Job ID = 6459307 SRX = SRX666357 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T13:06:16 prefetch.2.10.7: 1) Downloading 'SRR1532701'... 2020-06-21T13:06:16 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T13:19:27 prefetch.2.10.7: HTTPS download succeed 2020-06-21T13:19:27 prefetch.2.10.7: 1) 'SRR1532701' was downloaded successfully Read 29904815 spots for SRR1532701/SRR1532701.sra Written 29904815 spots for SRR1532701/SRR1532701.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: 00:11:24 29904815 reads; of these: 29904815 (100.00%) were unpaired; of these: 10792589 (36.09%) aligned 0 times 17172268 (57.42%) aligned exactly 1 time 1939958 (6.49%) aligned >1 times 63.91% overall alignment rate Time searching: 00:11:24 Overall time: 00:11:24 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] 15762171 / 19112226 = 0.8247 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 22:38:53: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX666357/SRX666357.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX666357/SRX666357.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX666357/SRX666357.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX666357/SRX666357.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 22:38:53: #1 read tag files... INFO @ Sun, 21 Jun 2020 22:38:53: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 22:39:00: 1000000 INFO @ Sun, 21 Jun 2020 22:39:08: 2000000 INFO @ Sun, 21 Jun 2020 22:39:16: 3000000 INFO @ Sun, 21 Jun 2020 22:39:19: #1 tag size is determined as 100 bps INFO @ Sun, 21 Jun 2020 22:39:19: #1 tag size = 100 INFO @ Sun, 21 Jun 2020 22:39:19: #1 total tags in treatment: 3350055 INFO @ Sun, 21 Jun 2020 22:39:19: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 22:39:19: #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 22:39:19: #1 tags after filtering in treatment: 3349799 INFO @ Sun, 21 Jun 2020 22:39:19: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 22:39:19: #1 finished! INFO @ Sun, 21 Jun 2020 22:39:19: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 22:39:19: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 22:39:20: #2 number of paired peaks: 1146 INFO @ Sun, 21 Jun 2020 22:39:20: start model_add_line... INFO @ Sun, 21 Jun 2020 22:39:20: start X-correlation... INFO @ Sun, 21 Jun 2020 22:39:20: end of X-cor INFO @ Sun, 21 Jun 2020 22:39:20: #2 finished! INFO @ Sun, 21 Jun 2020 22:39:20: #2 predicted fragment length is 111 bps INFO @ Sun, 21 Jun 2020 22:39:20: #2 alternative fragment length(s) may be 111 bps INFO @ Sun, 21 Jun 2020 22:39:20: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX666357/SRX666357.05_model.r WARNING @ Sun, 21 Jun 2020 22:39:20: #2 Since the d (111) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 22:39:20: #2 You may need to consider one of the other alternative d(s): 111 WARNING @ Sun, 21 Jun 2020 22:39:20: #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 22:39:20: #3 Call peaks... INFO @ Sun, 21 Jun 2020 22:39:20: #3 Pre-compute pvalue-qvalue table... 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 22:39:22: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX666357/SRX666357.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX666357/SRX666357.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX666357/SRX666357.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX666357/SRX666357.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 22:39:22: #1 read tag files... INFO @ Sun, 21 Jun 2020 22:39:22: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 22:39:29: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 22:39:30: 1000000 INFO @ Sun, 21 Jun 2020 22:39:33: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX666357/SRX666357.05_peaks.xls INFO @ Sun, 21 Jun 2020 22:39:33: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX666357/SRX666357.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 22:39:33: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX666357/SRX666357.05_summits.bed INFO @ Sun, 21 Jun 2020 22:39:33: Done! pass1 - making usageList (338 chroms): 1 millis pass2 - checking and writing primary data (2694 records, 4 fields): 14 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 22:39:38: 2000000 INFO @ Sun, 21 Jun 2020 22:39:46: 3000000 INFO @ Sun, 21 Jun 2020 22:39:49: #1 tag size is determined as 100 bps INFO @ Sun, 21 Jun 2020 22:39:49: #1 tag size = 100 INFO @ Sun, 21 Jun 2020 22:39:49: #1 total tags in treatment: 3350055 INFO @ Sun, 21 Jun 2020 22:39:49: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 22:39:49: #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 22:39:50: #1 tags