Job ID = 6367004 SRX = SRX257703 Genome = ce11 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-15T23:10:16 prefetch.2.10.7: 1) Downloading 'SRR800720'... 2020-06-15T23:10:16 prefetch.2.10.7: Downloading via HTTPS... 2020-06-15T23:11:59 prefetch.2.10.7: HTTPS download succeed 2020-06-15T23:12:00 prefetch.2.10.7: 'SRR800720' is valid 2020-06-15T23:12:00 prefetch.2.10.7: 1) 'SRR800720' was downloaded successfully Read 16311814 spots for SRR800720/SRR800720.sra Written 16311814 spots for SRR800720/SRR800720.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: 00:04:00 16311814 reads; of these: 16311814 (100.00%) were unpaired; of these: 562134 (3.45%) aligned 0 times 12341000 (75.66%) aligned exactly 1 time 3408680 (20.90%) aligned >1 times 96.55% overall alignment rate Time searching: 00:04:00 Overall time: 00:04:00 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_sort_core] merging from 8 files... [bam_rmdupse_core] 2795513 / 15749680 = 0.1775 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 08:21:05: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX257703/SRX257703.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX257703/SRX257703.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX257703/SRX257703.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX257703/SRX257703.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 08:21:05: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:21:05: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:21:11: 1000000 INFO @ Tue, 16 Jun 2020 08:21:16: 2000000 INFO @ Tue, 16 Jun 2020 08:21:22: 3000000 INFO @ Tue, 16 Jun 2020 08:21:28: 4000000 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 08:21:34: 5000000 INFO @ Tue, 16 Jun 2020 08:21:35: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX257703/SRX257703.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX257703/SRX257703.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX257703/SRX257703.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX257703/SRX257703.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 08:21:35: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:21:35: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:21:40: 6000000 INFO @ Tue, 16 Jun 2020 08:21:42: 1000000 INFO @ Tue, 16 Jun 2020 08:21:47: 7000000 INFO @ Tue, 16 Jun 2020 08:21:49: 2000000 INFO @ Tue, 16 Jun 2020 08:21:53: 8000000 INFO @ Tue, 16 Jun 2020 08:21:56: 3000000 INFO @ Tue, 16 Jun 2020 08:22:00: 9000000 INFO @ Tue, 16 Jun 2020 08:22:03: 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 @ Tue, 16 Jun 2020 08:22:05: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX257703/SRX257703.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX257703/SRX257703.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX257703/SRX257703.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX257703/SRX257703.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 08:22:05: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:22:05: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:22:07: 10000000 INFO @ Tue, 16 Jun 2020 08:22:10: 5000000 INFO @ Tue, 16 Jun 2020 08:22:12: 1000000 INFO @ Tue, 16 Jun 2020 08:22:14: 11000000 INFO @ Tue, 16 Jun 2020 08:22:17: 6000000 INFO @ Tue, 16 Jun 2020 08:22:19: 2000000 INFO @ Tue, 16 Jun 2020 08:22:20: 12000000 INFO @ Tue, 16 Jun 2020 08:22:24: 7000000 INFO @ Tue, 16 Jun 2020 08:22:26: 3000000 INFO @ Tue, 16 Jun 2020 08:22:27: #1 tag size is determined as 51 bps INFO @ Tue, 16 Jun 2020 08:22:27: #1 tag size = 51 INFO @ Tue, 16 Jun 2020 08:22:27: #1 total tags in treatment: 12954167 INFO @ Tue, 16 Jun 2020 08:22:27: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:22:27: #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 08:22:27: #1 tags after filtering in treatment: 12954167 INFO @ Tue, 16 Jun 2020 08:22:27: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:22:27: #1 finished! INFO @ Tue, 16 Jun 2020 08:22:27: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:22:27: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:22:28: #2 number of paired peaks: 500 WARNING @ Tue, 16 Jun 2020 08:22:28: Fewer paired peaks (500) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 500 pairs to build model! INFO @ Tue, 16 Jun 2020 08:22:28: start model_add_line... INFO @ Tue, 16 Jun 2020 08:22:28: start X-correlation... INFO @ Tue, 16 Jun 2020 08:22:28: end of X-cor INFO @ Tue, 16 Jun 2020 08:22:28: #2 finished! INFO @ Tue, 16 Jun 2020 08:22:28: #2 predicted fragment length is 45 bps INFO @ Tue, 16 Jun 2020 08:22:28: #2 alternative fragment length(s) may be 2,45 bps INFO @ Tue, 16 Jun 2020 08:22:28: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX257703/SRX257703.05_model.r WARNING @ Tue, 16 Jun 2020 08:22:28: #2 Since the d (45) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 08:22:28: #2 You may need to consider one of the other alternative d(s): 2,45 WARNING @ Tue, 16 Jun 2020 08:22:28: #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 08:22:28: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:22:28: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 08:22:31: 8000000 INFO @ Tue, 16 Jun 2020 08:22:32: 4000000 INFO @ Tue, 16 Jun 2020 08:22:38: 9000000 INFO @ Tue, 16 Jun 2020 08:22:39: 5000000 INFO @ Tue, 16 Jun 2020 08:22:45: 10000000 INFO @ Tue, 16 Jun 2020 08:22:46: 6000000 INFO @ Tue, 16 Jun 2020 08:22:52: 11000000 INFO @ Tue, 16 Jun 