Job ID = 6457969 SRX = SRX4933877 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T12:05:14 prefetch.2.10.7: 1) Downloading 'SRR8107267'... 2020-06-21T12:05:14 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T12:12:06 prefetch.2.10.7: HTTPS download succeed 2020-06-21T12:12:06 prefetch.2.10.7: 1) 'SRR8107267' was downloaded successfully Read 41067534 spots for SRR8107267/SRR8107267.sra Written 41067534 spots for SRR8107267/SRR8107267.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: 00:12:22 41067534 reads; of these: 41067534 (100.00%) were unpaired; of these: 14941165 (36.38%) aligned 0 times 16382822 (39.89%) aligned exactly 1 time 9743547 (23.73%) aligned >1 times 63.62% overall alignment rate Time searching: 00:12:22 Overall time: 00:12:22 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] 24088543 / 26126369 = 0.9220 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 21:31:01: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX4933877/SRX4933877.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX4933877/SRX4933877.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX4933877/SRX4933877.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX4933877/SRX4933877.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 21:31:01: #1 read tag files... INFO @ Sun, 21 Jun 2020 21:31:01: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 21:31:08: 1000000 INFO @ Sun, 21 Jun 2020 21:31:16: 2000000 INFO @ Sun, 21 Jun 2020 21:31:16: #1 tag size is determined as 51 bps INFO @ Sun, 21 Jun 2020 21:31:16: #1 tag size = 51 INFO @ Sun, 21 Jun 2020 21:31:16: #1 total tags in treatment: 2037826 INFO @ Sun, 21 Jun 2020 21:31:16: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 21:31:16: #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 21:31:16: #1 tags after filtering in treatment: 2037729 INFO @ Sun, 21 Jun 2020 21:31:16: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 21:31:16: #1 finished! INFO @ Sun, 21 Jun 2020 21:31:16: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 21:31:16: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 21:31:17: #2 number of paired peaks: 6237 INFO @ Sun, 21 Jun 2020 21:31:17: start model_add_line... INFO @ Sun, 21 Jun 2020 21:31:17: start X-correlation... INFO @ Sun, 21 Jun 2020 21:31:17: end of X-cor INFO @ Sun, 21 Jun 2020 21:31:17: #2 finished! INFO @ Sun, 21 Jun 2020 21:31:17: #2 predicted fragment length is 101 bps INFO @ Sun, 21 Jun 2020 21:31:17: #2 alternative fragment length(s) may be 101,103 bps INFO @ Sun, 21 Jun 2020 21:31:17: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX4933877/SRX4933877.05_model.r WARNING @ Sun, 21 Jun 2020 21:31:17: #2 Since the d (101) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 21:31:17: #2 You may need to consider one of the other alternative d(s): 101,103 WARNING @ Sun, 21 Jun 2020 21:31:17: #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 21:31:17: #3 Call peaks... INFO @ Sun, 21 Jun 2020 21:31:17: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 21:31:22: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 21:31:25: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX4933877/SRX4933877.05_peaks.xls INFO @ Sun, 21 Jun 2020 21:31:25: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX4933877/SRX4933877.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 21:31:25: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX4933877/SRX4933877.05_summits.bed INFO @ Sun, 21 Jun 2020 21:31:25: Done! pass1 - making usageList (925 chroms): 2 millis pass2 - checking and writing primary data (4018 records, 4 fields): 29 millis CompletedMACS2peakCalling 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 21:31:31: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX4933877/SRX4933877.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX4933877/SRX4933877.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX4933877/SRX4933877.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX4933877/SRX4933877.