Job ID = 5721034 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... spots read : 29,612,148 reads read : 59,224,296 reads written : 59,224,296 rm: cannot remove ‘[DSE]RR*’: No such file or directory fastq に変換しました。 bowtie でマッピング中... Time loading reference: 00:00:00 Time loading forward index: 00:00:00 Time loading mirror index: 00:00:00 Multiseed full-index search: 01:12:05 29612148 reads; of these: 29612148 (100.00%) were paired; of these: 4457497 (15.05%) aligned concordantly 0 times 21312372 (71.97%) aligned concordantly exactly 1 time 3842279 (12.98%) aligned concordantly >1 times ---- 4457497 pairs aligned concordantly 0 times; of these: 1599685 (35.89%) aligned discordantly 1 time ---- 2857812 pairs aligned 0 times concordantly or discordantly; of these: 5715624 mates make up the pairs; of these: 3877611 (67.84%) aligned 0 times 1070496 (18.73%) aligned exactly 1 time 767517 (13.43%) aligned >1 times 93.45% overall alignment rate Time searching: 01:12:05 Overall time: 01:12:05 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] 12893471 / 26625288 = 0.4843 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/3.5.2/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Thu, 16 Apr 2020 06:10:55: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX6386770/SRX6386770.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX6386770/SRX6386770.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX6386770/SRX6386770.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX6386770/SRX6386770.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 @ Thu, 16 Apr 2020 06:10:55: #1 read tag files... INFO @ Thu, 16 Apr 2020 06:10:55: #1 read treatment tags... INFO @ Thu, 16 Apr 2020 06:11:04: 1000000 INFO @ Thu, 16 Apr 2020 06:11:13: 2000000 INFO @ Thu, 16 Apr 2020 06:11:22: 3000000 WARNING: Skipping mount /opt/pkg/singularity/3.5.2/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Thu, 16 Apr 2020 06:11:25: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX6386770/SRX6386770.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX6386770/SRX6386770.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX6386770/SRX6386770.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX6386770/SRX6386770.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 @ Thu, 16 Apr 2020 06:11:25: #1 read tag files... INFO @ Thu, 16 Apr 2020 06:11:25: #1 read treatment tags... INFO @ Thu, 16 Apr 2020 06:11:31: 4000000 INFO @ Thu, 16 Apr 2020 06:11:35: 1000000 INFO @ Thu, 16 Apr 2020 06:11:41: 5000000 INFO @ Thu, 16 Apr 2020 06:11:45: 2000000 INFO @ Thu, 16 Apr 2020 06:11:50: 6000000 BedGraph に変換中... WARNING: Skipping mount /opt/pkg/singularity/3.5.2/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Thu, 16 Apr 2020 06:11:54: 3000000 INFO @ Thu, 16 Apr 2020 06:11:55: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX6386770/SRX6386770.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX6386770/SRX6386770.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX6386770/SRX6386770.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX6386770/SRX6386770.