Job ID = 6365891 SRX = SRX012299 Genome = ce11 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-15T22:34:06 prefetch.2.10.7: 1) Downloading 'SRR029218'... 2020-06-15T22:34:06 prefetch.2.10.7: Downloading via HTTPS... 2020-06-15T22:40:16 prefetch.2.10.7: HTTPS download succeed 2020-06-15T22:40:17 prefetch.2.10.7: 1) 'SRR029218' was downloaded successfully Read 11947205 spots for SRR029218/SRR029218.sra Written 11947205 spots for SRR029218/SRR029218.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: 00:01:24 11947205 reads; of these: 11947205 (100.00%) were unpaired; of these: 6394552 (53.52%) aligned 0 times 4723643 (39.54%) aligned exactly 1 time 829010 (6.94%) aligned >1 times 46.48% overall alignment rate Time searching: 00:01:24 Overall time: 00:01:24 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] 498004 / 5552653 = 0.0897 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 07:44:24: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX012299/SRX012299.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX012299/SRX012299.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX012299/SRX012299.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX012299/SRX012299.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 07:44:24: #1 read tag files... INFO @ Tue, 16 Jun 2020 07:44:24: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 07:44:29: 1000000 INFO @ Tue, 16 Jun 2020 07:44:34: 2000000 INFO @ Tue, 16 Jun 2020 07:44:39: 3000000 INFO @ Tue, 16 Jun 2020 07:44:44: 4000000 INFO @ Tue, 16 Jun 2020 07:44:49: 5000000 INFO @ Tue, 16 Jun 2020 07:44:49: #1 tag size is determined as 36 bps INFO @ Tue, 16 Jun 2020 07:44:49: #1 tag size = 36 INFO @ Tue, 16 Jun 2020 07:44:49: #1 total tags in treatment: 5054649 INFO @ Tue, 16 Jun 2020 07:44:49: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 07:44:49: #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 07:44:49: #1 tags after filtering in treatment: 5054649 INFO @ Tue, 16 Jun 2020 07:44:49: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 07:44:49: #1 finished! INFO @ Tue, 16 Jun 2020 07:44:49: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 07:44:49: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 07:44:49: #2 number of paired peaks: 232 WARNING @ Tue, 16 Jun 2020 07:44:49: Fewer paired peaks (232) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 232 pairs to build model! INFO @ Tue, 16 Jun 2020 07:44:49: start model_add_line... INFO @ Tue, 16 Jun 2020 07:44:49: start X-correlation... INFO @ Tue, 16 Jun 2020 07:44:49: end of X-cor INFO @ Tue, 16 Jun 2020 07:44:49: #2 finished! INFO @ Tue, 16 Jun 2020 07:44:49: #2 predicted fragment length is 36 bps INFO @ Tue, 16 Jun 2020 07:44:49: #2 alternative fragment length(s) may be 2,15,36,83,138,183,240,340,396,494,512,579,584,588 bps INFO @ Tue, 16 Jun 2020 07:44:49: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX012299/SRX012299.05_model.r WARNING @ Tue, 16 Jun 2020 07:44:49: #2 Since the d (36) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 07:44:49: #2 You may need to consider one of the other alternative d(s): 2,15,36,83,138,183,240,340,396,494,512,579,584,588 WARNING @ Tue, 16 Jun 2020 07:44:49: #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 07:44:49: #3 Call peaks... INFO @ Tue, 16 Jun 2020 07:44:49: #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 @ Tue, 16 Jun 2020 07:44:54: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX012299/SRX012299.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX012299/SRX012299.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX012299/SRX012299.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX012299/SRX012299.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 07:44:54: #1 read tag files... INFO @ Tue, 16 Jun 2020 07:44:54: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 07:44:59: 1000000 INFO @ Tue, 16 Jun 2020 07:45:01: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 07:45:04: 2000000 INFO @ Tue, 16 Jun 2020 07:45:07: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX012299/SRX012299.05_peaks.xls INFO @ Tue, 16 Jun 2020 07:45:07: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX012299/SRX012299.05_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 07:45:07: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX012299/SRX012299.05_summits.bed INFO @ Tue, 16 Jun 2020 07:45:07: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (197 records, 4 fields): 1 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 07:45:09: 3000000 INFO @ Tue, 16 Jun 2020 07:45:14: 4000000 INFO @ Tue, 16 Jun 2020 07:45:18: 5000000 INFO @ Tue, 16 Jun 2020 07:45:19: #1 tag size is determined as 36 bps INFO @ Tue, 16 Jun 2020 07:45:19: #1 tag size = 36 INFO @ Tue, 16 Jun 2020 07:45:19: #1 total tags in treatment: 5054649 INFO @ Tue, 16 Jun 2020 07:45:19: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 07:45:19: #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 07:45:19: #1 tags after filtering in treatment: 5054649 INFO @ Tue, 16 Jun 2020 07:45:19: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 