Job ID = 6456580 SRX = SRX365698 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T10:52:16 prefetch.2.10.7: 1) Downloading 'SRR1013776'... 2020-06-21T10:52:16 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T10:58:27 prefetch.2.10.7: HTTPS download succeed 2020-06-21T10:58:27 prefetch.2.10.7: 1) 'SRR1013776' was downloaded successfully Read 22204822 spots for SRR1013776/SRR1013776.sra Written 22204822 spots for SRR1013776/SRR1013776.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: 00:05:42 22204822 reads; of these: 22204822 (100.00%) were unpaired; of these: 1838746 (8.28%) aligned 0 times 14921546 (67.20%) aligned exactly 1 time 5444530 (24.52%) aligned >1 times 91.72% overall alignment rate Time searching: 00:05:42 Overall time: 00:05:42 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] 17336439 / 20366076 = 0.8512 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 20:09:00: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX365698/SRX365698.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX365698/SRX365698.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX365698/SRX365698.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX365698/SRX365698.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 20:09:00: #1 read tag files... INFO @ Sun, 21 Jun 2020 20:09:00: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 20:09:05: 1000000 INFO @ Sun, 21 Jun 2020 20:09:11: 2000000 INFO @ Sun, 21 Jun 2020 20:09:16: 3000000 INFO @ Sun, 21 Jun 2020 20:09:17: #1 tag size is determined as 51 bps INFO @ Sun, 21 Jun 2020 20:09:17: #1 tag size = 51 INFO @ Sun, 21 Jun 2020 20:09:17: #1 total tags in treatment: 3029637 INFO @ Sun, 21 Jun 2020 20:09:17: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 20:09:17: #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 20:09:17: #1 tags after filtering in treatment: 3029496 INFO @ Sun, 21 Jun 2020 20:09:17: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 20:09:17: #1 finished! INFO @ Sun, 21 Jun 2020 20:09:17: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 20:09:17: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 20:09:17: #2 number of paired peaks: 3904 INFO @ Sun, 21 Jun 2020 20:09:17: start model_add_line... INFO @ Sun, 21 Jun 2020 20:09:18: start X-correlation... INFO @ Sun, 21 Jun 2020 20:09:18: end of X-cor INFO @ Sun, 21 Jun 2020 20:09:18: #2 finished! INFO @ Sun, 21 Jun 2020 20:09:18: #2 predicted fragment length is 76 bps INFO @ Sun, 21 Jun 2020 20:09:18: #2 alternative fragment length(s) may be 76 bps INFO @ Sun, 21 Jun 2020 20:09:18: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX365698/SRX365698.05_model.r WARNING @ Sun, 21 Jun 2020 20:09:18: #2 Since the d (76) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 20:09:18: #2 You may need to consider one of the other alternative d(s): 76 WARNING @ Sun, 21 Jun 2020 20:09:18: #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 20:09:18: #3 Call peaks... INFO @ Sun, 21 Jun 2020 20:09:18: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 20:09:25: #3 Call peaks for each chromosome... 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 20:09:28: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX365698/SRX365698.05_peaks.xls INFO @ Sun, 21 Jun 2020 20:09:28: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX365698/SRX365698.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 20:09:28: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX365698/SRX365698.05_summits.bed INFO @ Sun, 21 Jun 2020 20:09:28: Done! pass1 - making usageList (715 chroms): 2 millis pass2 - checking and writing primary data (4944 records, 4 fields): 24 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 20:09:30: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX365698/SRX365698.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX365698/SRX365698.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX365698/SRX365698.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX365698/SRX365698.