Job ID = 6528276 SRX = SRX495786 Genome = dm3 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-29T14:53:46 prefetch.2.10.7: 1) Downloading 'SRR1199484'... 2020-06-29T14:53:46 prefetch.2.10.7: Downloading via HTTPS... 2020-06-29T14:56:49 prefetch.2.10.7: HTTPS download succeed 2020-06-29T14:56:49 prefetch.2.10.7: 1) 'SRR1199484' was downloaded successfully Read 25341638 spots for SRR1199484/SRR1199484.sra Written 25341638 spots for SRR1199484/SRR1199484.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: 00:09:20 25341638 reads; of these: 25341638 (100.00%) were unpaired; of these: 8856255 (34.95%) aligned 0 times 6206668 (24.49%) aligned exactly 1 time 10278715 (40.56%) aligned >1 times 65.05% overall alignment rate Time searching: 00:09:21 Overall time: 00:09:21 マッピングが完了しました。 samtools でBAM に変換中... [samopen] SAM header is present: 15 sequences. [bam_sort_core] merging from 8 files... [bam_rmdupse_core] 7095869 / 16485383 = 0.4304 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 @ Tue, 30 Jun 2020 00:17:09: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX495786/SRX495786.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX495786/SRX495786.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX495786/SRX495786.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX495786/SRX495786.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 @ Tue, 30 Jun 2020 00:17:09: #1 read tag files... INFO @ Tue, 30 Jun 2020 00:17:09: #1 read treatment tags... INFO @ Tue, 30 Jun 2020 00:17:15: 1000000 INFO @ Tue, 30 Jun 2020 00:17:21: 2000000 INFO @ Tue, 30 Jun 2020 00:17:27: 3000000 INFO @ Tue, 30 Jun 2020 00:17:32: 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 @ Tue, 30 Jun 2020 00:17:38: 5000000 INFO @ Tue, 30 Jun 2020 00:17:40: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX495786/SRX495786.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX495786/SRX495786.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX495786/SRX495786.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX495786/SRX495786.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 @ Tue, 30 Jun 2020 00:17:40: #1 read tag files... INFO @ Tue, 30 Jun 2020 00:17:40: #1 read treatment tags... INFO @ Tue, 30 Jun 2020 00:17:45: 6000000 INFO @ Tue, 30 Jun 2020 00:17:47: 1000000 INFO @ Tue, 30 Jun 2020 00:17:51: 7000000 INFO @ Tue, 30 Jun 2020 00:17:54: 2000000 INFO @ Tue, 30 Jun 2020 00:17:58: 8000000 INFO @ Tue, 30 Jun 2020 00:18:02: 3000000 INFO @ Tue, 30 Jun 2020 00:18:05: 9000000 INFO @ Tue, 30 Jun 2020 00:18:08: #1 tag size is determined as 50 bps INFO @ Tue, 30 Jun 2020 00:18:08: #1 tag size = 50 INFO @ Tue, 30 Jun 2020 00:18:08: #1 total tags in treatment: 9389514 INFO @ Tue, 30 Jun 2020 00:18:08: #1 user defined the maximum tags... INFO @ Tue, 30 Jun 2020 00:18:08: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) 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 @ Tue, 30 Jun 2020 00:18:08: #1 tags after filtering in treatment: 9389514 INFO @ Tue, 30 Jun 2020 00:18:08: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 30 Jun 2020 00:18:08: #1 finished! INFO @ Tue, 30 Jun 2020 00:18:08: #2 Build Peak Model... INFO @ Tue, 30 Jun 2020 00:18:08: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 30 Jun 2020 00:18:08: #2 number of paired peaks: 1102 INFO @ Tue, 30 Jun 2020 00:18:08: start model_add_line... INFO @ Tue, 30 Jun 2020 00:18:09: start X-correlation... INFO @ Tue, 30 Jun 2020 00:18:09: end of