Job ID = 6459411 SRX = SRX6747980 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T13:14:49 prefetch.2.10.7: 1) Downloading 'SRR10009755'... 2020-06-21T13:14:49 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T13:17:56 prefetch.2.10.7: HTTPS download succeed 2020-06-21T13:17:56 prefetch.2.10.7: 1) 'SRR10009755' was downloaded successfully 2020-06-21T13:17:56 prefetch.2.10.7: 'SRR10009755' has 0 unresolved dependencies Read 28488556 spots for SRR10009755/SRR10009755.sra Written 28488556 spots for SRR10009755/SRR10009755.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: 00:06:43 28488556 reads; of these: 28488556 (100.00%) were unpaired; of these: 15398975 (54.05%) aligned 0 times 9091668 (31.91%) aligned exactly 1 time 3997913 (14.03%) aligned >1 times 45.95% overall alignment rate Time searching: 00:06:43 Overall time: 00:06:43 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] 1871764 / 13089581 = 0.1430 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 22:30:00: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX6747980/SRX6747980.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX6747980/SRX6747980.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX6747980/SRX6747980.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX6747980/SRX6747980.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 22:30:00: #1 read tag files... INFO @ Sun, 21 Jun 2020 22:30:00: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 22:30:06: 1000000 INFO @ Sun, 21 Jun 2020 22:30:11: 2000000 INFO @ Sun, 21 Jun 2020 22:30:17: 3000000 INFO @ Sun, 21 Jun 2020 22:30:22: 4000000 INFO @ Sun, 21 Jun 2020 22:30:27: 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 22:30:30: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX6747980/SRX6747980.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX6747980/SRX6747980.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX6747980/SRX6747980.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX6747980/SRX6747980.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 22:30:30: #1 read tag files... INFO @ Sun, 21 Jun 2020 22:30:30: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 22:30:33: 6000000 INFO @ Sun, 21 Jun 2020 22:30:37: 1000000 INFO @ Sun, 21 Jun 2020 22:30:39: 7000000 INFO @ Sun, 21 Jun 2020 22:30:44: 2000000 INFO @ Sun, 21 Jun 2020 22:30:45: 8000000 INFO @ Sun, 21 Jun 2020 22:30:51: 3000000 INFO @ Sun, 21 Jun 2020 22:30:51: 9000000 INFO @ Sun, 21 Jun 2020 22:30:57: 10000000 INFO @ Sun, 21 Jun 2020 22:30:58: 4000000 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 22:31:00: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX6747980/SRX6747980.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX6747980/SRX6747980.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX6747980/SRX6747980.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX6747980/SRX6747980.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 22:31:00: #1 read tag files... INFO @ Sun, 21 Jun 2020 22:31:00: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 22:31:03: 11000000 INFO @ Sun, 21 Jun 2020 22:31:04: #1 tag size is determined as 73 bps INFO @ Sun, 21 Jun 2020 22:31:04: #1 tag size = 73 INFO @ Sun, 21 Jun 2020 22:31:04: #1 total tags in treatment: 11217817 INFO @ Sun, 21 Jun 2020 22:31:04: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 22:31:04: #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 22:31:04: 5000000 INFO @ Sun, 21 Jun 2020 22:31:05: #1 tags after filtering in treatment: 11217708 INFO @ Sun, 21 Jun 2020 22:31:05: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 22:31:05: #1 finished! INFO @ Sun, 21 Jun 2020 22:31:05: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 22:31:05: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 22:31:06: #2 number of paired peaks: 894 WARNING @ Sun, 21 Jun 2020 22:31:06: Fewer paired peaks (894) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 894 pairs to build model! INFO @ Sun, 21 Jun 2020 22:31:06: start model_add_line... INFO @ Sun, 21 Jun 2020 22:31:06: start X-correlation... INFO @ Sun, 21 Jun 2020 22:31:06: end of X-cor INFO @ Sun, 21 Jun 2020 22:31:06: #2 finished! INFO @ Sun, 21 Jun 2020 22:31:06: #2 predicted fragment length is 74 bps INFO @ Sun, 21 Jun 2020 22:31:06: #2 alternative fragment length(s) may be 4,74,584 bps INFO @ Sun, 21 Jun 2020 22:31:06: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX6747980/SRX6747980.05_model.r WARNING @ Sun, 21 Jun 2020 22:31:06: #2 Since the d (74) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 22:31:06: #2 You may need to consider one of the other alternative d(s): 4,74,584 WARNING @ Sun, 21 Jun 2020 22:31:06: #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 22:31:06: #3 Call peaks... INFO @ Sun, 21 Jun 2020 22:31:06: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 22:31:07: 1000000 INFO @ Sun, 21 Jun 2020 22:31:11: 6000000 INFO @ Sun, 21 Jun 2020 22:31:14: 2000000 INFO @ Sun, 21 Jun 2020 22:31:18: 7000000 INFO @ Sun, 21 Jun 2020 22:31:21: 3000000 INFO @ Sun, 21 Jun 2020 22:31:24: 8000000 INFO @ Sun, 21 Jun 2020 22:31:27: 4000000 INFO @ Sun, 21 Jun 2020 22:31:28: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 22:31:31: 9000000 INFO @ Sun, 21 Jun 2020 22:31:34: 5000000 INFO @ Sun, 21 Jun 2020 22:31:38: 10000000 INFO @ Sun, 21 Jun 2020 22:31:38: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX6747980/SRX6747980.05_peaks.xls INFO @ Sun, 21 Jun 2020 22:31:39: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX6747980/SRX6747980.