Job ID = 5721217 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 23,605,296 reads read : 23,605,296 reads written : 23,605,296 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: 00:08:02 23605296 reads; of these: 23605296 (100.00%) were unpaired; of these: 855726 (3.63%) aligned 0 times 15636946 (66.24%) aligned exactly 1 time 7112624 (30.13%) aligned >1 times 96.37% overall alignment rate Time searching: 00:08:02 Overall time: 00:08:02 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] 3711911 / 22749570 = 0.1632 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 06:09:01: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX6827677/SRX6827677.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX6827677/SRX6827677.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX6827677/SRX6827677.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX6827677/SRX6827677.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 06:09:01: #1 read tag files... INFO @ Thu, 16 Apr 2020 06:09:01: #1 read treatment tags... INFO @ Thu, 16 Apr 2020 06:09:07: 1000000 INFO @ Thu, 16 Apr 2020 06:09:12: 2000000 INFO @ Thu, 16 Apr 2020 06:09:18: 3000000 INFO @ Thu, 16 Apr 2020 06:09:23: 4000000 INFO @ Thu, 16 Apr 2020 06:09:29: 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 @ Thu, 16 Apr 2020 06:09:32: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX6827677/SRX6827677.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX6827677/SRX6827677.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX6827677/SRX6827677.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX6827677/SRX6827677.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 06:09:32: #1 read tag files... INFO @ Thu, 16 Apr 2020 06:09:32: #1 read treatment tags... INFO @ Thu, 16 Apr 2020 06:09:35: 6000000 INFO @ Thu, 16 Apr 2020 06:09:38: 1000000 INFO @ Thu, 16 Apr 2020 06:09:41: 7000000 INFO @ Thu, 16 Apr 2020 06:09:44: 2000000 INFO @ Thu, 16 Apr 2020 06:09:48: 8000000 INFO @ Thu, 16 Apr 2020 06:09:51: 3000000 INFO @ Thu, 16 Apr 2020 06:09:54: 9000000 INFO @ Thu, 16 Apr 2020 06:09:57: 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 @ Thu, 16 Apr 2020 06:10:00: 10000000 INFO @ Thu, 16 Apr 2020 06:10:01: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX6827677/SRX6827677.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX6827677/SRX6827677.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX6827677/SRX6827677.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX6827677/SRX6827677.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 06:10:01: #1 read tag files... INFO @ Thu, 16 Apr 2020 06:10:01: #1 read treatment tags... INFO @ Thu, 16 Apr 2020 06:10:03: 5000000 INFO @ Thu, 16 Apr 2020 06:10:07: 11000000 INFO @ Thu, 16 Apr 2020 06:10:08: 1000000 INFO @ Thu, 16 Apr 2020 06:10:10: 6000000 INFO @ Thu, 16 Apr 2020 06:10:13: 12000000 INFO @ Thu, 16 Apr 2020 06:10:14: 2000000 INFO @ Thu, 16 Apr 2020 06:10:16: 7000000 INFO @ Thu, 16 Apr 2020 06:10:19: 13000000 INFO @ Thu, 16 Apr 2020 06:10:21: 3000000 INFO @ Thu, 16 Apr 2020 06:10:23: 8000000 INFO @ Thu, 16 Apr 2020 06:10:26: 14000000 INFO @ Thu, 16 Apr 2020 06:10:27: 4000000 INFO @ Thu, 16 Apr 2020 06:10:29: 9000000 INFO @ Thu, 16 Apr 2020 06:10:33: 15000000 INFO @ Thu, 16 Apr 2020 06:10:34: 5000000 INFO @ Thu, 16 Apr 2020 06:10:36: 10000000 INFO @ Thu, 16 Apr 2020 06:10:39: 16000000 INFO @ Thu, 16 Apr 2020 06:10:40: 6000000 INFO @ Thu, 16 Apr 2020 06:10:42: 11000000 INFO @ Thu, 16 Apr 2020 06:10:46: 17000000 INFO @ Thu, 16 Apr 2020 06:10:47: 7000000 INFO @ Thu, 16 Apr 2020 06:10:49: 12000000 INFO @ Thu, 16 Apr 2020 06:10:53: 18000000 INFO @ Thu, 16 Apr 2020 06:10:53: 8000000 INFO @ Thu, 16 Apr 2020 06:10:56: 13000000 INFO @ Thu, 16 Apr 2020 06:10:59: 19000000 INFO @ Thu, 16 Apr 2020 06:10:59: #1 tag size is determined as 50 bps INFO @ Thu, 16 Apr 