Job ID = 5720761 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 24,430,431 reads read : 48,860,862 reads written : 24,430,431 reads 0-length : 24,430,431 rm: cannot remove ‘[DSE]RR*’: No such file or directory 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: 00:09:35 24430431 reads; of these: 24430431 (100.00%) were unpaired; of these: 917254 (3.75%) aligned 0 times 17517293 (71.70%) aligned exactly 1 time 5995884 (24.54%) aligned >1 times 96.25% overall alignment rate Time searching: 00:09:35 Overall time: 00:09:35 マッピングが完了しました。 samtools でBAM に変換中... [samopen] SAM header is present: 15 sequences. [bam_sort_core] merging from 12 files... [bam_rmdupse_core] 2746470 / 23513177 = 0.1168 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 @ Thu, 16 Apr 2020 01:42:01: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX5226998/SRX5226998.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX5226998/SRX5226998.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX5226998/SRX5226998.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX5226998/SRX5226998.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 @ Thu, 16 Apr 2020 01:42:01: #1 read tag files... INFO @ Thu, 16 Apr 2020 01:42:01: #1 read treatment tags... INFO @ Thu, 16 Apr 2020 01:42:12: 1000000 INFO @ Thu, 16 Apr 2020 01:42:19: 2000000 INFO @ Thu, 16 Apr 2020 01:42:27: 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 @ Thu, 16 Apr 2020 01:42:30: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX5226998/SRX5226998.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX5226998/SRX5226998.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX5226998/SRX5226998.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX5226998/SRX5226998.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 @ Thu, 16 Apr 2020 01:42:30: #1 read tag files... INFO @ Thu, 16 Apr 2020 01:42:30: #1 read treatment tags... INFO @ Thu, 16 Apr 2020 01:42:35: 4000000 INFO @ Thu, 16 Apr 2020 01:42:38: 1000000 INFO @ Thu, 16 Apr 2020 01:42:42: 5000000 INFO @ Thu, 16 Apr 2020 01:42:47: 2000000 INFO @ Thu, 16 Apr 2020 01:42:50: 6000000 INFO @ Thu, 16 Apr 2020 01:42:55: 3000000 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 @ Thu, 16 Apr 2020 01:42:58: 7000000 INFO @ Thu, 16 Apr 2020 01:43:00: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX5226998/SRX5226998.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX5226998/SRX5226998.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX5226998/SRX5226998.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX5226998/SRX5226998.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 @ Thu, 16 Apr 2020 01:43:00: #1 read tag files... INFO @ Thu, 16 Apr 2020 01:43:00: #1 read treatment tags... INFO @ Thu, 16 Apr 2020 01:43:03: 4000000 INFO @ Thu, 16 Apr 2020 01:43:07: 8000000 INFO @ Thu, 16 Apr 2020 01:43:09: 1000000 INFO @ Thu, 16 Apr 2020 01:43:11: 5000000 INFO @ Thu, 16 Apr 2020 01:43:15: 9000000 INFO @ Thu, 16 Apr 2020 01:43:17: 2000000 INFO @ Thu, 16 Apr 2020 01:43:19: 6000000 INFO @ Thu, 16 Apr 2020 01:43:23: 10000000 INFO @ Thu, 16 Apr 2020 01:43:25: 3000000 INFO @ Thu, 16 Apr 2020 01:43:27: 7000000 INFO @ Thu, 16 Apr 2020 01:43:31: 11000000 INFO @ Thu, 16 Apr 2020 01:43:33: 4000000 INFO @ Thu, 16 Apr 2020 01:43:36: 8000000 INFO @ Thu, 16 Apr 2020 01:43:39: 12000000 INFO @ Thu, 16 Apr 2020 01:43:41: 5000000 INFO @ Thu, 16 Apr 2020 01:43:44: 9000000 INFO @ Thu, 16 Apr 2020 01:43:47: 13000000 INFO @ Thu, 16 Apr 2020 01:43:49: 6000000 INFO @ Thu, 16 Apr 2020 01:43:52: 10000000 INFO @ Thu, 16 Apr 2020 01:43:55: 14000000 INFO @ Thu, 16 Apr 2020 01:43:57: 7000000 INFO @ Thu, 16 Apr 2020 01:44:00: 11000000 INFO @ Thu, 16 Apr 2020 01:44:03: 15000000 INFO @ Thu, 16 Apr 2020 01:44:05: 8000000 INFO @ Thu, 16 Apr 2020 01:44:09: 12000000 INFO @ Thu, 16 Apr 2020 01:44:11: 16000000 INFO @ Thu, 16 Apr 2020 01:44:14: 9000000 INFO @ Thu, 16 Apr 2020 01:44:17: 13000000 INFO @ Thu, 16 Apr 2020 01:44:19: 17000000 INFO @ Thu, 16 Apr 2020 01:44:22: 10000000 INFO @ Thu, 16 Apr 2020 01:44:25: 14000000 INFO @ Thu, 16 Apr 2020 01:44:27: 18000000 INFO @ Thu, 16 Apr 2020 01:44:30: 11000000 INFO @ Thu, 16 Apr 2020 01:44:33: 15000000 INFO @ Thu, 16 Apr 2020 01:44:35: 19000000 INFO @ Thu, 16 Apr 2020 01:44:38: 12000000 INFO @ Thu, 16 Apr 2020 01:44:41: 16000000 INFO @ Thu, 16 Apr 2020 01:44:43: 20000000 INFO @ Thu, 16 Apr 2020 01:44:46: 13000000 INFO @ Thu, 16 Apr 2020 01:44:49: #1 tag size is determined as 75 bps INFO @ Thu, 16 Apr 2020 01:44:49: #1 tag size = 75 INFO @ Thu, 16 Apr 2020 01:44:49: #1 total tags in treatment: 20766707 INFO @ Thu, 16 Apr 2020 01:44:49: #1 user defined the maximum tags... INFO @ Thu, 16 Apr 2020 01:44:49: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Thu, 16 Apr 2020 01:44:49: 17000000 INFO @ Thu, 16 Apr 2020 01:44:49: #1 tags after filtering in treatment: 20766707 INFO @ Thu, 16 Apr 2020 01:44:49: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 16 Apr 2020 01:44:49: #1 finished! INFO @ Thu, 16 Apr 2020 01:44:49: #2 Build Peak Model... INFO @ Thu, 16 Apr 2020 01:44:49: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 16 Apr 2020 01:44:50: #2 number of paired peaks: 460 WARNING @ Thu, 16 Apr 2020 01:44:50: Fewer paired peaks (460) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 460 pairs to build model! INFO @ Thu, 16 Apr 2020 01:44:50: start model_add_line... INFO @ Thu, 16 Apr 2020 01:44:50: start X-correlation... INFO @ Thu, 16 Apr 2020 01:44:50: end of X-cor INFO @ Thu, 16 Apr 2020 01:44:50: #2 finished! INFO @ Thu, 16 Apr 2020 01:44:50: #2 predicted fragment length is 69 bps INFO @ Thu, 16 Apr 2020 01:44:50: #2 alternative fragment length(s) may be 4,69 bps INFO @ Thu, 16 Apr 2020 01:44:50: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX5226998/SRX5226998.05_model.r WARNING @ Thu, 16 Apr 2020 01:44:50: #2 Since the d (69) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 16 Apr 2020 01:44:50: #2 You may need to consider one of the other alternative d(s): 4,69 WARNING @ Thu, 16 Apr 2020 01:44:50: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Thu, 16 Apr 2020 01:44:50: #3 Call peaks... INFO @ Thu, 16 Apr 2020 01:44:50: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 16 Apr 2020 01:44:54: 14000000 INFO @ Thu, 16 Apr 2020 01:44:57: 18000000 INFO @ Thu, 16 Apr 2020 01:45:02: 15000000 INFO @ Thu, 16 Apr 2020 01:45:05: 19000000 INFO @ Thu, 16 Apr 2020 01:45:10: 16000000 INFO @ Thu, 16 Apr 2020 01:45:12: 20000000 INFO @ Thu, 16 Apr 2020 01:45:18: #1 tag size is determined as 75 bps INFO @ Thu, 16 Apr 2020 01:45:18: #1 tag size = 75 INFO @ Thu, 16 Apr 2020 01:45:18: #1 total tags in treatment: 20766707 INFO @ Thu, 16 Apr 2020 01:45:18: #1 user defined the maximum tags... INFO @ Thu, 16 Apr 2020 01:45:18: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Thu, 16 Apr 2020 01:45:19: 17000000 INFO @ Thu, 16 Apr 2020 01:45:19: #1 tags after filtering in treatment: 20766707 INFO @ Thu, 16 Apr 2020 01:45:19: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 16 Apr 2020 01:45:19: #1 finished! INFO @ Thu, 16 Apr 2020 01:45:19: #2 Build Peak Model... INFO @ Thu, 16 Apr 2020 01:45:19: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 16 Apr 2020 01:45:20: #2 number of paired peaks: 460 WARNING @ Thu, 16 Apr 2020 01:45:20: Fewer paired peaks (460) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 460 pairs to build model! INFO @ Thu, 16 Apr 2020 01:45:20: start model_add_line... INFO @ Thu, 16 Apr 2020 01:45:20: start X-correlation... INFO @ Thu, 16 Apr 2020 01:45:20: end of X-cor INFO @ Thu, 16 Apr 2020 01:45:20: #2 finished! INFO @ Thu, 16 Apr 2020 01:45:20: #2 predicted fragment length is 69 bps INFO @ Thu, 16 Apr 2020 01:45:20: #2 alternative fragment length(s) may be 4,69 bps INFO @ Thu, 16 Apr 2020 01:45:20: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX5226998/SRX5226998.10_model.r WARNING @ Thu, 16 Apr 2020 01:45:20: #2 Since the d (69) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 16 Apr 2020 01:45:20: #2 You may need to