2020 08:22:52: 7000000 INFO @ Tue, 16 Jun 2020 08:22:54: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 08:22:58: 12000000 INFO @ Tue, 16 Jun 2020 08:22:59: 8000000 INFO @ Tue, 16 Jun 2020 08:23:05: #1 tag size is determined as 51 bps INFO @ Tue, 16 Jun 2020 08:23:05: #1 tag size = 51 INFO @ Tue, 16 Jun 2020 08:23:05: #1 total tags in treatment: 12954167 INFO @ Tue, 16 Jun 2020 08:23:05: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:23:05: #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 08:23:05: #1 tags after filtering in treatment: 12954167 INFO @ Tue, 16 Jun 2020 08:23:05: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:23:05: #1 finished! INFO @ Tue, 16 Jun 2020 08:23:05: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:23:05: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:23:05: 9000000 INFO @ Tue, 16 Jun 2020 08:23:06: #2 number of paired peaks: 500 WARNING @ Tue, 16 Jun 2020 08:23:06: Fewer paired peaks (500) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 500 pairs to build model! INFO @ Tue, 16 Jun 2020 08:23:06: start model_add_line... INFO @ Tue, 16 Jun 2020 08:23:06: start X-correlation... INFO @ Tue, 16 Jun 2020 08:23:06: end of X-cor INFO @ Tue, 16 Jun 2020 08:23:06: #2 finished! INFO @ Tue, 16 Jun 2020 08:23:06: #2 predicted fragment length is 45 bps INFO @ Tue, 16 Jun 2020 08:23:06: #2 alternative fragment length(s) may be 2,45 bps INFO @ Tue, 16 Jun 2020 08:23:06: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX257703/SRX257703.10_model.r WARNING @ Tue, 16 Jun 2020 08:23:06: #2 Since the d (45) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 08:23:06: #2 You may need to consider one of the other alternative d(s): 2,45 WARNING @ Tue, 16 Jun 2020 08:23:06: #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 08:23:06: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:23:06: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 08:23:07: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX257703/SRX257703.05_peaks.xls INFO @ Tue, 16 Jun 2020 08:23:07: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX257703/SRX257703.05_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:23:07: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX257703/SRX257703.05_summits.bed INFO @ Tue, 16 Jun 2020 08:23:07: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (809 records, 4 fields): 2 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 16 Jun 2020 08:23:11: 10000000 INFO @ Tue, 16 Jun 2020 08:23:17: 11000000 INFO @ Tue, 16 Jun 2020 08:23:23: 12000000 INFO @ Tue, 16 Jun 2020 08:23:28: #1 tag size is determined as 51 bps INFO @ Tue, 16 Jun 2020 08:23:28: #1 tag size = 51 INFO @ Tue, 16 Jun 2020 08:23:28: #1 total tags in treatment: 12954167 INFO @ Tue, 16 Jun 2020 08:23:28: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:23:28: #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 08:23:29: #1 tags after filtering in treatment: 12954167 INFO @ Tue, 16 Jun 2020 08:23:29: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:23:29: #1 finished! INFO @ Tue, 16 Jun 2020 08:23:29: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:23:29: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:23:29: #2 number of paired peaks: 500 WARNING @ Tue, 16 Jun 2020 08:23:29: Fewer paired peaks (500) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 500 pairs to build model! INFO @ Tue, 16 Jun 2020 08:23:29: start model_add_line... INFO @ Tue, 16 Jun 2020 08:23:29: start X-correlation... INFO @ Tue, 16 Jun 2020 08:23:30: end of X-cor INFO @ Tue, 16 Jun 2020 08:23:30: #2 finished! INFO @ Tue, 16 Jun 2020 08:23:30: #2 predicted fragment length is 45 bps INFO @ Tue, 16 Jun 2020 08:23:30: #2 alternative fragment length(s) may be 2,45 bps INFO @ Tue, 16 Jun 2020 08:23:30: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX257703/SRX257703.20_model.r WARNING @ Tue, 16 Jun 2020 08:23:30: #2 Since the d (45) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 08:23:30: #2 You may need to consider one of the other alternative d(s): 2,45 WARNING @ Tue, 16 Jun 2020 08:23:30: #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 08:23:30: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:23:30: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 08:23:30: #3 Call peaks for each chromosome... BigWig に変換しました。 INFO @ Tue, 16 Jun 2020 08:23:42: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX257703/SRX257703.10_peaks.xls INFO @ Tue, 16 Jun 2020 08:23:42: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX257703/SRX257703.10_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:23:42: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX257703/SRX257703.10_summits.bed INFO @ Tue, 16 Jun 2020 08:23:42: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (511 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 08:23:54: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 08:24:06: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX257703/SRX257703.20_peaks.xls INFO @ Tue, 16 Jun 2020 08:24:06: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX257703/SRX257703.20_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:24:06: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX257703/SRX257703.20_summits.bed INFO @ Tue, 16 Jun 2020 08:24:06: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (264 records, 4 fields): 1 millis CompletedMACS2peakCalling