Job ID = 6459096 SRX = SRX6386768 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T13:09:49 prefetch.2.10.7: 1) Downloading 'SRR9624500'... 2020-06-21T13:09:49 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T13:15:46 prefetch.2.10.7: HTTPS download succeed 2020-06-21T13:15:46 prefetch.2.10.7: 1) 'SRR9624500' was downloaded successfully Read 21424868 spots for SRR9624500/SRR9624500.sra Written 21424868 spots for SRR9624500/SRR9624500.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: 00:03:30 21424868 reads; of these: 21424868 (100.00%) were unpaired; of these: 12125968 (56.60%) aligned 0 times 6944036 (32.41%) aligned exactly 1 time 2354864 (10.99%) aligned >1 times 43.40% overall alignment rate Time searching: 00:03:30 Overall time: 00:03:30 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_rmdupse_core] 3845730 / 9298900 = 0.4136 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 22:22:55: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX6386768/SRX6386768.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX6386768/SRX6386768.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX6386768/SRX6386768.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX6386768/SRX6386768.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 22:22:55: #1 read tag files... INFO @ Sun, 21 Jun 2020 22:22:55: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 22:23:01: 1000000 INFO @ Sun, 21 Jun 2020 22:23:07: 2000000 INFO @ Sun, 21 Jun 2020 22:23:14: 3000000 INFO @ Sun, 21 Jun 2020 22:23:20: 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 22:23:25: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX6386768/SRX6386768.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX6386768/SRX6386768.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX6386768/SRX6386768.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX6386768/SRX6386768.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 22:23:25: #1 read tag files... INFO @ Sun, 21 Jun 2020 22:23:25: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 22:23:27: 5000000 INFO @ Sun, 21 Jun 2020 22:23:30: #1 tag size is determined as 51 bps INFO @ Sun, 21 Jun 2020 22:23:30: #1 tag size = 51 INFO @ Sun, 21 Jun 2020 22:23:30: #1 total tags in treatment: 5453170 INFO @ Sun, 21 Jun 2020 22:23:30: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 22:23:30: #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 22:23:30: #1 tags after filtering in treatment: 5453128 INFO @ Sun, 21 Jun 2020 22:23:30: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 22:23:30: #1 finished! INFO @ Sun, 21 Jun 2020 22:23:30: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 22:23:30: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 22:23:31: #2 number of paired peaks: 1340 INFO @ Sun, 21 Jun 2020 22:23:31: start model_add_line... INFO @ Sun, 21 Jun 2020 22:23:31: start X-correlation... INFO @ Sun, 21 Jun 2020 22:23:31: end of X-cor INFO @ Sun, 21 Jun 2020 22:23:31: #2 finished! INFO @ Sun, 21 Jun 2020 22:23:31: #2 predicted fragment length is 59 bps INFO @ Sun, 21 Jun 2020 22:23:31: #2 alternative fragment length(s) may be 4,59 bps INFO @ Sun, 21 Jun 2020 22:23:31: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX6386768/SRX6386768.05_model.r WARNING @ Sun, 21 Jun 2020 22:23:31: #2 Since the d (59) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 22:23:31: #2 You may need to consider one of the other alternative d(s): 4,59 WARNING @ Sun, 21 Jun 2020 22:23:31: #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 22:23:31: #3 Call peaks... INFO @ Sun, 21 Jun 2020 22:23:31: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 22:23:32: 1000000 INFO @ Sun, 21 Jun 2020 22:23:39: 2000000 INFO @ Sun, 21 Jun 2020 22:23:43: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 22:23:45: 3000000 INFO @ Sun, 21 Jun 2020 22:23:49: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX6386768/SRX6386768.05_peaks.xls INFO @ Sun, 21 Jun 2020 22:23:49: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX6386768/SRX6386768.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 22:23:49: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX6386768/SRX6386768.05_summits.bed INFO @ Sun, 21 Jun 2020 22:23:49: Done! pass1 - making usageList (592 chroms): 1 millis pass2 - checking and writing primary data (2328 records, 4 fields): 18 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 22:23:51: 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 22:23:55: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX6386768/SRX6386768.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX6386768/SRX6386768.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX6386768/SRX6386768.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX6386768/SRX6386768.