07:45:19: #1 finished! INFO @ Tue, 16 Jun 2020 07:45:19: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 07:45:19: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 07:45:19: #2 number of paired peaks: 232 WARNING @ Tue, 16 Jun 2020 07:45:19: Fewer paired peaks (232) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 232 pairs to build model! INFO @ Tue, 16 Jun 2020 07:45:19: start model_add_line... INFO @ Tue, 16 Jun 2020 07:45:19: start X-correlation... INFO @ Tue, 16 Jun 2020 07:45:19: end of X-cor INFO @ Tue, 16 Jun 2020 07:45:19: #2 finished! INFO @ Tue, 16 Jun 2020 07:45:19: #2 predicted fragment length is 36 bps INFO @ Tue, 16 Jun 2020 07:45:19: #2 alternative fragment length(s) may be 2,15,36,83,138,183,240,340,396,494,512,579,584,588 bps INFO @ Tue, 16 Jun 2020 07:45:19: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX012299/SRX012299.10_model.r WARNING @ Tue, 16 Jun 2020 07:45:19: #2 Since the d (36) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 07:45:19: #2 You may need to consider one of the other alternative d(s): 2,15,36,83,138,183,240,340,396,494,512,579,584,588 WARNING @ Tue, 16 Jun 2020 07:45:19: #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 07:45:19: #3 Call peaks... INFO @ Tue, 16 Jun 2020 07:45:19: #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 @ Tue, 16 Jun 2020 07:45:24: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX012299/SRX012299.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX012299/SRX012299.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX012299/SRX012299.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX012299/SRX012299.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 07:45:24: #1 read tag files... INFO @ Tue, 16 Jun 2020 07:45:24: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 07:45:29: 1000000 INFO @ Tue, 16 Jun 2020 07:45:31: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 07:45:34: 2000000 INFO @ Tue, 16 Jun 2020 07:45:36: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX012299/SRX012299.10_peaks.xls INFO @ Tue, 16 Jun 2020 07:45:36: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX012299/SRX012299.10_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 07:45:36: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX012299/SRX012299.10_summits.bed INFO @ Tue, 16 Jun 2020 07:45:36: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (67 records, 4 fields): 1 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 07:45:39: 3000000 INFO @ Tue, 16 Jun 2020 07:45:43: 4000000 INFO @ Tue, 16 Jun 2020 07:45:48: 5000000 INFO @ Tue, 16 Jun 2020 07:45:49: #1 tag size is determined as 36 bps INFO @ Tue, 16 Jun 2020 07:45:49: #1 tag size = 36 INFO @ Tue, 16 Jun 2020 07:45:49: #1 total tags in treatment: 5054649 INFO @ Tue, 16 Jun 2020 07:45:49: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 07:45:49: #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 07:45:49: #1 tags after filtering in treatment: 5054649 INFO @ Tue, 16 Jun 2020 07:45:49: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 07:45:49: #1 finished! INFO @ Tue, 16 Jun 2020 07:45:49: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 07:45:49: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 07:45:49: #2 number of paired peaks: 232 WARNING @ Tue, 16 Jun 2020 07:45:49: Fewer paired peaks (232) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 232 pairs to build model! INFO @ Tue, 16 Jun 2020 07:45:49: start model_add_line... INFO @ Tue, 16 Jun 2020 07:45:49: start X-correlation... INFO @ Tue, 16 Jun 2020 07:45:49: end of X-cor INFO @ Tue, 16 Jun 2020 07:45:49: #2 finished! INFO @ Tue, 16 Jun 2020 07:45:49: #2 predicted fragment length is 36 bps INFO @ Tue, 16 Jun 2020 07:45:49: #2 alternative fragment length(s) may be 2,15,36,83,138,183,240,340,396,494,512,579,584,588 bps INFO @ Tue, 16 Jun 2020 07:45:49: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX012299/SRX012299.20_model.r WARNING @ Tue, 16 Jun 2020 07:45:49: #2 Since the d (36) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 07:45:49: #2 You may need to consider one of the other alternative d(s): 2,15,36,83,138,183,240,340,396,494,512,579,584,588 WARNING @ Tue, 16 Jun 2020 07:45:49: #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 07:45:49: #3 Call peaks... INFO @ Tue, 16 Jun 2020 07:45:49: #3 Pre-compute pvalue-qvalue table... BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 16 Jun 2020 07:46:00: #3 Call peaks for each chromosome... BigWig に変換しました。 INFO @ Tue, 16 Jun 2020 07:46:06: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX012299/SRX012299.20_peaks.xls INFO @ Tue, 16 Jun 2020 07:46:06: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX012299/SRX012299.20_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 07:46:06: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX012299/SRX012299.20_summits.bed INFO @ Tue, 16 Jun 2020 07:46:06: Done! pass1 - making usageList (5 chroms): 0 millis pass2 - checking and writing primary data (10 records, 4 fields): 1 millis CompletedMACS2peakCalling