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 22:31:39: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX6747980/SRX6747980.05_summits.bed INFO @ Sun, 21 Jun 2020 22:31:39: Done! pass1 - making usageList (640 chroms): 1 millis pass2 - checking and writing primary data (2421 records, 4 fields): 18 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 22:31:40: 6000000 INFO @ Sun, 21 Jun 2020 22:31:45: 11000000 INFO @ Sun, 21 Jun 2020 22:31:46: #1 tag size is determined as 73 bps INFO @ Sun, 21 Jun 2020 22:31:46: #1 tag size = 73 INFO @ Sun, 21 Jun 2020 22:31:46: #1 total tags in treatment: 11217817 INFO @ Sun, 21 Jun 2020 22:31:46: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 22:31:46: #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 22:31:46: #1 tags after filtering in treatment: 11217708 INFO @ Sun, 21 Jun 2020 22:31:46: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 22:31:46: #1 finished! INFO @ Sun, 21 Jun 2020 22:31:46: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 22:31:46: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 22:31:47: 7000000 INFO @ Sun, 21 Jun 2020 22:31:47: #2 number of paired peaks: 894 WARNING @ Sun, 21 Jun 2020 22:31:47: Fewer paired peaks (894) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 894 pairs to build model! INFO @ Sun, 21 Jun 2020 22:31:47: start model_add_line... INFO @ Sun, 21 Jun 2020 22:31:47: start X-correlation... INFO @ Sun, 21 Jun 2020 22:31:47: end of X-cor INFO @ Sun, 21 Jun 2020 22:31:47: #2 finished! INFO @ Sun, 21 Jun 2020 22:31:47: #2 predicted fragment length is 74 bps INFO @ Sun, 21 Jun 2020 22:31:47: #2 alternative fragment length(s) may be 4,74,584 bps INFO @ Sun, 21 Jun 2020 22:31:47: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX6747980/SRX6747980.10_model.r WARNING @ Sun, 21 Jun 2020 22:31:47: #2 Since the d (74) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 22:31:47: #2 You may need to consider one of the other alternative d(s): 4,74,584 WARNING @ Sun, 21 Jun 2020 22:31:47: #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 22:31:47: #3 Call peaks... INFO @ Sun, 21 Jun 2020 22:31:47: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 22:31:53: 8000000 INFO @ Sun, 21 Jun 2020 22:32:00: 9000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 22:32:06: 10000000 INFO @ Sun, 21 Jun 2020 22:32:10: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 22:32:13: 11000000 INFO @ Sun, 21 Jun 2020 22:32:14: #1 tag size is determined as 73 bps INFO @ Sun, 21 Jun 2020 22:32:14: #1 tag size = 73 INFO @ Sun, 21 Jun 2020 22:32:14: #1 total tags in treatment: 11217817 INFO @ Sun, 21 Jun 2020 22:32:14: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 22:32:14: #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 22:32:15: #1 tags after filtering in treatment: 11217708 INFO @ Sun, 21 Jun 2020 22:32:15: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 22:32:15: #1 finished! INFO @ Sun, 21 Jun 2020 22:32:15: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 22:32:15: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 22:32:16: #2 number of paired peaks: 894 WARNING @ Sun, 21 Jun 2020 22:32:16: Fewer paired peaks (894) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 894 pairs to build model! INFO @ Sun, 21 Jun 2020 22:32:16: start model_add_line... INFO @ Sun, 21 Jun 2020 22:32:16: start X-correlation... INFO @ Sun, 21 Jun 2020 22:32:16: end of X-cor INFO @ Sun, 21 Jun 2020 22:32:16: #2 finished! INFO @ Sun, 21 Jun 2020 22:32:16: #2 predicted fragment length is 74 bps INFO @ Sun, 21 Jun 2020 22:32:16: #2 alternative fragment length(s) may be 4,74,584 bps INFO @ Sun, 21 Jun 2020 22:32:16: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX6747980/SRX6747980.20_model.r WARNING @ Sun, 21 Jun 2020 22:32:16: #2 Since the d (74) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 22:32:16: #2 You may need to consider one of the other alternative d(s): 4,74,584 WARNING @ Sun, 21 Jun 2020 22:32:16: #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 22:32:16: #3 Call peaks... INFO @ Sun, 21 Jun 2020 22:32:16: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 22:32:22: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX6747980/SRX6747980.10_peaks.xls INFO @ Sun, 21 Jun 2020 22:32:22: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX6747980/SRX6747980.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 22:32:22: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX6747980/SRX6747980.10_summits.bed INFO @ Sun, 21 Jun 2020 22:32:22: Done! pass1 - making usageList (564 chroms): 1 millis pass2 - checking and writing primary data (1619 records, 4 fields): 16 millis CompletedMACS2peakCalling BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 22:32:39: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 22:32:50: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX6747980/SRX6747980.20_peaks.xls INFO @ Sun, 21 Jun 2020 22:32:50: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX6747980/SRX6747980.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 22:32:50: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX6747980/SRX6747980.20_summits.bed INFO @ Sun, 21 Jun 2020 22:32:50: Done! pass1 - making usageList (412 chroms): 1 millis pass2 - checking and writing primary data (1001 records, 4 fields): 13 millis CompletedMACS2peakCalling