Job ID = 6454643 SRX = SRX2422644 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T09:24:14 prefetch.2.10.7: 1) Downloading 'SRR5110258'... 2020-06-21T09:24:14 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T09:27:29 prefetch.2.10.7: HTTPS download succeed 2020-06-21T09:27:30 prefetch.2.10.7: 'SRR5110258' is valid 2020-06-21T09:27:30 prefetch.2.10.7: 1) 'SRR5110258' was downloaded successfully Read 13292362 spots for SRR5110258/SRR5110258.sra Written 13292362 spots for SRR5110258/SRR5110258.sra 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: 00:04:55 13292362 reads; of these: 13292362 (100.00%) were unpaired; of these: 384208 (2.89%) aligned 0 times 8994362 (67.67%) aligned exactly 1 time 3913792 (29.44%) aligned >1 times 97.11% overall alignment rate Time searching: 00:04:55 Overall time: 00:04:55 マッピングが完了しました。 samtools でBAM に変換中... [samopen] SAM header is present: 1870 sequences. [bam_sort_core] merging from 8 files... [bam_rmdupse_core] 1553478 / 12908154 = 0.1203 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 @ Sun, 21 Jun 2020 18:37:03: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX2422644/SRX2422644.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX2422644/SRX2422644.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX2422644/SRX2422644.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX2422644/SRX2422644.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 @ Sun, 21 Jun 2020 18:37:03: #1 read tag files... INFO @ Sun, 21 Jun 2020 18:37:03: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 18:37:08: 1000000 INFO @ Sun, 21 Jun 2020 18:37:14: 2000000 INFO @ Sun, 21 Jun 2020 18:37:19: 3000000 INFO @ Sun, 21 Jun 2020 18:37:25: 4000000 INFO @ Sun, 21 Jun 2020 18:37:30: 5000000 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 @ Sun, 21 Jun 2020 18:37:33: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX2422644/SRX2422644.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX2422644/SRX2422644.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX2422644/SRX2422644.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX2422644/SRX2422644.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 @ Sun, 21 Jun 2020 18:37:33: #1 read tag files... INFO @ Sun, 21 Jun 2020 18:37:33: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 18:37:36: 6000000 INFO @ Sun, 21 Jun 2020 18:37:38: 1000000 INFO @ Sun, 21 Jun 2020 18:37:42: 7000000 INFO @ Sun, 21 Jun 2020 18:37:44: 2000000 INFO @ Sun, 21 Jun 2020 18:37:47: 8000000 INFO @ Sun, 21 Jun 2020 18:37:50: 3000000 INFO @ Sun, 21 Jun 2020 18:37:53: 9000000 INFO @ Sun, 21 Jun 2020 18:37:55: 4000000 INFO @ Sun, 21 Jun 2020 18:37:59: 10000000 INFO @ Sun, 21 Jun 2020 18:38:01: 5000000 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 @ Sun, 21 Jun 2020 18:38:03: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX2422644/SRX2422644.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX2422644/SRX2422644.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX2422644/SRX2422644.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX2422644/SRX2422644.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 @ Sun, 21 Jun 2020 18:38:03: #1 read tag files... INFO @ Sun, 21 Jun 2020 18:38:03: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 18:38:05: 11000000 INFO @ Sun, 21 Jun 2020 18:38:07: 6000000 INFO @ Sun, 21 Jun 2020 18:38:07: #1 tag size is determined as 68 bps INFO @ Sun, 21 Jun 2020 18:38:07: #1 tag size = 68 INFO @ Sun, 21 Jun 2020 18:38:07: #1 total tags in treatment: 11354676 INFO @ Sun, 21 Jun 2020 18:38:07: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 18:38:07: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sun, 21 Jun 2020 18:38:08: #1 tags after filtering in treatment: 11354558 INFO @ Sun, 21 Jun 2020 18:38:08: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 18:38:08: #1 finished! INFO @ Sun, 21 Jun 2020 18:38:08: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 18:38:08: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 18:38:09: 1000000 INFO @ Sun, 21 Jun 2020 18:38:09: #2 number of paired peaks: 1495 INFO @ Sun, 21 Jun 2020 18:38:09: start model_add_line... INFO @ Sun, 21 Jun 2020 18:38:09: start X-correlation... INFO @ Sun, 21 Jun 2020 18:38:09: end of X-cor INFO @ Sun, 21 Jun 2020 18:38:09: #2 finished! INFO @ Sun, 21 Jun 2020 18:38:09: #2 predicted fragment length is 79 bps INFO @ Sun, 21 Jun 2020 18:38:09: #2 alternative fragment length(s) may be 4,79 bps INFO @ Sun, 21 Jun 2020 18:38:09: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX2422644/SRX2422644.05_model.r WARNING @ Sun, 21 Jun 2020 18:38:09: #2 Since the d (79) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 18:38:09: #2 You may need to consider one of the other alternative d(s): 4,79 WARNING @ Sun, 21 Jun 2020 18:38:09: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sun, 21 Jun 2020 18:38:09: #3 Call peaks... INFO @ Sun, 21 Jun 2020 18:38:09: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 18:38:12: 7000000 INFO @ Sun, 21 Jun 2020 18:38:14: 2000000 INFO @ Sun, 21 Jun 2020 18:38:18: 8000000 INFO @ Sun, 21 Jun 2020 18:38:20: 3000000 INFO @ Sun, 21 Jun 2020 18:38:24: 9000000 INFO @ Sun, 21 Jun 2020 18:38:26: 4000000 INFO @ Sun, 21 Jun 2020 18:38:30: 10000000 INFO @ Sun, 21 Jun 2020 18:38:31: 5000000 INFO @ Sun, 21 Jun 2020 