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 21:31:31: #1 read tag files... INFO @ Sun, 21 Jun 2020 21:31:31: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 21:31:38: 1000000 INFO @ Sun, 21 Jun 2020 21:31:45: 2000000 INFO @ Sun, 21 Jun 2020 21:31:46: #1 tag size is determined as 51 bps INFO @ Sun, 21 Jun 2020 21:31:46: #1 tag size = 51 INFO @ Sun, 21 Jun 2020 21:31:46: #1 total tags in treatment: 2037826 INFO @ Sun, 21 Jun 2020 21:31:46: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 21:31:46: #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 21:31:46: #1 tags after filtering in treatment: 2037729 INFO @ Sun, 21 Jun 2020 21:31:46: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 21:31:46: #1 finished! INFO @ Sun, 21 Jun 2020 21:31:46: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 21:31:46: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 21:31:46: #2 number of paired peaks: 6237 INFO @ Sun, 21 Jun 2020 21:31:46: start model_add_line... INFO @ Sun, 21 Jun 2020 21:31:46: start X-correlation... INFO @ Sun, 21 Jun 2020 21:31:46: end of X-cor INFO @ Sun, 21 Jun 2020 21:31:46: #2 finished! INFO @ Sun, 21 Jun 2020 21:31:46: #2 predicted fragment length is 101 bps INFO @ Sun, 21 Jun 2020 21:31:46: #2 alternative fragment length(s) may be 101,103 bps INFO @ Sun, 21 Jun 2020 21:31:46: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX4933877/SRX4933877.10_model.r WARNING @ Sun, 21 Jun 2020 21:31:46: #2 Since the d (101) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 21:31:46: #2 You may need to consider one of the other alternative d(s): 101,103 WARNING @ Sun, 21 Jun 2020 21:31:46: #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 21:31:46: #3 Call peaks... INFO @ Sun, 21 Jun 2020 21:31:46: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 21:31:52: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 21:31:54: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX4933877/SRX4933877.10_peaks.xls INFO @ Sun, 21 Jun 2020 21:31:54: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX4933877/SRX4933877.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 21:31:54: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX4933877/SRX4933877.10_summits.bed INFO @ Sun, 21 Jun 2020 21:31:54: Done! pass1 - making usageList (689 chroms): 1 millis pass2 - checking and writing primary data (1926 records, 4 fields): 21 millis CompletedMACS2peakCalling 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 21:32:01: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX4933877/SRX4933877.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX4933877/SRX4933877.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX4933877/SRX4933877.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX4933877/SRX4933877.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 21:32:01: #1 read tag files... INFO @ Sun, 21 Jun 2020 21:32:01: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 21:32:07: 1000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 21:32:13: 2000000 BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 21:32:14: #1 tag size is determined as 51 bps INFO @ Sun, 21 Jun 2020 21:32:14: #1 tag size = 51 INFO @ Sun, 21 Jun 2020 21:32:14: #1 total tags in treatment: 2037826 INFO @ Sun, 21 Jun 2020 21:32:14: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 21:32:14: #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 21:32:14: #1 tags after filtering in treatment: 2037729 INFO @ Sun, 21 Jun 2020 21:32:14: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 21:32:14: #1 finished! INFO @ Sun, 21 Jun 2020 21:32:14: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 21:32:14: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 21:32:14: #2 number of paired peaks: 6237 INFO @ Sun, 21 Jun 2020 21:32:14: start model_add_line... INFO @ Sun, 21 Jun 2020 21:32:14: start X-correlation... INFO @ Sun, 21 Jun 2020 21:32:14: end of X-cor INFO @ Sun, 21 Jun 2020 21:32:14: #2 finished! INFO @ Sun, 21 Jun 2020 21:32:14: #2 predicted fragment length is 101 bps INFO @ Sun, 21 Jun 2020 21:32:14: #2 alternative fragment length(s) may be 101,103 bps INFO @ Sun, 21 Jun 2020 21:32:14: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX4933877/SRX4933877.20_model.r WARNING @ Sun, 21 Jun 2020 21:32:14: #2 Since the d (101) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 21:32:14: #2 You may need to consider one of the other alternative d(s): 101,103 WARNING @ Sun, 21 Jun 2020 21:32:14: #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 21:32:14: #3 Call peaks... INFO @ Sun, 21 Jun 2020 21:32:14: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 21:32:20: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 21:32:22: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX4933877/SRX4933877.20_peaks.xls INFO @ Sun, 21 Jun 2020 21:32:22: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX4933877/SRX4933877.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 21:32:22: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX4933877/SRX4933877.20_summits.bed INFO @ Sun, 21 Jun 2020 21:32:22: Done! pass1 - making usageList (429 chroms): 1 millis pass2 - checking and writing primary data (795 records, 4 fields): 14 millis CompletedMACS2peakCalling