Job ID = 6509073 SRX = SRX645116 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-26T14:57:14 prefetch.2.10.7: 1) Downloading 'SRR1505716'... 2020-06-26T14:57:14 prefetch.2.10.7: Downloading via HTTPS... 2020-06-26T15:01:28 prefetch.2.10.7: HTTPS download succeed 2020-06-26T15:01:28 prefetch.2.10.7: 1) 'SRR1505716' was downloaded successfully Read 25506879 spots for SRR1505716/SRR1505716.sra Written 25506879 spots for SRR1505716/SRR1505716.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: 00:08:39 25506879 reads; of these: 25506879 (100.00%) were unpaired; of these: 17907040 (70.20%) aligned 0 times 5482387 (21.49%) aligned exactly 1 time 2117452 (8.30%) aligned >1 times 29.80% overall alignment rate Time searching: 00:08:39 Overall time: 00:08:39 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] 4874435 / 7599839 = 0.6414 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 @ Sat, 27 Jun 2020 00:15:13: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX645116/SRX645116.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX645116/SRX645116.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX645116/SRX645116.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX645116/SRX645116.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 @ Sat, 27 Jun 2020 00:15:13: #1 read tag files... INFO @ Sat, 27 Jun 2020 00:15:13: #1 read treatment tags... INFO @ Sat, 27 Jun 2020 00:15:21: 1000000 INFO @ Sat, 27 Jun 2020 00:15:29: 2000000 INFO @ Sat, 27 Jun 2020 00:15:36: #1 tag size is determined as 100 bps INFO @ Sat, 27 Jun 2020 00:15:36: #1 tag size = 100 INFO @ Sat, 27 Jun 2020 00:15:36: #1 total tags in treatment: 2725404 INFO @ Sat, 27 Jun 2020 00:15:36: #1 user defined the maximum tags... INFO @ Sat, 27 Jun 2020 00:15:36: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 27 Jun 2020 00:15:36: #1 tags after filtering in treatment: 2725339 INFO @ Sat, 27 Jun 2020 00:15:36: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 27 Jun 2020 00:15:36: #1 finished! INFO @ Sat, 27 Jun 2020 00:15:36: #2 Build Peak Model... INFO @ Sat, 27 Jun 2020 00:15:36: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 27 Jun 2020 00:15:37: #2 number of paired peaks: 1633 INFO @ Sat, 27 Jun 2020 00:15:37: start model_add_line... INFO @ Sat, 27 Jun 2020 00:15:37: start X-correlation... INFO @ Sat, 27 Jun 2020 00:15:37: end of X-cor INFO @ Sat, 27 Jun 2020 00:15:37: #2 finished! INFO @ Sat, 27 Jun 2020 00:15:37: #2 predicted fragment length is 99 bps INFO @ Sat, 27 Jun 2020 00:15:37: #2 alternative fragment length(s) may be 99 bps INFO @ Sat, 27 Jun 2020 00:15:37: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX645116/SRX645116.05_model.r WARNING @ Sat, 27 Jun 2020 00:15:37: #2 Since the d (99) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 27 Jun 2020 00:15:37: #2 You may need to consider one of the other alternative d(s): 99 WARNING @ Sat, 27 Jun 2020 00:15:37: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sat, 27 Jun 2020 00:15:37: #3 Call peaks... INFO @ Sat, 27 Jun 2020 00:15:37: #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 @ Sat, 27 Jun 2020 00:15:42: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX645116/SRX645116.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX645116/SRX645116.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX645116/SRX645116.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX645116/SRX645116.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 @ Sat, 27 Jun 2020 00:15:42: #1 read tag files... INFO @ Sat, 27 Jun 2020 00:15:42: #1 read treatment tags... INFO @ Sat, 27 Jun 2020 00:15:43: #3 Call peaks for each chromosome... INFO @ Sat, 27 Jun 2020 00:15:46: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX645116/SRX645116.05_peaks.xls INFO @ Sat, 27 Jun 2020 00:15:46: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX645116/SRX645116.05_peaks.narrowPeak INFO @ Sat, 27 Jun 2020 00:15:46: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX645116/SRX645116.05_summits.bed INFO @ Sat, 27 Jun 2020 00:15:46: Done! pass1 - making usageList (672 chroms): 1 millis pass2 - checking and writing primary data (1812 records, 4 fields): 69 millis CompletedMACS2peakCalling INFO @ Sat, 27 Jun 2020 00:15:51: 1000000 INFO @ Sat, 27 Jun 2020 00:15:59: 2000000 INFO @ Sat, 27 Jun 2020 00:16:06: #1 tag size is determined as 100 bps INFO @ Sat, 27 Jun 2020 00:16:06: #1 tag size = 100 INFO @ Sat, 27 Jun 2020 00:16:06: #1 total tags in treatment: 2725404 INFO @ Sat, 27 Jun 2020 00:16:06: #1 user defined the maximum tags... INFO @ Sat, 27 Jun 2020 00:16:06: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 27 Jun 2020 00:16:06: #1 tags after filtering in treatment: 