X-cor INFO @ Tue, 30 Jun 2020 00:18:09: #2 finished! INFO @ Tue, 30 Jun 2020 00:18:09: #2 predicted fragment length is 57 bps INFO @ Tue, 30 Jun 2020 00:18:09: #2 alternative fragment length(s) may be 3,57,552 bps INFO @ Tue, 30 Jun 2020 00:18:09: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX495786/SRX495786.05_model.r WARNING @ Tue, 30 Jun 2020 00:18:09: #2 Since the d (57) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 30 Jun 2020 00:18:09: #2 You may need to consider one of the other alternative d(s): 3,57,552 WARNING @ Tue, 30 Jun 2020 00:18:09: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 30 Jun 2020 00:18:09: #3 Call peaks... INFO @ Tue, 30 Jun 2020 00:18:09: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 30 Jun 2020 00:18:09: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX495786/SRX495786.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX495786/SRX495786.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX495786/SRX495786.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX495786/SRX495786.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 @ Tue, 30 Jun 2020 00:18:09: #1 read tag files... INFO @ Tue, 30 Jun 2020 00:18:09: #1 read treatment tags... INFO @ Tue, 30 Jun 2020 00:18:10: 4000000 INFO @ Tue, 30 Jun 2020 00:18:17: 1000000 INFO @ Tue, 30 Jun 2020 00:18:17: 5000000 INFO @ Tue, 30 Jun 2020 00:18:24: 2000000 INFO @ Tue, 30 Jun 2020 00:18:25: 6000000 INFO @ Tue, 30 Jun 2020 00:18:28: #3 Call peaks for each chromosome... INFO @ Tue, 30 Jun 2020 00:18:32: 3000000 INFO @ Tue, 30 Jun 2020 00:18:33: 7000000 INFO @ Tue, 30 Jun 2020 00:18:38: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX495786/SRX495786.05_peaks.xls INFO @ Tue, 30 Jun 2020 00:18:38: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX495786/SRX495786.05_peaks.narrowPeak INFO @ Tue, 30 Jun 2020 00:18:38: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX495786/SRX495786.05_summits.bed INFO @ Tue, 30 Jun 2020 00:18:38: Done! pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (2800 records, 4 fields): 4 millis CompletedMACS2peakCalling INFO @ Tue, 30 Jun 2020 00:18:39: 4000000 INFO @ Tue, 30 Jun 2020 00:18:41: 8000000 INFO @ Tue, 30 Jun 2020 00:18:46: 5000000 INFO @ Tue, 30 Jun 2020 00:18:49: 9000000 INFO @ Tue, 30 Jun 2020 00:18:52: #1 tag size is determined as 50 bps INFO @ Tue, 30 Jun 2020 00:18:52: #1 tag size = 50 INFO @ Tue, 30 Jun 2020 00:18:52: #1 total tags in treatment: 9389514 INFO @ Tue, 30 Jun 2020 00:18:52: #1 user defined the maximum tags... INFO @ Tue, 30 Jun 2020 00:18:52: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 30 Jun 2020 00:18:52: #1 tags after filtering in treatment: 9389514 INFO @ Tue, 30 Jun 2020 00:18:52: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 30 Jun 2020 00:18:52: #1 finished! INFO @ Tue, 30 Jun 2020 00:18:52: #2 Build Peak Model... INFO @ Tue, 30 Jun 2020 00:18:52: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 30 Jun 2020 00:18:53: #2 number of paired peaks: 1102 INFO @ Tue, 30 Jun 2020 00:18:53: start model_add_line... INFO @ Tue, 30 Jun 2020 00:18:53: start X-correlation... INFO @ Tue, 30 Jun 2020 00:18:53: end of X-cor INFO @ Tue, 30 Jun 2020 00:18:53: #2 finished! INFO @ Tue, 30 Jun 2020 00:18:53: #2 predicted fragment length is 57 bps INFO @ Tue, 30 Jun 2020 00:18:53: #2 alternative fragment length(s) may be 3,57,552 bps INFO @ Tue, 30 Jun 2020 00:18:53: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX495786/SRX495786.10_model.r