Job ID = 14171469 SRX = SRX10971108 Genome = dm3 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... 2021-12-11T02:45:23 prefetch.2.10.7: 1) Downloading 'SRR14631232'... 2021-12-11T02:45:23 prefetch.2.10.7: Downloading via HTTPS... 2021-12-11T02:46:32 prefetch.2.10.7: HTTPS download succeed 2021-12-11T02:46:32 prefetch.2.10.7: 1) 'SRR14631232' was downloaded successfully 2021-12-11T02:46:32 prefetch.2.10.7: 'SRR14631232' has 0 unresolved dependencies Read 16938119 spots for SRR14631232/SRR14631232.sra Written 16938119 spots for SRR14631232/SRR14631232.sra fastq に変換しました。 bowtie でマッピング中... Your job 14172063 ("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: 00:29:48 16938119 reads; of these: 16938119 (100.00%) were paired; of these: 1673991 (9.88%) aligned concordantly 0 times 13100109 (77.34%) aligned concordantly exactly 1 time 2164019 (12.78%) aligned concordantly >1 times ---- 1673991 pairs aligned concordantly 0 times; of these: 132777 (7.93%) aligned discordantly 1 time ---- 1541214 pairs aligned 0 times concordantly or discordantly; of these: 3082428 mates make up the pairs; of these: 2429711 (78.82%) aligned 0 times 477662 (15.50%) aligned exactly 1 time 175055 (5.68%) aligned >1 times 92.83% overall alignment rate Time searching: 00:29:48 Overall time: 00:29:48 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] 5196115 / 15035885 = 0.3456 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 12:26:10: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX10971108/SRX10971108.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX10971108/SRX10971108.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX10971108/SRX10971108.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX10971108/SRX10971108.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 12:26:10: #1 read tag files... INFO @ Sat, 11 Dec 2021 12:26:10: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 12:26:17: 1000000 INFO @ Sat, 11 Dec 2021 12:26:24: 2000000 INFO @ Sat, 11 Dec 2021 12:26:30: 3000000 INFO @ Sat, 11 Dec 2021 12:26:37: 4000000 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 12:26:40: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX10971108/SRX10971108.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX10971108/SRX10971108.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX10971108/SRX10971108.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX10971108/SRX10971108.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 12:26:40: #1 read tag files... INFO @ Sat, 11 Dec 2021 12:26:40: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 12:26:44: 5000000 INFO @ Sat, 11 Dec 2021 12:26:50: 1000000 INFO @ Sat, 11 Dec 2021 12:26:53: 6000000 INFO @ Sat, 11 Dec 2021 12:27:00: 2000000 INFO @ Sat, 11 Dec 2021 12:27:02: 7000000 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 12:27:10: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX10971108/SRX10971108.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX10971108/SRX10971108.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX10971108/SRX10971108.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX10971108/SRX10971108.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 12:27:10: #1 read tag files... INFO @ Sat, 11 Dec 2021 12:27:10: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 12:27:10: 3000000 INFO @ Sat, 11 Dec 2021 12:27:10: 8000000 INFO @ Sat, 11 Dec 2021 12:27:19: 9000000 INFO @ Sat, 11 Dec 2021 12:27:20: 1000000 INFO @ Sat, 11 Dec 2021 12:27:20: 4000000 INFO @ Sat, 11 Dec 2021 12:27:28: 10000000 INFO @ Sat, 11 Dec 2021 12:27:30: 2000000 INFO @ Sat, 11 Dec 2021 12:27:30: 5000000 INFO @ Sat, 11 Dec 2021 12:27:37: 11000000 INFO @ Sat, 11 Dec 2021 12:27:40: 3000000 INFO @ Sat, 11 Dec 2021 12:27:40: 6000000 INFO @ Sat, 11 Dec 2021 12:27:45: 12000000 INFO @ Sat, 11 Dec 2021 12:27:50: 4000000 INFO @ Sat, 11 Dec 2021 12:27:50: 7000000 INFO @ Sat, 11 Dec 2021 12:27:54: 13000000 INFO @ Sat, 11 Dec 2021 12:27:59: 5000000 INFO @ Sat, 11 Dec 2021 12:28:00: 8000000 INFO @ Sat, 11 Dec 2021 12:28:03: 14000000 INFO @ Sat, 11 Dec 2021 12:28:09: 6000000 INFO @ Sat, 11 Dec 2021 12:28:11: 9000000 INFO @ Sat, 11 Dec 2021 12:28:12: 15000000 INFO @ Sat, 11 Dec 2021 12:28:19: 7000000 INFO @ Sat, 