2725339 INFO @ Sat, 27 Jun 2020 00:16:06: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 27 Jun 2020 00:16:06: #1 finished! INFO @ Sat, 27 Jun 2020 00:16:06: #2 Build Peak Model... INFO @ Sat, 27 Jun 2020 00:16:06: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 27 Jun 2020 00:16:07: #2 number of paired peaks: 1633 INFO @ Sat, 27 Jun 2020 00:16:07: start model_add_line... INFO @ Sat, 27 Jun 2020 00:16:07: start X-correlation... INFO @ Sat, 27 Jun 2020 00:16:07: end of X-cor INFO @ Sat, 27 Jun 2020 00:16:07: #2 finished! INFO @ Sat, 27 Jun 2020 00:16:07: #2 predicted fragment length is 99 bps INFO @ Sat, 27 Jun 2020 00:16:07: #2 alternative fragment length(s) may be 99 bps INFO @ Sat, 27 Jun 2020 00:16:07: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX645116/SRX645116.10_model.r WARNING @ Sat, 27 Jun 2020 00:16:07: #2 Since the d (99) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 27 Jun 2020 00:16:07: #2 You may need to consider one of the other alternative d(s): 99 WARNING @ Sat, 27 Jun 2020 00:16:07: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sat, 27 Jun 2020 00:16:07: #3 Call peaks... INFO @ Sat, 27 Jun 2020 00:16:07: #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 @ Sat, 27 Jun 2020 00:16:12: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX645116/SRX645116.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX645116/SRX645116.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX645116/SRX645116.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX645116/SRX645116.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 @ Sat, 27 Jun 2020 00:16:12: #1 read tag files... INFO @ Sat, 27 Jun 2020 00:16:12: #1 read treatment tags... INFO @ Sat, 27 Jun 2020 00:16:13: #3 Call peaks for each chromosome... INFO @ Sat, 27 Jun 2020 00:16:16: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX645116/SRX645116.10_peaks.xls INFO @ Sat, 27 Jun 2020 00:16:16: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX645116/SRX645116.10_peaks.narrowPeak INFO @ Sat, 27 Jun 2020 00:16:16: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX645116/SRX645116.10_summits.bed INFO @ Sat, 27 Jun 2020 00:16:16: Done! pass1 - making usageList (533 chroms): 1 millis pass2 - checking and writing primary data (1165 records, 4 fields): 38 millis CompletedMACS2peakCalling INFO @ Sat, 27 Jun 2020 00:16:21: 1000000 INFO @ Sat, 27 Jun 2020 00:16:29: 2000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 27 Jun 2020 00:16:36: #1 tag size is determined as 100 bps INFO @ Sat, 27 Jun 2020 00:16:36: #1 tag size = 100 INFO @ Sat, 27 Jun 2020 00:16:36: #1 total tags in treatment: 2725404 INFO @ Sat, 27 Jun 2020 00:16:36: #1 user defined the maximum tags... INFO @ Sat, 27 Jun 2020 00:16:36: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 27 Jun 2020 00:16:36: #1 tags after filtering in treatment: 2725339 INFO @ Sat, 27 Jun 2020 00:16:36: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 27 Jun 2020 00:16:36: #1 finished! INFO @ Sat, 27 Jun 2020 00:16:36: #2 Build Peak Model... INFO @ Sat, 27 Jun 2020 00:16:36: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 27 Jun 2020 00:16:37: #2 number of paired peaks: 1633 INFO @ Sat, 27 Jun 2020 00:16:37: start model_add_line... INFO @ Sat, 27 Jun 2020 00:16:37: start X-correlation... INFO @ Sat, 27 Jun 2020 00:16:37: end of X-cor INFO @ Sat, 27 Jun 2020 00:16:37: #2 finished! INFO @ Sat, 27 Jun 2020 00:16:37: #2 predicted fragment length is 99 bps INFO @ Sat, 27 Jun 2020 00:16:37: #2 alternative fragment length(s) may be 99 bps INFO @ Sat, 27 Jun 2020 00:16:37: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX645116/SRX645116.20_model.r WARNING @ Sat, 27 Jun 2020 00:16:37: #2 Since the d (99) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 27 Jun 2020 00:16:37: #2 You may need to consider one of the other alternative d(s): 99 WARNING @ Sat, 27 Jun 2020 00:16:37: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sat, 27 Jun 2020 00:16:37: #3 Call peaks... INFO @ Sat, 27 Jun 2020 00:16:37: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Sat, 27 Jun 2020 00:16:44: #3 Call peaks for each chromosome... INFO @ Sat, 27 Jun 2020 00:16:47: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX645116/SRX645116.20_peaks.xls INFO @ Sat, 27 Jun 2020 00:16:48: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX645116/SRX645116.20_peaks.narrowPeak INFO @ Sat, 27 Jun 2020 00:16:48: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX645116/SRX645116.20_summits.bed INFO @ Sat, 27 Jun 2020 00:16:48: Done! pass1 - making usageList (356 chroms): 1 millis pass2 - checking and writing primary data (605 records, 4 fields): 21 millis CompletedMACS2peakCalling