Job ID = 6457943 SRX = SRX4923187 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T12:00:17 prefetch.2.10.7: 1) Downloading 'SRR8096337'... 2020-06-21T12:00:17 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T12:03:26 prefetch.2.10.7: HTTPS download succeed 2020-06-21T12:03:27 prefetch.2.10.7: 'SRR8096337' is valid 2020-06-21T12:03:27 prefetch.2.10.7: 1) 'SRR8096337' was downloaded successfully 2020-06-21T12:03:27 prefetch.2.10.7: 'SRR8096337' has 0 unresolved dependencies Read 27404758 spots for SRR8096337/SRR8096337.sra Written 27404758 spots for SRR8096337/SRR8096337.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: 00:09:22 27404758 reads; of these: 27404758 (100.00%) were unpaired; of these: 616268 (2.25%) aligned 0 times 8500550 (31.02%) aligned exactly 1 time 18287940 (66.73%) aligned >1 times 97.75% overall alignment rate Time searching: 00:09:22 Overall time: 00:09:22 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] 11840066 / 26788490 = 0.4420 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 21:18:31: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX4923187/SRX4923187.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX4923187/SRX4923187.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX4923187/SRX4923187.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX4923187/SRX4923187.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 21:18:31: #1 read tag files... INFO @ Sun, 21 Jun 2020 21:18:31: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 21:18:37: 1000000 INFO @ Sun, 21 Jun 2020 21:18:43: 2000000 INFO @ Sun, 21 Jun 2020 21:18:50: 3000000 INFO @ Sun, 21 Jun 2020 21:18:56: 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 21:19:01: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX4923187/SRX4923187.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX4923187/SRX4923187.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX4923187/SRX4923187.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX4923187/SRX4923187.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 21:19:01: #1 read tag files... INFO @ Sun, 21 Jun 2020 21:19:01: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 21:19:03: 5000000 INFO @ Sun, 21 Jun 2020 21:19:08: 1000000 INFO @ Sun, 21 Jun 2020 21:19:10: 6000000 INFO @ Sun, 21 Jun 2020 21:19:15: 2000000 INFO @ Sun, 21 Jun 2020 21:19:17: 7000000 INFO @ Sun, 21 Jun 2020 21:19:22: 3000000 INFO @ Sun, 21 Jun 2020 21:19:24: 8000000 INFO @ Sun, 21 Jun 2020 21:19:28: 4000000 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 21:19:31: 9000000 INFO @ Sun, 21 Jun 2020 21:19:31: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX4923187/SRX4923187.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX4923187/SRX4923187.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX4923187/SRX4923187.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX4923187/SRX4923187.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 21:19:31: #1 read tag files... INFO @ Sun, 21 Jun 2020 21:19:31: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 21:19:36: 5000000 INFO @ Sun, 21 Jun 2020 21:19:38: 10000000 INFO @ Sun, 21 Jun 2020 21:19:38: 1000000 INFO @ Sun, 21 Jun 2020 21:19:43: 6000000 INFO @ Sun, 21 Jun 2020 21:19:45: 11000000 INFO @ Sun, 21 Jun 2020 21:19:46: 2000000 INFO @ Sun, 21 Jun 2020 21:19:50: 7000000 INFO @ Sun, 21 Jun 2020 21:19:53: 12000000 INFO @ Sun, 21 Jun 2020 21:19:53: 3000000 INFO @ Sun, 21 Jun 2020 21:19:57: 8000000 INFO @ Sun, 21 Jun 2020 21:20:00: 13000000 INFO @ Sun, 21 Jun 2020 21:20:01: 4000000 INFO @ Sun, 21 Jun 2020 21:20:04: 9000000 INFO @ Sun, 21 Jun 2020 21:20:07: 14000000 INFO @ Sun, 21 Jun 2020 21:20:08: 5000000 INFO @ Sun, 21 Jun 2020 21:20:11: 10000000 INFO @ Sun, 21 Jun 2020 21:20:14: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 21:20:14: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 21:20:14: #1 total tags in treatment: 14948424 INFO @ Sun, 21 Jun 2020 21:20:14: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 21:20:14: #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 21:20:14: #1 tags after filtering in treatment: 14948380 INFO @ Sun, 21 Jun 2020 21:20:14: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 21:20:14: #1 finished! INFO @ Sun, 21 Jun 2020 21:20:14: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 21:20:14: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 21:20:16: 6000000 INFO @ Sun, 21 Jun 2020 21:20:16: #2 number of paired peaks: 6491 INFO @ Sun, 21 Jun 2020 21:20:16: start model_add_line... INFO @ Sun, 21 Jun 2020 21:20:16: start X-correlation... INFO @ Sun, 21 Jun 2020 21:20:16: end of X-cor INFO @ Sun, 21 Jun 2020 21:20:16: #2 finished! INFO @ Sun, 21 Jun 2020 21:20:16: #2 predicted fragment length is 75 bps INFO @ Sun, 21 Jun 2020 21:20:16: #2 alternative fragment length(s) may be 2,75 bps INFO @ Sun, 21 Jun 2020 21:20:16: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX4923187/SRX4923187.05_model.r WARNING @ Sun, 21 Jun 2020 21:20:16: #2 Since the d (75) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 21:20:16: #2 You may need to consider one of the other alternative d(s): 2,75 WARNING @ Sun, 21 Jun 2020 21:20:16: #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 21:20:16: #3 Call peaks... INFO @ Sun, 21 Jun 2020 21:20:16: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 21:20:18: 11000000 INFO @ Sun, 21 Jun 2020 21:20:23: 7000000 INFO @ Sun, 21 Jun 2020 21:20:25: 12000000 INFO @ Sun, 21 Jun 2020 21:20:31: 8000000 INFO @ Sun, 21 Jun 2020 21:20:32: 13000000 INFO @ Sun, 21 Jun 2020 21:20:38: 9000000 INFO @ Sun, 21 Jun 2020 21:20:39: 14000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 21:20:45: 10000000 INFO @ Sun, 21 Jun 2020 21:20:45: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 21:20:45: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 21:20:45: #1 total tags in treatment: 14948424 INFO @ Sun, 21 Jun 2020 21:20:45: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 21:20:45: #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 21:20:46: #1 tags after filtering in treatment: 14948380 INFO @ Sun, 21 Jun 2020 21:20:46: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 21:20:46: #1 finished! INFO @ Sun, 21 Jun 2020 21:20:46: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 21:20:46: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 21:20:47: #2 number of paired peaks: 6491 INFO @ Sun, 21 Jun 2020 21:20:47: start model_add_line... INFO @ Sun, 21 Jun 2020 21:20:47: start X-correlation... INFO @ Sun, 21 Jun 2020 21:20:47: end of X-cor INFO @ Sun, 21 Jun 2020 21:20:47: #2 finished! INFO @ Sun, 21 Jun 2020 21:20:47: #2 predicted fragment length is 75 bps INFO @ Sun, 21 Jun 2020 21:20:47: #2 alternative fragment length(s) may be 2,75 bps INFO @ Sun, 21 Jun 2020 21:20:47: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX4923187/SRX4923187.10_model.r WARNING @ Sun, 21 Jun 2020 21:20:47: #2 Since the d (75) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 21:20:47: #2 You may need to consider one of the other alternative d(s): 2,75 WARNING @ Sun, 21 Jun 2020 21:20:47: #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 21:20:47: #3 Call peaks... INFO @ Sun, 21 Jun 2020 21:20:47: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 21:20:50: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 21:20:52: 11000000 INFO @ Sun, 21 Jun 2020 21:20:59: 12000000 INFO @ Sun, 21 Jun 2020 21:21:05: 13000000 INFO @ Sun, 21 Jun 2020 21:21:07: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX4923187/SRX4923187.05_peaks.xls INFO @ Sun, 21 Jun 2020 21:21:07: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX4923187/SRX4923187.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 21:21:07: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX4923187/SRX4923187.05_summits.bed INFO @ Sun, 21 Jun 2020 21:21:07: Done! pass1 - making usageList (1135 chroms): 3 millis pass2 - checking and writing primary data (9298 records, 4 fields): 37 millis CompletedMACS2peakCalling BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 21:21:11: 14000000 INFO @ Sun, 21 Jun 2020 21:21:17: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 21:21:17: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 21:21:17: #1 total tags in treatment: 14948424 INFO @ Sun, 21 Jun 2020 21:21:17: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 21:21:17: #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 21:21:17: #1 tags after filtering in treatment: 14948380 INFO @ Sun, 21 Jun 2020 21:21:17: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 21:21:17: #1 finished! INFO @ Sun, 21 Jun 2020 21:21:17: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 21:21:17: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 21:21:19: #2 number of paired peaks: 6491 INFO @ Sun, 21 Jun 2020 21:21:19: start model_add_line... INFO @ Sun, 21 Jun 2020 21:21:19: start X-correlation... INFO @ Sun, 21 Jun 2020 21:21:19: end of X-cor INFO @ Sun, 21 Jun 2020 21:21:19: #2 finished! INFO @ Sun, 21 Jun 2020 21:21:19: #2 predicted fragment length is 75 bps INFO @ Sun, 21 Jun 2020 21:21:19: #2 alternative fragment length(s) may be 2,75 bps INFO @ Sun, 21 Jun 2020 21:21:19: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX4923187/SRX4923187.20_model.r WARNING @ Sun, 21 Jun 2020 21:21:19: #2 Since the d (75) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 21:21:19: #2 You may need to consider one of the other alternative d(s): 2,75 WARNING @ Sun, 21 Jun 2020 21:21:19: #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 21:21:19: #3 Call peaks... INFO @ Sun, 21 Jun 2020 21:21:19: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 21:21:20: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 21:21:36: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX4923187/SRX4923187.10_peaks.xls INFO @ Sun, 21 Jun 2020 21:21:36: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX4923187/SRX4923187.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 21:21:36: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX4923187/SRX4923187.10_summits.bed INFO @ Sun, 21 Jun 2020 21:21:36: Done! pass1 - making usageList (993 chroms): 2 millis pass2 - checking and writing primary data (4633 records, 4 fields): 31 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 21:21:52: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 21:22:08: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX4923187/SRX4923187.20_peaks.xls INFO @ Sun, 21 Jun 2020 21:22:08: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX4923187/SRX4923187.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 21:22:08: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX4923187/SRX4923187.20_summits.bed INFO @ Sun, 21 Jun 2020 21:22:08: Done! pass1 - making usageList (785 chroms): 1 millis pass2 - checking and writing primary data (2468 records, 4 fields): 22 millis CompletedMACS2peakCalling