Job ID = 6455238 SRX = SRX287582 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T09:54:10 prefetch.2.10.7: 1) Downloading 'SRR869725'... 2020-06-21T09:54:10 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T09:58:19 prefetch.2.10.7: HTTPS download succeed 2020-06-21T09:58:19 prefetch.2.10.7: 1) 'SRR869725' was downloaded successfully Read 21266404 spots for SRR869725/SRR869725.sra Written 21266404 spots for SRR869725/SRR869725.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: 00:06:07 21266404 reads; of these: 21266404 (100.00%) were unpaired; of these: 1611458 (7.58%) aligned 0 times 13447225 (63.23%) aligned exactly 1 time 6207721 (29.19%) aligned >1 times 92.42% overall alignment rate Time searching: 00:06:07 Overall time: 00:06:07 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 12 files... [bam_rmdupse_core] 4582404 / 19654946 = 0.2331 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 19:10:20: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX287582/SRX287582.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX287582/SRX287582.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX287582/SRX287582.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX287582/SRX287582.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 19:10:20: #1 read tag files... INFO @ Sun, 21 Jun 2020 19:10:20: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 19:10:27: 1000000 INFO @ Sun, 21 Jun 2020 19:10:35: 2000000 INFO @ Sun, 21 Jun 2020 19:10:42: 3000000 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 19:10:49: 4000000 INFO @ Sun, 21 Jun 2020 19:10:50: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX287582/SRX287582.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX287582/SRX287582.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX287582/SRX287582.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX287582/SRX287582.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 19:10:50: #1 read tag files... INFO @ Sun, 21 Jun 2020 19:10:50: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 19:10:57: 1000000 INFO @ Sun, 21 Jun 2020 19:10:57: 5000000 INFO @ Sun, 21 Jun 2020 19:11:05: 2000000 INFO @ Sun, 21 Jun 2020 19:11:06: 6000000 INFO @ Sun, 21 Jun 2020 19:11:13: 3000000 INFO @ Sun, 21 Jun 2020 19:11:14: 7000000 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 19:11:20: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX287582/SRX287582.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX287582/SRX287582.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX287582/SRX287582.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX287582/SRX287582.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 19:11:20: #1 read tag files... INFO @ Sun, 21 Jun 2020 19:11:20: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 19:11:20: 4000000 INFO @ Sun, 21 Jun 2020 19:11:22: 8000000 INFO @ Sun, 21 Jun 2020 19:11:28: 1000000 INFO @ Sun, 21 Jun 2020 19:11:28: 5000000 INFO @ Sun, 21 Jun 2020 19:11:30: 9000000 INFO @ Sun, 21 Jun 2020 19:11:36: 2000000 INFO @ Sun, 21 Jun 2020 19:11:36: 6000000 INFO @ Sun, 21 Jun 2020 19:11:39: 10000000 INFO @ Sun, 21 Jun 2020 19:11:44: 3000000 INFO @ Sun, 21 Jun 2020 19:11:44: 7000000 INFO @ Sun, 21 Jun 2020 19:11:47: 11000000 INFO @ Sun, 21 Jun 2020 19:11:52: 4000000 INFO @ Sun, 21 Jun 2020 19:11:52: 8000000 INFO @ Sun, 21 Jun 2020 19:11:55: 12000000 INFO @ Sun, 21 Jun 2020 19:12:00: 5000000 INFO @ Sun, 21 Jun 2020 19:12:00: 9000000 INFO @ Sun, 21 Jun 2020 19:12:04: 13000000 INFO @ Sun, 21 Jun 2020 19:12:07: 6000000 INFO @ Sun, 21 Jun 2020 19:12:07: 10000000 INFO @ Sun, 21 Jun 2020 19:12:12: 14000000 INFO @ Sun, 21 Jun 2020 19:12:15: 11000000 INFO @ Sun, 21 Jun 2020 19:12:15: 7000000 INFO @ Sun, 21 Jun 2020 19:12:20: 15000000 INFO @ Sun, 21 Jun 2020 19:12:21: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 19:12:21: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 19:12:21: #1 total tags in treatment: 15072542 INFO @ Sun, 21 Jun 2020 19:12:21: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 19:12:21: #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 19:12:21: #1 tags after filtering in treatment: 15072542 INFO @ Sun, 21 Jun 2020 19:12:21: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 19:12:21: #1 finished! INFO @ Sun, 21 Jun 2020 19:12:21: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 19:12:21: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 19:12:22: #2 number of paired peaks: 724 WARNING @ Sun, 21 Jun 2020 19:12:22: Fewer paired peaks (724) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 724 pairs to build model! INFO @ Sun, 21 Jun 2020 19:12:22: start model_add_line... INFO @ Sun, 21 Jun 2020 19:12:22: start X-correlation... INFO @ Sun, 21 Jun 2020 19:12:22: end of X-cor INFO @ Sun, 21 Jun 2020 19:12:22: #2 finished! INFO @ Sun, 21 Jun 2020 19:12:22: #2 predicted fragment length is 31 bps INFO @ Sun, 21 Jun 2020 19:12:22: #2 alternative fragment length(s) may be 3,31,561 bps INFO @ Sun, 21 Jun 2020 19:12:22: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX287582/SRX287582.05_model.r WARNING @ Sun, 21 Jun 2020 19:12:22: #2 Since the d (31) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 19:12:22: #2 You may need to consider one of the other alternative d(s): 3,31,561 WARNING @ Sun, 21 Jun 2020 19:12:22: #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 19:12:22: #3 Call peaks... INFO @ Sun, 21 Jun 2020 19:12:22: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 19:12:23: 8000000 INFO @ Sun, 21 Jun 2020 19:12:23: 12000000 INFO @ Sun, 21 Jun 2020 19:12:30: 9000000 INFO @ Sun, 21 Jun 2020 19:12:30: 13000000 INFO @ Sun, 