Job ID = 6509259 SRX = SRX768487 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-26T15:32:37 prefetch.2.10.7: 1) Downloading 'SRR1663315'... 2020-06-26T15:32:37 prefetch.2.10.7: Downloading via HTTPS... 2020-06-26T15:33:42 prefetch.2.10.7: HTTPS download succeed 2020-06-26T15:33:43 prefetch.2.10.7: 'SRR1663315' is valid 2020-06-26T15:33:43 prefetch.2.10.7: 1) 'SRR1663315' was downloaded successfully Read 15385455 spots for SRR1663315/SRR1663315.sra Written 15385455 spots for SRR1663315/SRR1663315.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: 00:04:39 15385455 reads; of these: 15385455 (100.00%) were unpaired; of these: 1449909 (9.42%) aligned 0 times 9674875 (62.88%) aligned exactly 1 time 4260671 (27.69%) aligned >1 times 90.58% overall alignment rate Time searching: 00:04:39 Overall time: 00:04:39 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] 2033930 / 13935546 = 0.1460 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 @ Sat, 27 Jun 2020 00:43:08: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX768487/SRX768487.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX768487/SRX768487.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX768487/SRX768487.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX768487/SRX768487.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 @ Sat, 27 Jun 2020 00:43:08: #1 read tag files... INFO @ Sat, 27 Jun 2020 00:43:08: #1 read treatment tags... INFO @ Sat, 27 Jun 2020 00:43:13: 1000000 INFO @ Sat, 27 Jun 2020 00:43:18: 2000000 INFO @ Sat, 27 Jun 2020 00:43:24: 3000000 INFO @ Sat, 27 Jun 2020 00:43:29: 4000000 INFO @ Sat, 27 Jun 2020 00:43:35: 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 @ Sat, 27 Jun 2020 00:43:38: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX768487/SRX768487.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX768487/SRX768487.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX768487/SRX768487.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX768487/SRX768487.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 @ Sat, 27 Jun 2020 00:43:38: #1 read tag files... INFO @ Sat, 27 Jun 2020 00:43:38: #1 read treatment tags... INFO @ Sat, 27 Jun 2020 00:43:40: 6000000 INFO @ Sat, 27 Jun 2020 00:43:43: 1000000 INFO @ Sat, 27 Jun 2020 00:43:45: 7000000 INFO @ Sat, 27 Jun 2020 00:43:49: 2000000 INFO @ Sat, 27 Jun 2020 00:43:50: 8000000 INFO @ Sat, 27 Jun 2020 00:43:54: 3000000 INFO @ Sat, 27 Jun 2020 00:43:56: 9000000 INFO @ Sat, 27 Jun 2020 00:43:59: 4000000 INFO @ Sat, 27 Jun 2020 00:44:02: 10000000 INFO @ Sat, 27 Jun 2020 00:44:05: 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 @ Sat, 27 Jun 2020 00:44:07: 11000000 INFO @ Sat, 27 Jun 2020 00:44:08: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX768487/SRX768487.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX768487/SRX768487.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX768487/SRX768487.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX768487/SRX768487.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 @ Sat, 27 Jun 2020 00:44:08: #1 read tag files... INFO @ Sat, 27 Jun 2020 00:44:08: #1 read treatment tags... INFO @ Sat, 27 Jun 2020 00:44:10: 6000000 INFO @ Sat, 27 Jun 2020 00:44:12: #1 tag size is determined as 50 bps INFO @ Sat, 27 Jun 2020 00:44:12: #1 tag size = 50 INFO @ Sat, 27 Jun 2020 00:44:12: #1 total tags in treatment: 11901616 INFO @ Sat, 27 Jun 2020 00:44:12: #1 user defined the maximum tags... INFO @ Sat, 27 Jun 2020 00:44:12: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 27 Jun 2020 00:44:13: #1 tags after filtering in treatment: 11901537 INFO @ Sat, 27 Jun 2020 00:44:13: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 