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 @ Thu, 16 Apr 2020 06:11:55: #1 read tag files... INFO @ Thu, 16 Apr 2020 06:11:55: #1 read treatment tags... INFO @ Thu, 16 Apr 2020 06:12:00: 7000000 INFO @ Thu, 16 Apr 2020 06:12:04: 4000000 INFO @ Thu, 16 Apr 2020 06:12:05: 1000000 INFO @ Thu, 16 Apr 2020 06:12:10: 8000000 INFO @ Thu, 16 Apr 2020 06:12:14: 5000000 INFO @ Thu, 16 Apr 2020 06:12:15: 2000000 INFO @ Thu, 16 Apr 2020 06:12:20: 9000000 INFO @ Thu, 16 Apr 2020 06:12:24: 6000000 INFO @ Thu, 16 Apr 2020 06:12:24: 3000000 INFO @ Thu, 16 Apr 2020 06:12:30: 10000000 INFO @ Thu, 16 Apr 2020 06:12:34: 4000000 INFO @ Thu, 16 Apr 2020 06:12:34: 7000000 INFO @ Thu, 16 Apr 2020 06:12:39: 11000000 INFO @ Thu, 16 Apr 2020 06:12:43: 5000000 INFO @ Thu, 16 Apr 2020 06:12:44: 8000000 INFO @ Thu, 16 Apr 2020 06:12:49: 12000000 INFO @ Thu, 16 Apr 2020 06:12:53: 6000000 INFO @ Thu, 16 Apr 2020 06:12:54: 9000000 INFO @ Thu, 16 Apr 2020 06:12:58: 13000000 INFO @ Thu, 16 Apr 2020 06:13:03: 7000000 INFO @ Thu, 16 Apr 2020 06:13:04: 10000000 INFO @ Thu, 16 Apr 2020 06:13:08: 14000000 INFO @ Thu, 16 Apr 2020 06:13:12: 8000000 INFO @ Thu, 16 Apr 2020 06:13:13: 11000000 INFO @ Thu, 16 Apr 2020 06:13:17: 15000000 INFO @ Thu, 16 Apr 2020 06:13:22: 9000000 INFO @ Thu, 16 Apr 2020 06:13:23: 12000000 INFO @ Thu, 16 Apr 2020 06:13:27: 16000000 INFO @ Thu, 16 Apr 2020 06:13:32: 10000000 INFO @ Thu, 16 Apr 2020 06:13:33: 13000000 INFO @ Thu, 16 Apr 2020 06:13:37: 17000000 INFO @ Thu, 16 Apr 2020 06:13:41: 11000000 INFO @ Thu, 16 Apr 2020 06:13:43: 14000000 INFO @ Thu, 16 Apr 2020 06:13:46: 18000000 INFO @ Thu, 16 Apr 2020 06:13:51: 12000000 INFO @ Thu, 16 Apr 2020 06:13:52: 15000000 INFO @ Thu, 16 Apr 2020 06:13:56: 19000000 INFO @ Thu, 16 Apr 2020 06:14:00: 13000000 INFO @ Thu, 16 Apr 2020 06:14:02: 16000000 INFO @ Thu, 16 Apr 2020 06:14:05: 20000000 INFO @ Thu, 16 Apr 2020 06:14:09: 14000000 INFO @ Thu, 16 Apr 2020 06:14:12: 17000000 INFO @ Thu, 16 Apr 2020 06:14:15: 21000000 INFO @ Thu, 16 Apr 2020 06:14:19: 15000000 INFO @ Thu, 16 Apr 2020 06:14:21: 18000000 INFO @ Thu, 16 Apr 2020 06:14:25: 22000000 INFO @ Thu, 16 Apr 2020 06:14:28: 16000000 INFO @ Thu, 16 Apr 2020 06:14:31: 19000000 INFO @ Thu, 16 Apr 2020 06:14:34: 23000000 INFO @ Thu, 16 Apr 2020 06:14:38: 17000000 INFO @ Thu, 16 Apr 2020 06:14:41: 20000000 INFO @ Thu, 16 Apr 2020 06:14:44: 24000000 INFO @ Thu, 16 Apr 2020 06:14:47: 18000000 INFO @ Thu, 16 Apr 2020 06:14:51: 21000000 INFO @ Thu, 16 Apr 2020 06:14:54: 25000000 INFO @ Thu, 16 Apr 2020 06:14:57: 19000000 INFO @ Thu, 16 Apr 2020 06:15:00: 22000000 INFO @ Thu, 16 Apr 2020 06:15:04: 26000000 INFO @ Thu, 16 Apr 2020 06:15:06: 20000000 INFO @ Thu, 16 Apr 2020 06:15:10: 23000000 INFO @ Thu, 16 Apr 2020 06:15:13: 27000000 INFO @ Thu, 16 Apr 2020 06:15:15: 21000000 INFO @ Thu, 16 Apr 2020 06:15:20: 24000000 INFO @ Thu, 16 Apr 2020 06:15:23: 28000000 INFO @ Thu, 16 Apr 2020 06:15:25: 22000000 INFO @ Thu, 16 Apr 2020 06:15:30: 25000000 INFO @ Thu, 16 Apr 2020 06:15:32: 29000000 INFO @ Thu, 16 Apr 2020 06:15:35: 23000000 INFO @ Thu, 16 Apr 2020 06:15:38: #1 tag size is determined as 151 bps INFO @ Thu, 16 Apr 2020 06:15:38: #1 tag size = 151 INFO @ Thu, 16 Apr 2020 06:15:38: #1 total tags in treatment: 12773306 INFO @ Thu, 16 Apr 2020 06:15:38: #1 user defined the maximum tags... INFO @ Thu, 16 Apr 2020 06:15:38: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Thu, 16 Apr 2020 06:15:38: #1 tags after filtering in treatment: 12244505 INFO @ Thu, 16 Apr 2020 06:15:38: #1 Redundant rate of treatment: 0.04 INFO @ Thu, 16 Apr 2020 06:15:38: #1 finished! INFO @ Thu, 16 Apr 2020 06:15:38: #2 Build Peak Model... INFO @ Thu, 16 Apr 2020 06:15:38: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 16 Apr 2020 06:15:39: #2 number of paired peaks: 109 WARNING @ Thu, 16 Apr 2020 06:15:39: Fewer paired peaks (109) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 109 pairs to build model! INFO @ Thu, 16 Apr 2020 06:15:39: start model_add_line... INFO @ Thu, 16 Apr 2020 06:15:39: start X-correlation... INFO @ Thu, 16 Apr 2020 06:15:39: end of X-cor INFO @ Thu, 16 Apr 2020 06:15:39: #2 finished! INFO @ Thu, 16 Apr 2020 06:15:39: #2 predicted fragment length is 240 bps INFO @ Thu, 16 Apr 2020 06:15:39: #2 alternative fragment length(s) may be 240 bps INFO @ Thu, 16 Apr 2020 06:15:39: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX6386770/SRX6386770.05_model.r WARNING @ Thu, 16 Apr 2020 06:15:39: #2 Since the d (240) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 16 Apr 2020 06:15:39: #2 You may need to consider one of the other alternative d(s): 240 WARNING @ Thu, 16 Apr 2020 06:15:39: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Thu, 16 Apr 2020 06:15:39: #3 Call peaks... INFO @ Thu, 16 Apr 2020 06:15:39: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 16 Apr 2020 06:15:40: 26000000 INFO @ Thu, 16 Apr 2020 06:15:44: 24000000 INFO @ Thu, 16 Apr 2020 06:15:49: 27000000 INFO @ Thu, 16 Apr 2020 06:15:54: 25000000 INFO @ Thu, 16 Apr 2020 06:15:59: 28000000 INFO @ Thu, 16 Apr 2020 06:16:03: 26000000 INFO @ Thu, 16 Apr 2020 06:16:04: #3 Call peaks for each chromosome... INFO @ Thu, 16 Apr 2020 06:16:08: 29000000 INFO @ Thu, 16 Apr 2020 06:16:13: 27000000 INFO @ Thu, 16 Apr 2020 06:16:14: #1 tag size is determined as 151 bps INFO @ Thu, 16 Apr 2020 06:16:14: #1 tag size = 151 INFO @ Thu, 16 Apr 2020 06:16:14: #1 total tags in treatment: 12773306 INFO @ Thu, 16 Apr 2020 06:16:14: #1 user defined the maximum tags... INFO @ Thu, 16 Apr 2020 06:16:14: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Thu, 16 Apr 2020 06:16:14: #1 tags after filtering in treatment: 12244505 INFO @ Thu, 16 Apr 2020 06:16:14: #1 Redundant rate of treatment: 0.04 INFO @ Thu, 16 Apr 2020 06:16:14: #1 finished! INFO @ Thu, 16 Apr 2020 06:16:14: #2 Build Peak Model... INFO @ Thu, 16 Apr 2020 06:16:14: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 16 Apr 2020 06:16:15: #2 number of paired peaks: 109 WARNING @ Thu, 16 Apr 2020 06:16:15: Fewer paired peaks (109) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 109 pairs to build model! INFO @ Thu, 16 Apr 2020 06:16:15: start model_add_line... INFO @ Thu, 16 Apr 2020 06:16:15: start X-correlation... INFO @ Thu, 16 Apr 2020 06:16:15: end of X-cor INFO @ Thu, 16 Apr 2020 06:16:15: #2 finished! INFO @ Thu, 16 Apr 2020 06:16:15: #2 predicted fragment length is 240 bps INFO @ Thu, 16 Apr 2020 06:16:15: #2 alternative fragment length(s) may be 240 bps INFO @ Thu, 16 Apr 2020 06:16:15: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX6386770/SRX6386770.10_model.r WARNING @ Thu, 16 Apr 2020 06:16:15: #2 Since the d (240) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 16 Apr 2020 06:16:15: #2 You may need to consider one of the other alternative d(s): 240 WARNING @ Thu, 16 Apr 2020 06:16:15: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Thu, 16 Apr 2020 06:16:15: #3 Call peaks... INFO @ Thu, 16 Apr 2020 06:16:15: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 16 Apr 2020 06:16:17: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX6386770/SRX6386770.05_peaks.xls INFO @ Thu, 16 Apr 2020 