18:38:34: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 18:38:36: 11000000 INFO @ Sun, 21 Jun 2020 18:38:37: 6000000 INFO @ Sun, 21 Jun 2020 18:38:38: #1 tag size is determined as 68 bps INFO @ Sun, 21 Jun 2020 18:38:38: #1 tag size = 68 INFO @ Sun, 21 Jun 2020 18:38:38: #1 total tags in treatment: 11354676 INFO @ Sun, 21 Jun 2020 18:38:38: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 18:38:38: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sun, 21 Jun 2020 18:38:38: #1 tags after filtering in treatment: 11354558 INFO @ Sun, 21 Jun 2020 18:38:38: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 18:38:38: #1 finished! INFO @ Sun, 21 Jun 2020 18:38:38: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 18:38:38: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 18:38:39: #2 number of paired peaks: 1495 INFO @ Sun, 21 Jun 2020 18:38:39: start model_add_line... INFO @ Sun, 21 Jun 2020 18:38:39: start X-correlation... INFO @ Sun, 21 Jun 2020 18:38:39: end of X-cor INFO @ Sun, 21 Jun 2020 18:38:39: #2 finished! INFO @ Sun, 21 Jun 2020 18:38:39: #2 predicted fragment length is 79 bps INFO @ Sun, 21 Jun 2020 18:38:39: #2 alternative fragment length(s) may be 4,79 bps INFO @ Sun, 21 Jun 2020 18:38:39: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX2422644/SRX2422644.10_model.r WARNING @ Sun, 21 Jun 2020 18:38:39: #2 Since the d (79) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 18:38:39: #2 You may need to consider one of the other alternative d(s): 4,79 WARNING @ Sun, 21 Jun 2020 18:38:39: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sun, 21 Jun 2020 18:38:39: #3 Call peaks... INFO @ Sun, 21 Jun 2020 18:38:39: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 18:38:43: 7000000 INFO @ Sun, 21 Jun 2020 18:38:46: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX2422644/SRX2422644.05_peaks.xls INFO @ Sun, 21 Jun 2020 18:38:46: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX2422644/SRX2422644.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 18:38:46: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX2422644/SRX2422644.05_summits.bed INFO @ Sun, 21 Jun 2020 18:38:46: Done! pass1 - making usageList (595 chroms): 1 millis pass2 - checking and writing primary data (2842 records, 4 fields): 18 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 18:38:48: 8000000 INFO @ Sun, 21 Jun 2020 18:38:54: 9000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 18:39:00: 10000000 INFO @ Sun, 21 Jun 2020 18:39:04: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 18:39:05: 11000000 INFO @ Sun, 21 Jun 2020 18:39:07: #1 tag size is determined as 68 bps INFO @ Sun, 21 Jun 2020 18:39:07: #1 tag size = 68 INFO @ Sun, 21 Jun 2020 18:39:07: #1 total tags in treatment: 11354676 INFO @ Sun, 21 Jun 2020 18:39:07: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 18:39:07: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sun, 21 Jun 2020 18:39:08: #1 tags after filtering in treatment: 11354558 INFO @ Sun, 21 Jun 2020 18:39:08: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 18:39:08: #1 finished! INFO @ Sun, 21 Jun 2020 18:39:08: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 18:39:08: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 18:39:09: #2 number of paired peaks: 1495 INFO @ Sun, 21 Jun 2020 18:39:09: start model_add_line... INFO @ Sun, 21 Jun 2020 18:39:09: start X-correlation... INFO @ Sun, 21 Jun 2020 18:39:09: end of X-cor INFO @ Sun, 21 Jun 2020 18:39:09: #2 finished! INFO @ Sun, 21 Jun 2020 18:39:09: #2 predicted fragment length is 79 bps INFO @ Sun, 21 Jun 2020 18:39:09: #2 alternative fragment length(s) may be 4,79 bps INFO @ Sun, 21 Jun 2020 18:39:09: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX2422644/SRX2422644.20_model.r WARNING @ Sun, 21 Jun 2020 18:39:09: #2 Since the d (79) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 18:39:09: #2 You may need to consider one of the other alternative d(s): 4,79 WARNING @ Sun, 21 Jun 2020 18:39:09: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sun, 21 Jun 2020 18:39:09: #3 Call peaks... INFO @ Sun, 21 Jun 2020 18:39:09: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 18:39:16: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX2422644/SRX2422644.10_peaks.xls INFO @ Sun, 21 Jun 2020 18:39:16: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX2422644/SRX2422644.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 18:39:16: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX2422644/SRX2422644.10_summits.bed INFO @ Sun, 21 Jun 2020 18:39:16: Done! pass1 - making usageList (443 chroms): 1 millis pass2 - checking and writing primary data (1483 records, 4 fields): 14 millis CompletedMACS2peakCalling BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 18:39:33: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 18:39:45: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX2422644/SRX2422644.20_peaks.xls INFO @ Sun, 21 Jun 2020 18:39:45: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX2422644/SRX2422644.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 18:39:45: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX2422644/SRX2422644.20_summits.bed INFO @ Sun, 21 Jun 2020 18:39:45: Done! pass1 - making usageList (259 chroms): 1 millis pass2 - checking and writing primary data (585 records, 4 fields): 8 millis CompletedMACS2peakCalling