Job ID = 6458464 SRX = SRX5241028 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T12:37:26 prefetch.2.10.7: 1) Downloading 'SRR8433309'... 2020-06-21T12:37:26 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T12:40:00 prefetch.2.10.7: HTTPS download succeed 2020-06-21T12:40:01 prefetch.2.10.7: 'SRR8433309' is valid 2020-06-21T12:40:01 prefetch.2.10.7: 1) 'SRR8433309' was downloaded successfully 2020-06-21T12:40:01 prefetch.2.10.7: 'SRR8433309' has 0 unresolved dependencies Read 18678944 spots for SRR8433309/SRR8433309.sra Written 18678944 spots for SRR8433309/SRR8433309.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: 00:05:04 18678944 reads; of these: 18678944 (100.00%) were unpaired; of these: 458911 (2.46%) aligned 0 times 16912396 (90.54%) aligned exactly 1 time 1307637 (7.00%) aligned >1 times 97.54% overall alignment rate Time searching: 00:05:04 Overall time: 00:05:04 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] 9417672 / 18220033 = 0.5169 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 21:50:02: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX5241028/SRX5241028.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX5241028/SRX5241028.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX5241028/SRX5241028.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX5241028/SRX5241028.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 21:50:02: #1 read tag files... INFO @ Sun, 21 Jun 2020 21:50:02: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 21:50:09: 1000000 INFO @ Sun, 21 Jun 2020 21:50:16: 2000000 INFO @ Sun, 21 Jun 2020 21:50:24: 3000000 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 21:50:31: 4000000 INFO @ Sun, 21 Jun 2020 21:50:31: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX5241028/SRX5241028.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX5241028/SRX5241028.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX5241028/SRX5241028.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX5241028/SRX5241028.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 21:50:31: #1 read tag files... INFO @ Sun, 21 Jun 2020 21:50:31: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 21:50:39: 5000000 INFO @ Sun, 21 Jun 2020 21:50:40: 1000000 INFO @ Sun, 21 Jun 2020 21:50:47: 6000000 INFO @ Sun, 21 Jun 2020 21:50:48: 2000000 INFO @ Sun, 21 Jun 2020 21:50:55: 7000000 INFO @ Sun, 21 Jun 2020 21:50:56: 3000000 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 21:51:02: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX5241028/SRX5241028.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX5241028/SRX5241028.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX5241028/SRX5241028.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX5241028/SRX5241028.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 21:51:02: #1 read tag files... INFO @ Sun, 21 Jun 2020 21:51:02: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 21:51:04: 4000000 INFO @ Sun, 21 Jun 2020 21:51:04: 8000000 INFO @ Sun, 21 Jun 2020 21:51:10: 1000000 INFO @ Sun, 21 Jun 2020 21:51:11: #1 tag size is determined as 76 bps INFO @ Sun, 21 Jun 2020 21:51:11: #1 tag size = 76 INFO @ Sun, 21 Jun 2020 21:51:11: #1 total tags in treatment: 8802361 INFO @ Sun, 21 Jun 2020 21:51:11: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 21:51:11: #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 21:51:11: #1 tags after filtering in treatment: 8802047 INFO @ Sun, 21 Jun 2020 21:51:11: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 21:51:11: #1 finished! INFO @ Sun, 21 Jun 2020 21:51:11: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 21:51:11: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 21:51:12: 5000000 INFO @ Sun, 21 Jun 2020 21:51:13: #2 number of paired peaks: 12764 INFO @ Sun, 21 Jun 2020 21:51:13: start model_add_line... INFO @ Sun, 21 Jun 2020 21:51:13: start X-correlation... INFO @ Sun, 21 Jun 2020 21:51:13: end of X-cor INFO @ Sun, 21 Jun 2020 21:51:13: #2 finished! INFO @ Sun, 21 Jun 2020 21:51:13: #2 predicted fragment length is 118 bps INFO @ Sun, 21 Jun 2020 21:51:13: #2 alternative fragment length(s) may be 118 bps INFO @ Sun, 21 Jun 2020 21:51:13: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX5241028/SRX5241028.05_model.r WARNING @ Sun, 21 Jun 2020 21:51:13: #2 Since the d (118) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 21:51:13: #2 You may need to consider one of the other alternative d(s): 118 WARNING @ Sun, 21 Jun 2020 21:51:13: #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 21:51:13: #3 Call peaks... INFO @ Sun, 21 Jun 2020 21:51:13: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 21:51:18: 2000000 INFO @ Sun, 21 Jun 2020 21:51:20: 6000000 INFO @ Sun, 21 Jun 2020 21:51:26: 3000000 INFO @ Sun, 21 Jun 2020 21:51:28: 7000000 INFO @ Sun, 21 Jun 2020 21:51:34: 4000000 INFO @ Sun, 21 Jun 2020 21:51:35: #3 Call peaks for each chromosome... BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 21:51:36: 8000000 INFO @ Sun, 21 Jun 2020 21:51:42: 5000000 INFO @ Sun, 