Job ID = 6458954 SRX = SRX5827823 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T12:54:11 prefetch.2.10.7: 1) Downloading 'SRR9051574'... 2020-06-21T12:54:11 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T13:00:15 prefetch.2.10.7: HTTPS download succeed 2020-06-21T13:00:15 prefetch.2.10.7: 1) 'SRR9051574' was downloaded successfully 2020-06-21T13:00:15 prefetch.2.10.7: 'SRR9051574' has 0 unresolved dependencies Read 55291041 spots for SRR9051574/SRR9051574.sra Written 55291041 spots for SRR9051574/SRR9051574.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: 00:13:30 55291041 reads; of these: 55291041 (100.00%) were unpaired; of these: 5648435 (10.22%) aligned 0 times 41540589 (75.13%) aligned exactly 1 time 8102017 (14.65%) aligned >1 times 89.78% overall alignment rate Time searching: 00:13:30 Overall time: 00:13:30 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 24 files... [bam_rmdupse_core] 30113727 / 49642606 = 0.6066 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 22:27:57: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX5827823/SRX5827823.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX5827823/SRX5827823.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX5827823/SRX5827823.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX5827823/SRX5827823.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 22:27:57: #1 read tag files... INFO @ Sun, 21 Jun 2020 22:27:57: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 22:28:04: 1000000 INFO @ Sun, 21 Jun 2020 22:28:10: 2000000 INFO @ Sun, 21 Jun 2020 22:28:17: 3000000 INFO @ Sun, 21 Jun 2020 22:28:24: 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 22:28:27: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX5827823/SRX5827823.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX5827823/SRX5827823.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX5827823/SRX5827823.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX5827823/SRX5827823.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 22:28:27: #1 read tag files... INFO @ Sun, 21 Jun 2020 22:28:27: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 22:28:31: 5000000 INFO @ Sun, 21 Jun 2020 22:28:34: 1000000 INFO @ Sun, 21 Jun 2020 22:28:39: 6000000 INFO @ Sun, 21 Jun 2020 22:28:42: 2000000 INFO @ Sun, 21 Jun 2020 22:28:46: 7000000 INFO @ Sun, 21 Jun 2020 22:28:49: 3000000 INFO @ Sun, 21 Jun 2020 22:28:53: 8000000 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 22:28:56: 4000000 INFO @ Sun, 21 Jun 2020 22:28:57: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX5827823/SRX5827823.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX5827823/SRX5827823.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX5827823/SRX5827823.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX5827823/SRX5827823.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 22:28:57: #1 read tag files... INFO @ Sun, 21 Jun 2020 22:28:57: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 22:29:01: 9000000 INFO @ Sun, 21 Jun 2020 22:29:04: 5000000 INFO @ Sun, 21 Jun 2020 22:29:05: 1000000 INFO @ Sun, 21 Jun 2020 22:29:08: 10000000 INFO @ Sun, 21 Jun 2020 22:29:11: 6000000 INFO @ Sun, 21 Jun 2020 22:29:12: 2000000 INFO @ Sun, 21 Jun 2020 22:29:16: 11000000 INFO @ Sun, 21 Jun 2020 22:29:19: 7000000 INFO @ Sun, 21 Jun 2020 22:29:20: 3000000 INFO @ Sun, 21 Jun 2020 22:29:23: 12000000 INFO @ Sun, 21 Jun 2020 22:29:26: 8000000 INFO @ Sun, 21 Jun 2020 22:29:27: 4000000 INFO @ Sun, 21 Jun 2020 22:29:31: 13000000 INFO @ Sun, 21 Jun 2020 22:29:33: 9000000 INFO @ Sun, 21 Jun 2020 22:29:34: 5000000 INFO @ Sun, 21 Jun 2020 22:29:39: 14000000 INFO @ Sun, 21 Jun 2020 22:29:40: 10000000 INFO @ Sun, 21 Jun 2020 22:29:42: 6000000 INFO @ Sun, 21 Jun 2020 22:29:46: 15000000 INFO @ Sun, 21 Jun 2020 22:29:48: 11000000 INFO @ Sun, 21 Jun 2020 22:29:49: 7000000 INFO @ Sun, 21 Jun 2020 22:29:54: 16000000 INFO @ Sun, 21 Jun 2020 22:29:55: 12000000 INFO @ Sun, 21 Jun 2020 22:29:57: 8000000 