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 22:23:55: #1 read tag files... INFO @ Sun, 21 Jun 2020 22:23:55: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 22:23:58: 5000000 INFO @ Sun, 21 Jun 2020 22:24:01: #1 tag size is determined as 51 bps INFO @ Sun, 21 Jun 2020 22:24:01: #1 tag size = 51 INFO @ Sun, 21 Jun 2020 22:24:01: #1 total tags in treatment: 5453170 INFO @ Sun, 21 Jun 2020 22:24:01: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 22:24:01: #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 22:24:02: #1 tags after filtering in treatment: 5453128 INFO @ Sun, 21 Jun 2020 22:24:02: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 22:24:02: #1 finished! INFO @ Sun, 21 Jun 2020 22:24:02: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 22:24:02: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 22:24:02: 1000000 INFO @ Sun, 21 Jun 2020 22:24:02: #2 number of paired peaks: 1340 INFO @ Sun, 21 Jun 2020 22:24:02: start model_add_line... INFO @ Sun, 21 Jun 2020 22:24:02: start X-correlation... INFO @ Sun, 21 Jun 2020 22:24:02: end of X-cor INFO @ Sun, 21 Jun 2020 22:24:02: #2 finished! INFO @ Sun, 21 Jun 2020 22:24:02: #2 predicted fragment length is 59 bps INFO @ Sun, 21 Jun 2020 22:24:02: #2 alternative fragment length(s) may be 4,59 bps INFO @ Sun, 21 Jun 2020 22:24:02: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX6386768/SRX6386768.10_model.r WARNING @ Sun, 21 Jun 2020 22:24:02: #2 Since the d (59) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 22:24:02: #2 You may need to consider one of the other alternative d(s): 4,59 WARNING @ Sun, 21 Jun 2020 22:24:02: #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 22:24:02: #3 Call peaks... INFO @ Sun, 21 Jun 2020 22:24:02: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 22:24:08: 2000000 INFO @ Sun, 21 Jun 2020 22:24:15: 3000000 INFO @ Sun, 21 Jun 2020 22:24:15: #3 Call peaks for each chromosome... BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 22:24:21: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX6386768/SRX6386768.10_peaks.xls INFO @ Sun, 21 Jun 2020 22:24:21: 4000000 INFO @ Sun, 21 Jun 2020 22:24:21: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX6386768/SRX6386768.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 22:24:21: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX6386768/SRX6386768.10_summits.bed INFO @ Sun, 21 Jun 2020 22:24:21: Done! pass1 - making usageList (537 chroms): 2 millis pass2 - checking and writing primary data (1762 records, 4 fields): 17 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 22:24:28: 5000000 INFO @ Sun, 21 Jun 2020 22:24:31: #1 tag size is determined as 51 bps INFO @ Sun, 21 Jun 2020 22:24:31: #1 tag size = 51 INFO @ Sun, 21 Jun 2020 22:24:31: #1 total tags in treatment: 5453170 INFO @ Sun, 21 Jun 2020 22:24:31: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 22:24:31: #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 22:24:31: #1 tags after filtering in treatment: 5453128 INFO @ Sun, 21 Jun 2020 22:24:31: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 22:24:31: #1 finished! INFO @ Sun, 21 Jun 2020 22:24:31: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 22:24:31: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 22:24:32: #2 number of paired peaks: 1340 INFO @ Sun, 21 Jun 2020 22:24:32: start model_add_line... INFO @ Sun, 21 Jun 2020 22:24:32: start X-correlation... INFO @ Sun, 21 Jun 2020 22:24:32: end of X-cor INFO @ Sun, 21 Jun 2020 22:24:32: #2 finished! INFO @ Sun, 21 Jun 2020 22:24:32: #2 predicted fragment length is 59 bps INFO @ Sun, 21 Jun 2020 22:24:32: #2 alternative fragment length(s) may be 4,59 bps INFO @ Sun, 21 Jun 2020 22:24:32: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX6386768/SRX6386768.20_model.r WARNING @ Sun, 21 Jun 2020 22:24:32: #2 Since the d (59) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 22:24:32: #2 You may need to consider one of the other alternative d(s): 4,59 WARNING @ Sun, 21 Jun 2020 22:24:32: #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 22:24:32: #3 Call peaks... INFO @ Sun, 21 Jun 2020 22:24:32: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 22:24:44: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 22:24:50: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX6386768/SRX6386768.20_peaks.xls INFO @ Sun, 21 Jun 2020 22:24:50: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX6386768/SRX6386768.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 22:24:50: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX6386768/SRX6386768.20_summits.bed INFO @ Sun, 21 Jun 2020 22:24:50: Done! pass1 - making usageList (347 chroms): 1 millis pass2 - checking and writing primary data (709 records, 4 fields): 13 millis CompletedMACS2peakCalling