Job ID = 6366077 SRX = SRX059249 Genome = ce11 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-15T22:48:37 prefetch.2.10.7: 1) Downloading 'SRR190689'... 2020-06-15T22:48:37 prefetch.2.10.7: Downloading via HTTPS... 2020-06-15T22:49:14 prefetch.2.10.7: HTTPS download succeed 2020-06-15T22:49:14 prefetch.2.10.7: 'SRR190689' is valid 2020-06-15T22:49:14 prefetch.2.10.7: 1) 'SRR190689' was downloaded successfully Read 9011548 spots for SRR190689/SRR190689.sra Written 9011548 spots for SRR190689/SRR190689.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: 00:01:15 9011548 reads; of these: 9011548 (100.00%) were unpaired; of these: 24123 (0.27%) aligned 0 times 7440223 (82.56%) aligned exactly 1 time 1547202 (17.17%) aligned >1 times 99.73% overall alignment rate Time searching: 00:01:15 Overall time: 00:01:15 マッピングが完了しました。 samtools でBAM に変換中... [samopen] SAM header is present: 7 sequences. [bam_rmdupse_core] 570803 / 8987425 = 0.0635 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 @ Tue, 16 Jun 2020 07:53:29: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX059249/SRX059249.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX059249/SRX059249.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX059249/SRX059249.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX059249/SRX059249.bam'] # control file = None # effective genome size = 9.00e+07 # 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 @ Tue, 16 Jun 2020 07:53:29: #1 read tag files... INFO @ Tue, 16 Jun 2020 07:53:29: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 07:53:33: 1000000 INFO @ Tue, 16 Jun 2020 07:53:37: 2000000 INFO @ Tue, 16 Jun 2020 07:53:42: 3000000 INFO @ Tue, 16 Jun 2020 07:53:46: 4000000 INFO @ Tue, 16 Jun 2020 07:53:50: 5000000 INFO @ Tue, 16 Jun 2020 07:53:55: 6000000 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 @ Tue, 16 Jun 2020 07:53:59: 7000000 INFO @ Tue, 16 Jun 2020 07:53:59: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX059249/SRX059249.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX059249/SRX059249.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX059249/SRX059249.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX059249/SRX059249.bam'] # control file = None # effective genome size = 9.00e+07 # 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 @ Tue, 16 Jun 2020 07:53:59: #1 read tag files... INFO @ Tue, 16 Jun 2020 07:53:59: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 07:54:03: 8000000 INFO @ Tue, 16 Jun 2020 07:54:04: 1000000 INFO @ Tue, 16 Jun 2020 07:54:05: #1 tag size is determined as 28 bps INFO @ Tue, 16 Jun 2020 07:54:05: #1 tag size = 28 INFO @ Tue, 16 Jun 2020 07:54:05: #1 total tags in treatment: 8416622 INFO @ Tue, 16 Jun 2020 07:54:05: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 07:54:05: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 16 Jun 2020 07:54:05: #1 tags after filtering in treatment: 8416622 INFO @ Tue, 16 Jun 2020 07:54:05: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 07:54:05: #1 finished! INFO @ Tue, 16 Jun 2020 07:54:05: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 07:54:05: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 07:54:06: #2 number of paired peaks: 353 WARNING @ Tue, 16 Jun 2020 07:54:06: Fewer paired peaks (353) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 353 pairs to build model! INFO @ Tue, 16 Jun 2020 07:54:06: start model_add_line... INFO @ Tue, 16 Jun 2020 07:54:06: start X-correlation... INFO @ Tue, 16 Jun 2020 07:54:06: end of X-cor INFO @ Tue, 16 Jun 2020 07:54:06: #2 finished! INFO @ Tue, 16 Jun 2020 07:54:06: #2 predicted fragment length is 28 bps INFO @ Tue, 16 Jun 2020 07:54:06: #2 alternative fragment length(s) may be 2,28,97,100,524,538 bps INFO @ Tue, 16 Jun 2020 07:54:06: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX059249/SRX059249.05_model.r WARNING @ Tue, 16 Jun 2020 07:54:06: #2 Since the d (28) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 07:54:06: #2 You may need to consider one of the other alternative d(s): 2,28,97,100,524,538 WARNING @ Tue, 16 Jun 2020 07:54:06: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 16 Jun 2020 07:54:06: #3 Call peaks... INFO @ Tue, 16 Jun 2020 07:54:06: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 07:54:08: 2000000 INFO @ Tue, 16 Jun 2020 07:54:12: 3000000 INFO @ Tue, 16 Jun 2020 07:54:17: 4000000 INFO @ Tue, 16 Jun 2020 07:54:21: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 07:54:21: 5000000 INFO @ Tue, 16 Jun 2020 07:54:25: 6000000 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 @ Tue, 16 Jun 2020 07:54:28: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX059249/SRX059249.05_peaks.xls INFO @ Tue, 16 Jun 2020 07:54:28: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX059249/SRX059249.05_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 07:54:28: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX059249/SRX059249.05_summits.bed INFO @ Tue, 16 Jun 2020 07:54:28: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (535 records, 4 fields): 1 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 07:54:29: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX059249/SRX059249.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX059249/SRX059249.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX059249/SRX059249.