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 20:09:30: #1 read tag files... INFO @ Sun, 21 Jun 2020 20:09:30: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 20:09:36: 1000000 INFO @ Sun, 21 Jun 2020 20:09:43: 2000000 INFO @ Sun, 21 Jun 2020 20:09:49: 3000000 INFO @ Sun, 21 Jun 2020 20:09:50: #1 tag size is determined as 51 bps INFO @ Sun, 21 Jun 2020 20:09:50: #1 tag size = 51 INFO @ Sun, 21 Jun 2020 20:09:50: #1 total tags in treatment: 3029637 INFO @ Sun, 21 Jun 2020 20:09:50: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 20:09:50: #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 20:09:50: #1 tags after filtering in treatment: 3029496 INFO @ Sun, 21 Jun 2020 20:09:50: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 20:09:50: #1 finished! INFO @ Sun, 21 Jun 2020 20:09:50: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 20:09:50: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 20:09:50: #2 number of paired peaks: 3904 INFO @ Sun, 21 Jun 2020 20:09:50: start model_add_line... INFO @ Sun, 21 Jun 2020 20:09:50: start X-correlation... INFO @ Sun, 21 Jun 2020 20:09:50: end of X-cor INFO @ Sun, 21 Jun 2020 20:09:50: #2 finished! INFO @ Sun, 21 Jun 2020 20:09:50: #2 predicted fragment length is 76 bps INFO @ Sun, 21 Jun 2020 20:09:50: #2 alternative fragment length(s) may be 76 bps INFO @ Sun, 21 Jun 2020 20:09:50: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX365698/SRX365698.10_model.r WARNING @ Sun, 21 Jun 2020 20:09:50: #2 Since the d (76) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 20:09:50: #2 You may need to consider one of the other alternative d(s): 76 WARNING @ Sun, 21 Jun 2020 20:09:50: #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 20:09:50: #3 Call peaks... INFO @ Sun, 21 Jun 2020 20:09:50: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 20:09:58: #3 Call peaks for each chromosome... 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 20:10:00: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX365698/SRX365698.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX365698/SRX365698.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX365698/SRX365698.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX365698/SRX365698.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 20:10:00: #1 read tag files... INFO @ Sun, 21 Jun 2020 20:10:00: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 20:10:01: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX365698/SRX365698.10_peaks.xls INFO @ Sun, 21 Jun 2020 20:10:01: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX365698/SRX365698.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 20:10:01: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX365698/SRX365698.10_summits.bed INFO @ Sun, 21 Jun 2020 20:10:01: Done! pass1 - making usageList (472 chroms): 1 millis pass2 - checking and writing primary data (2314 records, 4 fields): 17 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 20:10:06: 1000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 20:10:13: 2000000 BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 20:10:19: 3000000 INFO @ Sun, 21 Jun 2020 20:10:20: #1 tag size is determined as 51 bps INFO @ Sun, 21 Jun 2020 20:10:20: #1 tag size = 51 INFO @ Sun, 21 Jun 2020 20:10:20: #1 total tags in treatment: 3029637 INFO @ Sun, 21 Jun 2020 20:10:20: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 20:10:20: #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 20:10:20: #1 tags after filtering in treatment: 3029496 INFO @ Sun, 21 Jun 2020 20:10:20: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 20:10:20: #1 finished! INFO @ Sun, 21 Jun 2020 20:10:20: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 20:10:20: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 20:10:20: #2 number of paired peaks: 3904 INFO @ Sun, 21 Jun 2020 20:10:20: start model_add_line... INFO @ Sun, 21 Jun 2020 20:10:20: start X-correlation... INFO @ Sun, 21 Jun 2020 20:10:20: end of X-cor INFO @ Sun, 21 Jun 2020 20:10:20: #2 finished! INFO @ Sun, 21 Jun 2020 20:10:20: #2 predicted fragment length is 76 bps INFO @ Sun, 21 Jun 2020 20:10:20: #2 alternative fragment length(s) may be 76 bps INFO @ Sun, 21 Jun 2020 20:10:20: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX365698/SRX365698.20_model.r WARNING @ Sun, 21 Jun 2020 20:10:20: #2 Since the d (76) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 20:10:20: #2 You may need to consider one of the other alternative d(s): 76 WARNING @ Sun, 21 Jun 2020 20:10:20: #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 20:10:20: #3 Call peaks... INFO @ Sun, 21 Jun 2020 20:10:20: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 20:10:28: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 20:10:31: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX365698/SRX365698.20_peaks.xls INFO @ Sun, 21 Jun 2020 20:10:31: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX365698/SRX365698.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 20:10:31: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX365698/SRX365698.20_summits.bed INFO @ Sun, 21 Jun 2020 20:10:31: Done! pass1 - making usageList (320 chroms): 1 millis pass2 - checking and writing primary data (907 records, 4 fields): 10 millis CompletedMACS2peakCalling