INFO @ Sun, 21 Jun 2020 22:30:02: 17000000 INFO @ Sun, 21 Jun 2020 22:30:02: 13000000 INFO @ Sun, 21 Jun 2020 22:30:05: 9000000 INFO @ Sun, 21 Jun 2020 22:30:09: 18000000 INFO @ Sun, 21 Jun 2020 22:30:10: 14000000 INFO @ Sun, 21 Jun 2020 22:30:12: 10000000 INFO @ Sun, 21 Jun 2020 22:30:17: 15000000 INFO @ Sun, 21 Jun 2020 22:30:17: 19000000 INFO @ Sun, 21 Jun 2020 22:30:20: 11000000 INFO @ Sun, 21 Jun 2020 22:30:22: #1 tag size is determined as 51 bps INFO @ Sun, 21 Jun 2020 22:30:22: #1 tag size = 51 INFO @ Sun, 21 Jun 2020 22:30:22: #1 total tags in treatment: 19528879 INFO @ Sun, 21 Jun 2020 22:30:22: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 22:30:22: #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 22:30:22: #1 tags after filtering in treatment: 19528879 INFO @ Sun, 21 Jun 2020 22:30:22: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 22:30:22: #1 finished! INFO @ Sun, 21 Jun 2020 22:30:22: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 22:30:22: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 22:30:23: #2 number of paired peaks: 529 WARNING @ Sun, 21 Jun 2020 22:30:23: Fewer paired peaks (529) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 529 pairs to build model! INFO @ Sun, 21 Jun 2020 22:30:23: start model_add_line... INFO @ Sun, 21 Jun 2020 22:30:24: start X-correlation... INFO @ Sun, 21 Jun 2020 22:30:24: end of X-cor INFO @ Sun, 21 Jun 2020 22:30:24: #2 finished! INFO @ Sun, 21 Jun 2020 22:30:24: #2 predicted fragment length is 102 bps INFO @ Sun, 21 Jun 2020 22:30:24: #2 alternative fragment length(s) may be 4,102 bps INFO @ Sun, 21 Jun 2020 22:30:24: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX5827823/SRX5827823.05_model.r WARNING @ Sun, 21 Jun 2020 22:30:24: #2 Since the d (102) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 22:30:24: #2 You may need to consider one of the other alternative d(s): 4,102 WARNING @ Sun, 21 Jun 2020 22:30:24: #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 22:30:24: #3 Call peaks... INFO @ Sun, 21 Jun 2020 22:30:24: #3 Pre-compute pvalue-qvalue table... BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 22:30:25: 16000000 INFO @ Sun, 21 Jun 2020 22:30:27: 12000000 INFO @ Sun, 21 Jun 2020 22:30:32: 17000000 INFO @ Sun, 21 Jun 2020 22:30:34: 13000000 INFO @ Sun, 21 Jun 2020 22:30:39: 18000000 INFO @ Sun, 21 Jun 2020 22:30:41: 14000000 INFO @ Sun, 21 Jun 2020 22:30:47: 19000000 INFO @ Sun, 21 Jun 2020 22:30:49: 15000000 INFO @ Sun, 21 Jun 2020 22:30:51: #1 tag size is determined as 51 bps INFO @ Sun, 21 Jun 2020 22:30:51: #1 tag size = 51 INFO @ Sun, 21 Jun 2020 22:30:51: #1 total tags in treatment: 19528879 INFO @ Sun, 21 Jun 2020 22:30:51: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 22:30:51: #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 22:30:51: #1 tags after filtering in treatment: 19528879 INFO @ Sun, 21 Jun 2020 22:30:51: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 22:30:51: #1 finished! INFO @ Sun, 21 Jun 2020 22:30:51: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 22:30:51: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 22:30:53: #2 number of paired peaks: 529 WARNING @ Sun, 21 Jun 2020 22:30:53: Fewer paired peaks (529) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 529 pairs to build model! INFO @ Sun, 21 Jun 2020 22:30:53: start model_add_line... INFO @ Sun, 21 Jun 2020 22:30:53: start X-correlation... INFO @ Sun, 21 Jun 2020 22:30:53: end of X-cor INFO @ Sun, 21 Jun 2020 22:30:53: #2 finished! INFO @ Sun, 21 Jun 2020 22:30:53: #2 predicted fragment length is 102 bps INFO @ Sun, 21 Jun 2020 22:30:53: #2 alternative fragment length(s) may be 4,102 bps INFO @ Sun, 21 Jun 2020 22:30:53: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX5827823/SRX5827823.10_model.r WARNING @ Sun, 21 Jun 2020 22:30:53: #2 Since the d (102) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 22:30:53: #2 You may need to consider one of the other alternative d(s): 