Job ID = 6459604 SRX = SRX7277044 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T13:17:04 prefetch.2.10.7: 1) Downloading 'SRR10597309'... 2020-06-21T13:17:04 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T13:19:24 prefetch.2.10.7: HTTPS download succeed 2020-06-21T13:19:25 prefetch.2.10.7: 'SRR10597309' is valid 2020-06-21T13:19:25 prefetch.2.10.7: 1) 'SRR10597309' was downloaded successfully 2020-06-21T13:19:25 prefetch.2.10.7: 'SRR10597309' has 0 unresolved dependencies Read 19882025 spots for SRR10597309/SRR10597309.sra Written 19882025 spots for SRR10597309/SRR10597309.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: 00:04:29 19882025 reads; of these: 19882025 (100.00%) were unpaired; of these: 4185986 (21.05%) aligned 0 times 11468900 (57.68%) aligned exactly 1 time 4227139 (21.26%) aligned >1 times 78.95% overall alignment rate Time searching: 00:04:29 Overall time: 00:04:29 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] 10679154 / 15696039 = 0.6804 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 22:27:39: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX7277044/SRX7277044.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX7277044/SRX7277044.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX7277044/SRX7277044.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX7277044/SRX7277044.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 22:27:39: #1 read tag files... INFO @ Sun, 21 Jun 2020 22:27:39: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 22:27:45: 1000000 INFO @ Sun, 21 Jun 2020 22:27:51: 2000000 INFO @ Sun, 21 Jun 2020 22:27:58: 3000000 INFO @ Sun, 21 Jun 2020 22:28:04: 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 22:28:09: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX7277044/SRX7277044.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX7277044/SRX7277044.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX7277044/SRX7277044.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX7277044/SRX7277044.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 22:28:09: #1 read tag files... INFO @ Sun, 21 Jun 2020 22:28:09: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 22:28:11: 5000000 INFO @ Sun, 21 Jun 2020 22:28:11: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 22:28:11: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 22:28:11: #1 total tags in treatment: 5016885 INFO @ Sun, 21 Jun 2020 22:28:11: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 22:28:11: #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 22:28:11: #1 tags after filtering in treatment: 5016876 INFO @ Sun, 21 Jun 2020 22:28:11: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 22:28:11: #1 finished! INFO @ Sun, 21 Jun 2020 22:28:11: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 22:28:11: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 22:28:12: #2 number of paired peaks: 1807 INFO @ Sun, 21 Jun 2020 22:28:12: start model_add_line... INFO @ Sun, 21 Jun 2020 22:28:12: start X-correlation... INFO @ Sun, 21 Jun 2020 22:28:12: end of X-cor INFO @ Sun, 21 Jun 2020 22:28:12: #2 finished! INFO @ Sun, 21 Jun 2020 22:28:12: #2 predicted fragment length is 91 bps INFO @ Sun, 21 Jun 2020 22:28:12: #2 alternative fragment length(s) may be 91 bps INFO @ Sun, 21 Jun 2020 22:28:12: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX7277044/SRX7277044.05_model.r WARNING @ Sun, 21 Jun 2020 22:28:12: #2 Since the d (91) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 22:28:12: #2 You may need to consider one of the other alternative d(s): 91 WARNING @ Sun, 21 Jun 2020 22:28:12: #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 22:28:12: #3 Call peaks... INFO @ Sun, 21 Jun 2020 22:28:12: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 22:28:16: 1000000 INFO @ Sun, 21 Jun 2020 22:28:22: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 22:28:23: 2000000 INFO @ Sun, 21 Jun 2020 22:28:28: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX7277044/SRX7277044.05_peaks.xls INFO @ Sun, 21 Jun 2020 22:28:28: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX7277044/SRX7277044.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 22:28:28: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX7277044/SRX7277044.05_summits.bed INFO @ Sun, 21 Jun 2020 22:28:28: Done! pass1 - making usageList (751 chroms): 2 millis pass2 - checking and writing primary data (2906 records, 4 fields): 21 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 22:28:30: 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 22:28:39: 4000000 INFO @ Sun, 21 Jun 2020 22:28:39: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX7277044/SRX7277044.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX7277044/SRX7277044.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX7277044/SRX7277044.