Job ID = 6458450 SRX = SRX5227004 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T12:25:34 prefetch.2.10.7: 1) Downloading 'SRR8417919'... 2020-06-21T12:25:34 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T12:29:30 prefetch.2.10.7: HTTPS download succeed 2020-06-21T12:29:30 prefetch.2.10.7: 1) 'SRR8417919' was downloaded successfully 2020-06-21T12:29:30 prefetch.2.10.7: 'SRR8417919' has 0 unresolved dependencies Read 20388222 spots for SRR8417919/SRR8417919.sra Written 20388222 spots for SRR8417919/SRR8417919.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: 00:07:40 20388222 reads; of these: 20388222 (100.00%) were unpaired; of these: 1722769 (8.45%) aligned 0 times 12651723 (62.05%) aligned exactly 1 time 6013730 (29.50%) aligned >1 times 91.55% overall alignment rate Time searching: 00:07:40 Overall time: 00:07:40 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] 3598435 / 18665453 = 0.1928 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 21:44:11: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX5227004/SRX5227004.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX5227004/SRX5227004.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX5227004/SRX5227004.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX5227004/SRX5227004.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 21:44:11: #1 read tag files... INFO @ Sun, 21 Jun 2020 21:44:11: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 21:44:17: 1000000 INFO @ Sun, 21 Jun 2020 21:44:22: 2000000 INFO @ Sun, 21 Jun 2020 21:44:28: 3000000 INFO @ Sun, 21 Jun 2020 21:44:33: 4000000 INFO @ Sun, 21 Jun 2020 21:44:38: 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 21:44:41: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX5227004/SRX5227004.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX5227004/SRX5227004.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX5227004/SRX5227004.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX5227004/SRX5227004.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 21:44:41: #1 read tag files... INFO @ Sun, 21 Jun 2020 21:44:41: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 21:44:44: 6000000 INFO @ Sun, 21 Jun 2020 21:44:48: 1000000 INFO @ Sun, 21 Jun 2020 21:44:50: 7000000 INFO @ Sun, 21 Jun 2020 21:44:54: 2000000 INFO @ Sun, 21 Jun 2020 21:44:55: 8000000 INFO @ Sun, 21 Jun 2020 21:45:01: 3000000 INFO @ Sun, 21 Jun 2020 21:45:01: 9000000 INFO @ Sun, 21 Jun 2020 21:45:07: 10000000 INFO @ Sun, 21 Jun 2020 21:45:07: 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 21:45:11: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX5227004/SRX5227004.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX5227004/SRX5227004.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX5227004/SRX5227004.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX5227004/SRX5227004.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 21:45:11: #1 read tag files... INFO @ Sun, 21 Jun 2020 21:45:11: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 21:45:13: 11000000 INFO @ Sun, 21 Jun 2020 21:45:14: 5000000 INFO @ Sun, 21 Jun 2020 21:45:17: 1000000 INFO @ Sun, 21 Jun 2020 21:45:18: 12000000 INFO @ Sun, 21 Jun 2020 21:45:20: 6000000 INFO @ Sun, 21 Jun 2020 21:45:23: 2000000 INFO @ Sun, 21 Jun 2020 21:45:24: 13000000 INFO @ Sun, 21 Jun 2020 21:45:27: 7000000 INFO @ Sun, 21 Jun 2020 21:45:28: 3000000 INFO @ Sun, 21 Jun 2020 21:45:30: 14000000 INFO @ Sun, 21 Jun 2020 21:45:33: 8000000 INFO @ Sun, 21 Jun 2020 21:45:34: 4000000 INFO @ Sun, 21 Jun 2020 21:45:36: 15000000 INFO @ Sun, 21 Jun 2020 21:45:36: #1 tag size is determined as 75 bps INFO @ Sun, 21 Jun 2020 21:45:36: #1 tag size = 75 INFO @ Sun, 21 Jun 2020 21:45:36: #1 total tags in treatment: 15067018 INFO @ Sun, 21 Jun 2020 21:45:36: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 21:45:36: #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 21:45:37: #1 tags after filtering in treatment: 15066892 INFO @ Sun, 21 Jun 2020 21:45:37: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 21:45:37: #1 finished! INFO @ Sun, 21 Jun 2020 21:45:37: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 21:45:37: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 21:45:38: #2 number of paired peaks: 1545 INFO @ Sun, 21 Jun 2020 21:45:38: start model_add_line... INFO @ Sun, 21 Jun 2020 21:45:38: start X-correlation... INFO @ Sun, 21 Jun 2020 21:45:38: end of X-cor INFO @ Sun, 21 Jun 2020 21:45:38: #2 finished! INFO @ Sun, 21 Jun 2020 21:45:38: #2 predicted fragment length is 106 bps INFO @ Sun, 21 Jun 2020 21:45:38: #2 alternative fragment length(s) may be 106 bps INFO @ Sun, 21 Jun 2020 21:45:38: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX5227004/SRX5227004.05_model.r WARNING @ Sun, 21 Jun 2020 21:45:38: #2 Since the d (106) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 21:45:38: #2 You may need to consider one of the other alternative d(s): 106 WARNING @ Sun, 21 Jun 2020 21:45:38: #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 21:45:38: #3 Call peaks... INFO @ Sun, 21 Jun 2020 21:45:38: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 21:45:39: 5000000 INFO @ Sun, 21 Jun 2020 21:45:40: 9000000 INFO @ Sun, 21 Jun 2020 21:45:45: 6000000 INFO @ Sun, 21 Jun 2020 21:45:46: 10000000 INFO @ Sun, 21 Jun 2020 21:45:50: 7000000 INFO @ Sun, 21 Jun 2020 21:45:52: 11000000 INFO @ Sun, 21 Jun 2020 21:45:56: 8000000 INFO @ Sun, 21 Jun 2020 21:45:58: 12000000 INFO @ Sun, 21 Jun 2020 