Job ID = 6457984 SRX = SRX4933891 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T12:02:35 prefetch.2.10.7: 1) Downloading 'SRR8107281'... 2020-06-21T12:02:35 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T12:09:36 prefetch.2.10.7: HTTPS download succeed 2020-06-21T12:09:36 prefetch.2.10.7: 1) 'SRR8107281' was downloaded successfully Read 41260960 spots for SRR8107281/SRR8107281.sra Written 41260960 spots for SRR8107281/SRR8107281.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: 00:14:10 41260960 reads; of these: 41260960 (100.00%) were unpaired; of these: 3546208 (8.59%) aligned 0 times 22728078 (55.08%) aligned exactly 1 time 14986674 (36.32%) aligned >1 times 91.41% overall alignment rate Time searching: 00:14:10 Overall time: 00:14:10 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 16 files... [bam_rmdupse_core] 31578123 / 37714752 = 0.8373 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 21:32:02: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX4933891/SRX4933891.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX4933891/SRX4933891.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX4933891/SRX4933891.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX4933891/SRX4933891.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 21:32:02: #1 read tag files... INFO @ Sun, 21 Jun 2020 21:32:02: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 21:32:08: 1000000 INFO @ Sun, 21 Jun 2020 21:32:14: 2000000 INFO @ Sun, 21 Jun 2020 21:32:20: 3000000 INFO @ Sun, 21 Jun 2020 21:32:26: 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 21:32:31: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX4933891/SRX4933891.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX4933891/SRX4933891.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX4933891/SRX4933891.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX4933891/SRX4933891.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 21:32:31: #1 read tag files... INFO @ Sun, 21 Jun 2020 21:32:31: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 21:32:33: 5000000 INFO @ Sun, 21 Jun 2020 21:32:37: 1000000 INFO @ Sun, 21 Jun 2020 21:32:39: 6000000 INFO @ Sun, 21 Jun 2020 21:32:40: #1 tag size is determined as 51 bps INFO @ Sun, 21 Jun 2020 21:32:40: #1 tag size = 51 INFO @ Sun, 21 Jun 2020 21:32:40: #1 total tags in treatment: 6136629 INFO @ Sun, 21 Jun 2020 21:32:40: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 21:32:40: #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 21:32:40: #1 tags after filtering in treatment: 6136620 INFO @ Sun, 21 Jun 2020 21:32:40: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 21:32:40: #1 finished! INFO @ Sun, 21 Jun 2020 21:32:40: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 21:32:40: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 21:32:41: #2 number of paired peaks: 2169 INFO @ Sun, 21 Jun 2020 21:32:41: start model_add_line... INFO @ Sun, 21 Jun 2020 21:32:41: start X-correlation... INFO @ Sun, 21 Jun 2020 21:32:41: end of X-cor INFO @ Sun, 21 Jun 2020 21:32:41: #2 finished! INFO @ Sun, 21 Jun 2020 21:32:41: #2 predicted fragment length is 45 bps INFO @ Sun, 21 Jun 2020 21:32:41: #2 alternative fragment length(s) may be 3,45 bps INFO @ Sun, 21 Jun 2020 21:32:41: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX4933891/SRX4933891.05_model.r WARNING @ Sun, 21 Jun 2020 21:32:41: #2 Since the d (45) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 21:32:41: #2 You may need to consider one of the other alternative d(s): 3,45 WARNING @ Sun, 21 Jun 2020 21:32:41: #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 21:32:41: #3 Call peaks... INFO @ Sun, 21 Jun 2020 21:32:41: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 21:32:43: 2000000 INFO @ Sun, 21 Jun 2020 21:32:49: 3000000 INFO @ Sun, 21 Jun 2020 21:32:53: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 21:32:55: 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 21:32:59: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX4933891/SRX4933891.05_peaks.xls INFO @ Sun, 21 Jun 2020 21:32:59: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX4933891/SRX4933891.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 21:32:59: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX4933891/SRX4933891.05_summits.bed INFO @ Sun, 21 Jun 2020 21:32:59: Done! pass1 - making usageList (783 chroms): 2 millis pass2 - checking and writing primary data (3397 records, 4 fields): 22 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 21:33:01: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX4933891/SRX4933891.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX4933891/SRX4933891.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX4933891/SRX4933891.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX4933891/SRX4933891.