Job ID = 6458935 SRX = SRX5775935 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T13:05:51 prefetch.2.10.7: 1) Downloading 'SRR8997138'... 2020-06-21T13:05:51 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T13:09:12 prefetch.2.10.7: HTTPS download succeed 2020-06-21T13:09:12 prefetch.2.10.7: 1) 'SRR8997138' was downloaded successfully Read 20506179 spots for SRR8997138/SRR8997138.sra Written 20506179 spots for SRR8997138/SRR8997138.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: 00:00:01 Time loading mirror index: 00:00:00 Multiseed full-index search: 00:04:41 20506179 reads; of these: 20506179 (100.00%) were unpaired; of these: 12527534 (61.09%) aligned 0 times 5867819 (28.61%) aligned exactly 1 time 2110826 (10.29%) aligned >1 times 38.91% overall alignment rate Time searching: 00:04:42 Overall time: 00:04:42 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_rmdupse_core] 3468532 / 7978645 = 0.4347 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 22:17:11: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX5775935/SRX5775935.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX5775935/SRX5775935.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX5775935/SRX5775935.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX5775935/SRX5775935.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 22:17:11: #1 read tag files... INFO @ Sun, 21 Jun 2020 22:17:11: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 22:17:18: 1000000 INFO @ Sun, 21 Jun 2020 22:17:24: 2000000 INFO @ Sun, 21 Jun 2020 22:17:31: 3000000 INFO @ Sun, 21 Jun 2020 22:17:37: 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 22:17:41: #1 tag size is determined as 75 bps INFO @ Sun, 21 Jun 2020 22:17:41: #1 tag size = 75 INFO @ Sun, 21 Jun 2020 22:17:41: #1 total tags in treatment: 4510113 INFO @ Sun, 21 Jun 2020 22:17:41: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 22:17:41: #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 22:17:41: #1 tags after filtering in treatment: 4510098 INFO @ Sun, 21 Jun 2020 22:17:41: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 22:17:41: #1 finished! INFO @ Sun, 21 Jun 2020 22:17:41: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 22:17:41: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 22:17:42: #2 number of paired peaks: 1084 INFO @ Sun, 21 Jun 2020 22:17:42: start model_add_line... INFO @ Sun, 21 Jun 2020 22:17:42: start X-correlation... INFO @ Sun, 21 Jun 2020 22:17:42: end of X-cor INFO @ Sun, 21 Jun 2020 22:17:42: #2 finished! INFO @ Sun, 21 Jun 2020 22:17:42: #2 predicted fragment length is 78 bps INFO @ Sun, 21 Jun 2020 22:17:42: #2 alternative fragment length(s) may be 78 bps INFO @ Sun, 21 Jun 2020 22:17:42: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX5775935/SRX5775935.05_model.r INFO @ Sun, 21 Jun 2020 22:17:42: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX5775935/SRX5775935.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX5775935/SRX5775935.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX5775935/SRX5775935.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX5775935/SRX5775935.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 22:17:42: #1 read tag files... INFO @ Sun, 21 Jun 2020 22:17:42: #1 read treatment tags... WARNING @ Sun, 21 Jun 2020 22:17:42: #2 Since the d (78) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 22:17:42: #2 You may need to consider one of the other alternative d(s): 78 WARNING @ Sun, 21 Jun 2020 22:17:42: #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 22:17:42: #3 Call peaks... INFO @ Sun, 21 Jun 2020 22:17:42: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 22:17:50: 1000000 INFO @ Sun, 21 Jun 2020 22:17:52: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 22:17:58: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX5775935/SRX5775935.05_peaks.xls INFO @ Sun, 21 Jun 2020 22:17:58: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX5775935/SRX5775935.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 22:17:58: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX5775935/SRX5775935.05_summits.bed INFO @ Sun, 21 Jun 2020 22:17:58: Done! pass1 - making usageList (631 chroms): 1 millis pass2 - checking and writing primary data (2280 records, 4 fields): 20 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 22:17:58: 2000000 INFO @ Sun, 21 Jun 2020 22:18:06: 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 22:18:12: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX5775935/SRX5775935.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX5775935/SRX5775935.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX5775935/SRX5775935.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX5775935/SRX5775935.