21:46:02: 9000000 INFO @ Sun, 21 Jun 2020 21:46:05: 13000000 INFO @ Sun, 21 Jun 2020 21:46:07: 10000000 INFO @ Sun, 21 Jun 2020 21:46:10: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 21:46:11: 14000000 INFO @ Sun, 21 Jun 2020 21:46:13: 11000000 INFO @ Sun, 21 Jun 2020 21:46:18: 15000000 INFO @ Sun, 21 Jun 2020 21:46:18: #1 tag size is determined as 75 bps INFO @ Sun, 21 Jun 2020 21:46:18: #1 tag size = 75 INFO @ Sun, 21 Jun 2020 21:46:18: #1 total tags in treatment: 15067018 INFO @ Sun, 21 Jun 2020 21:46:18: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 21:46:18: #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 21:46:18: 12000000 INFO @ Sun, 21 Jun 2020 21:46:19: #1 tags after filtering in treatment: 15066892 INFO @ Sun, 21 Jun 2020 21:46:19: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 21:46:19: #1 finished! INFO @ Sun, 21 Jun 2020 21:46:19: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 21:46:19: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 21:46:20: #2 number of paired peaks: 1545 INFO @ Sun, 21 Jun 2020 21:46:20: start model_add_line... INFO @ Sun, 21 Jun 2020 21:46:20: start X-correlation... INFO @ Sun, 21 Jun 2020 21:46:20: end of X-cor INFO @ Sun, 21 Jun 2020 21:46:20: #2 finished! INFO @ Sun, 21 Jun 2020 21:46:20: #2 predicted fragment length is 106 bps INFO @ Sun, 21 Jun 2020 21:46:20: #2 alternative fragment length(s) may be 106 bps INFO @ Sun, 21 Jun 2020 21:46:20: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX5227004/SRX5227004.10_model.r WARNING @ Sun, 21 Jun 2020 21:46:20: #2 Since the d (106) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 21:46:20: #2 You may need to consider one of the other alternative d(s): 106 WARNING @ Sun, 21 Jun 2020 21:46:20: #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 21:46:20: #3 Call peaks... INFO @ Sun, 21 Jun 2020 21:46:20: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 21:46:24: 13000000 INFO @ Sun, 21 Jun 2020 21:46:25: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX5227004/SRX5227004.05_peaks.xls INFO @ Sun, 21 Jun 2020 21:46:25: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX5227004/SRX5227004.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 21:46:25: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX5227004/SRX5227004.05_summits.bed INFO @ Sun, 21 Jun 2020 21:46:25: Done! pass1 - making usageList (713 chroms): 2 millis pass2 - checking and writing primary data (5344 records, 4 fields): 24 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 21:46:30: 14000000 INFO @ Sun, 21 Jun 2020 21:46:35: 15000000 INFO @ Sun, 21 Jun 2020 21:46:36: #1 tag size is determined as 75 bps INFO @ Sun, 21 Jun 2020 21:46:36: #1 tag size = 75 INFO @ Sun, 21 Jun 2020 21:46:36: #1 total tags in treatment: 15067018 INFO @ Sun, 21 Jun 2020 21:46:36: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 21:46:36: #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 21:46:36: #1 tags after filtering in treatment: 15066892 INFO @ Sun, 21 Jun 2020 21:46:36: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 21:46:36: #1 finished! INFO @ Sun, 21 Jun 2020 21:46:36: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 21:46:36: #2 looking for paired plus/minus strand peaks... BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 21:46:37: #2 number of paired peaks: 1545 INFO @ Sun, 21 Jun 2020 21:46:37: start model_add_line... INFO @ Sun, 21 Jun 2020 21:46:37: start X-correlation... INFO @ Sun, 21 Jun 2020 21:46:37: end of X-cor INFO @ Sun, 21 Jun 2020 21:46:37: #2 finished! INFO @ Sun, 21 Jun 2020 21:46:37: #2 predicted fragment length is 106 bps INFO @ Sun, 21 Jun 2020 21:46:37: #2 alternative fragment length(s) may be 106 bps INFO @ Sun, 21 Jun 2020 21:46:37: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX5227004/SRX5227004.20_model.r WARNING @ Sun, 21 Jun 2020 21:46:37: #2 Since the d (106) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 21:46:37: #2 You may need to consider one of the other alternative d(s): 106 WARNING @ Sun, 21 Jun 2020 21:46:37: #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 21:46:37: #3 Call peaks... INFO @ Sun, 21 Jun 2020 21:46:37: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 21:46:51: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 21:47:06: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX5227004/SRX5227004.10_peaks.xls INFO @ Sun, 21 Jun 2020 21:47:06: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX5227004/SRX5227004.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 21:47:06: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX5227004/SRX5227004.10_summits.bed INFO @ Sun, 21 Jun 2020 21:47:06: Done! pass1 - making usageList (595 chroms): 1 millis pass2 - checking and writing primary data (3017 records, 4 fields): 18 millis CompletedMACS2peakCalling BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 21:47:10: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 21:47:26: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX5227004/SRX5227004.20_peaks.xls INFO @ Sun, 21 Jun 2020 21:47:26: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX5227004/SRX5227004.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 21:47:26: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX5227004/SRX5227004.20_summits.bed INFO @ Sun, 21 Jun 2020 21:47:26: Done! pass1 - making usageList (340 chroms): 1 millis pass2 - checking and writing primary data (1231 records, 4 fields): 12 millis CompletedMACS2peakCalling