Job ID = 6458423 SRX = SRX5226982 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T12:34:23 prefetch.2.10.7: 1) Downloading 'SRR8417897'... 2020-06-21T12:34:23 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T12:36:31 prefetch.2.10.7: HTTPS download succeed 2020-06-21T12:36:31 prefetch.2.10.7: 'SRR8417897' is valid 2020-06-21T12:36:31 prefetch.2.10.7: 1) 'SRR8417897' was downloaded successfully 2020-06-21T12:36:32 prefetch.2.10.7: 'SRR8417897' has 0 unresolved dependencies Read 12142729 spots for SRR8417897/SRR8417897.sra Written 12142729 spots for SRR8417897/SRR8417897.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: 00:04:32 12142729 reads; of these: 12142729 (100.00%) were unpaired; of these: 1122126 (9.24%) aligned 0 times 8095397 (66.67%) aligned exactly 1 time 2925206 (24.09%) aligned >1 times 90.76% overall alignment rate Time searching: 00:04:32 Overall time: 00:04:32 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] 1099447 / 11020603 = 0.0998 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 21:45:59: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX5226982/SRX5226982.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX5226982/SRX5226982.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX5226982/SRX5226982.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX5226982/SRX5226982.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 21:45:59: #1 read tag files... INFO @ Sun, 21 Jun 2020 21:45:59: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 21:46:06: 1000000 INFO @ Sun, 21 Jun 2020 21:46:11: 2000000 INFO @ Sun, 21 Jun 2020 21:46:17: 3000000 INFO @ Sun, 21 Jun 2020 21:46:23: 4000000 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 21:46:29: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX5226982/SRX5226982.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX5226982/SRX5226982.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX5226982/SRX5226982.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX5226982/SRX5226982.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 21:46:29: #1 read tag files... INFO @ Sun, 21 Jun 2020 21:46:29: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 21:46:30: 5000000 INFO @ Sun, 21 Jun 2020 21:46:36: 6000000 INFO @ Sun, 21 Jun 2020 21:46:36: 1000000 INFO @ Sun, 21 Jun 2020 21:46:42: 7000000 INFO @ Sun, 21 Jun 2020 21:46:43: 2000000 INFO @ Sun, 21 Jun 2020 21:46:48: 8000000 INFO @ Sun, 21 Jun 2020 21:46:50: 3000000 INFO @ Sun, 21 Jun 2020 21:46:55: 9000000 INFO @ Sun, 21 Jun 2020 21:46:57: 4000000 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 21:46:59: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX5226982/SRX5226982.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX5226982/SRX5226982.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX5226982/SRX5226982.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX5226982/SRX5226982.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 21:46:59: #1 read tag files... INFO @ Sun, 21 Jun 2020 21:46:59: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 21:47:00: #1 tag size is determined as 75 bps INFO @ Sun, 21 Jun 2020 21:47:00: #1 tag size = 75 INFO @ Sun, 21 Jun 2020 21:47:00: #1 total tags in treatment: 9921156 INFO @ Sun, 21 Jun 2020 21:47:00: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 21:47:00: #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 21:47:01: #1 tags after filtering in treatment: 9921002 INFO @ Sun, 21 Jun 2020 21:47:01: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 21:47:01: #1 finished! INFO @ Sun, 21 Jun 2020 21:47:01: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 21:47:01: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 21:47:01: #2 number of paired peaks: 1200 INFO @ Sun, 21 Jun 2020 21:47:01: start model_add_line... INFO @ Sun, 21 Jun 2020 21:47:02: start X-correlation... INFO @ Sun, 21 Jun 2020 21:47:02: end of X-cor INFO @ Sun, 21 Jun 2020 21:47:02: #2 finished! INFO @ Sun, 21 Jun 2020 21:47:02: #2 predicted fragment length is 95 bps INFO @ Sun, 21 Jun 2020 21:47:02: #2 alternative fragment length(s) may be 95 bps INFO @ Sun, 21 Jun 2020 21:47:02: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX5226982/SRX5226982.05_model.r WARNING @ Sun, 21 Jun 2020 21:47:02: #2 Since the d (95) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 21:47:02: #2 You may need to consider one of the other alternative d(s): 95 WARNING @ Sun, 21 Jun 2020 21:47:02: #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 21:47:02: #3 Call peaks... INFO @ Sun, 21 Jun 2020 21:47:02: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 21:47:04: 5000000 INFO @ Sun, 21 Jun 2020 21:47:06: 1000000 INFO @ Sun, 21 Jun 2020 21:47:11: 6000000 INFO @ Sun, 21 Jun 2020 21:47:12: 2000000 INFO @ Sun, 21 Jun 2020 21:47:18: 7000000 INFO @ Sun, 21 Jun 2020 21:47:18: 3000000 INFO @ Sun, 21 Jun 2020 21:47:25: 4000000 INFO @ Sun, 21 Jun 2020 21:47:25: 8000000 INFO @ Sun, 21 Jun 2020 21:47:25: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 21:47:31: 5000000 INFO @ Sun, 21 Jun 2020 21:47:32: 9000000 INFO @ Sun, 21 Jun 2020 21:47:37: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX5226982/SRX5226982.05_peaks.xls INFO @ Sun, 21 Jun 2020 21:47:37: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX5226982/SRX5226982.