Fri, 10 Dec 2021 20:11:18: #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 20:11:19: #1 tags after filtering in treatment: 2971642 INFO @ Fri, 10 Dec 2021 20:11:19: #1 Redundant rate of treatment: 0.40 INFO @ Fri, 10 Dec 2021 20:11:19: #1 finished! INFO @ Fri, 10 Dec 2021 20:11:19: #2 Build Peak Model... INFO @ Fri, 10 Dec 2021 20:11:19: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Dec 2021 20:11:19: #2 number of paired peaks: 2846 INFO @ Fri, 10 Dec 2021 20:11:19: start model_add_line... INFO @ Fri, 10 Dec 2021 20:11:19: start X-correlation... INFO @ Fri, 10 Dec 2021 20:11:19: end of X-cor INFO @ Fri, 10 Dec 2021 20:11:19: #2 finished! INFO @ Fri, 10 Dec 2021 20:11:19: #2 predicted fragment length is 208 bps INFO @ Fri, 10 Dec 2021 20:11:19: #2 alternative fragment length(s) may be 208 bps INFO @ Fri, 10 Dec 2021 20:11:19: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/ERX3978757/ERX3978757.10_model.r WARNING @ Fri, 10 Dec 2021 20:11:19: #2 Since the d (208) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 10 Dec 2021 20:11:19: #2 You may need to consider one of the other alternative d(s): 208 WARNING @ Fri, 10 Dec 2021 20:11:19: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Fri, 10 Dec 2021 20:11:19: #3 Call peaks... INFO @ Fri, 10 Dec 2021 20:11:19: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 10 Dec 2021 20:11:26: 21000000 INFO @ Fri, 10 Dec 2021 20:11:26: #3 Call peaks for each chromosome... INFO @ Fri, 10 Dec 2021 20:11:29: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/ERX3978757/ERX3978757.10_peaks.xls INFO @ Fri, 10 Dec 2021 20:11:29: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/ERX3978757/ERX3978757.10_peaks.narrowPeak INFO @ Fri, 10 Dec 2021 20:11:29: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/ERX3978757/ERX3978757.10_summits.bed INFO @ Fri, 10 Dec 2021 20:11:29: Done! pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (2329 records, 4 fields): 4 millis CompletedMACS2peakCalling INFO @ Fri, 10 Dec 2021 20:11:33: 22000000 INFO @ Fri, 10 Dec 2021 20:11:41: 23000000 INFO @ Fri, 10 Dec 2021 20:11:46: #1 tag size is determined as 125 bps INFO @ Fri, 10 Dec 2021 20:11:46: #1 tag size = 125 INFO @ Fri, 10 Dec 2021 20:11:46: #1 total tags in treatment: 4958667 INFO @ Fri, 10 Dec 2021 20:11:46: #1 user defined the maximum tags... INFO @ Fri, 10 Dec 2021 20:11:46: #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 20:11:46: #1 tags after filtering in treatment: 2971642 INFO @ Fri, 10 Dec 2021 20:11:46: #1 Redundant rate of treatment: 0.40 INFO @ Fri, 10 Dec 2021 20:11:46: #1 finished! INFO @ Fri, 10 Dec 2021 20:11:46: #2 Build Peak Model... INFO @ Fri, 10 Dec 2021 20:11:46: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Dec 2021 20:11:46: #2 number of paired peaks: 2846 INFO @ Fri, 10 Dec 2021 20:11:46: start model_add_line... INFO @ Fri, 10 Dec 2021 20:11:46: start X-correlation... INFO @ Fri, 10 Dec 2021 20:11:46: end of X-cor INFO @ Fri, 10 Dec 2021 20:11:46: #2 finished! INFO @ Fri, 10 Dec 2021 20:11:46: #2 predicted fragment length is 208 bps INFO @ Fri, 10 Dec 2021 20:11:46: #2 alternative fragment length(s) may be 208 bps INFO @ Fri, 10 Dec 2021 20:11:46: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/ERX3978757/ERX3978757.20_model.r WARNING @ Fri, 10 Dec 2021 20:11:46: #2 Since the d (208) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 10 Dec 2021 20:11:46: #2 You may need to consider one of the other alternative d(s): 208 WARNING @ Fri, 10 Dec 2021 20:11:46: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Fri, 10 Dec 2021 20:11:46: #3 Call peaks... INFO @ Fri, 10 Dec 2021 20:11:46: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 10 Dec 2021 20:11:53: #3 Call peaks for each chromosome... INFO @ Fri, 10 Dec 2021 20:11:56: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/ERX3978757/ERX3978757.20_peaks.xls INFO @ Fri, 10 Dec 2021 20:11:56: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/ERX3978757/ERX3978757.20_peaks.narrowPeak INFO @ Fri, 10 Dec 2021 20:11:56: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/ERX3978757/ERX3978757.20_summits.bed INFO @ Fri, 10 Dec 2021 20:11:56: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (641 records, 4 fields): 2 millis CompletedMACS2peakCalling