Job ID = 6367439 SRX = SRX331197 Genome = ce11 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-15T23:31:20 prefetch.2.10.7: 1) Downloading 'SRR947429'... 2020-06-15T23:31:20 prefetch.2.10.7: Downloading via HTTPS... 2020-06-15T23:31:52 prefetch.2.10.7: HTTPS download succeed 2020-06-15T23:31:52 prefetch.2.10.7: 'SRR947429' is valid 2020-06-15T23:31:52 prefetch.2.10.7: 1) 'SRR947429' was downloaded successfully Read 5162172 spots for SRR947429/SRR947429.sra Written 5162172 spots for SRR947429/SRR947429.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: 00:00:01 Multiseed full-index search: 00:00:50 5162172 reads; of these: 5162172 (100.00%) were unpaired; of these: 26340 (0.51%) aligned 0 times 4312685 (83.54%) aligned exactly 1 time 823147 (15.95%) aligned >1 times 99.49% overall alignment rate Time searching: 00:00:51 Overall time: 00:00:51 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] 298524 / 5135832 = 0.0581 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 08:34:22: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX331197/SRX331197.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX331197/SRX331197.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX331197/SRX331197.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX331197/SRX331197.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 08:34:22: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:34:22: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:34:27: 1000000 INFO @ Tue, 16 Jun 2020 08:34:32: 2000000 INFO @ Tue, 16 Jun 2020 08:34:37: 3000000 INFO @ Tue, 16 Jun 2020 08:34:43: 4000000 INFO @ Tue, 16 Jun 2020 08:34:47: #1 tag size is determined as 32 bps INFO @ Tue, 16 Jun 2020 08:34:47: #1 tag size = 32 INFO @ Tue, 16 Jun 2020 08:34:47: #1 total tags in treatment: 4837308 INFO @ Tue, 16 Jun 2020 08:34:47: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:34:47: #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 08:34:47: #1 tags after filtering in treatment: 4837308 INFO @ Tue, 16 Jun 2020 08:34:47: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:34:47: #1 finished! INFO @ Tue, 16 Jun 2020 08:34:47: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:34:47: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:34:47: #2 number of paired peaks: 345 WARNING @ Tue, 16 Jun 2020 08:34:47: Fewer paired peaks (345) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 345 pairs to build model! INFO @ Tue, 16 Jun 2020 08:34:47: start model_add_line... INFO @ Tue, 16 Jun 2020 08:34:47: start X-correlation... INFO @ Tue, 16 Jun 2020 08:34:47: end of X-cor INFO @ Tue, 16 Jun 2020 08:34:47: #2 finished! INFO @ Tue, 16 Jun 2020 08:34:47: #2 predicted fragment length is 30 bps INFO @ Tue, 16 Jun 2020 08:34:47: #2 alternative fragment length(s) may be 4,30,538,589 bps INFO @ Tue, 16 Jun 2020 08:34:47: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX331197/SRX331197.05_model.r WARNING @ Tue, 16 Jun 2020 08:34:47: #2 Since the d (30) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 08:34:47: #2 You may need to consider one of the other alternative d(s): 4,30,538,589 WARNING @ Tue, 16 Jun 2020 08:34:47: #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 08:34:47: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:34:47: #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 08:34:52: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX331197/SRX331197.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX331197/SRX331197.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX331197/SRX331197.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX331197/SRX331197.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 08:34:52: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:34:52: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:34:57: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 08:34:58: 1000000 INFO @ Tue, 16 Jun 2020 08:35:03: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX331197/SRX331197.05_peaks.xls INFO @ Tue, 16 Jun 2020 08:35:03: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX331197/SRX331197.05_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:35:03: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX331197/SRX331197.05_summits.bed INFO @ Tue, 16 Jun 2020 08:35:03: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (356 records, 4 fields): 1 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 08:35:05: 2000000 INFO @ Tue, 16 Jun 2020 08:35:11: 3000000 INFO @ Tue, 16 Jun 2020 08:35:17: 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 08:35:22: #1 tag size is determined as 32 bps INFO @ Tue, 16 Jun 2020 08:35:22: #1 tag size = 32 INFO @ Tue, 16 Jun 2020 08:35:22: #1 total tags in treatment: 4837308 INFO @ Tue, 16 Jun 2020 08:35:22: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:35:22: #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 08:35:22: #1 tags after filtering in treatment: 4837308 INFO @ Tue, 16 Jun 2020 08:35:22: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:35:22: #1 finished! INFO @ Tue, 16 Jun 2020 08:35:22: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:35:22: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:35:22: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX331197/SRX331197.