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX059249/SRX059249.bam'] # control file = None # effective genome size = 9.00e+07 # 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 @ Tue, 16 Jun 2020 07:54:29: #1 read tag files... INFO @ Tue, 16 Jun 2020 07:54:29: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 07:54:30: 7000000 INFO @ Tue, 16 Jun 2020 07:54:34: 1000000 INFO @ Tue, 16 Jun 2020 07:54:34: 8000000 INFO @ Tue, 16 Jun 2020 07:54:36: #1 tag size is determined as 28 bps INFO @ Tue, 16 Jun 2020 07:54:36: #1 tag size = 28 INFO @ Tue, 16 Jun 2020 07:54:36: #1 total tags in treatment: 8416622 INFO @ Tue, 16 Jun 2020 07:54:36: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 07:54:36: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 16 Jun 2020 07:54:36: #1 tags after filtering in treatment: 8416622 INFO @ Tue, 16 Jun 2020 07:54:36: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 07:54:36: #1 finished! INFO @ Tue, 16 Jun 2020 07:54:36: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 07:54:36: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 07:54:37: #2 number of paired peaks: 353 WARNING @ Tue, 16 Jun 2020 07:54:37: Fewer paired peaks (353) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 353 pairs to build model! INFO @ Tue, 16 Jun 2020 07:54:37: start model_add_line... INFO @ Tue, 16 Jun 2020 07:54:37: start X-correlation... INFO @ Tue, 16 Jun 2020 07:54:37: end of X-cor INFO @ Tue, 16 Jun 2020 07:54:37: #2 finished! INFO @ Tue, 16 Jun 2020 07:54:37: #2 predicted fragment length is 28 bps INFO @ Tue, 16 Jun 2020 07:54:37: #2 alternative fragment length(s) may be 2,28,97,100,524,538 bps INFO @ Tue, 16 Jun 2020 07:54:37: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX059249/SRX059249.10_model.r WARNING @ Tue, 16 Jun 2020 07:54:37: #2 Since the d (28) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 07:54:37: #2 You may need to consider one of the other alternative d(s): 2,28,97,100,524,538 WARNING @ Tue, 16 Jun 2020 07:54:37: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 16 Jun 2020 07:54:37: #3 Call peaks... INFO @ Tue, 16 Jun 2020 07:54:37: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 07:54:38: 2000000 INFO @ Tue, 16 Jun 2020 07:54:43: 3000000 INFO @ Tue, 16 Jun 2020 07:54:47: 4000000 INFO @ Tue, 16 Jun 2020 07:54:51: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 07:54:52: 5000000 INFO @ Tue, 16 Jun 2020 07:54:57: 6000000 INFO @ Tue, 16 Jun 2020 07:54:59: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX059249/SRX059249.10_peaks.xls INFO @ Tue, 16 Jun 2020 07:54:59: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX059249/SRX059249.10_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 07:54:59: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX059249/SRX059249.10_summits.bed INFO @ Tue, 16 Jun 2020 07:54:59: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (234 records, 4 fields): 1 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 07:55:01: 7000000 INFO @ Tue, 16 Jun 2020 07:55:06: 8000000 INFO @ Tue, 16 Jun 2020 07:55:08: #1 tag size is determined as 28 bps INFO @ Tue, 16 Jun 2020 07:55:08: #1 tag size = 28 INFO @ Tue, 16 Jun 2020 07:55:08: #1 total tags in treatment: 8416622 INFO @ Tue, 16 Jun 2020 07:55:08: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 07:55:08: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 16 Jun 2020 07:55:08: #1 tags after filtering in treatment: 8416622 INFO @ Tue, 16 Jun 2020 07:55:08: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 07:55:08: #1 finished! INFO @ Tue, 16 Jun 2020 07:55:08: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 07:55:08: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 07:55:08: #2 number of paired peaks: 353 WARNING @ Tue, 16 Jun 2020 07:55:08: Fewer paired peaks (353) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 353 pairs to build model! INFO @ Tue, 16 Jun 2020 07:55:08: start model_add_line... INFO @ Tue, 16 Jun 2020 07:55:08: start X-correlation... INFO @ Tue, 16 Jun 2020 07:55:08: end of X-cor INFO @ Tue, 16 Jun 2020 07:55:08: #2 finished! INFO @ Tue, 16 Jun 2020 07:55:08: #2 predicted fragment length is 28 bps INFO @ Tue, 16 Jun 2020 07:55:08: #2 alternative fragment length(s) may be 2,28,97,100,524,538 bps INFO @ Tue, 16 Jun 2020 07:55:08: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX059249/SRX059249.20_model.r WARNING @ Tue, 16 Jun 2020 07:55:08: #2 Since the d (28) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 07:55:08: #2 You may need to consider one of the other alternative d(s): 2,28,97,100,524,538 WARNING @ Tue, 16 Jun 2020 07:55:08: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 16 Jun 2020 07:55:08: #3 Call peaks... INFO @ Tue, 16 Jun 2020 07:55:08: #3 Pre-compute pvalue-qvalue table... BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 16 Jun 2020 07:55:23: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 07:55:31: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX059249/SRX059249.20_peaks.xls INFO @ Tue, 16 Jun 2020 07:55:31: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX059249/SRX059249.20_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 07:55:31: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX059249/SRX059249.20_summits.bed INFO @ Tue, 16 Jun 2020 07:55:31: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (66 records, 4 fields): 1 millis CompletedMACS2peakCalling BigWig に変換しました。