Job ID = 6455745 SRX = SRX288039 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T10:16:07 prefetch.2.10.7: 1) Downloading 'SRR870228'... 2020-06-21T10:16:07 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T10:18:58 prefetch.2.10.7: HTTPS download succeed 2020-06-21T10:18:58 prefetch.2.10.7: 1) 'SRR870228' was downloaded successfully Read 17355751 spots for SRR870228/SRR870228.sra Written 17355751 spots for SRR870228/SRR870228.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: 00:05:05 17355751 reads; of these: 17355751 (100.00%) were unpaired; of these: 1248864 (7.20%) aligned 0 times 10894851 (62.77%) aligned exactly 1 time 5212036 (30.03%) aligned >1 times 92.80% overall alignment rate Time searching: 00:05:05 Overall time: 00:05:05 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] 3083328 / 16106887 = 0.1914 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 19:29:03: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX288039/SRX288039.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX288039/SRX288039.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX288039/SRX288039.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX288039/SRX288039.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 19:29:03: #1 read tag files... INFO @ Sun, 21 Jun 2020 19:29:03: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 19:29:09: 1000000 INFO @ Sun, 21 Jun 2020 19:29:14: 2000000 INFO @ Sun, 21 Jun 2020 19:29:20: 3000000 INFO @ Sun, 21 Jun 2020 19:29:25: 4000000 INFO @ Sun, 21 Jun 2020 19:29:31: 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 19:29:33: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX288039/SRX288039.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX288039/SRX288039.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX288039/SRX288039.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX288039/SRX288039.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 19:29:33: #1 read tag files... INFO @ Sun, 21 Jun 2020 19:29:33: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 19:29:36: 6000000 INFO @ Sun, 21 Jun 2020 19:29:39: 1000000 INFO @ Sun, 21 Jun 2020 19:29:42: 7000000 INFO @ Sun, 21 Jun 2020 19:29:44: 2000000 INFO @ Sun, 21 Jun 2020 19:29:47: 8000000 INFO @ Sun, 21 Jun 2020 19:29:50: 3000000 INFO @ Sun, 21 Jun 2020 19:29:52: 9000000 INFO @ Sun, 21 Jun 2020 19:29:55: 4000000 INFO @ Sun, 21 Jun 2020 19:29:58: 10000000 INFO @ Sun, 21 Jun 2020 19:30:00: 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 19:30:03: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX288039/SRX288039.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX288039/SRX288039.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX288039/SRX288039.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX288039/SRX288039.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 19:30:03: #1 read tag files... INFO @ Sun, 21 Jun 2020 19:30:03: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 19:30:04: 11000000 INFO @ Sun, 21 Jun 2020 19:30:06: 6000000 INFO @ Sun, 21 Jun 2020 19:30:09: 1000000 INFO @ Sun, 21 Jun 2020 19:30:09: 12000000 INFO @ Sun, 21 Jun 2020 19:30:11: 7000000 INFO @ Sun, 21 Jun 2020 19:30:14: 2000000 INFO @ Sun, 21 Jun 2020 19:30:15: 13000000 INFO @ Sun, 21 Jun 2020 19:30:15: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 19:30:15: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 19:30:15: #1 total tags in treatment: 13023559 INFO @ Sun, 21 Jun 2020 19:30:15: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 19:30:15: #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 19:30:15: #1 tags after filtering in treatment: 13023559 INFO @ Sun, 21 Jun 2020 19:30:15: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 19:30:15: #1 finished! INFO @ Sun, 21 Jun 2020 19:30:15: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 19:30:15: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 19:30:16: 8000000 INFO @ Sun, 21 Jun 2020 19:30:16: #2 number of paired peaks: 852 WARNING @ Sun, 21 Jun 2020 19:30:16: Fewer paired peaks (852) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 852 pairs to build model! INFO @ Sun, 21 Jun 2020 19:30:16: start model_add_line... INFO @ Sun, 21 Jun 2020 19:30:17: start X-correlation... INFO @ Sun, 21 Jun 2020 19:30:17: end of X-cor INFO @ Sun, 21 Jun 2020 19:30:17: #2 finished! INFO @ Sun, 21 Jun 2020 19:30:17: #2 predicted fragment length is 39 bps INFO @ Sun, 21 Jun 2020 19:30:17: #2 alternative fragment length(s) may be 3,39 bps INFO @ Sun, 21 Jun 2020 19:30:17: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX288039/SRX288039.05_model.r WARNING @ Sun, 21 Jun 2020 19:30:17: #2 Since the d (39) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 19:30:17: #2 You may need to consider one of the other alternative d(s): 3,39 WARNING @ Sun, 21 Jun 2020 19:30:17: #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 19:30:17: #3 Call peaks... INFO @ Sun, 21 Jun 2020 19:30:17: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 19:30:19: 3000000 INFO @ Sun, 21 Jun 2020 19:30:21: 9000000 INFO @ Sun, 21 Jun 2020 19:30:25: 4000000 INFO @ Sun, 21 Jun 2020 19:30:27: 10000000 INFO @ Sun, 21 Jun 2020 19:30:30: 5000000 INFO @ Sun, 21 Jun 2020 19:30:32: 11000000 INFO @ Sun, 21 Jun 2020 19:30:35: 6000000 INFO @ Sun, 21 Jun 2020 19:30:38: 12000000 INFO @ Sun, 21 Jun 2020 19:30:40: 7000000 INFO @ Sun, 21 Jun 2020 19:30:43: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 19:30:43: 13000000 INFO @ Sun, 21 Jun 2020 