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 21:47:37: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX5226982/SRX5226982.05_summits.bed INFO @ Sun, 21 Jun 2020 21:47:37: Done! INFO @ Sun, 21 Jun 2020 21:47:37: 6000000 pass1 - making usageList (428 chroms): 2 millis pass2 - checking and writing primary data (3731 records, 4 fields): 15 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 21:47:38: #1 tag size is determined as 75 bps INFO @ Sun, 21 Jun 2020 21:47:38: #1 tag size = 75 INFO @ Sun, 21 Jun 2020 21:47:38: #1 total tags in treatment: 9921156 INFO @ Sun, 21 Jun 2020 21:47:38: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 21:47:38: #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 21:47:39: #1 tags after filtering in treatment: 9921002 INFO @ Sun, 21 Jun 2020 21:47:39: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 21:47:39: #1 finished! INFO @ Sun, 21 Jun 2020 21:47:39: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 21:47:39: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 21:47:40: #2 number of paired peaks: 1200 INFO @ Sun, 21 Jun 2020 21:47:40: start model_add_line... INFO @ Sun, 21 Jun 2020 21:47:40: start X-correlation... INFO @ Sun, 21 Jun 2020 21:47:40: end of X-cor INFO @ Sun, 21 Jun 2020 21:47:40: #2 finished! INFO @ Sun, 21 Jun 2020 21:47:40: #2 predicted fragment length is 95 bps INFO @ Sun, 21 Jun 2020 21:47:40: #2 alternative fragment length(s) may be 95 bps INFO @ Sun, 21 Jun 2020 21:47:40: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX5226982/SRX5226982.10_model.r WARNING @ Sun, 21 Jun 2020 21:47:40: #2 Since the d (95) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 21:47:40: #2 You may need to consider one of the other alternative d(s): 95 WARNING @ Sun, 21 Jun 2020 21:47:40: #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 21:47:40: #3 Call peaks... INFO @ Sun, 21 Jun 2020 21:47:40: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 21:47:44: 7000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 21:47:50: 8000000 INFO @ Sun, 21 Jun 2020 21:47:56: 9000000 INFO @ Sun, 21 Jun 2020 21:48:02: #1 tag size is determined as 75 bps INFO @ Sun, 21 Jun 2020 21:48:02: #1 tag size = 75 INFO @ Sun, 21 Jun 2020 21:48:02: #1 total tags in treatment: 9921156 INFO @ Sun, 21 Jun 2020 21:48:02: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 21:48:02: #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 21:48:02: #1 tags after filtering in treatment: 9921002 INFO @ Sun, 21 Jun 2020 21:48:02: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 21:48:02: #1 finished! INFO @ Sun, 21 Jun 2020 21:48:02: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 21:48:02: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 21:48:03: #2 number of paired peaks: 1200 INFO @ Sun, 21 Jun 2020 21:48:03: start model_add_line... INFO @ Sun, 21 Jun 2020 21:48:03: start X-correlation... INFO @ Sun, 21 Jun 2020 21:48:03: end of X-cor INFO @ Sun, 21 Jun 2020 21:48:03: #2 finished! INFO @ Sun, 21 Jun 2020 21:48:03: #2 predicted fragment length is 95 bps INFO @ Sun, 21 Jun 2020 21:48:03: #2 alternative fragment length(s) may be 95 bps INFO @ Sun, 21 Jun 2020 21:48:03: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX5226982/SRX5226982.20_model.r WARNING @ Sun, 21 Jun 2020 21:48:03: #2 Since the d (95) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 21:48:03: #2 You may need to consider one of the other alternative d(s): 95 WARNING @ Sun, 21 Jun 2020 21:48:03: #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 21:48:03: #3 Call peaks... INFO @ Sun, 21 Jun 2020 21:48:03: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 21:48:04: #3 Call peaks for each chromosome... BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 21:48:15: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX5226982/SRX5226982.10_peaks.xls INFO @ Sun, 21 Jun 2020 21:48:16: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX5226982/SRX5226982.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 21:48:16: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX5226982/SRX5226982.10_summits.bed INFO @ Sun, 21 Jun 2020 21:48:16: Done! pass1 - making usageList (324 chroms): 1 millis pass2 - checking and writing primary data (1781 records, 4 fields): 13 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 21:48:27: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 21:48:39: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX5226982/SRX5226982.20_peaks.xls INFO @ Sun, 21 Jun 2020 21:48:39: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX5226982/SRX5226982.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 21:48:39: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX5226982/SRX5226982.20_summits.bed INFO @ Sun, 21 Jun 2020 21:48:39: Done! pass1 - making usageList (196 chroms): 1 millis pass2 - checking and writing primary data (665 records, 4 fields): 7 millis CompletedMACS2peakCalling