Job ID = 6457839 SRX = SRX4801803 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T12:06:24 prefetch.2.10.7: 1) Downloading 'SRR7968388'... 2020-06-21T12:06:24 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T12:09:57 prefetch.2.10.7: HTTPS download succeed 2020-06-21T12:09:57 prefetch.2.10.7: 1) 'SRR7968388' was downloaded successfully Read 19478435 spots for SRR7968388/SRR7968388.sra Written 19478435 spots for SRR7968388/SRR7968388.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: 00:07:01 19478435 reads; of these: 19478435 (100.00%) were unpaired; of these: 802631 (4.12%) aligned 0 times 12884751 (66.15%) aligned exactly 1 time 5791053 (29.73%) aligned >1 times 95.88% overall alignment rate Time searching: 00:07:01 Overall time: 00:07:01 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] 2754185 / 18675804 = 0.1475 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 21:23:07: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX4801803/SRX4801803.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX4801803/SRX4801803.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX4801803/SRX4801803.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX4801803/SRX4801803.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 21:23:07: #1 read tag files... INFO @ Sun, 21 Jun 2020 21:23:07: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 21:23:14: 1000000 INFO @ Sun, 21 Jun 2020 21:23:21: 2000000 INFO @ Sun, 21 Jun 2020 21:23:27: 3000000 INFO @ Sun, 21 Jun 2020 21:23:34: 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 21:23:38: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX4801803/SRX4801803.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX4801803/SRX4801803.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX4801803/SRX4801803.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX4801803/SRX4801803.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 21:23:38: #1 read tag files... INFO @ Sun, 21 Jun 2020 21:23:38: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 21:23:40: 5000000 INFO @ Sun, 21 Jun 2020 21:23:45: 1000000 INFO @ Sun, 21 Jun 2020 21:23:48: 6000000 INFO @ Sun, 21 Jun 2020 21:23:53: 2000000 INFO @ Sun, 21 Jun 2020 21:23:55: 7000000 INFO @ Sun, 21 Jun 2020 21:24:01: 3000000 INFO @ Sun, 21 Jun 2020 21:24:03: 8000000 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 21:24:07: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX4801803/SRX4801803.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX4801803/SRX4801803.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX4801803/SRX4801803.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX4801803/SRX4801803.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 21:24:07: #1 read tag files... INFO @ Sun, 21 Jun 2020 21:24:07: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 21:24:08: 4000000 INFO @ Sun, 21 Jun 2020 21:24:10: 9000000 INFO @ Sun, 21 Jun 2020 21:24:15: 1000000 INFO @ Sun, 21 Jun 2020 21:24:16: 5000000 INFO @ Sun, 21 Jun 2020 21:24:17: 10000000 INFO @ Sun, 21 Jun 2020 21:24:22: 2000000 INFO @ Sun, 21 Jun 2020 21:24:23: 6000000 INFO @ Sun, 21 Jun 2020 21:24:24: 11000000 INFO @ Sun, 21 Jun 2020 21:24:30: 3000000 INFO @ Sun, 21 Jun 2020 21:24:31: 7000000 INFO @ Sun, 21 Jun 2020 21:24:32: 12000000 INFO @ Sun, 21 Jun 2020 21:24:37: 4000000 INFO @ Sun, 21 Jun 2020 21:24:38: 8000000 INFO @ Sun, 21 Jun 2020 21:24:39: 13000000 INFO @ Sun, 21 Jun 2020 21:24:44: 5000000 INFO @ Sun, 21 Jun 2020 21:24:45: 9000000 INFO @ Sun, 21 Jun 2020 21:24:46: 14000000 INFO @ Sun, 21 Jun 2020 21:24:52: 6000000 INFO @ Sun, 21 Jun 2020 21:24:52: 10000000 INFO @ Sun, 21 Jun 2020 21:24:53: 15000000 INFO @ Sun, 21 Jun 2020 21:24:59: 7000000 INFO @ Sun, 21 Jun 2020 21:25:00: 11000000 INFO @ Sun, 21 Jun 2020 21:25:00: #1 tag size is determined as 68 bps INFO @ Sun, 21 Jun 2020 21:25:00: #1 tag size = 68 INFO @ Sun, 21 Jun 2020 21:25:00: #1 total tags in treatment: 15921619 INFO @ Sun, 21 Jun 2020 21:25:00: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 21:25:00: #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 21:25:01: #1 tags after filtering in treatment: 15921527 INFO @ Sun, 21 Jun 2020 21:25:01: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 21:25:01: #1 finished! INFO @ Sun, 21 Jun 2020 21:25:01: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 21:25:01: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 21:25:02: #2 number of paired peaks: 1475 INFO @ Sun, 21 Jun 2020 21:25:02: start model_add_line... INFO @ Sun, 21 Jun 2020 21:25:02: start X-correlation... INFO @ Sun, 21 Jun 2020 21:25:02: end of X-cor INFO @ Sun, 21 Jun 2020 21:25:02: #2 finished! INFO @ Sun, 21 Jun 2020 21:25:02: #2 predicted fragment length is 71 bps INFO @ Sun, 21 Jun 2020 21:25:02: #2 alternative fragment length(s) may be 3,71,590 bps INFO @ Sun, 21 Jun 2020 21:25:02: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX4801803/SRX4801803.05_model.r WARNING @ Sun, 21 Jun 2020 21:25:02: #2 Since the d (71) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 21:25:02: #2 You may need to consider one of the other alternative d(s): 3,71,590 WARNING @ Sun, 21 Jun 2020 21:25:02: #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 21:25:02: #3 Call peaks... INFO @ Sun, 21 Jun 2020 21:25:02: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 21:25:06: 8000000 INFO @ Sun, 21 Jun 2020 21:25:07: 12000000 INFO @ Sun, 21 Jun 2020 21:25:13: 9000000 INFO @ Sun, 