Job ID = 5720234 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 34,218,469 reads read : 34,218,469 reads written : 34,218,469 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: 00:07:08 34218469 reads; of these: 34218469 (100.00%) were unpaired; of these: 1783343 (5.21%) aligned 0 times 26868181 (78.52%) aligned exactly 1 time 5566945 (16.27%) aligned >1 times 94.79% overall alignment rate Time searching: 00:07:08 Overall time: 00:07:08 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 16 files... [bam_rmdupse_core] 16438694 / 32435126 = 0.5068 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 @ Wed, 15 Apr 2020 22:56:18: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX6720165/SRX6720165.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX6720165/SRX6720165.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX6720165/SRX6720165.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX6720165/SRX6720165.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 @ Wed, 15 Apr 2020 22:56:18: #1 read tag files... INFO @ Wed, 15 Apr 2020 22:56:18: #1 read treatment tags... INFO @ Wed, 15 Apr 2020 22:56:23: 1000000 INFO @ Wed, 15 Apr 2020 22:56:28: 2000000 INFO @ Wed, 15 Apr 2020 22:56:33: 3000000 INFO @ Wed, 15 Apr 2020 22:56:38: 4000000 INFO @ Wed, 15 Apr 2020 22:56:44: 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 @ Wed, 15 Apr 2020 22:56:48: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX6720165/SRX6720165.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX6720165/SRX6720165.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX6720165/SRX6720165.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX6720165/SRX6720165.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 @ Wed, 15 Apr 2020 22:56:48: #1 read tag files... INFO @ Wed, 15 Apr 2020 22:56:48: #1 read treatment tags... INFO @ Wed, 15 Apr 2020 22:56:49: 6000000 INFO @ Wed, 15 Apr 2020 22:56:54: 1000000 INFO @ Wed, 15 Apr 2020 22:56:54: 7000000 INFO @ Wed, 15 Apr 2020 22:57:00: 2000000 INFO @ Wed, 15 Apr 2020 22:57:00: 8000000 INFO @ Wed, 15 Apr 2020 22:57:05: 3000000 INFO @ Wed, 15 Apr 2020 22:57:05: 9000000 INFO @ Wed, 15 Apr 2020 22:57:11: 4000000 INFO @ Wed, 15 Apr 2020 22:57:11: 10000000 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 @ Wed, 15 Apr 2020 22:57:16: 5000000 INFO @ Wed, 15 Apr 2020 22:57:16: 11000000 INFO @ Wed, 15 Apr 2020 22:57:18: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX6720165/SRX6720165.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX6720165/SRX6720165.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX6720165/SRX6720165.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX6720165/SRX6720165.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 @ Wed, 15 Apr 2020 22:57:18: #1 read tag files... INFO @ Wed, 15 Apr 2020 22:57:18: #1 read treatment tags... INFO @ Wed, 15 Apr 2020 22:57:22: 12000000 INFO @ Wed, 15 Apr 2020 22:57:22: 6000000 INFO @ Wed, 15 Apr 2020 22:57:24: 1000000 INFO @ Wed, 15 Apr 2020 22:57:27: 13000000 INFO @ Wed, 15 Apr 2020 22:57:27: 7000000 INFO @ Wed, 15 Apr 2020 22:57:30: 2000000 INFO @ Wed, 15 Apr 2020 22:57:32: 14000000 INFO @ Wed, 15 Apr 2020 22:57:33: 8000000 INFO @ Wed, 15 Apr 2020 22:57:35: 3000000 INFO @ Wed, 15 Apr 2020 22:57:38: 15000000 INFO @ Wed, 15 Apr 2020 22:57:38: 9000000 INFO @ Wed, 15 Apr 2020 22:57:41: 4000000 INFO @ Wed, 15 Apr 2020 22:57:43: #1 tag size is determined as 50 bps INFO @ Wed, 15 Apr 2020 22:57:43: #1 tag size = 50 INFO @ Wed, 15 Apr 2020 22:57:43: #1 total tags in treatment: 15996432 INFO @ Wed, 15 Apr 2020 22:57:43: #1 user defined the maximum tags... INFO @ Wed, 15 Apr 2020 22:57:43: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Wed, 