Job ID = 6458560 SRX = SRX5343095 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T12:30:22 prefetch.2.10.7: 1) Downloading 'SRR8540872'... 2020-06-21T12:30:22 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T12:31:50 prefetch.2.10.7: HTTPS download succeed 2020-06-21T12:31:51 prefetch.2.10.7: 'SRR8540872' is valid 2020-06-21T12:31:51 prefetch.2.10.7: 1) 'SRR8540872' was downloaded successfully 2020-06-21T12:31:51 prefetch.2.10.7: 'SRR8540872' has 0 unresolved dependencies Read 11365061 spots for SRR8540872/SRR8540872.sra Written 11365061 spots for SRR8540872/SRR8540872.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: 00:04:54 11365061 reads; of these: 11365061 (100.00%) were unpaired; of these: 1554160 (13.67%) aligned 0 times 4635621 (40.79%) aligned exactly 1 time 5175280 (45.54%) aligned >1 times 86.33% overall alignment rate Time searching: 00:04:54 Overall time: 00:04:54 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_rmdupse_core] 2756713 / 9810901 = 0.2810 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 21:40:12: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX5343095/SRX5343095.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX5343095/SRX5343095.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX5343095/SRX5343095.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX5343095/SRX5343095.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 21:40:12: #1 read tag files... INFO @ Sun, 21 Jun 2020 21:40:12: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 21:40:18: 1000000 INFO @ Sun, 21 Jun 2020 21:40:24: 2000000 INFO @ Sun, 21 Jun 2020 21:40:29: 3000000 INFO @ Sun, 21 Jun 2020 21:40:35: 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 21:40:41: 5000000 INFO @ Sun, 21 Jun 2020 21:40:42: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX5343095/SRX5343095.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX5343095/SRX5343095.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX5343095/SRX5343095.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX5343095/SRX5343095.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 21:40:42: #1 read tag files... INFO @ Sun, 21 Jun 2020 21:40:42: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 21:40:48: 6000000 INFO @ Sun, 21 Jun 2020 21:40:50: 1000000 INFO @ Sun, 21 Jun 2020 21:40:56: 7000000 INFO @ Sun, 21 Jun 2020 21:40:56: #1 tag size is determined as 65 bps INFO @ Sun, 21 Jun 2020 21:40:56: #1 tag size = 65 INFO @ Sun, 21 Jun 2020 21:40:56: #1 total tags in treatment: 7054188 INFO @ Sun, 21 Jun 2020 21:40:56: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 21:40:56: #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 21:40:57: #1 tags after filtering in treatment: 7054185 INFO @ Sun, 21 Jun 2020 21:40:57: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 21:40:57: #1 finished! INFO @ Sun, 21 Jun 2020 21:40:57: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 21:40:57: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 21:40:57: #2 number of paired peaks: 2339 INFO @ Sun, 21 Jun 2020 21:40:57: start model_add_line... INFO @ Sun, 21 Jun 2020 21:40:57: start X-correlation... INFO @ Sun, 21 Jun 2020 21:40:57: end of X-cor INFO @ Sun, 21 Jun 2020 21:40:57: #2 finished! INFO @ Sun, 21 Jun 2020 21:40:57: #2 predicted fragment length is 72 bps INFO @ Sun, 21 Jun 2020 21:40:57: #2 alternative fragment length(s) may be 4,72 bps INFO @ Sun, 21 Jun 2020 21:40:57: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX5343095/SRX5343095.05_model.r WARNING @ Sun, 21 Jun 2020 21:40:57: #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 21:40:57: #2 You may need to consider one of the other alternative d(s): 4,72 WARNING @ Sun, 21 Jun 2020 21:40:57: #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 21:40:57: #3 Call peaks... INFO @ Sun, 21 Jun 2020 21:40:57: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 21:40:58: 2000000 INFO @ Sun, 21 Jun 2020 21:41:05: 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 21:41:12: 4000000 INFO @ Sun, 21 Jun 2020 21:41:12: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 21:41:16: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX5343095/SRX5343095.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX5343095/SRX5343095.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX5343095/SRX5343095.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX5343095/SRX5343095.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 21:41:16: #1 read tag files... INFO @ Sun, 21 Jun 2020 21:41:16: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 21:41:20: 5000000 INFO @ Sun, 21 Jun 2020 21:41:20: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX5343095/SRX5343095.05_peaks.xls INFO @ Sun, 21 Jun 2020 21:41:20: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX5343095/SRX5343095.