19:30:43: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 19:30:43: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 19:30:43: #1 total tags in treatment: 13023559 INFO @ Sun, 21 Jun 2020 19:30:43: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 19:30:43: #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 19:30:43: #1 tags after filtering in treatment: 13023559 INFO @ Sun, 21 Jun 2020 19:30:43: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 19:30:43: #1 finished! INFO @ Sun, 21 Jun 2020 19:30:43: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 19:30:43: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 19:30:44: #2 number of paired peaks: 852 WARNING @ Sun, 21 Jun 2020 19:30:44: Fewer paired peaks (852) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 852 pairs to build model! INFO @ Sun, 21 Jun 2020 19:30:44: start model_add_line... INFO @ Sun, 21 Jun 2020 19:30:44: start X-correlation... INFO @ Sun, 21 Jun 2020 19:30:44: end of X-cor INFO @ Sun, 21 Jun 2020 19:30:44: #2 finished! INFO @ Sun, 21 Jun 2020 19:30:44: #2 predicted fragment length is 39 bps INFO @ Sun, 21 Jun 2020 19:30:44: #2 alternative fragment length(s) may be 3,39 bps INFO @ Sun, 21 Jun 2020 19:30:44: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX288039/SRX288039.10_model.r WARNING @ Sun, 21 Jun 2020 19:30:45: #2 Since the d (39) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 19:30:45: #2 You may need to consider one of the other alternative d(s): 3,39 WARNING @ Sun, 21 Jun 2020 19:30:45: #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 19:30:45: #3 Call peaks... INFO @ Sun, 21 Jun 2020 19:30:45: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 19:30:45: 8000000 INFO @ Sun, 21 Jun 2020 19:30:50: 9000000 INFO @ Sun, 21 Jun 2020 19:30:55: 10000000 INFO @ Sun, 21 Jun 2020 19:30:55: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX288039/SRX288039.05_peaks.xls INFO @ Sun, 21 Jun 2020 19:30:55: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX288039/SRX288039.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 19:30:55: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX288039/SRX288039.05_summits.bed INFO @ Sun, 21 Jun 2020 19:30:55: Done! pass1 - making usageList (638 chroms): 1 millis pass2 - checking and writing primary data (2347 records, 4 fields): 19 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 19:31:01: 11000000 INFO @ Sun, 21 Jun 2020 19:31:06: 12000000 INFO @ Sun, 21 Jun 2020 19:31:10: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 19:31:11: 13000000 INFO @ Sun, 21 Jun 2020 19:31:11: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 19:31:11: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 19:31:11: #1 total tags in treatment: 13023559 INFO @ Sun, 21 Jun 2020 19:31:11: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 19:31:11: #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 19:31:11: #1 tags after filtering in treatment: 13023559 INFO @ Sun, 21 Jun 2020 19:31:11: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 19:31:11: #1 finished! INFO @ Sun, 21 Jun 2020 19:31:11: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 19:31:11: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 19:31:12: #2 number of paired peaks: 852 WARNING @ Sun, 21 Jun 2020 19:31:12: Fewer paired peaks (852) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 852 pairs to build model! INFO @ Sun, 21 Jun 2020 19:31:12: start model_add_line... INFO @ Sun, 21 Jun 2020 19:31:12: start X-correlation... INFO @ Sun, 21 Jun 2020 19:31:12: end of X-cor INFO @ Sun, 21 Jun 2020 19:31:12: #2 finished! INFO @ Sun, 21 Jun 2020 19:31:12: #2 predicted fragment length is 39 bps INFO @ Sun, 21 Jun 2020 19:31:12: #2 alternative fragment length(s) may be 3,39 bps INFO @ Sun, 21 Jun 2020 19:31:12: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX288039/SRX288039.20_model.r WARNING @ Sun, 21 Jun 2020 19:31:12: #2 Since the d (39) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 19:31:12: #2 You may need to consider one of the other alternative d(s): 3,39 WARNING @ Sun, 21 Jun 2020 19:31:12: #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 19:31:12: #3 Call peaks... INFO @ Sun, 21 Jun 2020 19:31:12: #3 Pre-compute pvalue-qvalue table... BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 19:31:22: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX288039/SRX288039.10_peaks.xls INFO @ Sun, 21 Jun 2020 19:31:22: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX288039/SRX288039.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 19:31:22: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX288039/SRX288039.10_summits.bed INFO @ Sun, 21 Jun 2020 19:31:22: Done! pass1 - making usageList (532 chroms): 1 millis pass2 - checking and writing primary data (2020 records, 4 fields): 16 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 19:31:37: #3 Call peaks for each chromosome... BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 19:31:49: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX288039/SRX288039.20_peaks.xls INFO @ Sun, 21 Jun 2020 19:31:49: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX288039/SRX288039.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 19:31:49: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX288039/SRX288039.20_summits.bed INFO @ Sun, 21 Jun 2020 19:31:49: Done! pass1 - making usageList (397 chroms): 1 millis pass2 - checking and writing primary data (1074 records, 4 fields): 12 millis CompletedMACS2peakCalling