15 Apr 2020 22:57:44: #1 tags after filtering in treatment: 15996432 INFO @ Wed, 15 Apr 2020 22:57:44: #1 Redundant rate of treatment: 0.00 INFO @ Wed, 15 Apr 2020 22:57:44: #1 finished! INFO @ Wed, 15 Apr 2020 22:57:44: #2 Build Peak Model... INFO @ Wed, 15 Apr 2020 22:57:44: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 15 Apr 2020 22:57:44: 10000000 INFO @ Wed, 15 Apr 2020 22:57:45: #2 number of paired peaks: 433 WARNING @ Wed, 15 Apr 2020 22:57:45: Fewer paired peaks (433) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 433 pairs to build model! INFO @ Wed, 15 Apr 2020 22:57:45: start model_add_line... INFO @ Wed, 15 Apr 2020 22:57:45: start X-correlation... INFO @ Wed, 15 Apr 2020 22:57:45: end of X-cor INFO @ Wed, 15 Apr 2020 22:57:45: #2 finished! INFO @ Wed, 15 Apr 2020 22:57:45: #2 predicted fragment length is 1 bps INFO @ Wed, 15 Apr 2020 22:57:45: #2 alternative fragment length(s) may be 1,34,577 bps INFO @ Wed, 15 Apr 2020 22:57:45: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX6720165/SRX6720165.05_model.r WARNING @ Wed, 15 Apr 2020 22:57:45: #2 Since the d (1) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Wed, 15 Apr 2020 22:57:45: #2 You may need to consider one of the other alternative d(s): 1,34,577 WARNING @ Wed, 15 Apr 2020 22:57:45: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Wed, 15 Apr 2020 22:57:45: #3 Call peaks... INFO @ Wed, 15 Apr 2020 22:57:45: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 15 Apr 2020 22:57:46: 5000000 INFO @ Wed, 15 Apr 2020 22:57:49: 11000000 INFO @ Wed, 15 Apr 2020 22:57:52: 6000000 INFO @ Wed, 15 Apr 2020 22:57:54: 12000000 INFO @ Wed, 15 Apr 2020 22:57:57: 7000000 INFO @ Wed, 15 Apr 2020 22:58:00: 13000000 INFO @ Wed, 15 Apr 2020 22:58:03: 8000000 INFO @ Wed, 15 Apr 2020 22:58:05: 14000000 INFO @ Wed, 15 Apr 2020 22:58:08: 9000000 INFO @ Wed, 15 Apr 2020 22:58:11: 15000000 INFO @ Wed, 15 Apr 2020 22:58:11: #3 Call peaks for each chromosome... INFO @ Wed, 15 Apr 2020 22:58:13: 10000000 INFO @ Wed, 15 Apr 2020 22:58:16: #1 tag size is determined as 50 bps INFO @ Wed, 15 Apr 2020 22:58:16: #1 tag size = 50 INFO @ Wed, 15 Apr 2020 22:58:16: #1 total tags in treatment: 15996432 INFO @ Wed, 15 Apr 2020 22:58:16: #1 user defined the maximum tags... INFO @ Wed, 15 Apr 2020 22:58:16: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Wed, 15 Apr 2020 22:58:16: #1 tags after filtering in treatment: 15996432 INFO @ Wed, 15 Apr 2020 22:58:16: #1 Redundant rate of treatment: 0.00 INFO @ Wed, 15 Apr 2020 22:58:16: #1 finished! INFO @ Wed, 15 Apr 2020 22:58:16: #2 Build Peak Model... INFO @ Wed, 15 Apr 2020 22:58:16: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 15 Apr 2020 22:58:17: #2 number of paired peaks: 433 WARNING @ Wed, 15 Apr 2020 22:58:17: Fewer paired peaks (433) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 433 pairs to build model! INFO @ Wed, 15 Apr 2020 22:58:17: start model_add_line... INFO @ Wed, 15 Apr 2020 22:58:17: start X-correlation... INFO @ Wed, 15 Apr 2020 22:58:17: end of X-cor INFO @ Wed, 15 Apr 2020 22:58:17: #2 finished! INFO @ Wed, 15 Apr 2020 22:58:17: #2 predicted fragment length is 1 bps INFO @ Wed, 15 Apr 2020 22:58:17: #2 alternative fragment length(s) may be 1,34,577 bps INFO @ Wed, 15 Apr 2020 22:58:17: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX6720165/SRX6720165.10_model.r WARNING @ Wed, 15 Apr 2020 22:58:17: #2 Since the d (1) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Wed, 15 Apr 2020 22:58:17: #2 You may need to consider one of the other alternative d(s): 1,34,577 WARNING @ Wed, 15 Apr 2020 22:58:17: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Wed, 15 Apr 2020 