4,102 WARNING @ Sun, 21 Jun 2020 22:30:53: #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 22:30:53: #3 Call peaks... INFO @ Sun, 21 Jun 2020 22:30:53: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 22:30:56: 16000000 INFO @ Sun, 21 Jun 2020 22:31:03: 17000000 INFO @ Sun, 21 Jun 2020 22:31:04: #3 Call peaks for each chromosome... BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 22:31:09: 18000000 INFO @ Sun, 21 Jun 2020 22:31:16: 19000000 INFO @ Sun, 21 Jun 2020 22:31:20: #1 tag size is determined as 51 bps INFO @ Sun, 21 Jun 2020 22:31:20: #1 tag size = 51 INFO @ Sun, 21 Jun 2020 22:31:20: #1 total tags in treatment: 19528879 INFO @ Sun, 21 Jun 2020 22:31:20: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 22:31:20: #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 22:31:20: #1 tags after filtering in treatment: 19528879 INFO @ Sun, 21 Jun 2020 22:31:20: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 22:31:20: #1 finished! INFO @ Sun, 21 Jun 2020 22:31:20: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 22:31:20: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 22:31:22: #2 number of paired peaks: 529 WARNING @ Sun, 21 Jun 2020 22:31:22: Fewer paired peaks (529) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 529 pairs to build model! INFO @ Sun, 21 Jun 2020 22:31:22: start model_add_line... INFO @ Sun, 21 Jun 2020 22:31:22: start X-correlation... INFO @ Sun, 21 Jun 2020 22:31:22: end of X-cor INFO @ Sun, 21 Jun 2020 22:31:22: #2 finished! INFO @ Sun, 21 Jun 2020 22:31:22: #2 predicted fragment length is 102 bps INFO @ Sun, 21 Jun 2020 22:31:22: #2 alternative fragment length(s) may be 4,102 bps INFO @ Sun, 21 Jun 2020 22:31:22: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX5827823/SRX5827823.20_model.r WARNING @ Sun, 21 Jun 2020 22:31:22: #2 Since the d (102) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 22:31:22: #2 You may need to consider one of the other alternative d(s): 4,102 WARNING @ Sun, 21 Jun 2020 22:31:22: #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 22:31:22: #3 Call peaks... INFO @ Sun, 21 Jun 2020 22:31:22: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 22:31:24: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX5827823/SRX5827823.05_peaks.xls INFO @ Sun, 21 Jun 2020 22:31:24: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX5827823/SRX5827823.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 22:31:24: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX5827823/SRX5827823.05_summits.bed INFO @ Sun, 21 Jun 2020 22:31:24: Done! pass1 - making usageList (707 chroms): 2 millis pass2 - checking and writing primary data (6426 records, 4 fields): 26 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 22:31:31: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 22:31:50: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX5827823/SRX5827823.10_peaks.xls INFO @ Sun, 21 Jun 2020 22:31:50: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX5827823/SRX5827823.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 22:31:50: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX5827823/SRX5827823.10_summits.bed INFO @ Sun, 21 Jun 2020 22:31:50: Done! pass1 - making usageList (581 chroms): 1 millis pass2 - checking and writing primary data (3441 records, 4 fields): 19 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 22:32:00: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 22:32:19: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX5827823/SRX5827823.20_peaks.xls INFO @ Sun, 21 Jun 2020 22:32:19: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX5827823/SRX5827823.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 22:32:19: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX5827823/SRX5827823.20_summits.bed INFO @ Sun, 21 Jun 2020 22:32:19: Done! pass1 - making usageList (405 chroms): 1 millis pass2 - checking and writing primary data (1619 records, 4 fields): 13 millis CompletedMACS2peakCalling