Job ID = 6497535 SRX = SRX514567 Genome = ce10 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-25T22:12:29 prefetch.2.10.7: 1) Downloading 'SRR1230855'... 2020-06-25T22:12:31 prefetch.2.10.7: Downloading via HTTPS... 2020-06-25T22:13:32 prefetch.2.10.7: HTTPS download succeed 2020-06-25T22:13:33 prefetch.2.10.7: 'SRR1230855' is valid 2020-06-25T22:13:33 prefetch.2.10.7: 1) 'SRR1230855' was downloaded successfully Read 5046407 spots for SRR1230855/SRR1230855.sra Written 5046407 spots for SRR1230855/SRR1230855.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: 00:00:55 5046407 reads; of these: 5046407 (100.00%) were unpaired; of these: 923296 (18.30%) aligned 0 times 3656977 (72.47%) aligned exactly 1 time 466134 (9.24%) aligned >1 times 81.70% overall alignment rate Time searching: 00:00:55 Overall time: 00:00:55 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] 722841 / 4123111 = 0.1753 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 @ Fri, 26 Jun 2020 07:16:11: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX514567/SRX514567.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX514567/SRX514567.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX514567/SRX514567.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX514567/SRX514567.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 @ Fri, 26 Jun 2020 07:16:11: #1 read tag files... INFO @ Fri, 26 Jun 2020 07:16:11: #1 read treatment tags... INFO @ Fri, 26 Jun 2020 07:16:17: 1000000 INFO @ Fri, 26 Jun 2020 07:16:22: 2000000 INFO @ Fri, 26 Jun 2020 07:16:27: 3000000 INFO @ Fri, 26 Jun 2020 07:16:30: #1 tag size is determined as 50 bps INFO @ Fri, 26 Jun 2020 07:16:30: #1 tag size = 50 INFO @ Fri, 26 Jun 2020 07:16:30: #1 total tags in treatment: 3400270 INFO @ Fri, 26 Jun 2020 07:16:30: #1 user defined the maximum tags... INFO @ Fri, 26 Jun 2020 07:16:30: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 26 Jun 2020 07:16:30: #1 tags after filtering in treatment: 3400270 INFO @ Fri, 26 Jun 2020 07:16:30: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 26 Jun 2020 07:16:30: #1 finished! INFO @ Fri, 26 Jun 2020 07:16:30: #2 Build Peak Model... INFO @ Fri, 26 Jun 2020 07:16:30: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 26 Jun 2020 07:16:30: #2 number of paired peaks: 136 WARNING @ Fri, 26 Jun 2020 07:16:30: Fewer paired peaks (136) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 136 pairs to build model! INFO @ Fri, 26 Jun 2020 07:16:30: start model_add_line... INFO @ Fri, 26 Jun 2020 07:16:30: start X-correlation... INFO @ Fri, 26 Jun 2020 07:16:30: end of X-cor INFO @ Fri, 26 Jun 2020 07:16:30: #2 finished! INFO @ Fri, 26 Jun 2020 07:16:30: #2 predicted fragment length is 49 bps INFO @ Fri, 26 Jun 2020 07:16:30: #2 alternative fragment length(s) may be 49,130,201,233,489 bps INFO @ Fri, 26 Jun 2020 07:16:30: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX514567/SRX514567.05_model.r WARNING @ Fri, 26 Jun 2020 07:16:30: #2 Since the d (49) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 26 Jun 2020 07:16:30: #2 You may need to consider one of the other alternative d(s): 49,130,201,233,489 WARNING @ Fri, 26 Jun 2020 07:16:30: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Fri, 26 Jun 2020 07:16:30: #3 Call peaks... INFO @ Fri, 26 Jun 2020 07:16:30: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 26 Jun 2020 07:16:37: #3 Call peaks for each chromosome... 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 @ Fri, 26 Jun 2020 07:16:41: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX514567/SRX514567.05_peaks.xls INFO @ Fri, 26 Jun 2020 07:16:41: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX514567/SRX514567.05_peaks.narrowPeak INFO @ Fri, 26 Jun 2020 07:16:41: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX514567/SRX514567.05_summits.bed INFO @ Fri, 26 Jun 2020 07:16:41: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (270 records, 4 fields): 1 millis CompletedMACS2peakCalling INFO @ Fri, 26 Jun 2020 07:16:41: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX514567/SRX514567.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX514567/SRX514567.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX514567/SRX514567.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX514567/SRX514567.