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX331197/SRX331197.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX331197/SRX331197.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX331197/SRX331197.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 08:35:22: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:35:22: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:35:22: #2 number of paired peaks: 345 WARNING @ Tue, 16 Jun 2020 08:35:22: Fewer paired peaks (345) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 345 pairs to build model! INFO @ Tue, 16 Jun 2020 08:35:22: start model_add_line... INFO @ Tue, 16 Jun 2020 08:35:22: start X-correlation... INFO @ Tue, 16 Jun 2020 08:35:22: end of X-cor INFO @ Tue, 16 Jun 2020 08:35:22: #2 finished! INFO @ Tue, 16 Jun 2020 08:35:22: #2 predicted fragment length is 30 bps INFO @ Tue, 16 Jun 2020 08:35:22: #2 alternative fragment length(s) may be 4,30,538,589 bps INFO @ Tue, 16 Jun 2020 08:35:22: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX331197/SRX331197.10_model.r WARNING @ Tue, 16 Jun 2020 08:35:22: #2 Since the d (30) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 08:35:22: #2 You may need to consider one of the other alternative d(s): 4,30,538,589 WARNING @ Tue, 16 Jun 2020 08:35:22: #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 08:35:22: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:35:22: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 08:35:29: 1000000 INFO @ Tue, 16 Jun 2020 08:35:33: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 08:35:35: 2000000 INFO @ Tue, 16 Jun 2020 08:35:39: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX331197/SRX331197.10_peaks.xls INFO @ Tue, 16 Jun 2020 08:35:39: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX331197/SRX331197.10_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:35:39: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX331197/SRX331197.10_summits.bed INFO @ Tue, 16 Jun 2020 08:35:39: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (164 records, 4 fields): 1 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 08:35:42: 3000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 16 Jun 2020 08:35:48: 4000000 INFO @ Tue, 16 Jun 2020 08:35:54: #1 tag size is determined as 32 bps INFO @ Tue, 16 Jun 2020 08:35:54: #1 tag size = 32 INFO @ Tue, 16 Jun 2020 08:35:54: #1 total tags in treatment: 4837308 INFO @ Tue, 16 Jun 2020 08:35:54: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:35:54: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) BigWig に変換しました。 INFO @ Tue, 16 Jun 2020 08:35:54: #1 tags after filtering in treatment: 4837308 INFO @ Tue, 16 Jun 2020 08:35:54: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:35:54: #1 finished! INFO @ Tue, 16 Jun 2020 08:35:54: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:35:54: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:35:54: #2 number of paired peaks: 345 WARNING @ Tue, 16 Jun 2020 08:35:54: Fewer paired peaks (345) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 345 pairs to build model! INFO @ Tue, 16 Jun 2020 08:35:54: start model_add_line... INFO @ Tue, 16 Jun 2020 08:35:54: start X-correlation... INFO @ Tue, 16 Jun 2020 08:35:54: end of X-cor INFO @ Tue, 16 Jun 2020 08:35:54: #2 finished! INFO @ Tue, 16 Jun 2020 08:35:54: #2 predicted fragment length is 30 bps INFO @ Tue, 16 Jun 2020 08:35:54: #2 alternative fragment length(s) may be 4,30,538,589 bps INFO @ Tue, 16 Jun 2020 08:35:54: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX331197/SRX331197.20_model.r WARNING @ Tue, 16 Jun 2020 08:35:54: #2 Since the d (30) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 08:35:54: #2 You may need to consider one of the other alternative d(s): 4,30,538,589 WARNING @ Tue, 16 Jun 2020 08:35:54: #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 08:35:54: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:35:54: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 08:36:05: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 08:36:10: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX331197/SRX331197.20_peaks.xls INFO @ Tue, 16 Jun 2020 08:36:10: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX331197/SRX331197.20_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:36:10: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX331197/SRX331197.20_summits.bed INFO @ Tue, 16 Jun 2020 08:36:10: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (49 records, 4 fields): 1 millis CompletedMACS2peakCalling