Job ID = 6454483 SRX = SRX2165270 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T08:59:19 prefetch.2.10.7: 1) Downloading 'SRR4244769'... 2020-06-21T08:59:19 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T09:03:39 prefetch.2.10.7: HTTPS download succeed 2020-06-21T09:03:39 prefetch.2.10.7: 1) 'SRR4244769' was downloaded successfully Read 15068330 spots for SRR4244769/SRR4244769.sra Written 15068330 spots for SRR4244769/SRR4244769.sra 2020-06-21T09:04:47 prefetch.2.10.7: 1) Downloading 'SRR4244770'... 2020-06-21T09:04:47 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T09:08:39 prefetch.2.10.7: HTTPS download succeed 2020-06-21T09:08:39 prefetch.2.10.7: 1) 'SRR4244770' was downloaded successfully Read 15221560 spots for SRR4244770/SRR4244770.sra Written 15221560 spots for SRR4244770/SRR4244770.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: 00:10:20 30289890 reads; of these: 30289890 (100.00%) were unpaired; of these: 5985571 (19.76%) aligned 0 times 17220926 (56.85%) aligned exactly 1 time 7083393 (23.39%) aligned >1 times 80.24% overall alignment rate Time searching: 00:10:21 Overall time: 00:10:21 マッピングが完了しました。 samtools でBAM に変換中... [samopen] SAM header is present: 1870 sequences. [bam_sort_core] merging from 12 files... [bam_rmdupse_core] 18024573 / 24304319 = 0.7416 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 18:27:37: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX2165270/SRX2165270.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX2165270/SRX2165270.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX2165270/SRX2165270.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX2165270/SRX2165270.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 18:27:37: #1 read tag files... INFO @ Sun, 21 Jun 2020 18:27:37: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 18:27:42: 1000000 INFO @ Sun, 21 Jun 2020 18:27:48: 2000000 INFO @ Sun, 21 Jun 2020 18:27:53: 3000000 INFO @ Sun, 21 Jun 2020 18:27:59: 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 18:28:05: 5000000 INFO @ Sun, 21 Jun 2020 18:28:06: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX2165270/SRX2165270.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX2165270/SRX2165270.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX2165270/SRX2165270.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX2165270/SRX2165270.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 18:28:06: #1 read tag files... INFO @ Sun, 21 Jun 2020 18:28:06: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 18:28:11: 6000000 INFO @ Sun, 21 Jun 2020 18:28:13: 1000000 INFO @ Sun, 21 Jun 2020 18:28:13: #1 tag size is determined as 67 bps INFO @ Sun, 21 Jun 2020 18:28:13: #1 tag size = 67 INFO @ Sun, 21 Jun 2020 18:28:13: #1 total tags in treatment: 6279746 INFO @ Sun, 21 Jun 2020 18:28:13: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 18:28:13: #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 18:28:13: #1 tags after filtering in treatment: 6279734 INFO @ Sun, 21 Jun 2020 18:28:13: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 18:28:13: #1 finished! INFO @ Sun, 21 Jun 2020 18:28:13: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 18:28:13: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 18:28:14: #2 number of paired peaks: 1750 INFO @ Sun, 21 Jun 2020 18:28:14: start model_add_line... INFO @ Sun, 21 Jun 2020 18:28:14: start X-correlation... INFO @ Sun, 21 Jun 2020 18:28:14: end of X-cor INFO @ Sun, 21 Jun 2020 18:28:14: #2 finished! INFO @ Sun, 21 Jun 2020 18:28:14: #2 predicted fragment length is 72 bps INFO @ Sun, 21 Jun 2020 18:28:14: #2 alternative fragment length(s) may be 72 bps INFO @ Sun, 21 Jun 2020 18:28:14: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX2165270/SRX2165270.05_model.r WARNING @ Sun, 21 Jun 2020 18:28:14: #2 Since the d (72) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 18:28:14: #2 You may need to consider one of the other alternative d(s): 72 WARNING @ Sun, 21 Jun 2020 18:28:14: #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 18:28:14: #3 Call peaks... INFO @ Sun, 21 Jun 2020 18:28:14: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 18:28:19: 2000000 INFO @ Sun, 21 Jun 2020 18:28:24: 3000000 INFO @ Sun, 21 Jun 2020 18:28:29: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 18:28:30: 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 18:28:36: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX2165270/SRX2165270.05_peaks.xls INFO @ Sun, 21 Jun 2020 18:28:36: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX2165270/SRX2165270.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 18:28:36: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX2165270/SRX2165270.05_summits.bed INFO @ Sun, 21 Jun 2020 18:28:36: Done! pass1 - making usageList (796 chroms): 2 millis pass2 - checking and writing primary data (2905 records, 4 fields): 25 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 18:28:36: 5000000 INFO @ Sun, 21 Jun 2020 18:28:37: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX2165270/SRX2165270.