Job ID = 6454343 SRX = SRX2011092 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T09:00:49 prefetch.2.10.7: 1) Downloading 'SRR4017245'... 2020-06-21T09:00:49 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T09:04:22 prefetch.2.10.7: HTTPS download succeed 2020-06-21T09:04:22 prefetch.2.10.7: 1) 'SRR4017245' was downloaded successfully Read 17793839 spots for SRR4017245/SRR4017245.sra Written 17793839 spots for SRR4017245/SRR4017245.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: 00:09:40 17793839 reads; of these: 17793839 (100.00%) were unpaired; of these: 725123 (4.08%) aligned 0 times 11669467 (65.58%) aligned exactly 1 time 5399249 (30.34%) aligned >1 times 95.92% overall alignment rate Time searching: 00:09:40 Overall time: 00:09:40 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 8 files... [bam_rmdupse_core] 2024956 / 17068716 = 0.1186 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 18:20:58: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX2011092/SRX2011092.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX2011092/SRX2011092.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX2011092/SRX2011092.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX2011092/SRX2011092.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 18:20:58: #1 read tag files... INFO @ Sun, 21 Jun 2020 18:20:58: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 18:21:04: 1000000 INFO @ Sun, 21 Jun 2020 18:21:10: 2000000 INFO @ Sun, 21 Jun 2020 18:21:16: 3000000 INFO @ Sun, 21 Jun 2020 18:21:22: 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 18:21:28: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX2011092/SRX2011092.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX2011092/SRX2011092.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX2011092/SRX2011092.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX2011092/SRX2011092.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 18:21:28: #1 read tag files... INFO @ Sun, 21 Jun 2020 18:21:28: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 18:21:28: 5000000 INFO @ Sun, 21 Jun 2020 18:21:35: 1000000 INFO @ Sun, 21 Jun 2020 18:21:35: 6000000 INFO @ Sun, 21 Jun 2020 18:21:41: 2000000 INFO @ Sun, 21 Jun 2020 18:21:42: 7000000 INFO @ Sun, 21 Jun 2020 18:21:48: 3000000 INFO @ Sun, 21 Jun 2020 18:21:48: 8000000 INFO @ Sun, 21 Jun 2020 18:21:55: 4000000 INFO @ Sun, 21 Jun 2020 18:21:55: 9000000 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 18:21:58: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX2011092/SRX2011092.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX2011092/SRX2011092.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX2011092/SRX2011092.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX2011092/SRX2011092.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 18:21:58: #1 read tag files... INFO @ Sun, 21 Jun 2020 18:21:58: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 18:22:01: 5000000 INFO @ Sun, 21 Jun 2020 18:22:02: 10000000 INFO @ Sun, 21 Jun 2020 18:22:05: 1000000 INFO @ Sun, 21 Jun 2020 18:22:08: 11000000 INFO @ Sun, 21 Jun 2020 18:22:08: 6000000 INFO @ Sun, 21 Jun 2020 18:22:12: 2000000 INFO @ Sun, 21 Jun 2020 18:22:15: 12000000 INFO @ Sun, 21 Jun 2020 18:22:15: 7000000 INFO @ Sun, 21 Jun 2020 18:22:18: 3000000 INFO @ Sun, 21 Jun 2020 18:22:22: 13000000 INFO @ Sun, 21 Jun 2020 18:22:22: 8000000 INFO @ Sun, 21 Jun 2020 18:22:25: 4000000 INFO @ Sun, 21 Jun 2020 18:22:29: 9000000 INFO @ Sun, 21 Jun 2020 18:22:29: 14000000 INFO @ Sun, 21 Jun 2020 18:22:32: 5000000 INFO @ Sun, 21 Jun 2020 18:22:35: 10000000 INFO @ Sun, 21 Jun 2020 18:22:36: 15000000 INFO @ Sun, 21 Jun 2020 18:22:36: #1 tag size is determined as 100 bps INFO @ Sun, 21 Jun 2020 18:22:36: #1 tag size = 100 INFO @ Sun, 21 Jun 2020 18:22:36: #1 total tags in treatment: 15043760 INFO @ Sun, 21 Jun 2020 18:22:36: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 18:22:36: #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 18:22:37: #1 tags after filtering in treatment: 15043755 INFO @ Sun, 21 Jun 2020 18:22:37: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 18:22:37: #1 finished! INFO @ Sun, 21 Jun 2020 18:22:37: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 18:22:37: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 18:22:38: #2 number of paired peaks: 459 WARNING @ Sun, 21 Jun 2020 18:22:38: Fewer paired peaks (459) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 459 pairs to build model! INFO @ Sun, 21 Jun 2020 18:22:38: start model_add_line... INFO @ Sun, 21 Jun 2020 18:22:38: start X-correlation... INFO @ Sun, 21 Jun 2020 18:22:38: end of X-cor INFO @ Sun, 21 Jun 2020 18:22:38: #2 finished! INFO @ Sun, 21 Jun 2020 18:22:38: #2 predicted fragment length is 94 bps INFO @ Sun, 21 Jun 2020 18:22:38: #2 alternative fragment length(s) may be 4,94 bps INFO @ Sun, 21 Jun 2020 18:22:38: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX2011092/SRX2011092.05_model.r WARNING @ Sun, 21 Jun 2020 18:22:38: #2 Since the d (94) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 18:22:38: #2 You may need to consider one of the other alternative d(s): 4,94 WARNING @ Sun, 21 Jun 2020 18:22:38: #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 18:22:38: #3 Call peaks... INFO @ Sun, 21 Jun 2020 18:22:38: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 18:22:39: 6000000 INFO @ Sun, 21 Jun 2020 18:22:42: 11000000 INFO @ Sun, 21 Jun 2020 18:22:46: 7000000 INFO @ Sun, 21 Jun 2020 18:22:49: 12000000 INFO @ Sun, 21 Jun 2020 18:22:53: 8000000 INFO @ Sun, 21 Jun 2020 18:22:56: 13000000 INFO @ Sun, 21 Jun 2020 18:22:59: 9000000 INFO @ Sun, 21 Jun 2020 18:23:03: 14000000 INFO @ Sun, 21 Jun 2020 18:23:06: 10000000 INFO @ Sun, 21 Jun 2020 18:23:08: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 18:23:10: 15000000 INFO @ Sun, 21 Jun 2020 18:23:10: #1 tag size is determined as 100 bps INFO @ Sun, 21 Jun 2020 18:23:10: #1 tag size = 100 INFO @ Sun, 21 Jun 2020 18:23:10: #1 total tags in treatment: 15043760 INFO @ Sun, 21 Jun 2020 18:23:10: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 18:23:10: #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 18:23:11: #1 tags after filtering in treatment: 15043755 INFO @ Sun, 21 Jun 2020 18:23:11: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 18:23:11: #1 finished! INFO @ Sun, 21 Jun 2020 18:23:11: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 18:23:11: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 18:23:12: #2 number of paired peaks: 459 WARNING @ Sun, 21 Jun 2020 18:23:12: Fewer paired peaks (459) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 459 pairs to build model! INFO @ Sun, 21 Jun 2020 18:23:12: start model_add_line... INFO @ Sun, 21 Jun 2020 18:23:12: start X-correlation... INFO @ Sun, 21 Jun 2020 18:23:12: end of X-cor INFO @ Sun, 21 Jun 2020 18:23:12: #2 finished! INFO @ Sun, 21 Jun 2020 18:23:12: #2 predicted fragment length is 94 bps INFO @ Sun, 21 Jun 2020 18:23:12: #2 alternative fragment length(s) may be 4,94 bps INFO @ Sun, 21 Jun 2020 18:23:12: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX2011092/SRX2011092.10_model.r WARNING @ Sun, 21 Jun 2020 18:23:12: #2 Since the d (94) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 18:23:12: #2 You may need to consider one of the other alternative d(s): 4,94 WARNING @ Sun, 21 Jun 2020 18:23:12: #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 18:23:12: #3 Call peaks... INFO @ Sun, 21 Jun 2020 18:23:12: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 18:23:12: 11000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 18:23:18: 12000000 INFO @ Sun, 21 Jun 2020 18:23:22: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX2011092/SRX2011092.05_peaks.xls INFO @ Sun, 21 Jun 2020 18:23:22: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX2011092/SRX2011092.