22:58:17: #3 Call peaks... INFO @ Wed, 15 Apr 2020 22:58:17: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 15 Apr 2020 22:58:19: 11000000 INFO @ Wed, 15 Apr 2020 22:58:23: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX6720165/SRX6720165.05_peaks.xls INFO @ Wed, 15 Apr 2020 22:58:23: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX6720165/SRX6720165.05_peaks.narrowPeak INFO @ Wed, 15 Apr 2020 22:58:23: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX6720165/SRX6720165.05_summits.bed INFO @ Wed, 15 Apr 2020 22:58:23: Done! INFO @ Wed, 15 Apr 2020 22:58:24: 12000000 pass1 - making usageList (0 chroms): 0 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling INFO @ Wed, 15 Apr 2020 22:58:29: 13000000 INFO @ Wed, 15 Apr 2020 22:58:35: 14000000 INFO @ Wed, 15 Apr 2020 22:58:40: 15000000 INFO @ Wed, 15 Apr 2020 22:58:43: #3 Call peaks for each chromosome... INFO @ Wed, 15 Apr 2020 22:58:45: #1 tag size is determined as 50 bps INFO @ Wed, 15 Apr 2020 22:58:45: #1 tag size = 50 INFO @ Wed, 15 Apr 2020 22:58:45: #1 total tags in treatment: 15996432 INFO @ Wed, 15 Apr 2020 22:58:45: #1 user defined the maximum tags... INFO @ Wed, 15 Apr 2020 22:58:45: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Wed, 15 Apr 2020 22:58:45: #1 tags after filtering in treatment: 15996432 INFO @ Wed, 15 Apr 2020 22:58:45: #1 Redundant rate of treatment: 0.00 INFO @ Wed, 15 Apr 2020 22:58:45: #1 finished! INFO @ Wed, 15 Apr 2020 22:58:45: #2 Build Peak Model... INFO @ Wed, 15 Apr 2020 22:58:45: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 15 Apr 2020 22:58:46: #2 number of paired peaks: 433 WARNING @ Wed, 15 Apr 2020 22:58:46: Fewer paired peaks (433) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 433 pairs to build model! INFO @ Wed, 15 Apr 2020 22:58:46: start model_add_line... INFO @ Wed, 15 Apr 2020 22:58:46: start X-correlation... INFO @ Wed, 15 Apr 2020 22:58:46: end of X-cor INFO @ Wed, 15 Apr 2020 22:58:46: #2 finished! INFO @ Wed, 15 Apr 2020 22:58:46: #2 predicted fragment length is 1 bps INFO @ Wed, 15 Apr 2020 22:58:46: #2 alternative fragment length(s) may be 1,34,577 bps INFO @ Wed, 15 Apr 2020 22:58:46: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX6720165/SRX6720165.20_model.r WARNING @ Wed, 15 Apr 2020 22:58:46: #2 Since the d (1) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Wed, 15 Apr 2020 22:58:46: #2 You may need to consider one of the other alternative d(s): 1,34,577 WARNING @ Wed, 15 Apr 2020 22:58:46: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Wed, 15 Apr 2020 22:58:46: #3 Call peaks... INFO @ Wed, 15 Apr 2020 22:58:46: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 15 Apr 2020 22:58:55: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX6720165/SRX6720165.10_peaks.xls INFO @ Wed, 15 Apr 2020 22:58:55: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX6720165/SRX6720165.10_peaks.narrowPeak INFO @ Wed, 15 Apr 2020 22:58:55: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX6720165/SRX6720165.10_summits.bed INFO @ Wed, 15 Apr 2020 22:58:55: Done! pass1 - making usageList (0 chroms): 0 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling INFO @ Wed, 15 Apr 2020 22:59:12: #3 Call peaks for each chromosome... INFO @ Wed, 15 Apr 2020 22:59:23: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX6720165/SRX6720165.20_peaks.xls INFO @ Wed, 15 Apr 2020 22:59:23: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX6720165/SRX6720165.20_peaks.narrowPeak INFO @ Wed, 15 Apr 2020 22:59:23: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX6720165/SRX6720165.20_summits.bed INFO @ Wed, 15 Apr 2020 22:59:23: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。