Job ID = 6457868 SRX = SRX4823784 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T12:02:20 prefetch.2.10.7: 1) Downloading 'SRR7992742'... 2020-06-21T12:02:20 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T12:06:42 prefetch.2.10.7: HTTPS download succeed 2020-06-21T12:06:42 prefetch.2.10.7: 1) 'SRR7992742' was downloaded successfully 2020-06-21T12:06:42 prefetch.2.10.7: 'SRR7992742' has 0 unresolved dependencies Read 41239710 spots for SRR7992742/SRR7992742.sra Written 41239710 spots for SRR7992742/SRR7992742.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: 00:14:11 41239710 reads; of these: 41239710 (100.00%) were unpaired; of these: 4061901 (9.85%) aligned 0 times 26233620 (63.61%) aligned exactly 1 time 10944189 (26.54%) aligned >1 times 90.15% overall alignment rate Time searching: 00:14:11 Overall time: 00:14:11 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 16 files... [bam_rmdupse_core] 22883885 / 37177809 = 0.6155 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 21:29:39: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX4823784/SRX4823784.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX4823784/SRX4823784.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX4823784/SRX4823784.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX4823784/SRX4823784.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 21:29:39: #1 read tag files... INFO @ Sun, 21 Jun 2020 21:29:39: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 21:29:44: 1000000 INFO @ Sun, 21 Jun 2020 21:29:49: 2000000 INFO @ Sun, 21 Jun 2020 21:29:54: 3000000 INFO @ Sun, 21 Jun 2020 21:29:59: 4000000 INFO @ Sun, 21 Jun 2020 21:30:04: 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 21:30:09: 6000000 INFO @ Sun, 21 Jun 2020 21:30:09: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX4823784/SRX4823784.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX4823784/SRX4823784.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX4823784/SRX4823784.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX4823784/SRX4823784.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 21:30:09: #1 read tag files... INFO @ Sun, 21 Jun 2020 21:30:09: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 21:30:14: 7000000 INFO @ Sun, 21 Jun 2020 21:30:15: 1000000 INFO @ Sun, 21 Jun 2020 21:30:18: 8000000 INFO @ Sun, 21 Jun 2020 21:30:20: 2000000 INFO @ Sun, 21 Jun 2020 21:30:23: 9000000 INFO @ Sun, 21 Jun 2020 21:30:25: 3000000 INFO @ Sun, 21 Jun 2020 21:30:28: 10000000 INFO @ Sun, 21 Jun 2020 21:30:30: 4000000 INFO @ Sun, 21 Jun 2020 21:30:34: 11000000 INFO @ Sun, 21 Jun 2020 21:30:35: 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 21:30:39: 12000000 INFO @ Sun, 21 Jun 2020 21:30:39: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX4823784/SRX4823784.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX4823784/SRX4823784.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX4823784/SRX4823784.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX4823784/SRX4823784.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 21:30:39: #1 read tag files... INFO @ Sun, 21 Jun 2020 21:30:39: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 21:30:40: 6000000 INFO @ Sun, 21 Jun 2020 21:30:44: 13000000 INFO @ Sun, 21 Jun 2020 21:30:45: 1000000 INFO @ Sun, 21 Jun 2020 21:30:45: 7000000 INFO @ Sun, 21 Jun 2020 21:30:49: 14000000 INFO @ Sun, 21 Jun 2020 21:30:50: 2000000 INFO @ Sun, 21 Jun 2020 21:30:50: 8000000 INFO @ Sun, 21 Jun 2020 21:30:51: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 21:30:51: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 21:30:51: #1 total tags in treatment: 14293924 INFO @ Sun, 21 Jun 2020 21:30:51: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 21:30:51: #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 21:30:51: #1 tags after filtering in treatment: 14293854 INFO @ Sun, 21 Jun 2020 21:30:51: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 21:30:51: #1 finished! INFO @ Sun, 21 Jun 2020 21:30:51: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 21:30:51: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 21:30:53: #2 number of paired peaks: 1843 INFO @ Sun, 21 Jun 2020 21:30:53: start model_add_line... INFO @ Sun, 21 Jun 2020 21:30:53: start X-correlation... INFO @ Sun, 21 Jun 2020 21:30:53: end of X-cor INFO @ Sun, 21 Jun 2020 21:30:53: #2 finished! INFO @ Sun, 21 Jun 2020 21:30:53: #2 predicted fragment length is 96 bps INFO @ Sun, 21 Jun 2020 21:30:53: #2 alternative fragment length(s) may be 4,96 bps INFO @ Sun, 21 Jun 2020 21:30:53: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX4823784/SRX4823784.05_model.r WARNING @ Sun, 21 Jun 2020 21:30:53: #2 Since the d (96) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 21:30:53: #2 You may need to consider one of the other alternative d(s): 4,96 WARNING @ Sun, 21 Jun 2020 21:30:53: #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 21:30:53: #3 Call peaks... INFO @ Sun, 21 Jun 2020 21:30:53: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 21:30:55: 3000000 INFO @ Sun, 21 Jun 2020 21:30:55: 9000000 INFO @ Sun, 21 Jun 2020 21:31:00: 4000000 INFO @ Sun, 21 Jun 2020 21:31:00: 10000000 INFO @ Sun, 21 Jun 2020 21:31:05: 5000000 INFO @ Sun, 21 Jun 2020 21:31:06: 11000000 INFO @ Sun, 21 Jun 2020 21:31:10: 6000000 INFO @ Sun, 21 Jun 2020 21:31:11: 12000000 INFO @ Sun, 21 Jun 2020 21:31:16: 7000000 INFO @ Sun, 21 Jun 2020 