Job ID = 6458244 SRX = SRX5011011 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T12:15:49 prefetch.2.10.7: 1) Downloading 'SRR8191460'... 2020-06-21T12:15:49 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T12:17:22 prefetch.2.10.7: HTTPS download succeed 2020-06-21T12:17:23 prefetch.2.10.7: 'SRR8191460' is valid 2020-06-21T12:17:23 prefetch.2.10.7: 1) 'SRR8191460' was downloaded successfully 2020-06-21T12:17:23 prefetch.2.10.7: 'SRR8191460' has 0 unresolved dependencies Read 27181802 spots for SRR8191460/SRR8191460.sra Written 27181802 spots for SRR8191460/SRR8191460.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: 00:07:47 27181802 reads; of these: 27181802 (100.00%) were unpaired; of these: 697598 (2.57%) aligned 0 times 18430527 (67.80%) aligned exactly 1 time 8053677 (29.63%) aligned >1 times 97.43% overall alignment rate Time searching: 00:07:47 Overall time: 00:07:47 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 12 files... [bam_rmdupse_core] 12408616 / 26484204 = 0.4685 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 21:31:06: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX5011011/SRX5011011.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX5011011/SRX5011011.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX5011011/SRX5011011.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX5011011/SRX5011011.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 21:31:06: #1 read tag files... INFO @ Sun, 21 Jun 2020 21:31:06: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 21:31:12: 1000000 INFO @ Sun, 21 Jun 2020 21:31:17: 2000000 INFO @ Sun, 21 Jun 2020 21:31:22: 3000000 INFO @ Sun, 21 Jun 2020 21:31:28: 4000000 INFO @ Sun, 21 Jun 2020 21:31:33: 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 21:31:36: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX5011011/SRX5011011.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX5011011/SRX5011011.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX5011011/SRX5011011.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX5011011/SRX5011011.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 21:31:36: #1 read tag files... INFO @ Sun, 21 Jun 2020 21:31:36: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 21:31:39: 6000000 INFO @ Sun, 21 Jun 2020 21:31:43: 1000000 INFO @ Sun, 21 Jun 2020 21:31:45: 7000000 INFO @ Sun, 21 Jun 2020 21:31:49: 2000000 INFO @ Sun, 21 Jun 2020 21:31:51: 8000000 INFO @ Sun, 21 Jun 2020 21:31:55: 3000000 INFO @ Sun, 21 Jun 2020 21:31:57: 9000000 INFO @ Sun, 21 Jun 2020 21:32:01: 4000000 INFO @ Sun, 21 Jun 2020 21:32:03: 10000000 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 21:32:06: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX5011011/SRX5011011.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX5011011/SRX5011011.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX5011011/SRX5011011.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX5011011/SRX5011011.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 21:32:06: #1 read tag files... INFO @ Sun, 21 Jun 2020 21:32:06: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 21:32:08: 5000000 INFO @ Sun, 21 Jun 2020 21:32:10: 11000000 INFO @ Sun, 21 Jun 2020 21:32:13: 1000000 INFO @ Sun, 21 Jun 2020 21:32:14: 6000000 INFO @ Sun, 21 Jun 2020 21:32:16: 12000000 INFO @ Sun, 21 Jun 2020 21:32:20: 2000000 INFO @ Sun, 21 Jun 2020 21:32:21: 7000000 INFO @ Sun, 21 Jun 2020 21:32:22: 13000000 INFO @ Sun, 21 Jun 2020 21:32:27: 8000000 INFO @ Sun, 21 Jun 2020 21:32:27: 3000000 INFO @ Sun, 21 Jun 2020 21:32:29: 14000000 INFO @ Sun, 21 Jun 2020 21:32:29: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 21:32:29: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 21:32:29: #1 total tags in treatment: 14075588 INFO @ Sun, 21 Jun 2020 21:32:29: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 21:32:29: #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 21:32:30: #1 tags after filtering in treatment: 14075534 INFO @ Sun, 21 Jun 2020 21:32:30: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 21:32:30: #1 finished! INFO @ Sun, 21 Jun 2020 21:32:30: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 21:32:30: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 21:32:31: #2 number of paired peaks: 1683 INFO @ Sun, 21 Jun 2020 21:32:31: start model_add_line... INFO @ Sun, 21 Jun 2020 21:32:31: start X-correlation... INFO @ Sun, 21 Jun 2020 21:32:31: end of X-cor INFO @ Sun, 21 Jun 2020 21:32:31: #2 finished! INFO @ Sun, 21 Jun 2020 21:32:31: #2 predicted fragment length is 49 bps INFO @ Sun, 21 Jun 2020 21:32:31: #2 alternative fragment length(s) may be 2,49 bps INFO @ Sun, 21 Jun 2020 21:32:31: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX5011011/SRX5011011.05_model.r WARNING @ Sun, 21 Jun 2020 21:32:31: #2 Since the d (49) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 21:32:31: #2 You may need to consider one of the other alternative d(s): 2,49 WARNING @ Sun, 21 Jun 2020 21:32:31: #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 21:32:31: #3 Call peaks... INFO @ Sun, 21 Jun 2020 21:32:31: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 21:32:33: 9000000 INFO @ Sun, 21 Jun 2020 21:32:34: 4000000 INFO @ Sun, 21 Jun 2020 21:32:39: 10000000 INFO @ Sun, 21 Jun 2020 21:32:41: 5000000 INFO @ Sun, 21 Jun 2020 21:32:46: 11000000 INFO @ Sun, 21 Jun 2020 21:32:48: 6000000 INFO @ Sun, 21 Jun 2020 21:32:53: 12000000 INFO @ Sun, 21 Jun 