after filtering in treatment: 3349799 INFO @ Sun, 21 Jun 2020 22:39:50: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 22:39:50: #1 finished! INFO @ Sun, 21 Jun 2020 22:39:50: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 22:39:50: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 22:39:50: #2 number of paired peaks: 1146 INFO @ Sun, 21 Jun 2020 22:39:50: start model_add_line... INFO @ Sun, 21 Jun 2020 22:39:50: start X-correlation... INFO @ Sun, 21 Jun 2020 22:39:50: end of X-cor INFO @ Sun, 21 Jun 2020 22:39:50: #2 finished! INFO @ Sun, 21 Jun 2020 22:39:50: #2 predicted fragment length is 111 bps INFO @ Sun, 21 Jun 2020 22:39:50: #2 alternative fragment length(s) may be 111 bps INFO @ Sun, 21 Jun 2020 22:39:50: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX666357/SRX666357.10_model.r WARNING @ Sun, 21 Jun 2020 22:39:50: #2 Since the d (111) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 22:39:50: #2 You may need to consider one of the other alternative d(s): 111 WARNING @ Sun, 21 Jun 2020 22:39:50: #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 22:39:50: #3 Call peaks... INFO @ Sun, 21 Jun 2020 22:39:50: #3 Pre-compute pvalue-qvalue table... 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 22:39:52: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX666357/SRX666357.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX666357/SRX666357.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX666357/SRX666357.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX666357/SRX666357.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 22:39:52: #1 read tag files... INFO @ Sun, 21 Jun 2020 22:39:52: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 22:39:59: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 22:40:00: 1000000 INFO @ Sun, 21 Jun 2020 22:40:03: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX666357/SRX666357.10_peaks.xls INFO @ Sun, 21 Jun 2020 22:40:03: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX666357/SRX666357.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 22:40:03: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX666357/SRX666357.10_summits.bed INFO @ Sun, 21 Jun 2020 22:40:03: Done! pass1 - making usageList (226 chroms): 1 millis pass2 - checking and writing primary data (798 records, 4 fields): 8 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 22:40:08: 2000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 22:40:16: 3000000 INFO @ Sun, 21 Jun 2020 22:40:19: #1 tag size is determined as 100 bps INFO @ Sun, 21 Jun 2020 22:40:19: #1 tag size = 100 INFO @ Sun, 21 Jun 2020 22:40:19: #1 total tags in treatment: 3350055 INFO @ Sun, 21 Jun 2020 22:40:19: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 22:40:19: #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 22:40:20: #1 tags after filtering in treatment: 3349799 INFO @ Sun, 21 Jun 2020 22:40:20: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 22:40:20: #1 finished! INFO @ Sun, 21 Jun 2020 22:40:20: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 22:40:20: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 22:40:20: #2 number of paired peaks: 1146 INFO @ Sun, 21 Jun 2020 22:40:20: start model_add_line... INFO @ Sun, 21 Jun 2020 22:40:20: start X-correlation... INFO @ Sun, 21 Jun 2020 22:40:20: end of X-cor INFO @ Sun, 21 Jun 2020 22:40:20: #2 finished! INFO @ Sun, 21 Jun 2020 22:40:20: #2 predicted fragment length is 111 bps INFO @ Sun, 21 Jun 2020 22:40:20: #2 alternative fragment length(s) may be 111 bps INFO @ Sun, 21 Jun 2020 22:40:20: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX666357/SRX666357.20_model.r WARNING @ Sun, 21 Jun 2020 22:40:20: #2 Since the d (111) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 22:40:20: #2 You may need to consider one of the other alternative d(s): 111 WARNING @ Sun, 21 Jun 2020 22:40:20: #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 22:40:20: #3 Call peaks... INFO @ Sun, 21 Jun 2020 22:40:20: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 22:40:29: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 22:40:34: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX666357/SRX666357.20_peaks.xls INFO @ Sun, 21 Jun 2020 22:40:34: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX666357/SRX666357.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 22:40:34: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX666357/SRX666357.20_summits.bed INFO @ Sun, 21 Jun 2020 22:40:34: Done! pass1 - making usageList (121 chroms): 1 millis pass2 - checking and writing primary data (257 records, 4 fields): 5 millis CompletedMACS2peakCalling