06:16:17: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX6386770/SRX6386770.05_peaks.narrowPeak INFO @ Thu, 16 Apr 2020 06:16:17: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX6386770/SRX6386770.05_summits.bed INFO @ Thu, 16 Apr 2020 06:16:17: Done! pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (5461 records, 4 fields): 7 millis CompletedMACS2peakCalling INFO @ Thu, 16 Apr 2020 06:16:22: 28000000 INFO @ Thu, 16 Apr 2020 06:16:31: 29000000 INFO @ Thu, 16 Apr 2020 06:16:36: #1 tag size is determined as 151 bps INFO @ Thu, 16 Apr 2020 06:16:36: #1 tag size = 151 INFO @ Thu, 16 Apr 2020 06:16:36: #1 total tags in treatment: 12773306 INFO @ Thu, 16 Apr 2020 06:16:36: #1 user defined the maximum tags... INFO @ Thu, 16 Apr 2020 06:16:36: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Thu, 16 Apr 2020 06:16:36: #1 tags after filtering in treatment: 12244505 INFO @ Thu, 16 Apr 2020 06:16:36: #1 Redundant rate of treatment: 0.04 INFO @ Thu, 16 Apr 2020 06:16:36: #1 finished! INFO @ Thu, 16 Apr 2020 06:16:36: #2 Build Peak Model... INFO @ Thu, 16 Apr 2020 06:16:36: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 16 Apr 2020 06:16:37: #2 number of paired peaks: 109 WARNING @ Thu, 16 Apr 2020 06:16:37: Fewer paired peaks (109) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 109 pairs to build model! INFO @ Thu, 16 Apr 2020 06:16:37: start model_add_line... INFO @ Thu, 16 Apr 2020 06:16:37: start X-correlation... INFO @ Thu, 16 Apr 2020 06:16:37: end of X-cor INFO @ Thu, 16 Apr 2020 06:16:37: #2 finished! INFO @ Thu, 16 Apr 2020 06:16:37: #2 predicted fragment length is 240 bps INFO @ Thu, 16 Apr 2020 06:16:37: #2 alternative fragment length(s) may be 240 bps INFO @ Thu, 16 Apr 2020 06:16:37: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX6386770/SRX6386770.20_model.r WARNING @ Thu, 16 Apr 2020 06:16:37: #2 Since the d (240) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 16 Apr 2020 06:16:37: #2 You may need to consider one of the other alternative d(s): 240 WARNING @ Thu, 16 Apr 2020 06:16:37: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Thu, 16 Apr 2020 06:16:37: #3 Call peaks... INFO @ Thu, 16 Apr 2020 06:16:37: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 16 Apr 2020 06:16:39: #3 Call peaks for each chromosome... INFO @ Thu, 16 Apr 2020 06:16:51: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX6386770/SRX6386770.10_peaks.xls INFO @ Thu, 16 Apr 2020 06:16:51: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX6386770/SRX6386770.10_peaks.narrowPeak INFO @ Thu, 16 Apr 2020 06:16:51: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX6386770/SRX6386770.10_summits.bed INFO @ Thu, 16 Apr 2020 06:16:51: Done! pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (2679 records, 4 fields): 4 millis CompletedMACS2peakCalling INFO @ Thu, 16 Apr 2020 06:17:01: #3 Call peaks for each chromosome... INFO @ Thu, 16 Apr 2020 06:17:13: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX6386770/SRX6386770.20_peaks.xls INFO @ Thu, 16 Apr 2020 06:17:13: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX6386770/SRX6386770.20_peaks.narrowPeak INFO @ Thu, 16 Apr 2020 06:17:13: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX6386770/SRX6386770.20_summits.bed INFO @ Thu, 16 Apr 2020 06:17:13: Done! pass1 - making usageList (15 chroms): 0 millis pass2 - checking and writing primary data (849 records, 4 fields): 2 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。