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 22:18:12: #1 read tag files... INFO @ Sun, 21 Jun 2020 22:18:12: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 22:18:15: 4000000 INFO @ Sun, 21 Jun 2020 22:18:20: #1 tag size is determined as 75 bps INFO @ Sun, 21 Jun 2020 22:18:20: #1 tag size = 75 INFO @ Sun, 21 Jun 2020 22:18:20: #1 total tags in treatment: 4510113 INFO @ Sun, 21 Jun 2020 22:18:20: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 22:18:20: #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 22:18:20: #1 tags after filtering in treatment: 4510098 INFO @ Sun, 21 Jun 2020 22:18:20: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 22:18:20: #1 finished! INFO @ Sun, 21 Jun 2020 22:18:20: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 22:18:20: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 22:18:20: 1000000 INFO @ Sun, 21 Jun 2020 22:18:21: #2 number of paired peaks: 1084 INFO @ Sun, 21 Jun 2020 22:18:21: start model_add_line... INFO @ Sun, 21 Jun 2020 22:18:21: start X-correlation... INFO @ Sun, 21 Jun 2020 22:18:21: end of X-cor INFO @ Sun, 21 Jun 2020 22:18:21: #2 finished! INFO @ Sun, 21 Jun 2020 22:18:21: #2 predicted fragment length is 78 bps INFO @ Sun, 21 Jun 2020 22:18:21: #2 alternative fragment length(s) may be 78 bps INFO @ Sun, 21 Jun 2020 22:18:21: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX5775935/SRX5775935.10_model.r WARNING @ Sun, 21 Jun 2020 22:18:21: #2 Since the d (78) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 22:18:21: #2 You may need to consider one of the other alternative d(s): 78 WARNING @ Sun, 21 Jun 2020 22:18:21: #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 22:18:21: #3 Call peaks... INFO @ Sun, 21 Jun 2020 22:18:21: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 22:18:28: 2000000 INFO @ Sun, 21 Jun 2020 22:18:32: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 22:18:36: 3000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 22:18:37: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX5775935/SRX5775935.10_peaks.xls INFO @ Sun, 21 Jun 2020 22:18:38: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX5775935/SRX5775935.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 22:18:38: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX5775935/SRX5775935.10_summits.bed INFO @ Sun, 21 Jun 2020 22:18:38: Done! pass1 - making usageList (501 chroms): 1 millis pass2 - checking and writing primary data (1419 records, 4 fields): 17 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 22:18:44: 4000000 INFO @ Sun, 21 Jun 2020 22:18:48: #1 tag size is determined as 75 bps INFO @ Sun, 21 Jun 2020 22:18:48: #1 tag size = 75 INFO @ Sun, 21 Jun 2020 22:18:48: #1 total tags in treatment: 4510113 INFO @ Sun, 21 Jun 2020 22:18:48: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 22:18:48: #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 22:18:48: #1 tags after filtering in treatment: 4510098 INFO @ Sun, 21 Jun 2020 22:18:48: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 22:18:48: #1 finished! INFO @ Sun, 21 Jun 2020 22:18:48: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 22:18:48: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 22:18:49: #2 number of paired peaks: 1084 INFO @ Sun, 21 Jun 2020 22:18:49: start model_add_line... INFO @ Sun, 21 Jun 2020 22:18:49: start X-correlation... INFO @ Sun, 21 Jun 2020 22:18:49: end of X-cor INFO @ Sun, 21 Jun 2020 22:18:49: #2 finished! INFO @ Sun, 21 Jun 2020 22:18:49: #2 predicted fragment length is 78 bps INFO @ Sun, 21 Jun 2020 22:18:49: #2 alternative fragment length(s) may be 78 bps INFO @ Sun, 21 Jun 2020 22:18:49: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX5775935/SRX5775935.20_model.r WARNING @ Sun, 21 Jun 2020 22:18:49: #2 Since the d (78) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 22:18:49: #2 You may need to consider one of the other alternative d(s): 78 WARNING @ Sun, 21 Jun 2020 22:18:49: #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 22:18:49: #3 Call peaks... INFO @ Sun, 21 Jun 2020 22:18:49: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 22:19:00: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 22:19:05: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX5775935/SRX5775935.20_peaks.xls INFO @ Sun, 21 Jun 2020 22:19:05: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX5775935/SRX5775935.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 22:19:05: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX5775935/SRX5775935.20_summits.bed INFO @ Sun, 21 Jun 2020 22:19:05: Done! pass1 - making usageList (338 chroms): 2 millis pass2 - checking and writing primary data (669 records, 4 fields): 10 millis CompletedMACS2peakCalling