Job ID = 6453254 SRX = SRX110772 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T08:13:18 prefetch.2.10.7: 1) Downloading 'SRR388354'... 2020-06-21T08:13:18 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T08:15:12 prefetch.2.10.7: HTTPS download succeed 2020-06-21T08:15:13 prefetch.2.10.7: 'SRR388354' is valid 2020-06-21T08:15:13 prefetch.2.10.7: 1) 'SRR388354' was downloaded successfully Read 14101314 spots for SRR388354/SRR388354.sra Written 14101314 spots for SRR388354/SRR388354.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: 00:02:45 14101314 reads; of these: 14101314 (100.00%) were unpaired; of these: 1638733 (11.62%) aligned 0 times 9505315 (67.41%) aligned exactly 1 time 2957266 (20.97%) aligned >1 times 88.38% overall alignment rate Time searching: 00:02:45 Overall time: 00:02:45 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] 3265030 / 12462581 = 0.2620 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 17:21:59: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX110772/SRX110772.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX110772/SRX110772.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX110772/SRX110772.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX110772/SRX110772.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 17:21:59: #1 read tag files... INFO @ Sun, 21 Jun 2020 17:21:59: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 17:22:04: 1000000 INFO @ Sun, 21 Jun 2020 17:22:09: 2000000 INFO @ Sun, 21 Jun 2020 17:22:14: 3000000 INFO @ Sun, 21 Jun 2020 17:22:18: 4000000 INFO @ Sun, 21 Jun 2020 17:22:23: 5000000 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 17:22:28: 6000000 INFO @ Sun, 21 Jun 2020 17:22:29: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX110772/SRX110772.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX110772/SRX110772.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX110772/SRX110772.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX110772/SRX110772.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 17:22:29: #1 read tag files... INFO @ Sun, 21 Jun 2020 17:22:29: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 17:22:32: 7000000 INFO @ Sun, 21 Jun 2020 17:22:34: 1000000 INFO @ Sun, 21 Jun 2020 17:22:37: 8000000 INFO @ Sun, 21 Jun 2020 17:22:39: 2000000 INFO @ Sun, 21 Jun 2020 17:22:42: 9000000 INFO @ Sun, 21 Jun 2020 17:22:44: #1 tag size is determined as 40 bps INFO @ Sun, 21 Jun 2020 17:22:44: #1 tag size = 40 INFO @ Sun, 21 Jun 2020 17:22:44: #1 total tags in treatment: 9197551 INFO @ Sun, 21 Jun 2020 17:22:44: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 17:22:44: #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 17:22:44: 3000000 INFO @ Sun, 21 Jun 2020 17:22:44: #1 tags after filtering in treatment: 9197524 INFO @ Sun, 21 Jun 2020 17:22:44: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 17:22:44: #1 finished! INFO @ Sun, 21 Jun 2020 17:22:44: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 17:22:44: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 17:22:45: #2 number of paired peaks: 4151 INFO @ Sun, 21 Jun 2020 17:22:45: start model_add_line... INFO @ Sun, 21 Jun 2020 17:22:45: start X-correlation... INFO @ Sun, 21 Jun 2020 17:22:45: end of X-cor INFO @ Sun, 21 Jun 2020 17:22:45: #2 finished! INFO @ Sun, 21 Jun 2020 17:22:45: #2 predicted fragment length is 78 bps INFO @ Sun, 21 Jun 2020 17:22:45: #2 alternative fragment length(s) may be 78 bps INFO @ Sun, 21 Jun 2020 17:22:45: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX110772/SRX110772.05_model.r WARNING @ Sun, 21 Jun 2020 17:22:45: #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 17:22:45: #2 You may need to consider one of the other alternative d(s): 78 WARNING @ Sun, 21 Jun 2020 17:22:45: #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 17:22:45: #3 Call peaks... INFO @ Sun, 21 Jun 2020 17:22:45: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 17:22:48: 4000000 INFO @ Sun, 21 Jun 2020 17:22:53: 5000000 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 17:22:58: 6000000 INFO @ Sun, 21 Jun 2020 17:22:59: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX110772/SRX110772.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX110772/SRX110772.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX110772/SRX110772.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX110772/SRX110772.