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 21:41:20: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX5343095/SRX5343095.05_summits.bed INFO @ Sun, 21 Jun 2020 21:41:20: Done! pass1 - making usageList (871 chroms): 1 millis pass2 - checking and writing primary data (3066 records, 4 fields): 25 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 21:41:23: 1000000 INFO @ Sun, 21 Jun 2020 21:41:28: 6000000 INFO @ Sun, 21 Jun 2020 21:41:31: 2000000 INFO @ Sun, 21 Jun 2020 21:41:35: 7000000 INFO @ Sun, 21 Jun 2020 21:41:36: #1 tag size is determined as 65 bps INFO @ Sun, 21 Jun 2020 21:41:36: #1 tag size = 65 INFO @ Sun, 21 Jun 2020 21:41:36: #1 total tags in treatment: 7054188 INFO @ Sun, 21 Jun 2020 21:41:36: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 21:41:36: #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 21:41:36: #1 tags after filtering in treatment: 7054185 INFO @ Sun, 21 Jun 2020 21:41:36: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 21:41:36: #1 finished! INFO @ Sun, 21 Jun 2020 21:41:36: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 21:41:36: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 21:41:37: #2 number of paired peaks: 2339 INFO @ Sun, 21 Jun 2020 21:41:37: start model_add_line... INFO @ Sun, 21 Jun 2020 21:41:37: start X-correlation... INFO @ Sun, 21 Jun 2020 21:41:37: end of X-cor INFO @ Sun, 21 Jun 2020 21:41:37: #2 finished! INFO @ Sun, 21 Jun 2020 21:41:37: #2 predicted fragment length is 72 bps INFO @ Sun, 21 Jun 2020 21:41:37: #2 alternative fragment length(s) may be 4,72 bps INFO @ Sun, 21 Jun 2020 21:41:37: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX5343095/SRX5343095.10_model.r WARNING @ Sun, 21 Jun 2020 21:41:37: #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 21:41:37: #2 You may need to consider one of the other alternative d(s): 4,72 WARNING @ Sun, 21 Jun 2020 21:41:37: #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 21:41:37: #3 Call peaks... INFO @ Sun, 21 Jun 2020 21:41:37: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 21:41:38: 3000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 21:41:44: 4000000 INFO @ Sun, 21 Jun 2020 21:41:50: 5000000 INFO @ Sun, 21 Jun 2020 21:41:52: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 21:41:57: 6000000 INFO @ Sun, 21 Jun 2020 21:41:59: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX5343095/SRX5343095.10_peaks.xls INFO @ Sun, 21 Jun 2020 21:41:59: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX5343095/SRX5343095.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 21:41:59: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX5343095/SRX5343095.10_summits.bed INFO @ Sun, 21 Jun 2020 21:41:59: Done! pass1 - making usageList (557 chroms): 1 millis pass2 - checking and writing primary data (1494 records, 4 fields): 15 millis CompletedMACS2peakCalling BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 21:42:03: 7000000 INFO @ Sun, 21 Jun 2020 21:42:04: #1 tag size is determined as 65 bps INFO @ Sun, 21 Jun 2020 21:42:04: #1 tag size = 65 INFO @ Sun, 21 Jun 2020 21:42:04: #1 total tags in treatment: 7054188 INFO @ Sun, 21 Jun 2020 21:42:04: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 21:42:04: #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 21:42:04: #1 tags after filtering in treatment: 7054185 INFO @ Sun, 21 Jun 2020 21:42:04: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 21:42:04: #1 finished! INFO @ Sun, 21 Jun 2020 21:42:04: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 21:42:04: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 21:42:05: #2 number of paired peaks: 2339 INFO @ Sun, 21 Jun 2020 21:42:05: start model_add_line... INFO @ Sun, 21 Jun 2020 21:42:05: start X-correlation... INFO @ Sun, 21 Jun 2020 21:42:05: end of X-cor INFO @ Sun, 21 Jun 2020 21:42:05: #2 finished! INFO @ Sun, 21 Jun 2020 21:42:05: #2 predicted fragment length is 72 bps INFO @ Sun, 21 Jun 2020 21:42:05: #2 alternative fragment length(s) may be 4,72 bps INFO @ Sun, 21 Jun 2020 21:42:05: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX5343095/SRX5343095.20_model.r WARNING @ Sun, 21 Jun 2020 21:42:05: #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 21:42:05: #2 You may need to consider one of the other alternative d(s): 4,72 WARNING @ Sun, 21 Jun 2020 21:42:05: #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 21:42:05: #3 Call peaks... INFO @ Sun, 21 Jun 2020 21:42:05: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 21:42:19: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 21:42:26: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX5343095/SRX5343095.20_peaks.xls INFO @ Sun, 21 Jun 2020 21:42:26: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX5343095/SRX5343095.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 21:42:26: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX5343095/SRX5343095.20_summits.bed INFO @ Sun, 21 Jun 2020 21:42:26: Done! pass1 - making usageList (327 chroms): 1 millis pass2 - checking and writing primary data (659 records, 4 fields): 10 millis CompletedMACS2peakCalling