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 18:23:22: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX2011092/SRX2011092.05_summits.bed INFO @ Sun, 21 Jun 2020 18:23:22: Done! pass1 - making usageList (735 chroms): 2 millis pass2 - checking and writing primary data (2457 records, 4 fields): 20 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 18:23:25: 13000000 INFO @ Sun, 21 Jun 2020 18:23:32: 14000000 INFO @ Sun, 21 Jun 2020 18:23:38: 15000000 INFO @ Sun, 21 Jun 2020 18:23:38: #1 tag size is determined as 100 bps INFO @ Sun, 21 Jun 2020 18:23:38: #1 tag size = 100 INFO @ Sun, 21 Jun 2020 18:23:38: #1 total tags in treatment: 15043760 INFO @ Sun, 21 Jun 2020 18:23:38: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 18:23:38: #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 18:23:39: #1 tags after filtering in treatment: 15043755 INFO @ Sun, 21 Jun 2020 18:23:39: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 18:23:39: #1 finished! INFO @ Sun, 21 Jun 2020 18:23:39: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 18:23:39: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 18:23:40: #2 number of paired peaks: 459 WARNING @ Sun, 21 Jun 2020 18:23:40: Fewer paired peaks (459) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 459 pairs to build model! INFO @ Sun, 21 Jun 2020 18:23:40: start model_add_line... INFO @ Sun, 21 Jun 2020 18:23:40: start X-correlation... INFO @ Sun, 21 Jun 2020 18:23:40: end of X-cor INFO @ Sun, 21 Jun 2020 18:23:40: #2 finished! INFO @ Sun, 21 Jun 2020 18:23:40: #2 predicted fragment length is 94 bps INFO @ Sun, 21 Jun 2020 18:23:40: #2 alternative fragment length(s) may be 4,94 bps INFO @ Sun, 21 Jun 2020 18:23:40: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX2011092/SRX2011092.20_model.r WARNING @ Sun, 21 Jun 2020 18:23:40: #2 Since the d (94) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 18:23:40: #2 You may need to consider one of the other alternative d(s): 4,94 WARNING @ Sun, 21 Jun 2020 18:23:40: #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 18:23:40: #3 Call peaks... INFO @ Sun, 21 Jun 2020 18:23:40: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 18:23:42: #3 Call peaks for each chromosome... BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 18:23:57: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX2011092/SRX2011092.10_peaks.xls INFO @ Sun, 21 Jun 2020 18:23:57: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX2011092/SRX2011092.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 18:23:57: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX2011092/SRX2011092.10_summits.bed INFO @ Sun, 21 Jun 2020 18:23:57: Done! pass1 - making usageList (629 chroms): 1 millis pass2 - checking and writing primary data (1705 records, 4 fields): 17 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 18:24:10: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 18:24:24: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX2011092/SRX2011092.20_peaks.xls INFO @ Sun, 21 Jun 2020 18:24:24: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX2011092/SRX2011092.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 18:24:24: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX2011092/SRX2011092.20_summits.bed INFO @ Sun, 21 Jun 2020 18:24:24: Done! pass1 - making usageList (472 chroms): 1 millis pass2 - checking and writing primary data (994 records, 4 fields): 13 millis CompletedMACS2peakCalling