Job ID = 5721194 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 23,683,209 reads read : 23,683,209 reads written : 23,683,209 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: 00:08:32 23683209 reads; of these: 23683209 (100.00%) were unpaired; of these: 731045 (3.09%) aligned 0 times 15362714 (64.87%) aligned exactly 1 time 7589450 (32.05%) aligned >1 times 96.91% overall alignment rate Time searching: 00:08:32 Overall time: 00:08:32 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] 3376858 / 22952164 = 0.1471 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 06:02:01: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX6827663/SRX6827663.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX6827663/SRX6827663.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX6827663/SRX6827663.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX6827663/SRX6827663.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 06:02:01: #1 read tag files... INFO @ Thu, 16 Apr 2020 06:02:01: #1 read treatment tags... INFO @ Thu, 16 Apr 2020 06:02:06: 1000000 INFO @ Thu, 16 Apr 2020 06:02:12: 2000000 INFO @ Thu, 16 Apr 2020 06:02:17: 3000000 INFO @ Thu, 16 Apr 2020 06:02:22: 4000000 INFO @ Thu, 16 Apr 2020 06:02:27: 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 @ Thu, 16 Apr 2020 06:02:31: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX6827663/SRX6827663.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX6827663/SRX6827663.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX6827663/SRX6827663.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX6827663/SRX6827663.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 06:02:31: #1 read tag files... INFO @ Thu, 16 Apr 2020 06:02:31: #1 read treatment tags... INFO @ Thu, 16 Apr 2020 06:02:32: 6000000 INFO @ Thu, 16 Apr 2020 06:02:37: 1000000 INFO @ Thu, 16 Apr 2020 06:02:38: 7000000 INFO @ Thu, 16 Apr 2020 06:02:42: 2000000 INFO @ Thu, 16 Apr 2020 06:02:44: 8000000 INFO @ Thu, 16 Apr 2020 06:02:48: 3000000 INFO @ Thu, 16 Apr 2020 06:02:49: 9000000 INFO @ Thu, 16 Apr 2020 06:02:53: 4000000 INFO @ Thu, 16 Apr 2020 06:02:55: 10000000 INFO @ Thu, 16 Apr 2020 06:02:59: 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 @ Thu, 16 Apr 2020 06:03:00: 11000000 INFO @ Thu, 16 Apr 2020 06:03:01: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX6827663/SRX6827663.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX6827663/SRX6827663.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX6827663/SRX6827663.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX6827663/SRX6827663.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 06:03:01: #1 read tag files... INFO @ Thu, 16 Apr 2020 06:03:01: #1 read treatment tags... INFO @ Thu, 16 Apr 2020 06:03:04: 6000000 INFO @ Thu, 16 Apr 2020 06:03:06: 12000000 INFO @ Thu, 16 Apr 2020 06:03:07: 1000000 INFO @ Thu, 16 Apr 2020 06:03:10: 7000000 INFO @ Thu, 16 Apr 2020 06:03:12: 2000000 INFO @ Thu, 16 Apr 2020 06:03:12: 13000000 INFO @ Thu, 16 Apr 2020 06:03:16: 8000000 INFO @ Thu, 16 Apr 2020 06:03:18: 3000000 INFO @ Thu, 16 Apr 2020 06:03:18: 14000000 INFO @ Thu, 16 Apr 2020 06:03:22: 9000000 INFO @ Thu, 16 Apr 2020 06:03:23: 4000000 INFO @ Thu, 16 Apr 2020 06:03:24: 15000000 INFO @ Thu, 16 Apr 2020 06:03:27: 10000000 INFO @ Thu, 16 Apr 2020 06:03:29: 5000000 INFO @ Thu, 16 Apr 2020 06:03:30: 16000000 INFO @ Thu, 16 Apr 2020 06:03:33: 11000000 INFO @ Thu, 16 Apr 2020 06:03:35: 6000000 INFO @ Thu, 16 Apr 2020 06:03:35: 17000000 INFO @ Thu, 16 Apr 2020 06:03:39: 12000000 INFO @ Thu, 16 Apr 2020 06:03:40: 7000000 INFO @ Thu, 16 Apr 2020 06:03:41: 18000000 INFO @ Thu, 16 Apr 2020 06:03:44: 13000000 INFO @ Thu, 16 Apr 2020 06:03:46: 8000000 INFO @ Thu, 16 Apr 2020 06:03:47: 19000000 INFO @ Thu, 16 Apr 2020 06:03:50: 14000000 INFO @ Thu, 16 Apr 2020 06:03:50: #1 tag