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX7277044/SRX7277044.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 22:28:39: #1 read tag files... INFO @ Sun, 21 Jun 2020 22:28:39: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 22:28:46: 1000000 INFO @ Sun, 21 Jun 2020 22:28:47: 5000000 INFO @ Sun, 21 Jun 2020 22:28:47: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 22:28:47: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 22:28:47: #1 total tags in treatment: 5016885 INFO @ Sun, 21 Jun 2020 22:28:47: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 22:28:47: #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 22:28:47: #1 tags after filtering in treatment: 5016876 INFO @ Sun, 21 Jun 2020 22:28:47: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 22:28:47: #1 finished! INFO @ Sun, 21 Jun 2020 22:28:47: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 22:28:47: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 22:28:48: #2 number of paired peaks: 1807 INFO @ Sun, 21 Jun 2020 22:28:48: start model_add_line... INFO @ Sun, 21 Jun 2020 22:28:48: start X-correlation... INFO @ Sun, 21 Jun 2020 22:28:48: end of X-cor INFO @ Sun, 21 Jun 2020 22:28:48: #2 finished! INFO @ Sun, 21 Jun 2020 22:28:48: #2 predicted fragment length is 91 bps INFO @ Sun, 21 Jun 2020 22:28:48: #2 alternative fragment length(s) may be 91 bps INFO @ Sun, 21 Jun 2020 22:28:48: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX7277044/SRX7277044.10_model.r WARNING @ Sun, 21 Jun 2020 22:28:48: #2 Since the d (91) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 22:28:48: #2 You may need to consider one of the other alternative d(s): 91 WARNING @ Sun, 21 Jun 2020 22:28:48: #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 22:28:48: #3 Call peaks... INFO @ Sun, 21 Jun 2020 22:28:48: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 22:28:53: 2000000 INFO @ Sun, 21 Jun 2020 22:28:59: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 22:29:00: 3000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 22:29:05: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX7277044/SRX7277044.10_peaks.xls INFO @ Sun, 21 Jun 2020 22:29:05: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX7277044/SRX7277044.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 22:29:05: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX7277044/SRX7277044.10_summits.bed INFO @ Sun, 21 Jun 2020 22:29:05: Done! pass1 - making usageList (614 chroms): 1 millis pass2 - checking and writing primary data (1946 records, 4 fields): 17 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 22:29:07: 4000000 INFO @ Sun, 21 Jun 2020 22:29:13: 5000000 INFO @ Sun, 21 Jun 2020 22:29:13: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 22:29:13: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 22:29:13: #1 total tags in treatment: 5016885 INFO @ Sun, 21 Jun 2020 22:29:13: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 22:29:13: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 22:29:13: #1 tags after filtering in treatment: 5016876 INFO @ Sun, 21 Jun 2020 22:29:13: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 22:29:13: #1 finished! INFO @ Sun, 21 Jun 2020 22:29:13: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 22:29:13: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 22:29:14: #2 number of paired peaks: 1807 INFO @ Sun, 21 Jun 2020 22:29:14: start model_add_line... INFO @ Sun, 21 Jun 2020 22:29:14: start X-correlation... INFO @ Sun, 21 Jun 2020 22:29:14: end of X-cor INFO @ Sun, 21 Jun 2020 22:29:14: #2 finished! INFO @ Sun, 21 Jun 2020 22:29:14: #2 predicted fragment length is 91 bps INFO @ Sun, 21 Jun 2020 22:29:14: #2 alternative fragment length(s) may be 91 bps INFO @ Sun, 21 Jun 2020 22:29:14: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX7277044/SRX7277044.20_model.r WARNING @ Sun, 21 Jun 2020 22:29:14: #2 Since the d (91) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 22:29:14: #2 You may need to consider one of the other alternative d(s): 91 WARNING @ Sun, 21 Jun 2020 22:29:14: #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 22:29:14: #3 Call peaks... INFO @ Sun, 21 Jun 2020 22:29:14: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 22:29:24: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 22:29:29: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX7277044/SRX7277044.20_peaks.xls INFO @ Sun, 21 Jun 2020 22:29:29: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX7277044/SRX7277044.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 22:29:29: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX7277044/SRX7277044.20_summits.bed INFO @ Sun, 21 Jun 2020 22:29:29: Done! pass1 - making usageList (412 chroms): 1 millis pass2 - checking and writing primary data (951 records, 4 fields): 11 millis CompletedMACS2peakCalling