Job ID = 6458941 SRX = SRX5775941 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T12:49:10 prefetch.2.10.7: 1) Downloading 'SRR8997144'... 2020-06-21T12:49:10 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T12:53:14 prefetch.2.10.7: HTTPS download succeed 2020-06-21T12:53:14 prefetch.2.10.7: 1) 'SRR8997144' was downloaded successfully 2020-06-21T12:53:14 prefetch.2.10.7: 'SRR8997144' has 0 unresolved dependencies Read 30020667 spots for SRR8997144/SRR8997144.sra Written 30020667 spots for SRR8997144/SRR8997144.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: 00:06:18 30020667 reads; of these: 30020667 (100.00%) were unpaired; of these: 20905554 (69.64%) aligned 0 times 6601202 (21.99%) aligned exactly 1 time 2513911 (8.37%) aligned >1 times 30.36% overall alignment rate Time searching: 00:06:18 Overall time: 00:06:18 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] 5474550 / 9115113 = 0.6006 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 22:03:44: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX5775941/SRX5775941.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX5775941/SRX5775941.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX5775941/SRX5775941.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX5775941/SRX5775941.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 22:03:44: #1 read tag files... INFO @ Sun, 21 Jun 2020 22:03:44: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 22:03:52: 1000000 INFO @ Sun, 21 Jun 2020 22:04:00: 2000000 INFO @ Sun, 21 Jun 2020 22:04:08: 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 22:04:13: #1 tag size is determined as 74 bps INFO @ Sun, 21 Jun 2020 22:04:13: #1 tag size = 74 INFO @ Sun, 21 Jun 2020 22:04:13: #1 total tags in treatment: 3640563 INFO @ Sun, 21 Jun 2020 22:04:13: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 22:04:13: #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 22:04:13: #1 tags after filtering in treatment: 3640553 INFO @ Sun, 21 Jun 2020 22:04:13: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 22:04:13: #1 finished! INFO @ Sun, 21 Jun 2020 22:04:13: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 22:04:13: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 22:04:13: #2 number of paired peaks: 1308 INFO @ Sun, 21 Jun 2020 22:04:13: start model_add_line... INFO @ Sun, 21 Jun 2020 22:04:13: start X-correlation... INFO @ Sun, 21 Jun 2020 22:04:13: end of X-cor INFO @ Sun, 21 Jun 2020 22:04:13: #2 finished! INFO @ Sun, 21 Jun 2020 22:04:13: #2 predicted fragment length is 77 bps INFO @ Sun, 21 Jun 2020 22:04:13: #2 alternative fragment length(s) may be 77 bps INFO @ Sun, 21 Jun 2020 22:04:13: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX5775941/SRX5775941.05_model.r WARNING @ Sun, 21 Jun 2020 22:04:13: #2 Since the d (77) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 22:04:13: #2 You may need to consider one of the other alternative d(s): 77 WARNING @ Sun, 21 Jun 2020 22:04:13: #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 22:04:13: #3 Call peaks... INFO @ Sun, 21 Jun 2020 22:04:13: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 22:04:14: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX5775941/SRX5775941.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX5775941/SRX5775941.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX5775941/SRX5775941.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX5775941/SRX5775941.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 22:04:14: #1 read tag files... INFO @ Sun, 21 Jun 2020 22:04:14: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 22:04:22: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 22:04:22: 1000000 INFO @ Sun, 21 Jun 2020 22:04:26: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX5775941/SRX5775941.05_peaks.xls INFO @ Sun, 21 Jun 2020 22:04:26: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX5775941/SRX5775941.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 22:04:26: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX5775941/SRX5775941.05_summits.bed INFO @ Sun, 21 Jun 2020 22:04:26: Done! pass1 - making usageList (690 chroms): 1 millis pass2 - checking and writing primary data (2080 records, 4 fields): 21 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 22:04:30: 2000000 INFO @ Sun, 21 Jun 2020 22:04:38: 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 22:04:43: #1 tag size is determined as 74 bps INFO @ Sun, 21 Jun 2020 22:04:43: #1 tag size = 74 INFO @ Sun, 21 Jun 2020 22:04:43: #1 total tags in treatment: 3640563 INFO @ Sun, 21 Jun 2020 22:04:43: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 22:04:43: #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 