11 Dec 2021 12:28:20: 16000000 INFO @ Sat, 11 Dec 2021 12:28:21: 10000000 INFO @ Sat, 11 Dec 2021 12:28:29: 17000000 INFO @ Sat, 11 Dec 2021 12:28:29: 8000000 INFO @ Sat, 11 Dec 2021 12:28:31: 11000000 INFO @ Sat, 11 Dec 2021 12:28:38: 18000000 INFO @ Sat, 11 Dec 2021 12:28:39: 9000000 INFO @ Sat, 11 Dec 2021 12:28:41: 12000000 INFO @ Sat, 11 Dec 2021 12:28:47: 19000000 INFO @ Sat, 11 Dec 2021 12:28:49: 10000000 INFO @ Sat, 11 Dec 2021 12:28:51: 13000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 11 Dec 2021 12:28:56: 20000000 INFO @ Sat, 11 Dec 2021 12:28:59: 11000000 INFO @ Sat, 11 Dec 2021 12:29:01: 14000000 INFO @ Sat, 11 Dec 2021 12:29:05: 21000000 INFO @ Sat, 11 Dec 2021 12:29:05: #1 tag size is determined as 99 bps INFO @ Sat, 11 Dec 2021 12:29:05: #1 tag size = 99 INFO @ Sat, 11 Dec 2021 12:29:05: #1 total tags in treatment: 10073332 INFO @ Sat, 11 Dec 2021 12:29:05: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 12:29:05: #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 12:29:05: #1 tags after filtering in treatment: 8655545 INFO @ Sat, 11 Dec 2021 12:29:05: #1 Redundant rate of treatment: 0.14 INFO @ Sat, 11 Dec 2021 12:29:05: #1 finished! INFO @ Sat, 11 Dec 2021 12:29:05: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 12:29:05: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 12:29:06: #2 number of paired peaks: 813 WARNING @ Sat, 11 Dec 2021 12:29:06: Fewer paired peaks (813) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 813 pairs to build model! INFO @ Sat, 11 Dec 2021 12:29:06: start model_add_line... INFO @ Sat, 11 Dec 2021 12:29:06: start X-correlation... INFO @ Sat, 11 Dec 2021 12:29:06: end of X-cor INFO @ Sat, 11 Dec 2021 12:29:06: #2 finished! INFO @ Sat, 11 Dec 2021 12:29:06: #2 predicted fragment length is 194 bps INFO @ Sat, 11 Dec 2021 12:29:06: #2 alternative fragment length(s) may be 194 bps INFO @ Sat, 11 Dec 2021 12:29:06: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX10971108/SRX10971108.05_model.r WARNING @ Sat, 11 Dec 2021 12:29:06: #2 Since the d (194) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 11 Dec 2021 12:29:06: #2 You may need to consider one of the other alternative d(s): 194 WARNING @ Sat, 11 Dec 2021 12:29:06: #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 12:29:06: #3 Call peaks... INFO @ Sat, 11 Dec 2021 12:29:06: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Dec 2021 12:29:09: 12000000 INFO @ Sat, 11 Dec 2021 12:29:11: 15000000 INFO @ Sat, 11 Dec 2021 12:29:19: 13000000 INFO @ Sat, 11 Dec 2021 12:29:21: 16000000 INFO @ Sat, 11 Dec 2021 12:29:25: #3 Call peaks for each chromosome... BigWig に変換しました。 INFO @ Sat, 11 Dec 2021 12:29:29: 14000000 INFO @ Sat, 11 Dec 2021 12:29:31: 17000000 INFO @ Sat, 11 Dec 2021 12:29:34: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX10971108/SRX10971108.05_peaks.xls INFO @ Sat, 11 Dec 2021 12:29:34: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX10971108/SRX10971108.05_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 12:29:34: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX10971108/SRX10971108.05_summits.bed INFO @ Sat, 11 Dec 2021 12:29:34: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (1369 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Sat, 11 Dec 2021 12:29:39: 15000000 INFO @ Sat, 11 Dec 2021 12:29:42: 18000000 INFO @ Sat, 11 Dec 2021 12:29:49: 16000000 INFO @ Sat, 11 Dec 2021 12:29:52: 19000000 INFO @ Sat, 11 Dec 2021 12:29:59: 17000000 INFO @ Sat, 11 Dec 2021 12:30:02: 20000000 INFO @ Sat, 11 Dec 2021 12:30:09: 18000000 INFO @ Sat, 11 Dec 2021 12:30:11: 21000000 INFO @ Sat, 11 Dec 2021 12:30:12: #1 tag size is determined as 99 bps INFO @ Sat, 11 Dec 2021 12:30:12: #1 tag size = 99 INFO @ Sat, 11 Dec 2021 12:30:12: #1 total tags in treatment: 10073332 INFO @ Sat, 11 Dec 2021 12:30:12: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 12:30:12: #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 12:30:12: #1 tags after filtering in treatment: 8655545 INFO @ Sat, 11 Dec 2021 12:30:12: #1 Redundant rate of treatment: 0.14 INFO @ Sat, 11 Dec 2021 12:30:12: #1 finished! INFO @ Sat, 11 Dec 2021 12:30:12: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 