21 Jun 2020 21:51:43: #1 tag size is determined as 76 bps INFO @ Sun, 21 Jun 2020 21:51:43: #1 tag size = 76 INFO @ Sun, 21 Jun 2020 21:51:43: #1 total tags in treatment: 8802361 INFO @ Sun, 21 Jun 2020 21:51:43: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 21:51:43: #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 21:51:43: #1 tags after filtering in treatment: 8802047 INFO @ Sun, 21 Jun 2020 21:51:43: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 21:51:43: #1 finished! INFO @ Sun, 21 Jun 2020 21:51:43: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 21:51:43: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 21:51:44: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX5241028/SRX5241028.05_peaks.xls INFO @ Sun, 21 Jun 2020 21:51:44: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX5241028/SRX5241028.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 21:51:44: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX5241028/SRX5241028.05_summits.bed INFO @ Sun, 21 Jun 2020 21:51:44: Done! pass1 - making usageList (111 chroms): 2 millis pass2 - checking and writing primary data (8849 records, 4 fields): 13 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 21:51:45: #2 number of paired peaks: 12764 INFO @ Sun, 21 Jun 2020 21:51:45: start model_add_line... INFO @ Sun, 21 Jun 2020 21:51:45: start X-correlation... INFO @ Sun, 21 Jun 2020 21:51:45: end of X-cor INFO @ Sun, 21 Jun 2020 21:51:45: #2 finished! INFO @ Sun, 21 Jun 2020 21:51:45: #2 predicted fragment length is 118 bps INFO @ Sun, 21 Jun 2020 21:51:45: #2 alternative fragment length(s) may be 118 bps INFO @ Sun, 21 Jun 2020 21:51:45: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX5241028/SRX5241028.10_model.r WARNING @ Sun, 21 Jun 2020 21:51:45: #2 Since the d (118) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 21:51:45: #2 You may need to consider one of the other alternative d(s): 118 WARNING @ Sun, 21 Jun 2020 21:51:45: #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 21:51:45: #3 Call peaks... INFO @ Sun, 21 Jun 2020 21:51:45: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 21:51:50: 6000000 INFO @ Sun, 21 Jun 2020 21:51:57: 7000000 INFO @ Sun, 21 Jun 2020 21:52:05: 8000000 INFO @ Sun, 21 Jun 2020 21:52:08: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 21:52:11: #1 tag size is determined as 76 bps INFO @ Sun, 21 Jun 2020 21:52:11: #1 tag size = 76 INFO @ Sun, 21 Jun 2020 21:52:11: #1 total tags in treatment: 8802361 INFO @ Sun, 21 Jun 2020 21:52:11: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 21:52:11: #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 21:52:11: #1 tags after filtering in treatment: 8802047 INFO @ Sun, 21 Jun 2020 21:52:11: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 21:52:11: #1 finished! INFO @ Sun, 21 Jun 2020 21:52:11: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 21:52:11: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 21:52:12: #2 number of paired peaks: 12764 INFO @ Sun, 21 Jun 2020 21:52:12: start model_add_line... INFO @ Sun, 21 Jun 2020 21:52:13: start X-correlation... INFO @ Sun, 21 Jun 2020 21:52:13: end of X-cor INFO @ Sun, 21 Jun 2020 21:52:13: #2 finished! INFO @ Sun, 21 Jun 2020 21:52:13: #2 predicted fragment length is 118 bps INFO @ Sun, 21 Jun 2020 21:52:13: #2 alternative fragment length(s) may be 118 bps INFO @ Sun, 21 Jun 2020 21:52:13: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX5241028/SRX5241028.20_model.r WARNING @ Sun, 21 Jun 2020 21:52:13: #2 Since the d (118) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 21:52:13: #2 You may need to consider one of the other alternative d(s): 118 WARNING @ Sun, 21 Jun 2020 21:52:13: #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 21:52:13: #3 Call peaks... INFO @ Sun, 21 Jun 2020 21:52:13: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 21:52:17: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX5241028/SRX5241028.10_peaks.xls INFO @ Sun, 21 Jun 2020 21:52:17: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX5241028/SRX5241028.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 21:52:17: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX5241028/SRX5241028.10_summits.bed INFO @ Sun, 21 Jun 2020 21:52:17: Done! pass1 - making usageList (89 chroms): 2 millis pass2 - checking and writing primary data (8314 records, 4 fields): 12 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 21:52:35: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 21:52:44: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX5241028/SRX5241028.20_peaks.xls INFO @ Sun, 21 Jun 2020 21:52:44: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX5241028/SRX5241028.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 21:52:44: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX5241028/SRX5241028.20_summits.bed INFO @ Sun, 21 Jun 2020 21:52:44: Done! pass1 - making usageList (61 chroms): 1 millis pass2 - checking and writing primary data (7434 records, 4 fields): 12 millis CompletedMACS2peakCalling