size is determined as 50 bps INFO @ Thu, 16 Apr 2020 06:03:50: #1 tag size = 50 INFO @ Thu, 16 Apr 2020 06:03:50: #1 total tags in treatment: 19575306 INFO @ Thu, 16 Apr 2020 06:03:50: #1 user defined the maximum tags... INFO @ Thu, 16 Apr 2020 06:03:50: #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 06:03:51: #1 tags after filtering in treatment: 19575306 INFO @ Thu, 16 Apr 2020 06:03:51: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 16 Apr 2020 06:03:51: #1 finished! INFO @ Thu, 16 Apr 2020 06:03:51: #2 Build Peak Model... INFO @ Thu, 16 Apr 2020 06:03:51: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 16 Apr 2020 06:03:52: 9000000 INFO @ Thu, 16 Apr 2020 06:03:52: #2 number of paired peaks: 438 WARNING @ Thu, 16 Apr 2020 06:03:52: Fewer paired peaks (438) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 438 pairs to build model! INFO @ Thu, 16 Apr 2020 06:03:52: start model_add_line... INFO @ Thu, 16 Apr 2020 06:03:52: start X-correlation... INFO @ Thu, 16 Apr 2020 06:03:52: end of X-cor INFO @ Thu, 16 Apr 2020 06:03:52: #2 finished! INFO @ Thu, 16 Apr 2020 06:03:52: #2 predicted fragment length is 47 bps INFO @ Thu, 16 Apr 2020 06:03:52: #2 alternative fragment length(s) may be 4,47 bps INFO @ Thu, 16 Apr 2020 06:03:52: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX6827663/SRX6827663.05_model.r WARNING @ Thu, 16 Apr 2020 06:03:52: #2 Since the d (47) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 16 Apr 2020 06:03:52: #2 You may need to consider one of the other alternative d(s): 4,47 WARNING @ Thu, 16 Apr 2020 06:03:52: #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 06:03:52: #3 Call peaks... INFO @ Thu, 16 Apr 2020 06:03:52: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 16 Apr 2020 06:03:56: 15000000 INFO @ Thu, 16 Apr 2020 06:03:57: 10000000 INFO @ Thu, 16 Apr 2020 06:04:01: 16000000 INFO @ Thu, 16 Apr 2020 06:04:03: 11000000 INFO @ Thu, 16 Apr 2020 06:04:07: 17000000 INFO @ Thu, 16 Apr 2020 06:04:08: 12000000 INFO @ Thu, 16 Apr 2020 06:04:13: 18000000 INFO @ Thu, 16 Apr 2020 06:04:14: 13000000 INFO @ Thu, 16 Apr 2020 06:04:18: 19000000 INFO @ Thu, 16 Apr 2020 06:04:20: 14000000 INFO @ Thu, 16 Apr 2020 06:04:22: #1 tag size is determined as 50 bps INFO @ Thu, 16 Apr 2020 06:04:22: #1 tag size = 50 INFO @ Thu, 16 Apr 2020 06:04:22: #1 total tags in treatment: 19575306 INFO @ Thu, 16 Apr 2020 06:04:22: #1 user defined the maximum tags... INFO @ Thu, 16 Apr 2020 06:04:22: #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 06:04:22: #1 tags after filtering in treatment: 19575306 INFO @ Thu, 16 Apr 2020 06:04:22: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 16 Apr 2020 06:04:22: #1 finished! INFO @ Thu, 16 Apr 2020 06:04:22: #2 Build Peak Model... INFO @ Thu, 16 Apr 2020 06:04:22: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 16 Apr 2020 06:04:23: #2 number of paired peaks: 438 WARNING @ Thu, 16 Apr 2020 06:04:23: Fewer paired peaks (438) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 438 pairs to build model! INFO @ Thu, 16 Apr 2020 06:04:23: start model_add_line... INFO @ Thu, 16 Apr 2020 06:04:23: start X-correlation... INFO @ Thu, 16 Apr 2020 06:04:23: end of X-cor INFO @ Thu, 16 Apr 2020 06:04:23: #2 finished! INFO @ Thu, 16 Apr 2020 06:04:23: #2 predicted fragment length is 47 bps INFO @ Thu, 16 Apr 2020 06:04:23: #2 alternative fragment length(s) may be 4,47 bps INFO @ Thu, 16 Apr 2020 06:04:23: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX6827663/SRX6827663.10_model.r WARNING @ Thu, 16 Apr 2020 06:04:23: #2 Since the d (47) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 16 Apr 2020 06:04:23: #2 You may need to consider one of the other alternative d(s): 4,47 WARNING @ Thu, 16 Apr 2020 06:04:23: #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 06:04:23: #3 Call