2020 06:10:59: #1 tag size = 50 INFO @ Thu, 16 Apr 2020 06:10:59: #1 total tags in treatment: 19037659 INFO @ Thu, 16 Apr 2020 06:10:59: #1 user defined the maximum tags... INFO @ Thu, 16 Apr 2020 06:10:59: #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 06:10:59: 9000000 INFO @ Thu, 16 Apr 2020 06:11:00: #1 tags after filtering in treatment: 19037659 INFO @ Thu, 16 Apr 2020 06:11:00: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 16 Apr 2020 06:11:00: #1 finished! INFO @ Thu, 16 Apr 2020 06:11:00: #2 Build Peak Model... INFO @ Thu, 16 Apr 2020 06:11:00: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 16 Apr 2020 06:11:01: #2 number of paired peaks: 423 WARNING @ Thu, 16 Apr 2020 06:11:01: Fewer paired peaks (423) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 423 pairs to build model! INFO @ Thu, 16 Apr 2020 06:11:01: start model_add_line... INFO @ Thu, 16 Apr 2020 06:11:01: start X-correlation... INFO @ Thu, 16 Apr 2020 06:11:01: end of X-cor INFO @ Thu, 16 Apr 2020 06:11:01: #2 finished! INFO @ Thu, 16 Apr 2020 06:11:01: #2 predicted fragment length is 48 bps INFO @ Thu, 16 Apr 2020 06:11:01: #2 alternative fragment length(s) may be 48 bps INFO @ Thu, 16 Apr 2020 06:11:01: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX6827677/SRX6827677.05_model.r WARNING @ Thu, 16 Apr 2020 06:11:01: #2 Since the d (48) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 16 Apr 2020 06:11:01: #2 You may need to consider one of the other alternative d(s): 48 WARNING @ Thu, 16 Apr 2020 06:11:01: #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 06:11:01: #3 Call peaks... INFO @ Thu, 16 Apr 2020 06:11:01: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 16 Apr 2020 06:11:02: 14000000 INFO @ Thu, 16 Apr 2020 06:11:06: 10000000 INFO @ Thu, 16 Apr 2020 06:11:08: 15000000 INFO @ Thu, 16 Apr 2020 06:11:12: 11000000 INFO @ Thu, 16 Apr 2020 06:11:15: 16000000 INFO @ Thu, 16 Apr 2020 06:11:18: 12000000 INFO @ Thu, 16 Apr 2020 06:11:21: 17000000 INFO @ Thu, 16 Apr 2020 06:11:25: 13000000 INFO @ Thu, 16 Apr 2020 06:11:28: 18000000 INFO @ Thu, 16 Apr 2020 06:11:31: 14000000 INFO @ Thu, 16 Apr 2020 06:11:34: 19000000 INFO @ Thu, 16 Apr 2020 06:11:34: #1 tag size is determined as 50 bps INFO @ Thu, 16 Apr 2020 06:11:34: #1 tag size = 50 INFO @ Thu, 16 Apr 2020 06:11:34: #1 total tags in treatment: 19037659 INFO @ Thu, 16 Apr 2020 06:11:34: #1 user defined the maximum tags... INFO @ Thu, 16 Apr 2020 06:11:34: #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 06:11:34: #1 tags after filtering in treatment: 19037659 INFO @ Thu, 16 Apr 2020 06:11:34: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 16 Apr 2020 06:11:34: #1 finished! INFO @ Thu, 16 Apr 2020 06:11:34: #2 Build Peak Model... INFO @ Thu, 16 Apr 2020 06:11:34: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 16 Apr 2020 06:11:36: #2 number of paired peaks: 423 WARNING @ Thu, 16 Apr 2020 06:11:36: Fewer paired peaks (423) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 423 pairs to build model! INFO @ Thu, 16 Apr 2020 06:11:36: start model_add_line... INFO @ Thu, 16 Apr 2020 06:11:36: start X-correlation... INFO @ Thu, 16 Apr 2020 06:11:36: end of X-cor INFO @ Thu, 16 Apr 2020 06:11:36: #2 finished! INFO @ Thu, 16 Apr 2020 06:11:36: #2 predicted fragment length is 48 bps INFO @ Thu, 16 Apr 2020 06:11:36: #2 alternative fragment length(s) may be 48 bps INFO @ Thu, 16 Apr 2020 06:11:36: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX6827677/SRX6827677.10_model.r WARNING @ Thu, 16 Apr 2020 06:11:36: #2 Since the d (48) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 16 Apr 2020 06:11:36: #2 You may need to consider one of the other alternative d(s): 48 WARNING @ Thu, 16 Apr 2020 06:11:36: #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 06:11:36: #3 Call peaks... INFO @ Thu, 16 Apr 2020 06:11:36: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 16 Apr 2020 06:11:36: #3 Call peaks for each chromosome... INFO @ Thu, 16 Apr 2020 06:11:37: 15000000 INFO @ Thu, 16 Apr 2020 06:11:43: 16000000 INFO @ Thu, 16 Apr 2020 06:11:49: 17000000 INFO @ Thu, 16 Apr 2020 06:11:53: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX6827677/SRX6827677.05_peaks.xls INFO @ Thu, 16 Apr 2020 06:11:53: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX6827677/SRX6827677.05_peaks.narrowPeak INFO @ Thu, 16 Apr 2020 06:11:53: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX6827677/SRX6827677.05_summits.bed INFO @ Thu, 16 Apr 2020 06:11:53: Done! pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (3345 records, 4 fields): 4 millis CompletedMACS2peakCalling INFO @ Thu, 16 Apr 2020 06:11:55: 18000000 INFO @ Thu, 16 Apr 2020 06:12:00: 19000000 INFO @ Thu, 16 Apr 2020 06:12:01: #1 tag size is determined as 50 bps INFO @ Thu, 16 Apr 2020 06:12:01: #1 tag size = 50 INFO @ Thu, 16 Apr 2020 06:12:01: #1 total tags in treatment: 19037659 INFO @ Thu, 16 Apr 2020 06:12:01: #1 user defined the maximum tags... INFO @ Thu, 16 Apr 2020 06:12:01: #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 06:12:01: #1 tags after filtering in treatment: 19037659 INFO @ Thu, 16 Apr 2020 06:12:01: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 16 Apr 2020 06:12:01: #1 finished! INFO @ Thu, 16 Apr 2020 06:12:01: #2 Build Peak Model... INFO @ Thu, 16 Apr 2020 06:12:01: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 16 Apr 2020 06:12:02: #2 number of paired peaks: 423 WARNING @ Thu, 16 Apr 2020 06:12:02: Fewer paired peaks (423) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 423 pairs to build model! INFO @ Thu, 16 Apr 2020 06:12:02: start model_add_line... INFO @ Thu, 16 Apr 2020 06:12:02: start X-correlation... INFO @ Thu, 16 Apr 2020 06:12:02: end of X-cor INFO @ Thu, 16 Apr 2020 06:12:02: #2 finished! INFO @ Thu, 16 Apr 2020 06:12:02: #2 predicted fragment length is 48 bps INFO @ Thu, 16 Apr 2020 06:12:02: #2 alternative fragment length(s) may be 48 bps INFO @ Thu, 16 Apr 2020 06:12:02: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX6827677/SRX6827677.20_model.r WARNING @ Thu, 16 Apr 2020 06:12:02: #2 Since the d (48) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 16 Apr 2020 06:12:02: #2 You may need to consider one of the other alternative d(s): 48 WARNING @ Thu, 16 Apr 2020 06:12:02: #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 06:12:02: #3 Call peaks... INFO @ Thu, 16 Apr 2020 06:12:02: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 16 Apr 2020 06:12:10: #3 Call peaks for each chromosome... INFO @ Thu, 16 Apr 2020 06:12:27: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX6827677/SRX6827677.10_peaks.xls INFO @ Thu, 16 Apr 2020 06:12:27: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX6827677/SRX6827677.10_peaks.narrowPeak INFO @ Thu, 16 Apr 2020 06:12:27: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX6827677/SRX6827677.10_summits.bed INFO @ Thu, 16 Apr 2020 06:12:27: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (2296 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Thu, 16 Apr 2020 06:12:37: #3 Call peaks for each chromosome... INFO @ Thu, 16 Apr 2020 06:12:55: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX6827677/SRX6827677.20_peaks.xls INFO @ Thu, 16 Apr 2020 06:12:55: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX6827677/SRX6827677.20_peaks.narrowPeak INFO @ Thu, 16 Apr 2020 06:12:55: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX6827677/SRX6827677.20_summits.bed INFO @ Thu, 16 Apr 2020 06:12:55: Done! pass1 - making usageList (12 chroms): 1 millis pass2 - checking and writing primary data (1245 records, 4 fields): 2 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。