27 Jun 2020 00:44:13: #1 finished! INFO @ Sat, 27 Jun 2020 00:44:13: #2 Build Peak Model... INFO @ Sat, 27 Jun 2020 00:44:13: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 27 Jun 2020 00:44:13: 1000000 INFO @ Sat, 27 Jun 2020 00:44:13: #2 number of paired peaks: 784 WARNING @ Sat, 27 Jun 2020 00:44:13: Fewer paired peaks (784) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 784 pairs to build model! INFO @ Sat, 27 Jun 2020 00:44:13: start model_add_line... INFO @ Sat, 27 Jun 2020 00:44:14: start X-correlation... INFO @ Sat, 27 Jun 2020 00:44:14: end of X-cor INFO @ Sat, 27 Jun 2020 00:44:14: #2 finished! INFO @ Sat, 27 Jun 2020 00:44:14: #2 predicted fragment length is 53 bps INFO @ Sat, 27 Jun 2020 00:44:14: #2 alternative fragment length(s) may be 53 bps INFO @ Sat, 27 Jun 2020 00:44:14: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX768487/SRX768487.05_model.r WARNING @ Sat, 27 Jun 2020 00:44:14: #2 Since the d (53) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 27 Jun 2020 00:44:14: #2 You may need to consider one of the other alternative d(s): 53 WARNING @ Sat, 27 Jun 2020 00:44:14: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sat, 27 Jun 2020 00:44:14: #3 Call peaks... INFO @ Sat, 27 Jun 2020 00:44:14: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 27 Jun 2020 00:44:15: 7000000 INFO @ Sat, 27 Jun 2020 00:44:19: 2000000 INFO @ Sat, 27 Jun 2020 00:44:21: 8000000 INFO @ Sat, 27 Jun 2020 00:44:24: 3000000 INFO @ Sat, 27 Jun 2020 00:44:26: 9000000 INFO @ Sat, 27 Jun 2020 00:44:30: 4000000 INFO @ Sat, 27 Jun 2020 00:44:32: 10000000 INFO @ Sat, 27 Jun 2020 00:44:35: 5000000 INFO @ Sat, 27 Jun 2020 00:44:36: #3 Call peaks for each chromosome... INFO @ Sat, 27 Jun 2020 00:44:37: 11000000 INFO @ Sat, 27 Jun 2020 00:44:41: 6000000 INFO @ Sat, 27 Jun 2020 00:44:42: #1 tag size is determined as 50 bps INFO @ Sat, 27 Jun 2020 00:44:42: #1 tag size = 50 INFO @ Sat, 27 Jun 2020 00:44:42: #1 total tags in treatment: 11901616 INFO @ Sat, 27 Jun 2020 00:44:42: #1 user defined the maximum tags... INFO @ Sat, 27 Jun 2020 00:44:42: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 27 Jun 2020 00:44:43: #1 tags after filtering in treatment: 11901537 INFO @ Sat, 27 Jun 2020 00:44:43: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 27 Jun 2020 00:44:43: #1 finished! INFO @ Sat, 27 Jun 2020 00:44:43: #2 Build Peak Model... INFO @ Sat, 27 Jun 2020 00:44:43: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 27 Jun 2020 00:44:44: #2 number of paired peaks: 784 WARNING @ Sat, 27 Jun 2020 00:44:44: Fewer paired peaks (784) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 784 pairs to build model! INFO @ Sat, 27 Jun 2020 00:44:44: start model_add_line... INFO @ Sat, 27 Jun 2020 00:44:44: start X-correlation... INFO @ Sat, 27 Jun 2020 00:44:44: end of X-cor INFO @ Sat, 27 Jun 2020 00:44:44: #2 finished! INFO @ Sat, 27 Jun 2020 00:44:44: #2 predicted fragment length is 53 bps INFO @ Sat, 27 Jun 2020 00:44:44: #2 alternative fragment length(s) may be 53 bps INFO @ Sat, 27 Jun 2020 00:44:44: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX768487/SRX768487.10_model.r WARNING @ Sat, 27 Jun 2020 00:44:44: #2 Since the d (53) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 27 Jun 2020 00:44:44: #2 You may need to consider one of the other alternative d(s): 53 WARNING @ Sat, 27 Jun 2020 00:44:44: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sat, 27 Jun 2020 00:44:44: #3 Call peaks... INFO @ Sat, 27 Jun 2020 00:44:44: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 27 Jun 2020 00:44:46: 7000000 INFO @ Sat, 27 Jun 2020 00:44:48: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX768487/SRX768487.05_peaks.xls