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 21:33:01: #1 read tag files... INFO @ Sun, 21 Jun 2020 21:33:01: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 21:33:02: 5000000 INFO @ Sun, 21 Jun 2020 21:33:07: 1000000 INFO @ Sun, 21 Jun 2020 21:33:08: 6000000 INFO @ Sun, 21 Jun 2020 21:33:09: #1 tag size is determined as 51 bps INFO @ Sun, 21 Jun 2020 21:33:09: #1 tag size = 51 INFO @ Sun, 21 Jun 2020 21:33:09: #1 total tags in treatment: 6136629 INFO @ Sun, 21 Jun 2020 21:33:09: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 21:33:09: #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 21:33:10: #1 tags after filtering in treatment: 6136620 INFO @ Sun, 21 Jun 2020 21:33:10: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 21:33:10: #1 finished! INFO @ Sun, 21 Jun 2020 21:33:10: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 21:33:10: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 21:33:10: #2 number of paired peaks: 2169 INFO @ Sun, 21 Jun 2020 21:33:10: start model_add_line... INFO @ Sun, 21 Jun 2020 21:33:10: start X-correlation... INFO @ Sun, 21 Jun 2020 21:33:10: end of X-cor INFO @ Sun, 21 Jun 2020 21:33:10: #2 finished! INFO @ Sun, 21 Jun 2020 21:33:10: #2 predicted fragment length is 45 bps INFO @ Sun, 21 Jun 2020 21:33:10: #2 alternative fragment length(s) may be 3,45 bps INFO @ Sun, 21 Jun 2020 21:33:10: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX4933891/SRX4933891.10_model.r WARNING @ Sun, 21 Jun 2020 21:33:10: #2 Since the d (45) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 21:33:10: #2 You may need to consider one of the other alternative d(s): 3,45 WARNING @ Sun, 21 Jun 2020 21:33:10: #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 21:33:10: #3 Call peaks... INFO @ Sun, 21 Jun 2020 21:33:10: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 21:33:13: 2000000 INFO @ Sun, 21 Jun 2020 21:33:20: 3000000 INFO @ Sun, 21 Jun 2020 21:33:22: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 21:33:26: 4000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 21:33:28: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX4933891/SRX4933891.10_peaks.xls INFO @ Sun, 21 Jun 2020 21:33:28: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX4933891/SRX4933891.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 21:33:28: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX4933891/SRX4933891.10_summits.bed INFO @ Sun, 21 Jun 2020 21:33:28: Done! pass1 - making usageList (641 chroms): 2 millis pass2 - checking and writing primary data (2425 records, 4 fields): 18 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 21:33:32: 5000000 INFO @ Sun, 21 Jun 2020 21:33:37: 6000000 INFO @ Sun, 21 Jun 2020 21:33:38: #1 tag size is determined as 51 bps INFO @ Sun, 21 Jun 2020 21:33:38: #1 tag size = 51 INFO @ Sun, 21 Jun 2020 21:33:38: #1 total tags in treatment: 6136629 INFO @ Sun, 21 Jun 2020 21:33:38: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 21:33:38: #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 21:33:39: #1 tags after filtering in treatment: 6136620 INFO @ Sun, 21 Jun 2020 21:33:39: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 21:33:39: #1 finished! INFO @ Sun, 21 Jun 2020 21:33:39: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 21:33:39: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 21:33:39: #2 number of paired peaks: 2169 INFO @ Sun, 21 Jun 2020 21:33:39: start model_add_line... INFO @ Sun, 21 Jun 2020 21:33:39: start X-correlation... INFO @ Sun, 21 Jun 2020 21:33:39: end of X-cor INFO @ Sun, 21 Jun 2020 21:33:39: #2 finished! INFO @ Sun, 21 Jun 2020 21:33:39: #2 predicted fragment length is 45 bps INFO @ Sun, 21 Jun 2020 21:33:39: #2 alternative fragment length(s) may be 3,45 bps INFO @ Sun, 21 Jun 2020 21:33:39: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX4933891/SRX4933891.20_model.r WARNING @ Sun, 21 Jun 2020 21:33:39: #2 Since the d (45) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 21:33:39: #2 You may need to consider one of the other alternative d(s): 3,45 WARNING @ Sun, 21 Jun 2020 21:33:39: #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 21:33:39: #3 Call peaks... INFO @ Sun, 21 Jun 2020 21:33:39: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 21:33:51: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 21:33:57: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX4933891/SRX4933891.20_peaks.xls INFO @ Sun, 21 Jun 2020 21:33:57: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX4933891/SRX4933891.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 21:33:57: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX4933891/SRX4933891.20_summits.bed INFO @ Sun, 21 Jun 2020 21:33:57: Done! pass1 - making usageList (524 chroms): 1 millis pass2 - checking and writing primary data (1891 records, 4 fields): 15 millis CompletedMACS2peakCalling