12:30:12: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 12:30:13: #2 number of paired peaks: 813 WARNING @ Sat, 11 Dec 2021 12:30:13: Fewer paired peaks (813) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 813 pairs to build model! INFO @ Sat, 11 Dec 2021 12:30:13: start model_add_line... INFO @ Sat, 11 Dec 2021 12:30:13: start X-correlation... INFO @ Sat, 11 Dec 2021 12:30:13: end of X-cor INFO @ Sat, 11 Dec 2021 12:30:13: #2 finished! INFO @ Sat, 11 Dec 2021 12:30:13: #2 predicted fragment length is 194 bps INFO @ Sat, 11 Dec 2021 12:30:13: #2 alternative fragment length(s) may be 194 bps INFO @ Sat, 11 Dec 2021 12:30:13: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX10971108/SRX10971108.10_model.r WARNING @ Sat, 11 Dec 2021 12:30:13: #2 Since the d (194) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 11 Dec 2021 12:30:13: #2 You may need to consider one of the other alternative d(s): 194 WARNING @ Sat, 11 Dec 2021 12:30:13: #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 12:30:13: #3 Call peaks... INFO @ Sat, 11 Dec 2021 12:30:13: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Dec 2021 12:30:18: 19000000 INFO @ Sat, 11 Dec 2021 12:30:27: 20000000 INFO @ Sat, 11 Dec 2021 12:30:31: #3 Call peaks for each chromosome... INFO @ Sat, 11 Dec 2021 12:30:36: 21000000 INFO @ Sat, 11 Dec 2021 12:30:37: #1 tag size is determined as 99 bps INFO @ Sat, 11 Dec 2021 12:30:37: #1 tag size = 99 INFO @ Sat, 11 Dec 2021 12:30:37: #1 total tags in treatment: 10073332 INFO @ Sat, 11 Dec 2021 12:30:37: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 12:30:37: #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 12:30:37: #1 tags after filtering in treatment: 8655545 INFO @ Sat, 11 Dec 2021 12:30:37: #1 Redundant rate of treatment: 0.14 INFO @ Sat, 11 Dec 2021 12:30:37: #1 finished! INFO @ Sat, 11 Dec 2021 12:30:37: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 12:30:37: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 12:30:37: #2 number of paired peaks: 813 WARNING @ Sat, 11 Dec 2021 12:30:37: Fewer paired peaks (813) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 813 pairs to build model! INFO @ Sat, 11 Dec 2021 12:30:37: start model_add_line... INFO @ Sat, 11 Dec 2021 12:30:38: start X-correlation... INFO @ Sat, 11 Dec 2021 12:30:38: end of X-cor INFO @ Sat, 11 Dec 2021 12:30:38: #2 finished! INFO @ Sat, 11 Dec 2021 12:30:38: #2 predicted fragment length is 194 bps INFO @ Sat, 11 Dec 2021 12:30:38: #2 alternative fragment length(s) may be 194 bps INFO @ Sat, 11 Dec 2021 12:30:38: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX10971108/SRX10971108.20_model.r WARNING @ Sat, 11 Dec 2021 12:30:38: #2 Since the d (194) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 11 Dec 2021 12:30:38: #2 You may need to consider one of the other alternative d(s): 194 WARNING @ Sat, 11 Dec 2021 12:30:38: #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 12:30:38: #3 Call peaks... INFO @ Sat, 11 Dec 2021 12:30:38: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Dec 2021 12:30:40: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX10971108/SRX10971108.10_peaks.xls INFO @ Sat, 11 Dec 2021 12:30:40: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX10971108/SRX10971108.10_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 12:30:40: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX10971108/SRX10971108.10_summits.bed INFO @ Sat, 11 Dec 2021 12:30:40: Done! pass1 - making usageList (12 chroms): 1 millis pass2 - checking and writing primary data (952 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Sat, 11 Dec 2021 12:30:56: #3 Call peaks for each chromosome... INFO @ Sat, 11 Dec 2021 12:31:04: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX10971108/SRX10971108.20_peaks.xls INFO @ Sat, 11 Dec 2021 12:31:05: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX10971108/SRX10971108.20_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 12:31:05: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX10971108/SRX10971108.20_summits.bed INFO @ Sat, 11 Dec 2021 12:31:05: Done! pass1 - making usageList (11 chroms): 1 millis pass2 - checking and writing primary data (667 records, 4 fields): 2 millis CompletedMACS2peakCalling