peaks... INFO @ Thu, 16 Apr 2020 06:04:23: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 16 Apr 2020 06:04:26: 15000000 INFO @ Thu, 16 Apr 2020 06:04:30: #3 Call peaks for each chromosome... INFO @ Thu, 16 Apr 2020 06:04:31: 16000000 INFO @ Thu, 16 Apr 2020 06:04:37: 17000000 INFO @ Thu, 16 Apr 2020 06:04:42: 18000000 INFO @ Thu, 16 Apr 2020 06:04:48: 19000000 INFO @ Thu, 16 Apr 2020 06:04:48: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX6827663/SRX6827663.05_peaks.xls INFO @ Thu, 16 Apr 2020 06:04:48: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX6827663/SRX6827663.05_peaks.narrowPeak INFO @ Thu, 16 Apr 2020 06:04:48: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX6827663/SRX6827663.05_summits.bed INFO @ Thu, 16 Apr 2020 06:04:48: Done! pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (3368 records, 4 fields): 5 millis CompletedMACS2peakCalling INFO @ Thu, 16 Apr 2020 06:04:51: #1 tag size is determined as 50 bps INFO @ Thu, 16 Apr 2020 06:04:51: #1 tag size = 50 INFO @ Thu, 16 Apr 2020 06:04:51: #1 total tags in treatment: 19575306 INFO @ Thu, 16 Apr 2020 06:04:51: #1 user defined the maximum tags... INFO @ Thu, 16 Apr 2020 06:04:51: #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 06:04:51: #1 tags after filtering in treatment: 19575306 INFO @ Thu, 16 Apr 2020 06:04:51: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 16 Apr 2020 06:04:51: #1 finished! INFO @ Thu, 16 Apr 2020 06:04:51: #2 Build Peak Model... INFO @ Thu, 16 Apr 2020 06:04:51: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 16 Apr 2020 06:04:52: #2 number of paired peaks: 438 WARNING @ Thu, 16 Apr 2020 06:04:52: Fewer paired peaks (438) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 438 pairs to build model! INFO @ Thu, 16 Apr 2020 06:04:52: start model_add_line... INFO @ Thu, 16 Apr 2020 06:04:53: start X-correlation... INFO @ Thu, 16 Apr 2020 06:04:53: end of X-cor INFO @ Thu, 16 Apr 2020 06:04:53: #2 finished! INFO @ Thu, 16 Apr 2020 06:04:53: #2 predicted fragment length is 47 bps INFO @ Thu, 16 Apr 2020 06:04:53: #2 alternative fragment length(s) may be 4,47 bps INFO @ Thu, 16 Apr 2020 06:04:53: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX6827663/SRX6827663.20_model.r WARNING @ Thu, 16 Apr 2020 06:04:53: #2 Since the d (47) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 16 Apr 2020 06:04:53: #2 You may need to consider one of the other alternative d(s): 4,47 WARNING @ Thu, 16 Apr 2020 06:04:53: #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 06:04:53: #3 Call peaks... INFO @ Thu, 16 Apr 2020 06:04:53: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 16 Apr 2020 06:05:01: #3 Call peaks for each chromosome... INFO @ Thu, 16 Apr 2020 06:05:19: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX6827663/SRX6827663.10_peaks.xls INFO @ Thu, 16 Apr 2020 06:05:19: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX6827663/SRX6827663.10_peaks.narrowPeak INFO @ Thu, 16 Apr 2020 06:05:19: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX6827663/SRX6827663.10_summits.bed INFO @ Thu, 16 Apr 2020 06:05:19: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (2419 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Thu, 16 Apr 2020 06:05:28: #3 Call peaks for each chromosome... INFO @ Thu, 16 Apr 2020 06:05:46: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX6827663/SRX6827663.20_peaks.xls INFO @ Thu, 16 Apr 2020 06:05:46: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX6827663/SRX6827663.20_peaks.narrowPeak INFO @ Thu, 16 Apr 2020 06:05:46: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX6827663/SRX6827663.20_summits.bed INFO @ Thu, 16 Apr 2020 06:05:46: Done! pass1 - making usageList (12 chroms): 1 millis pass2 - checking and writing primary data (1285 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。