Job ID = 6497536 SRX = SRX514568 Genome = ce10 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-25T22:26:35 prefetch.2.10.7: 1) Downloading 'SRR1230856'... 2020-06-25T22:26:35 prefetch.2.10.7: Downloading via HTTPS... 2020-06-25T22:27:19 prefetch.2.10.7: HTTPS download succeed 2020-06-25T22:27:20 prefetch.2.10.7: 'SRR1230856' is valid 2020-06-25T22:27:20 prefetch.2.10.7: 1) 'SRR1230856' was downloaded successfully Read 5096702 spots for SRR1230856/SRR1230856.sra Written 5096702 spots for SRR1230856/SRR1230856.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: 00:01:05 5096702 reads; of these: 5096702 (100.00%) were unpaired; of these: 942223 (18.49%) aligned 0 times 3602793 (70.69%) aligned exactly 1 time 551686 (10.82%) aligned >1 times 81.51% overall alignment rate Time searching: 00:01:05 Overall time: 00:01:05 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] 310174 / 4154479 = 0.0747 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 07:30:13: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX514568/SRX514568.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX514568/SRX514568.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX514568/SRX514568.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX514568/SRX514568.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 07:30:13: #1 read tag files... INFO @ Fri, 26 Jun 2020 07:30:13: #1 read treatment tags... INFO @ Fri, 26 Jun 2020 07:30:19: 1000000 INFO @ Fri, 26 Jun 2020 07:30:25: 2000000 INFO @ Fri, 26 Jun 2020 07:30:31: 3000000 INFO @ Fri, 26 Jun 2020 07:30:36: #1 tag size is determined as 50 bps INFO @ Fri, 26 Jun 2020 07:30:36: #1 tag size = 50 INFO @ Fri, 26 Jun 2020 07:30:36: #1 total tags in treatment: 3844305 INFO @ Fri, 26 Jun 2020 07:30:36: #1 user defined the maximum tags... INFO @ Fri, 26 Jun 2020 07:30:36: #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 07:30:36: #1 tags after filtering in treatment: 3844305 INFO @ Fri, 26 Jun 2020 07:30:36: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 26 Jun 2020 07:30:36: #1 finished! INFO @ Fri, 26 Jun 2020 07:30:36: #2 Build Peak Model... INFO @ Fri, 26 Jun 2020 07:30:36: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 26 Jun 2020 07:30:36: #2 number of paired peaks: 176 WARNING @ Fri, 26 Jun 2020 07:30:36: Fewer paired peaks (176) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 176 pairs to build model! INFO @ Fri, 26 Jun 2020 07:30:36: start model_add_line... INFO @ Fri, 26 Jun 2020 07:30:36: start X-correlation... INFO @ Fri, 26 Jun 2020 07:30:36: end of X-cor INFO @ Fri, 26 Jun 2020 07:30:36: #2 finished! INFO @ Fri, 26 Jun 2020 07:30:36: #2 predicted fragment length is 45 bps INFO @ Fri, 26 Jun 2020 07:30:36: #2 alternative fragment length(s) may be 45,171,285,394,413,495 bps INFO @ Fri, 26 Jun 2020 07:30:36: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX514568/SRX514568.05_model.r WARNING @ Fri, 26 Jun 2020 07:30:36: #2 Since the d (45) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 26 Jun 2020 07:30:36: #2 You may need to consider one of the other alternative d(s): 45,171,285,394,413,495 WARNING @ Fri, 26 Jun 2020 07:30:36: #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 07:30:36: #3 Call peaks... INFO @ Fri, 26 Jun 2020 07:30:36: #3 Pre-compute pvalue-qvalue table... 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 07:30:43: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX514568/SRX514568.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX514568/SRX514568.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX514568/SRX514568.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX514568/SRX514568.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 07:30:43: #1 read tag files... INFO @ Fri, 26 Jun 2020 07:30:43: #1 read treatment tags... INFO @ Fri, 26 Jun 2020 07:30:44: #3 Call peaks for each chromosome... INFO @ Fri, 26 Jun 2020 07:30:49: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX514568/SRX514568.05_peaks.xls INFO @ Fri, 26 Jun 2020 07:30:49: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX514568/SRX514568.05_peaks.narrowPeak INFO @ Fri, 26 Jun 2020 07:30:49: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX514568/SRX514568.05_summits.bed INFO @ Fri, 26 Jun 2020 07:30:49: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (402 records, 4 fields): 25 millis CompletedMACS2peakCalling INFO @ Fri, 26 Jun 2020 07:30:49: 1000000 INFO @ Fri, 26 Jun 2020 07:30:55: 2000000 INFO @ Fri, 26 Jun 2020 07:31:01: 3000000 INFO @ Fri, 26 Jun 2020 07:31:05: #1 tag size is determined as 50 bps INFO @ Fri, 26 Jun 2020 07:31:05: #1 tag size = 50 INFO @ Fri, 26 Jun 2020 07:31:05: #1 total tags in treatment: 3844305 INFO @ Fri, 26 Jun 2020 07:31:05: #1 user defined the maximum tags... INFO @ Fri, 26 Jun 2020 07:31:05: #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 07:31:05: #1 tags after filtering in treatment: 3844305 