21 Jun 2020 21:25:14: 13000000 INFO @ Sun, 21 Jun 2020 21:25:20: 10000000 INFO @ Sun, 21 Jun 2020 21:25:22: 14000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 21:25:28: 11000000 INFO @ Sun, 21 Jun 2020 21:25:29: 15000000 INFO @ Sun, 21 Jun 2020 21:25:35: 12000000 INFO @ Sun, 21 Jun 2020 21:25:36: #1 tag size is determined as 68 bps INFO @ Sun, 21 Jun 2020 21:25:36: #1 tag size = 68 INFO @ Sun, 21 Jun 2020 21:25:36: #1 total tags in treatment: 15921619 INFO @ Sun, 21 Jun 2020 21:25:36: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 21:25:36: #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 21:25:37: #1 tags after filtering in treatment: 15921527 INFO @ Sun, 21 Jun 2020 21:25:37: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 21:25:37: #1 finished! INFO @ Sun, 21 Jun 2020 21:25:37: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 21:25:37: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 21:25:38: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 21:25:38: #2 number of paired peaks: 1475 INFO @ Sun, 21 Jun 2020 21:25:38: start model_add_line... INFO @ Sun, 21 Jun 2020 21:25:38: start X-correlation... INFO @ Sun, 21 Jun 2020 21:25:38: end of X-cor INFO @ Sun, 21 Jun 2020 21:25:38: #2 finished! INFO @ Sun, 21 Jun 2020 21:25:38: #2 predicted fragment length is 71 bps INFO @ Sun, 21 Jun 2020 21:25:38: #2 alternative fragment length(s) may be 3,71,590 bps INFO @ Sun, 21 Jun 2020 21:25:38: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX4801803/SRX4801803.10_model.r WARNING @ Sun, 21 Jun 2020 21:25:38: #2 Since the d (71) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 21:25:38: #2 You may need to consider one of the other alternative d(s): 3,71,590 WARNING @ Sun, 21 Jun 2020 21:25:38: #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 21:25:38: #3 Call peaks... INFO @ Sun, 21 Jun 2020 21:25:38: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 21:25:42: 13000000 INFO @ Sun, 21 Jun 2020 21:25:49: 14000000 INFO @ Sun, 21 Jun 2020 21:25:54: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX4801803/SRX4801803.05_peaks.xls INFO @ Sun, 21 Jun 2020 21:25:54: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX4801803/SRX4801803.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 21:25:54: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX4801803/SRX4801803.05_summits.bed INFO @ Sun, 21 Jun 2020 21:25:54: Done! pass1 - making usageList (659 chroms): 1 millis pass2 - checking and writing primary data (3405 records, 4 fields): 21 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 21:25:56: 15000000 BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 21:26:02: #1 tag size is determined as 68 bps INFO @ Sun, 21 Jun 2020 21:26:02: #1 tag size = 68 INFO @ Sun, 21 Jun 2020 21:26:02: #1 total tags in treatment: 15921619 INFO @ Sun, 21 Jun 2020 21:26:02: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 21:26:02: #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 21:26:02: #1 tags after filtering in treatment: 15921527 INFO @ Sun, 21 Jun 2020 21:26:02: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 21:26:02: #1 finished! INFO @ Sun, 21 Jun 2020 21:26:02: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 21:26:02: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 21:26:03: #2 number of paired peaks: 1475 INFO @ Sun, 21 Jun 2020 21:26:03: start model_add_line... INFO @ Sun, 21 Jun 2020 21:26:04: start X-correlation... INFO @ Sun, 21 Jun 2020 21:26:04: end of X-cor INFO @ Sun, 21 Jun 2020 21:26:04: #2 finished! INFO @ Sun, 21 Jun 2020 21:26:04: #2 predicted fragment length is 71 bps INFO @ Sun, 21 Jun 2020 21:26:04: #2 alternative fragment length(s) may be 3,71,590 bps INFO @ Sun, 21 Jun 2020 21:26:04: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX4801803/SRX4801803.20_model.r WARNING @ Sun, 21 Jun 2020 21:26:04: #2 Since the d (71) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 21:26:04: #2 You may need to consider one of the other alternative d(s): 3,71,590 WARNING @ Sun, 21 Jun 2020 21:26:04: #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 21:26:04: #3 Call peaks... INFO @ Sun, 21 Jun 2020 21:26:04: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 21:26:12: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 21:26:28: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX4801803/SRX4801803.10_peaks.xls INFO @ Sun, 21 Jun 2020 21:26:28: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX4801803/SRX4801803.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 21:26:28: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX4801803/SRX4801803.10_summits.bed INFO @ Sun, 21 Jun 2020 21:26:28: Done! pass1 - making usageList (537 chroms): 1 millis pass2 - checking and writing primary data (1977 records, 4 fields): 16 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 21:26:38: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 21:26:54: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX4801803/SRX4801803.20_peaks.xls INFO @ Sun, 21 Jun 2020 21:26:54: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX4801803/SRX4801803.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 21:26:54: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX4801803/SRX4801803.20_summits.bed INFO @ Sun, 21 Jun 2020 21:26:54: Done! pass1 - making usageList (378 chroms): 1 millis pass2 - checking and writing primary data (909 records, 4 fields): 12 millis CompletedMACS2peakCalling