21:31:16: 13000000 INFO @ Sun, 21 Jun 2020 21:31:21: 8000000 INFO @ Sun, 21 Jun 2020 21:31:22: 14000000 INFO @ Sun, 21 Jun 2020 21:31:23: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 21:31:23: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 21:31:23: #1 total tags in treatment: 14293924 INFO @ Sun, 21 Jun 2020 21:31:23: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 21:31:23: #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 21:31:24: #1 tags after filtering in treatment: 14293854 INFO @ Sun, 21 Jun 2020 21:31:24: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 21:31:24: #1 finished! INFO @ Sun, 21 Jun 2020 21:31:24: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 21:31:24: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 21:31:25: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 21:31:25: #2 number of paired peaks: 1843 INFO @ Sun, 21 Jun 2020 21:31:25: start model_add_line... INFO @ Sun, 21 Jun 2020 21:31:25: start X-correlation... INFO @ Sun, 21 Jun 2020 21:31:25: end of X-cor INFO @ Sun, 21 Jun 2020 21:31:25: #2 finished! INFO @ Sun, 21 Jun 2020 21:31:25: #2 predicted fragment length is 96 bps INFO @ Sun, 21 Jun 2020 21:31:25: #2 alternative fragment length(s) may be 4,96 bps INFO @ Sun, 21 Jun 2020 21:31:25: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX4823784/SRX4823784.10_model.r WARNING @ Sun, 21 Jun 2020 21:31:25: #2 Since the d (96) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 21:31:25: #2 You may need to consider one of the other alternative d(s): 4,96 WARNING @ Sun, 21 Jun 2020 21:31:25: #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 21:31:25: #3 Call peaks... INFO @ Sun, 21 Jun 2020 21:31:25: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 21:31:26: 9000000 INFO @ Sun, 21 Jun 2020 21:31:31: 10000000 INFO @ Sun, 21 Jun 2020 21:31:37: 11000000 INFO @ Sun, 21 Jun 2020 21:31:41: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX4823784/SRX4823784.05_peaks.xls INFO @ Sun, 21 Jun 2020 21:31:41: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX4823784/SRX4823784.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 21:31:41: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX4823784/SRX4823784.05_summits.bed INFO @ Sun, 21 Jun 2020 21:31:42: Done! INFO @ Sun, 21 Jun 2020 21:31:42: 12000000 pass1 - making usageList (809 chroms): 2 millis pass2 - checking and writing primary data (12064 records, 4 fields): 36 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 21:31:47: 13000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 21:31:52: 14000000 INFO @ Sun, 21 Jun 2020 21:31:54: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 21:31:54: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 21:31:54: #1 total tags in treatment: 14293924 INFO @ Sun, 21 Jun 2020 21:31:54: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 21:31:54: #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 21:31:54: #1 tags after filtering in treatment: 14293854 INFO @ Sun, 21 Jun 2020 21:31:54: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 21:31:54: #1 finished! INFO @ Sun, 21 Jun 2020 21:31:54: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 21:31:54: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 21:31:55: #2 number of paired peaks: 1843 INFO @ Sun, 21 Jun 2020 21:31:55: start model_add_line... INFO @ Sun, 21 Jun 2020 21:31:56: start X-correlation... INFO @ Sun, 21 Jun 2020 21:31:56: end of X-cor INFO @ Sun, 21 Jun 2020 21:31:56: #2 finished! INFO @ Sun, 21 Jun 2020 21:31:56: #2 predicted fragment length is 96 bps INFO @ Sun, 21 Jun 2020 21:31:56: #2 alternative fragment length(s) may be 4,96 bps INFO @ Sun, 21 Jun 2020 21:31:56: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX4823784/SRX4823784.20_model.r WARNING @ Sun, 21 Jun 2020 21:31:56: #2 Since the d (96) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 21:31:56: #2 You may need to consider one of the other alternative d(s): 4,96 WARNING @ Sun, 21 Jun 2020 21:31:56: #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 21:31:56: #3 Call peaks... INFO @ Sun, 21 Jun 2020 21:31:56: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 21:31:59: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 21:32:16: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX4823784/SRX4823784.10_peaks.xls INFO @ Sun, 21 Jun 2020 21:32:16: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX4823784/SRX4823784.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 21:32:16: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX4823784/SRX4823784.10_summits.bed INFO @ Sun, 21 Jun 2020 21:32:16: Done! pass1 - making usageList (692 chroms): 2 millis pass2 - checking and writing primary data (7177 records, 4 fields): 27 millis CompletedMACS2peakCalling BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 21:32:29: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 21:32:44: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX4823784/SRX4823784.20_peaks.xls INFO @ Sun, 21 Jun 2020 21:32:44: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX4823784/SRX4823784.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 21:32:44: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX4823784/SRX4823784.20_summits.bed INFO @ Sun, 21 Jun 2020 21:32:44: Done! pass1 - making usageList (597 chroms): 2 millis pass2 - checking and writing primary data (3508 records, 4 fields): 22 millis CompletedMACS2peakCalling