2020 21:32:55: 7000000 INFO @ Sun, 21 Jun 2020 21:32:59: 13000000 INFO @ Sun, 21 Jun 2020 21:33:02: 8000000 INFO @ Sun, 21 Jun 2020 21:33:02: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 21:33:06: 14000000 INFO @ Sun, 21 Jun 2020 21:33:06: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 21:33:06: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 21:33:06: #1 total tags in treatment: 14075588 INFO @ Sun, 21 Jun 2020 21:33:06: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 21:33:06: #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 21:33:07: #1 tags after filtering in treatment: 14075534 INFO @ Sun, 21 Jun 2020 21:33:07: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 21:33:07: #1 finished! INFO @ Sun, 21 Jun 2020 21:33:07: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 21:33:07: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 21:33:08: #2 number of paired peaks: 1683 INFO @ Sun, 21 Jun 2020 21:33:08: start model_add_line... INFO @ Sun, 21 Jun 2020 21:33:08: start X-correlation... INFO @ Sun, 21 Jun 2020 21:33:08: end of X-cor INFO @ Sun, 21 Jun 2020 21:33:08: #2 finished! INFO @ Sun, 21 Jun 2020 21:33:08: #2 predicted fragment length is 49 bps INFO @ Sun, 21 Jun 2020 21:33:08: #2 alternative fragment length(s) may be 2,49 bps INFO @ Sun, 21 Jun 2020 21:33:08: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX5011011/SRX5011011.10_model.r WARNING @ Sun, 21 Jun 2020 21:33:08: #2 Since the d (49) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 21:33:08: #2 You may need to consider one of the other alternative d(s): 2,49 WARNING @ Sun, 21 Jun 2020 21:33:08: #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 21:33:08: #3 Call peaks... INFO @ Sun, 21 Jun 2020 21:33:08: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 21:33:08: 9000000 INFO @ Sun, 21 Jun 2020 21:33:15: 10000000 INFO @ Sun, 21 Jun 2020 21:33:16: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX5011011/SRX5011011.05_peaks.xls INFO @ Sun, 21 Jun 2020 21:33:17: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX5011011/SRX5011011.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 21:33:17: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX5011011/SRX5011011.05_summits.bed INFO @ Sun, 21 Jun 2020 21:33:17: Done! pass1 - making usageList (787 chroms): 2 millis pass2 - checking and writing primary data (4255 records, 4 fields): 25 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 21:33:22: 11000000 INFO @ Sun, 21 Jun 2020 21:33:28: 12000000 INFO @ Sun, 21 Jun 2020 21:33:35: 13000000 INFO @ Sun, 21 Jun 2020 21:33:37: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 21:33:41: 14000000 INFO @ Sun, 21 Jun 2020 21:33:42: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 21:33:42: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 21:33:42: #1 total tags in treatment: 14075588 INFO @ Sun, 21 Jun 2020 21:33:42: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 21:33:42: #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 21:33:42: #1 tags after filtering in treatment: 14075534 INFO @ Sun, 21 Jun 2020 21:33:42: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 21:33:42: #1 finished! INFO @ Sun, 21 Jun 2020 21:33:42: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 21:33:42: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 21:33:43: #2 number of paired peaks: 1683 INFO @ Sun, 21 Jun 2020 21:33:43: start model_add_line... INFO @ Sun, 21 Jun 2020 21:33:43: start X-correlation... INFO @ Sun, 21 Jun 2020 21:33:43: end of X-cor INFO @ Sun, 21 Jun 2020 21:33:43: #2 finished! INFO @ Sun, 21 Jun 2020 21:33:43: #2 predicted fragment length is 49 bps INFO @ Sun, 21 Jun 2020 21:33:43: #2 alternative fragment length(s) may be 2,49 bps INFO @ Sun, 21 Jun 2020 21:33:43: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX5011011/SRX5011011.20_model.r WARNING @ Sun, 21 Jun 2020 21:33:43: #2 Since the d (49) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 21:33:43: #2 You may need to consider one of the other alternative d(s): 2,49 WARNING @ Sun, 21 Jun 2020 21:33:43: #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 21:33:43: #3 Call peaks... INFO @ Sun, 21 Jun 2020 21:33:43: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 21:33:51: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX5011011/SRX5011011.10_peaks.xls INFO @ Sun, 21 Jun 2020 21:33:51: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX5011011/SRX5011011.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 21:33:51: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX5011011/SRX5011011.10_summits.bed INFO @ Sun, 21 Jun 2020 21:33:51: Done! pass1 - making usageList (661 chroms): 2 millis pass2 - checking and writing primary data (2662 records, 4 fields): 19 millis CompletedMACS2peakCalling BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 21:34:13: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 21:34:27: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX5011011/SRX5011011.20_peaks.xls INFO @ Sun, 21 Jun 2020 21:34:27: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX5011011/SRX5011011.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 21:34:27: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX5011011/SRX5011011.20_summits.bed INFO @ Sun, 21 Jun 2020 21:34:27: Done! pass1 - making usageList (356 chroms): 1 millis pass2 - checking and writing primary data (814 records, 4 fields): 11 millis CompletedMACS2peakCalling