INFO @ Fri, 26 Jun 2020 07:31:05: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 26 Jun 2020 07:31:05: #1 finished! INFO @ Fri, 26 Jun 2020 07:31:05: #2 Build Peak Model... INFO @ Fri, 26 Jun 2020 07:31:05: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 26 Jun 2020 07:31:06: #2 number of paired peaks: 176 WARNING @ Fri, 26 Jun 2020 07:31:06: Fewer paired peaks (176) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 176 pairs to build model! INFO @ Fri, 26 Jun 2020 07:31:06: start model_add_line... INFO @ Fri, 26 Jun 2020 07:31:06: start X-correlation... INFO @ Fri, 26 Jun 2020 07:31:06: end of X-cor INFO @ Fri, 26 Jun 2020 07:31:06: #2 finished! INFO @ Fri, 26 Jun 2020 07:31:06: #2 predicted fragment length is 45 bps INFO @ Fri, 26 Jun 2020 07:31:06: #2 alternative fragment length(s) may be 45,171,285,394,413,495 bps INFO @ Fri, 26 Jun 2020 07:31:06: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX514568/SRX514568.10_model.r WARNING @ Fri, 26 Jun 2020 07:31:06: #2 Since the d (45) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 26 Jun 2020 07:31:06: #2 You may need to consider one of the other alternative d(s): 45,171,285,394,413,495 WARNING @ Fri, 26 Jun 2020 07:31:06: #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 07:31:06: #3 Call peaks... INFO @ Fri, 26 Jun 2020 07:31:06: #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 07:31:13: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX514568/SRX514568.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX514568/SRX514568.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX514568/SRX514568.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX514568/SRX514568.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 07:31:13: #1 read tag files... INFO @ Fri, 26 Jun 2020 07:31:13: #1 read treatment tags... INFO @ Fri, 26 Jun 2020 07:31:14: #3 Call peaks for each chromosome... INFO @ Fri, 26 Jun 2020 07:31:18: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX514568/SRX514568.10_peaks.xls INFO @ Fri, 26 Jun 2020 07:31:18: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX514568/SRX514568.10_peaks.narrowPeak INFO @ Fri, 26 Jun 2020 07:31:18: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX514568/SRX514568.10_summits.bed INFO @ Fri, 26 Jun 2020 07:31:18: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (120 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Fri, 26 Jun 2020 07:31:20: 1000000 INFO @ Fri, 26 Jun 2020 07:31:26: 2000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Fri, 26 Jun 2020 07:31:33: 3000000 INFO @ Fri, 26 Jun 2020 07:31:39: #1 tag size is determined as 50 bps INFO @ Fri, 26 Jun 2020 07:31:39: #1 tag size = 50 INFO @ Fri, 26 Jun 2020 07:31:39: #1 total tags in treatment: 3844305 INFO @ Fri, 26 Jun 2020 07:31:39: #1 user defined the maximum tags... INFO @ Fri, 26 Jun 2020 07:31:39: #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 07:31:39: #1 tags after filtering in treatment: 3844305 INFO @ Fri, 26 Jun 2020 07:31:39: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 26 Jun 2020 07:31:39: #1 finished! INFO @ Fri, 26 Jun 2020 07:31:39: #2 Build Peak Model... INFO @ Fri, 26 Jun 2020 07:31:39: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 26 Jun 2020 07:31:39: #2 number of paired peaks: 176 WARNING @ Fri, 26 Jun 2020 07:31:39: Fewer paired peaks (176) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 176 pairs to build model! INFO @ Fri, 26 Jun 2020 07:31:39: start model_add_line... INFO @ Fri, 26 Jun 2020 07:31:39: start X-correlation... INFO @ Fri, 26 Jun 2020 07:31:39: end of X-cor INFO @ Fri, 26 Jun 2020 07:31:39: #2 finished! INFO @ Fri, 26 Jun 2020 07:31:39: #2 predicted fragment length is 45 bps INFO @ Fri, 26 Jun 2020 07:31:39: #2 alternative fragment length(s) may be 45,171,285,394,413,495 bps INFO @ Fri, 26 Jun 2020 07:31:39: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX514568/SRX514568.20_model.r WARNING @ Fri, 26 Jun 2020 07:31:39: #2 Since the d (45) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 26 Jun 2020 07:31:39: #2 You may need to consider one of the other alternative d(s): 45,171,285,394,413,495 WARNING @ Fri, 26 Jun 2020 07:31:39: #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 07:31:39: #3 Call peaks... INFO @ Fri, 26 Jun 2020 07:31:39: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Fri, 26 Jun 2020 07:31:48: #3 Call peaks for each chromosome... INFO @ Fri, 26 Jun 2020 07:31:52: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX514568/SRX514568.20_peaks.xls INFO @ Fri, 26 Jun 2020 07:31:52: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX514568/SRX514568.20_peaks.narrowPeak INFO @ Fri, 26 Jun 2020 07:31:52: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX514568/SRX514568.20_summits.bed INFO @ Fri, 26 Jun 2020 07:31:52: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (39 records, 4 fields): 1 millis CompletedMACS2peakCalling