21 Jun 2020 19:12:37: 10000000 INFO @ Sun, 21 Jun 2020 19:12:37: 14000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 19:12:44: 11000000 INFO @ Sun, 21 Jun 2020 19:12:44: 15000000 INFO @ Sun, 21 Jun 2020 19:12:45: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 19:12:45: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 19:12:45: #1 total tags in treatment: 15072542 INFO @ Sun, 21 Jun 2020 19:12:45: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 19:12:45: #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 19:12:45: #1 tags after filtering in treatment: 15072542 INFO @ Sun, 21 Jun 2020 19:12:45: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 19:12:45: #1 finished! INFO @ Sun, 21 Jun 2020 19:12:45: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 19:12:45: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 19:12:46: #2 number of paired peaks: 724 WARNING @ Sun, 21 Jun 2020 19:12:46: Fewer paired peaks (724) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 724 pairs to build model! INFO @ Sun, 21 Jun 2020 19:12:46: start model_add_line... INFO @ Sun, 21 Jun 2020 19:12:47: start X-correlation... INFO @ Sun, 21 Jun 2020 19:12:47: end of X-cor INFO @ Sun, 21 Jun 2020 19:12:47: #2 finished! INFO @ Sun, 21 Jun 2020 19:12:47: #2 predicted fragment length is 31 bps INFO @ Sun, 21 Jun 2020 19:12:47: #2 alternative fragment length(s) may be 3,31,561 bps INFO @ Sun, 21 Jun 2020 19:12:47: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX287582/SRX287582.10_model.r WARNING @ Sun, 21 Jun 2020 19:12:47: #2 Since the d (31) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 19:12:47: #2 You may need to consider one of the other alternative d(s): 3,31,561 WARNING @ Sun, 21 Jun 2020 19:12:47: #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 19:12:47: #3 Call peaks... INFO @ Sun, 21 Jun 2020 19:12:47: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 19:12:50: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 19:12:51: 12000000 INFO @ Sun, 21 Jun 2020 19:12:57: 13000000 INFO @ Sun, 21 Jun 2020 19:13:03: 14000000 INFO @ Sun, 21 Jun 2020 19:13:04: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX287582/SRX287582.05_peaks.xls INFO @ Sun, 21 Jun 2020 19:13:04: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX287582/SRX287582.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 19:13:04: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX287582/SRX287582.05_summits.bed INFO @ Sun, 21 Jun 2020 19:13:04: Done! pass1 - making usageList (622 chroms): 1 millis pass2 - checking and writing primary data (2413 records, 4 fields): 18 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 19:13:10: 15000000 INFO @ Sun, 21 Jun 2020 19:13:10: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 19:13:10: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 19:13:10: #1 total tags in treatment: 15072542 INFO @ Sun, 21 Jun 2020 19:13:10: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 19:13:10: #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 19:13:11: #1 tags after filtering in treatment: 15072542 INFO @ Sun, 21 Jun 2020 19:13:11: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 19:13:11: #1 finished! INFO @ Sun, 21 Jun 2020 19:13:11: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 19:13:11: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 19:13:12: #2 number of paired peaks: 724 WARNING @ Sun, 21 Jun 2020 19:13:12: Fewer paired peaks (724) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 724 pairs to build model! INFO @ Sun, 21 Jun 2020 19:13:12: start model_add_line... INFO @ Sun, 21 Jun 2020 19:13:12: start X-correlation... INFO @ Sun, 21 Jun 2020 19:13:12: end of X-cor INFO @ Sun, 21 Jun 2020 19:13:12: #2 finished! INFO @ Sun, 21 Jun 2020 19:13:12: #2 predicted fragment length is 31 bps INFO @ Sun, 21 Jun 2020 19:13:12: #2 alternative fragment length(s) may be 3,31,561 bps INFO @ Sun, 21 Jun 2020 19:13:12: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX287582/SRX287582.20_model.r WARNING @ Sun, 21 Jun 2020 19:13:12: #2 Since the d (31) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 19:13:12: #2 You may need to consider one of the other alternative d(s): 3,31,561 WARNING @ Sun, 21 Jun 2020 19:13:12: #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 19:13:12: #3 Call peaks... INFO @ Sun, 21 Jun 2020 19:13:12: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 19:13:15: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 19:13:28: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX287582/SRX287582.10_peaks.xls INFO @ Sun, 21 Jun 2020 19:13:28: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX287582/SRX287582.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 19:13:28: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX287582/SRX287582.10_summits.bed INFO @ Sun, 21 Jun 2020 19:13:28: Done! pass1 - making usageList (498 chroms): 1 millis pass2 - checking and writing primary data (2002 records, 4 fields): 15 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 19:13:40: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 19:13:54: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX287582/SRX287582.20_peaks.xls INFO @ Sun, 21 Jun 2020 19:13:54: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX287582/SRX287582.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 19:13:54: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX287582/SRX287582.20_summits.bed INFO @ Sun, 21 Jun 2020 19:13:54: Done! pass1 - making usageList (289 chroms): 1 millis pass2 - checking and writing primary data (609 records, 4 fields): 9 millis CompletedMACS2peakCalling