22:04:43: #1 tags after filtering in treatment: 3640553 INFO @ Sun, 21 Jun 2020 22:04:43: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 22:04:43: #1 finished! INFO @ Sun, 21 Jun 2020 22:04:43: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 22:04:43: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 22:04:44: #2 number of paired peaks: 1308 INFO @ Sun, 21 Jun 2020 22:04:44: start model_add_line... INFO @ Sun, 21 Jun 2020 22:04:44: start X-correlation... INFO @ Sun, 21 Jun 2020 22:04:44: end of X-cor INFO @ Sun, 21 Jun 2020 22:04:44: #2 finished! INFO @ Sun, 21 Jun 2020 22:04:44: #2 predicted fragment length is 77 bps INFO @ Sun, 21 Jun 2020 22:04:44: #2 alternative fragment length(s) may be 77 bps INFO @ Sun, 21 Jun 2020 22:04:44: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX5775941/SRX5775941.10_model.r WARNING @ Sun, 21 Jun 2020 22:04:44: #2 Since the d (77) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 22:04:44: #2 You may need to consider one of the other alternative d(s): 77 WARNING @ Sun, 21 Jun 2020 22:04:44: #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 22:04:44: #3 Call peaks... INFO @ Sun, 21 Jun 2020 22:04:44: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 22:04:44: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX5775941/SRX5775941.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX5775941/SRX5775941.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX5775941/SRX5775941.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX5775941/SRX5775941.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 22:04:44: #1 read tag files... INFO @ Sun, 21 Jun 2020 22:04:44: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 22:04:52: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 22:04:52: 1000000 INFO @ Sun, 21 Jun 2020 22:04:56: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX5775941/SRX5775941.10_peaks.xls INFO @ Sun, 21 Jun 2020 22:04:56: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX5775941/SRX5775941.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 22:04:56: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX5775941/SRX5775941.10_summits.bed INFO @ Sun, 21 Jun 2020 22:04:56: Done! pass1 - making usageList (531 chroms): 1 millis pass2 - checking and writing primary data (1361 records, 4 fields): 15 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 22:05:00: 2000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 22:05:08: 3000000 BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 22:05:12: #1 tag size is determined as 74 bps INFO @ Sun, 21 Jun 2020 22:05:12: #1 tag size = 74 INFO @ Sun, 21 Jun 2020 22:05:12: #1 total tags in treatment: 3640563 INFO @ Sun, 21 Jun 2020 22:05:12: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 22:05:12: #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 22:05:13: #1 tags after filtering in treatment: 3640553 INFO @ Sun, 21 Jun 2020 22:05:13: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 22:05:13: #1 finished! INFO @ Sun, 21 Jun 2020 22:05:13: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 22:05:13: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 22:05:13: #2 number of paired peaks: 1308 INFO @ Sun, 21 Jun 2020 22:05:13: start model_add_line... INFO @ Sun, 21 Jun 2020 22:05:13: start X-correlation... INFO @ Sun, 21 Jun 2020 22:05:13: end of X-cor INFO @ Sun, 21 Jun 2020 22:05:13: #2 finished! INFO @ Sun, 21 Jun 2020 22:05:13: #2 predicted fragment length is 77 bps INFO @ Sun, 21 Jun 2020 22:05:13: #2 alternative fragment length(s) may be 77 bps INFO @ Sun, 21 Jun 2020 22:05:13: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX5775941/SRX5775941.20_model.r WARNING @ Sun, 21 Jun 2020 22:05:13: #2 Since the d (77) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 22:05:13: #2 You may need to consider one of the other alternative d(s): 77 WARNING @ Sun, 21 Jun 2020 22:05:13: #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 22:05:13: #3 Call peaks... INFO @ Sun, 21 Jun 2020 22:05:13: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 22:05:22: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 22:05:26: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX5775941/SRX5775941.20_peaks.xls INFO @ Sun, 21 Jun 2020 22:05:26: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX5775941/SRX5775941.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 22:05:26: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX5775941/SRX5775941.20_summits.bed INFO @ Sun, 21 Jun 2020 22:05:26: Done! pass1 - making usageList (346 chroms): 1 millis pass2 - checking and writing primary data (665 records, 4 fields): 10 millis CompletedMACS2peakCalling