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 17:22:59: #1 read tag files... INFO @ Sun, 21 Jun 2020 17:22:59: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 17:23:02: 7000000 INFO @ Sun, 21 Jun 2020 17:23:04: 1000000 INFO @ Sun, 21 Jun 2020 17:23:08: 8000000 INFO @ Sun, 21 Jun 2020 17:23:09: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 17:23:09: 2000000 INFO @ Sun, 21 Jun 2020 17:23:12: 9000000 INFO @ Sun, 21 Jun 2020 17:23:13: #1 tag size is determined as 40 bps INFO @ Sun, 21 Jun 2020 17:23:13: #1 tag size = 40 INFO @ Sun, 21 Jun 2020 17:23:13: #1 total tags in treatment: 9197551 INFO @ Sun, 21 Jun 2020 17:23:13: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 17:23:13: #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 17:23:14: 3000000 INFO @ Sun, 21 Jun 2020 17:23:14: #1 tags after filtering in treatment: 9197524 INFO @ Sun, 21 Jun 2020 17:23:14: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 17:23:14: #1 finished! INFO @ Sun, 21 Jun 2020 17:23:14: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 17:23:14: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 17:23:15: #2 number of paired peaks: 4151 INFO @ Sun, 21 Jun 2020 17:23:15: start model_add_line... INFO @ Sun, 21 Jun 2020 17:23:15: start X-correlation... INFO @ Sun, 21 Jun 2020 17:23:15: end of X-cor INFO @ Sun, 21 Jun 2020 17:23:15: #2 finished! INFO @ Sun, 21 Jun 2020 17:23:15: #2 predicted fragment length is 78 bps INFO @ Sun, 21 Jun 2020 17:23:15: #2 alternative fragment length(s) may be 78 bps INFO @ Sun, 21 Jun 2020 17:23:15: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX110772/SRX110772.10_model.r WARNING @ Sun, 21 Jun 2020 17:23:15: #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 17:23:15: #2 You may need to consider one of the other alternative d(s): 78 WARNING @ Sun, 21 Jun 2020 17:23:15: #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 17:23:15: #3 Call peaks... INFO @ Sun, 21 Jun 2020 17:23:15: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 17:23:18: 4000000 INFO @ Sun, 21 Jun 2020 17:23:21: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX110772/SRX110772.05_peaks.xls INFO @ Sun, 21 Jun 2020 17:23:21: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX110772/SRX110772.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 17:23:21: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX110772/SRX110772.05_summits.bed INFO @ Sun, 21 Jun 2020 17:23:21: Done! pass1 - making usageList (186 chroms): 1 millis pass2 - checking and writing primary data (7942 records, 4 fields): 15 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 17:23:23: 5000000 INFO @ Sun, 21 Jun 2020 17:23:28: 6000000 INFO @ Sun, 21 Jun 2020 17:23:32: 7000000 INFO @ Sun, 21 Jun 2020 17:23:37: 8000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 17:23:38: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 17:23:42: 9000000 INFO @ Sun, 21 Jun 2020 17:23:43: #1 tag size is determined as 40 bps INFO @ Sun, 21 Jun 2020 17:23:43: #1 tag size = 40 INFO @ Sun, 21 Jun 2020 17:23:43: #1 total tags in treatment: 9197551 INFO @ Sun, 21 Jun 2020 17:23:43: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 17:23:43: #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 17:23:43: #1 tags after filtering in treatment: 9197524 INFO @ Sun, 21 Jun 2020 17:23:43: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 17:23:43: #1 finished! INFO @ Sun, 21 Jun 2020 17:23:43: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 17:23:43: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 17:23:44: #2 number of paired peaks: 4151 INFO @ Sun, 21 Jun 2020 17:23:44: start model_add_line... INFO @ Sun, 21 Jun 2020 17:23:44: start X-correlation... INFO @ Sun, 21 Jun 2020 17:23:44: end of X-cor INFO @ Sun, 21 Jun 2020 17:23:44: #2 finished! INFO @ Sun, 21 Jun 2020 17:23:44: #2 predicted fragment length is 78 bps INFO @ Sun, 21 Jun 2020 17:23:44: #2 alternative fragment length(s) may be 78 bps INFO @ Sun, 21 Jun 2020 17:23:44: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX110772/SRX110772.20_model.r WARNING @ Sun, 21 Jun 2020 17:23:44: #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 17:23:44: #2 You may need to consider one of the other alternative d(s): 78 WARNING @ Sun, 21 Jun 2020 17:23:44: #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 17:23:44: #3 Call peaks... INFO @ Sun, 21 Jun 2020 17:23:44: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 17:23:50: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX110772/SRX110772.10_peaks.xls INFO @ Sun, 21 Jun 2020 17:23:50: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX110772/SRX110772.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 17:23:50: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX110772/SRX110772.10_summits.bed INFO @ Sun, 21 Jun 2020 17:23:50: Done! pass1 - making usageList (138 chroms): 1 millis pass2 - checking and writing primary data (5337 records, 4 fields): 11 millis CompletedMACS2peakCalling BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 17:24:08: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 17:24:20: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX110772/SRX110772.20_peaks.xls INFO @ Sun, 21 Jun 2020 17:24:20: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX110772/SRX110772.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 17:24:20: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX110772/SRX110772.20_summits.bed INFO @ Sun, 21 Jun 2020 17:24:20: Done! pass1 - making usageList (97 chroms): 1 millis pass2 - checking and writing primary data (3399 records, 4 fields): 8 millis CompletedMACS2peakCalling