consider one of the other alternative d(s): 4,69 WARNING @ Thu, 16 Apr 2020 01:45:20: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Thu, 16 Apr 2020 01:45:20: #3 Call peaks... INFO @ Thu, 16 Apr 2020 01:45:20: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 16 Apr 2020 01:45:26: #3 Call peaks for each chromosome... INFO @ Thu, 16 Apr 2020 01:45:26: 18000000 INFO @ Thu, 16 Apr 2020 01:45:34: 19000000 INFO @ Thu, 16 Apr 2020 01:45:42: 20000000 INFO @ Thu, 16 Apr 2020 01:45:45: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX5226998/SRX5226998.05_peaks.xls INFO @ Thu, 16 Apr 2020 01:45:45: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX5226998/SRX5226998.05_peaks.narrowPeak INFO @ Thu, 16 Apr 2020 01:45:45: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX5226998/SRX5226998.05_summits.bed INFO @ Thu, 16 Apr 2020 01:45:45: Done! INFO @ Thu, 16 Apr 2020 01:45:48: #1 tag size is determined as 75 bps INFO @ Thu, 16 Apr 2020 01:45:48: #1 tag size = 75 INFO @ Thu, 16 Apr 2020 01:45:48: #1 total tags in treatment: 20766707 INFO @ Thu, 16 Apr 2020 01:45:48: #1 user defined the maximum tags... INFO @ Thu, 16 Apr 2020 01:45:48: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Thu, 16 Apr 2020 01:45:48: #1 tags after filtering in treatment: 20766707 INFO @ Thu, 16 Apr 2020 01:45:48: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 16 Apr 2020 01:45:48: #1 finished! INFO @ Thu, 16 Apr 2020 01:45:48: #2 Build Peak Model... INFO @ Thu, 16 Apr 2020 01:45:48: #2 looking for paired plus/minus strand peaks... pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (6201 records, 4 fields): 7 millis CompletedMACS2peakCalling INFO @ Thu, 16 Apr 2020 01:45:50: #2 number of paired peaks: 460 WARNING @ Thu, 16 Apr 2020 01:45:50: Fewer paired peaks (460) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 460 pairs to build model! INFO @ Thu, 16 Apr 2020 01:45:50: start model_add_line... INFO @ Thu, 16 Apr 2020 01:45:50: start X-correlation... INFO @ Thu, 16 Apr 2020 01:45:50: end of X-cor INFO @ Thu, 16 Apr 2020 01:45:50: #2 finished! INFO @ Thu, 16 Apr 2020 01:45:50: #2 predicted fragment length is 69 bps INFO @ Thu, 16 Apr 2020 01:45:50: #2 alternative fragment length(s) may be 4,69 bps INFO @ Thu, 16 Apr 2020 01:45:50: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX5226998/SRX5226998.20_model.r WARNING @ Thu, 16 Apr 2020 01:45:50: #2 Since the d (69) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 16 Apr 2020 01:45:50: #2 You may need to consider one of the other alternative d(s): 4,69 WARNING @ Thu, 16 Apr 2020 01:45:50: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Thu, 16 Apr 2020 01:45:50: #3 Call peaks... INFO @ Thu, 16 Apr 2020 01:45:50: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 16 Apr 2020 01:45:58: #3 Call peaks for each chromosome... INFO @ Thu, 16 Apr 2020 01:46:17: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX5226998/SRX5226998.10_peaks.xls INFO @ Thu, 16 Apr 2020 01:46:17: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX5226998/SRX5226998.10_peaks.narrowPeak INFO @ Thu, 16 Apr 2020 01:46:17: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX5226998/SRX5226998.10_summits.bed INFO @ Thu, 16 Apr 2020 01:46:17: Done! pass1 - making usageList (15 chroms): 0 millis pass2 - checking and writing primary data (2768 records, 4 fields): 4 millis CompletedMACS2peakCalling INFO @ Thu, 16 Apr 2020 01:46:27: #3 Call peaks for each chromosome... BedGraph に変換しました。 BigWig に変換中... INFO @ Thu, 16 Apr 2020 01:46:46: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX5226998/SRX5226998.20_peaks.xls INFO @ Thu, 16 Apr 2020 01:46:46: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX5226998/SRX5226998.20_peaks.narrowPeak INFO @ Thu, 16 Apr 2020 01:46:46: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX5226998/SRX5226998.20_summits.bed INFO @ Thu, 16 Apr 2020 01:46:46: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (1067 records, 4 fields): 3 millis CompletedMACS2peakCalling BigWig に変換しました。