WARNING @ Tue, 30 Jun 2020 00:18:53: #2 Since the d (57) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 30 Jun 2020 00:18:53: #2 You may need to consider one of the other alternative d(s): 3,57,552 WARNING @ Tue, 30 Jun 2020 00:18:53: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 30 Jun 2020 00:18:53: #3 Call peaks... INFO @ Tue, 30 Jun 2020 00:18:53: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 30 Jun 2020 00:18:53: 6000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 30 Jun 2020 00:19:00: 7000000 INFO @ Tue, 30 Jun 2020 00:19:06: 8000000 INFO @ Tue, 30 Jun 2020 00:19:12: #3 Call peaks for each chromosome... INFO @ Tue, 30 Jun 2020 00:19:12: 9000000 INFO @ Tue, 30 Jun 2020 00:19:15: #1 tag size is determined as 50 bps INFO @ Tue, 30 Jun 2020 00:19:15: #1 tag size = 50 INFO @ Tue, 30 Jun 2020 00:19:15: #1 total tags in treatment: 9389514 INFO @ Tue, 30 Jun 2020 00:19:15: #1 user defined the maximum tags... INFO @ Tue, 30 Jun 2020 00:19:15: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 30 Jun 2020 00:19:15: #1 tags after filtering in treatment: 9389514 INFO @ Tue, 30 Jun 2020 00:19:15: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 30 Jun 2020 00:19:15: #1 finished! INFO @ Tue, 30 Jun 2020 00:19:15: #2 Build Peak Model... INFO @ Tue, 30 Jun 2020 00:19:15: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 30 Jun 2020 00:19:16: #2 number of paired peaks: 1102 INFO @ Tue, 30 Jun 2020 00:19:16: start model_add_line... INFO @ Tue, 30 Jun 2020 00:19:16: start X-correlation... INFO @ Tue, 30 Jun 2020 00:19:16: end of X-cor INFO @ Tue, 30 Jun 2020 00:19:16: #2 finished! INFO @ Tue, 30 Jun 2020 00:19:16: #2 predicted fragment length is 57 bps INFO @ Tue, 30 Jun 2020 00:19:16: #2 alternative fragment length(s) may be 3,57,552 bps INFO @ Tue, 30 Jun 2020 00:19:16: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX495786/SRX495786.20_model.r WARNING @ Tue, 30 Jun 2020 00:19:16: #2 Since the d (57) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 30 Jun 2020 00:19:16: #2 You may need to consider one of the other alternative d(s): 3,57,552 WARNING @ Tue, 30 Jun 2020 00:19:16: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 30 Jun 2020 00:19:16: #3 Call peaks... INFO @ Tue, 30 Jun 2020 00:19:16: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Tue, 30 Jun 2020 00:19:22: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX495786/SRX495786.10_peaks.xls INFO @ Tue, 30 Jun 2020 00:19:22: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX495786/SRX495786.10_peaks.narrowPeak INFO @ Tue, 30 Jun 2020 00:19:22: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX495786/SRX495786.10_summits.bed INFO @ Tue, 30 Jun 2020 00:19:23: Done! pass1 - making usageList (10 chroms): 1 millis pass2 - checking and writing primary data (1417 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Tue, 30 Jun 2020 00:19:35: #3 Call peaks for each chromosome... INFO @ Tue, 30 Jun 2020 00:19:45: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX495786/SRX495786.20_peaks.xls INFO @ Tue, 30 Jun 2020 00:19:46: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX495786/SRX495786.20_peaks.narrowPeak INFO @ Tue, 30 Jun 2020 00:19:46: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX495786/SRX495786.20_summits.bed INFO @ Tue, 30 Jun 2020 00:19:46: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (696 records, 4 fields): 2 millis CompletedMACS2peakCalling