INFO @ Sat, 27 Jun 2020 00:44:48: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX768487/SRX768487.05_peaks.narrowPeak INFO @ Sat, 27 Jun 2020 00:44:48: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX768487/SRX768487.05_summits.bed INFO @ Sat, 27 Jun 2020 00:44:48: Done! pass1 - making usageList (736 chroms): 2 millis pass2 - checking and writing primary data (5975 records, 4 fields): 25 millis CompletedMACS2peakCalling INFO @ Sat, 27 Jun 2020 00:44:51: 8000000 INFO @ Sat, 27 Jun 2020 00:44:56: 9000000 INFO @ Sat, 27 Jun 2020 00:45:02: 10000000 INFO @ Sat, 27 Jun 2020 00:45:08: 11000000 INFO @ Sat, 27 Jun 2020 00:45:08: #3 Call peaks for each chromosome... BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 27 Jun 2020 00:45:13: #1 tag size is determined as 50 bps INFO @ Sat, 27 Jun 2020 00:45:13: #1 tag size = 50 INFO @ Sat, 27 Jun 2020 00:45:13: #1 total tags in treatment: 11901616 INFO @ Sat, 27 Jun 2020 00:45:13: #1 user defined the maximum tags... INFO @ Sat, 27 Jun 2020 00:45:13: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 27 Jun 2020 00:45:13: #1 tags after filtering in treatment: 11901537 INFO @ Sat, 27 Jun 2020 00:45:13: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 27 Jun 2020 00:45:13: #1 finished! INFO @ Sat, 27 Jun 2020 00:45:13: #2 Build Peak Model... INFO @ Sat, 27 Jun 2020 00:45:13: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 27 Jun 2020 00:45:14: #2 number of paired peaks: 784 WARNING @ Sat, 27 Jun 2020 00:45:14: Fewer paired peaks (784) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 784 pairs to build model! INFO @ Sat, 27 Jun 2020 00:45:14: start model_add_line... INFO @ Sat, 27 Jun 2020 00:45:14: start X-correlation... INFO @ Sat, 27 Jun 2020 00:45:14: end of X-cor INFO @ Sat, 27 Jun 2020 00:45:14: #2 finished! INFO @ Sat, 27 Jun 2020 00:45:14: #2 predicted fragment length is 53 bps INFO @ Sat, 27 Jun 2020 00:45:14: #2 alternative fragment length(s) may be 53 bps INFO @ Sat, 27 Jun 2020 00:45:14: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX768487/SRX768487.20_model.r WARNING @ Sat, 27 Jun 2020 00:45:14: #2 Since the d (53) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 27 Jun 2020 00:45:14: #2 You may need to consider one of the other alternative d(s): 53 WARNING @ Sat, 27 Jun 2020 00:45:14: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sat, 27 Jun 2020 00:45:14: #3 Call peaks... INFO @ Sat, 27 Jun 2020 00:45:14: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 27 Jun 2020 00:45:20: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX768487/SRX768487.10_peaks.xls INFO @ Sat, 27 Jun 2020 00:45:20: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX768487/SRX768487.10_peaks.narrowPeak INFO @ Sat, 27 Jun 2020 00:45:20: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX768487/SRX768487.10_summits.bed INFO @ Sat, 27 Jun 2020 00:45:20: Done! pass1 - making usageList (523 chroms): 1 millis pass2 - checking and writing primary data (2326 records, 4 fields): 16 millis CompletedMACS2peakCalling BigWig に変換しました。 INFO @ Sat, 27 Jun 2020 00:45:38: #3 Call peaks for each chromosome... INFO @ Sat, 27 Jun 2020 00:45:49: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX768487/SRX768487.20_peaks.xls INFO @ Sat, 27 Jun 2020 00:45:49: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX768487/SRX768487.20_peaks.narrowPeak INFO @ Sat, 27 Jun 2020 00:45:49: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX768487/SRX768487.20_summits.bed INFO @ Sat, 27 Jun 2020 00:45:49: Done! pass1 - making usageList (254 chroms): 1 millis pass2 - checking and writing primary data (647 records, 4 fields): 9 millis CompletedMACS2peakCalling