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX2165270/SRX2165270.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX2165270/SRX2165270.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX2165270/SRX2165270.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 18:28:37: #1 read tag files... INFO @ Sun, 21 Jun 2020 18:28:37: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 18:28:43: 6000000 INFO @ Sun, 21 Jun 2020 18:28:43: 1000000 INFO @ Sun, 21 Jun 2020 18:28:44: #1 tag size is determined as 67 bps INFO @ Sun, 21 Jun 2020 18:28:44: #1 tag size = 67 INFO @ Sun, 21 Jun 2020 18:28:44: #1 total tags in treatment: 6279746 INFO @ Sun, 21 Jun 2020 18:28:44: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 18:28:44: #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 18:28:45: #1 tags after filtering in treatment: 6279734 INFO @ Sun, 21 Jun 2020 18:28:45: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 18:28:45: #1 finished! INFO @ Sun, 21 Jun 2020 18:28:45: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 18:28:45: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 18:28:45: #2 number of paired peaks: 1750 INFO @ Sun, 21 Jun 2020 18:28:45: start model_add_line... INFO @ Sun, 21 Jun 2020 18:28:46: start X-correlation... INFO @ Sun, 21 Jun 2020 18:28:46: end of X-cor INFO @ Sun, 21 Jun 2020 18:28:46: #2 finished! INFO @ Sun, 21 Jun 2020 18:28:46: #2 predicted fragment length is 72 bps INFO @ Sun, 21 Jun 2020 18:28:46: #2 alternative fragment length(s) may be 72 bps INFO @ Sun, 21 Jun 2020 18:28:46: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX2165270/SRX2165270.10_model.r WARNING @ Sun, 21 Jun 2020 18:28:46: #2 Since the d (72) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 18:28:46: #2 You may need to consider one of the other alternative d(s): 72 WARNING @ Sun, 21 Jun 2020 18:28:46: #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 18:28:46: #3 Call peaks... INFO @ Sun, 21 Jun 2020 18:28:46: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 18:28:49: 2000000 INFO @ Sun, 21 Jun 2020 18:28:55: 3000000 INFO @ Sun, 21 Jun 2020 18:29:00: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 18:29:01: 4000000 INFO @ Sun, 21 Jun 2020 18:29:07: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX2165270/SRX2165270.10_peaks.xls INFO @ Sun, 21 Jun 2020 18:29:07: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX2165270/SRX2165270.10_peaks.narrowPeak BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 18:29:07: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX2165270/SRX2165270.10_summits.bed INFO @ Sun, 21 Jun 2020 18:29:07: Done! INFO @ Sun, 21 Jun 2020 18:29:07: 5000000 pass1 - making usageList (625 chroms): 1 millis pass2 - checking and writing primary data (2001 records, 4 fields): 19 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 18:29:14: 6000000 INFO @ Sun, 21 Jun 2020 18:29:15: #1 tag size is determined as 67 bps INFO @ Sun, 21 Jun 2020 18:29:15: #1 tag size = 67 INFO @ Sun, 21 Jun 2020 18:29:15: #1 total tags in treatment: 6279746 INFO @ Sun, 21 Jun 2020 18:29:15: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 18:29:15: #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 18:29:16: #1 tags after filtering in treatment: 6279734 INFO @ Sun, 21 Jun 2020 18:29:16: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 18:29:16: #1 finished! INFO @ Sun, 21 Jun 2020 18:29:16: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 18:29:16: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 18:29:16: #2 number of paired peaks: 1750 INFO @ Sun, 21 Jun 2020 18:29:16: start model_add_line... INFO @ Sun, 21 Jun 2020 18:29:16: start X-correlation... INFO @ Sun, 21 Jun 2020 18:29:16: end of X-cor INFO @ Sun, 21 Jun 2020 18:29:16: #2 finished! INFO @ Sun, 21 Jun 2020 18:29:16: #2 predicted fragment length is 72 bps INFO @ Sun, 21 Jun 2020 18:29:16: #2 alternative fragment length(s) may be 72 bps INFO @ Sun, 21 Jun 2020 18:29:16: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX2165270/SRX2165270.20_model.r WARNING @ Sun, 21 Jun 2020 18:29:16: #2 Since the d (72) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 18:29:16: #2 You may need to consider one of the other alternative d(s): 72 WARNING @ Sun, 21 Jun 2020 18:29:16: #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 18:29:16: #3 Call peaks... INFO @ Sun, 21 Jun 2020 18:29:16: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 18:29:32: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 18:29:39: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX2165270/SRX2165270.20_peaks.xls INFO @ Sun, 21 Jun 2020 18:29:39: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX2165270/SRX2165270.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 18:29:39: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX2165270/SRX2165270.20_summits.bed INFO @ Sun, 21 Jun 2020 18:29:39: Done! pass1 - making usageList (508 chroms): 1 millis pass2 - checking and writing primary data (1338 records, 4 fields): 16 millis CompletedMACS2peakCalling