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 @ Fri, 26 Jun 2020 07:16:41: #1 read tag files... INFO @ Fri, 26 Jun 2020 07:16:41: #1 read treatment tags... INFO @ Fri, 26 Jun 2020 07:16:47: 1000000 INFO @ Fri, 26 Jun 2020 07:16:52: 2000000 INFO @ Fri, 26 Jun 2020 07:16:57: 3000000 INFO @ Fri, 26 Jun 2020 07:17:00: #1 tag size is determined as 50 bps INFO @ Fri, 26 Jun 2020 07:17:00: #1 tag size = 50 INFO @ Fri, 26 Jun 2020 07:17:00: #1 total tags in treatment: 3400270 INFO @ Fri, 26 Jun 2020 07:17:00: #1 user defined the maximum tags... INFO @ Fri, 26 Jun 2020 07:17:00: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 26 Jun 2020 07:17:00: #1 tags after filtering in treatment: 3400270 INFO @ Fri, 26 Jun 2020 07:17:00: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 26 Jun 2020 07:17:00: #1 finished! INFO @ Fri, 26 Jun 2020 07:17:00: #2 Build Peak Model... INFO @ Fri, 26 Jun 2020 07:17:00: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 26 Jun 2020 07:17:00: #2 number of paired peaks: 136 WARNING @ Fri, 26 Jun 2020 07:17:00: Fewer paired peaks (136) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 136 pairs to build model! INFO @ Fri, 26 Jun 2020 07:17:00: start model_add_line... INFO @ Fri, 26 Jun 2020 07:17:00: start X-correlation... INFO @ Fri, 26 Jun 2020 07:17:00: end of X-cor INFO @ Fri, 26 Jun 2020 07:17:00: #2 finished! INFO @ Fri, 26 Jun 2020 07:17:00: #2 predicted fragment length is 49 bps INFO @ Fri, 26 Jun 2020 07:17:00: #2 alternative fragment length(s) may be 49,130,201,233,489 bps INFO @ Fri, 26 Jun 2020 07:17:00: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX514567/SRX514567.10_model.r WARNING @ Fri, 26 Jun 2020 07:17:07: #2 Since the d (49) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 26 Jun 2020 07:17:07: #2 You may need to consider one of the other alternative d(s): 49,130,201,233,489 WARNING @ Fri, 26 Jun 2020 07:17:07: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Fri, 26 Jun 2020 07:17:07: #3 Call peaks... INFO @ Fri, 26 Jun 2020 07:17:07: #3 Pre-compute pvalue-qvalue table... 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 @ Fri, 26 Jun 2020 07:17:11: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX514567/SRX514567.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX514567/SRX514567.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX514567/SRX514567.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX514567/SRX514567.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 @ Fri, 26 Jun 2020 07:17:11: #1 read tag files... INFO @ Fri, 26 Jun 2020 07:17:11: #1 read treatment tags... INFO @ Fri, 26 Jun 2020 07:17:14: #3 Call peaks for each chromosome... INFO @ Fri, 26 Jun 2020 07:17:17: 1000000 INFO @ Fri, 26 Jun 2020 07:17:17: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX514567/SRX514567.10_peaks.xls INFO @ Fri, 26 Jun 2020 07:17:17: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX514567/SRX514567.10_peaks.narrowPeak INFO @ Fri, 26 Jun 2020 07:17:17: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX514567/SRX514567.10_summits.bed INFO @ Fri, 26 Jun 2020 07:17:17: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (75 records, 4 fields): 1 millis CompletedMACS2peakCalling INFO @ Fri, 26 Jun 2020 07:17:22: 2000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Fri, 26 Jun 2020 07:17:27: 3000000 INFO @ Fri, 26 Jun 2020 07:17:30: #1 tag size is determined as 50 bps INFO @ Fri, 26 Jun 2020 07:17:30: #1 tag size = 50 INFO @ Fri, 26 Jun 2020 07:17:30: #1 total tags in treatment: 3400270 INFO @ Fri, 26 Jun 2020 07:17:30: #1 user defined the maximum tags... INFO @ Fri, 26 Jun 2020 07:17:30: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 26 Jun 2020 07:17:30: #1 tags after filtering in treatment: 3400270 INFO @ Fri, 26 Jun 2020 07:17:30: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 26 Jun 2020 07:17:30: #1 finished! INFO @ Fri, 26 Jun 2020 07:17:30: #2 Build Peak Model... INFO @ Fri, 26 Jun 2020 07:17:30: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 26 Jun 2020 07:17:30: #2 number of paired peaks: 136 WARNING @ Fri, 26 Jun 2020 07:17:30: Fewer paired peaks (136) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 136 pairs to build model! INFO @ Fri, 26 Jun 2020 07:17:30: start model_add_line... INFO @ Fri, 26 Jun 2020 07:17:30: start X-correlation... INFO @ Fri, 26 Jun 2020 07:17:30: end of X-cor INFO @ Fri, 26 Jun 2020 07:17:30: #2 finished! INFO @ Fri, 26 Jun 2020 07:17:30: #2 predicted fragment length is 49 bps INFO @ Fri, 26 Jun 2020 07:17:30: #2 alternative fragment length(s) may be 49,130,201,233,489 bps INFO @ Fri, 26 Jun 2020 07:17:30: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX514567/SRX514567.20_model.r WARNING @ Fri, 26 Jun 2020 07:17:30: #2 Since the d (49) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 26 Jun 2020 07:17:30: #2 You may need to consider one of the other alternative d(s): 49,130,201,233,489 WARNING @ Fri, 26 Jun 2020 07:17:30: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Fri, 26 Jun 2020 07:17:30: #3 Call peaks... INFO @ Fri, 26 Jun 2020 07:17:30: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Fri, 26 Jun 2020 07:17:37: #3 Call peaks for each chromosome... INFO @ Fri, 26 Jun 2020 07:17:41: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX514567/SRX514567.20_peaks.xls INFO @ Fri, 26 Jun 2020 07:17:41: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX514567/SRX514567.20_peaks.narrowPeak INFO @ Fri, 26 Jun 2020 07:17:41: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX514567/SRX514567.20_summits.bed INFO @ Fri, 26 Jun 2020 07:17:41: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (18 records, 4 fields): 1 millis CompletedMACS2peakCalling