Job ID = 12265164 SRX = SRX2969573 Genome = ce11 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 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: 00:08:25 41403819 reads; of these: 41403819 (100.00%) were unpaired; of these: 3079484 (7.44%) aligned 0 times 33830589 (81.71%) aligned exactly 1 time 4493746 (10.85%) aligned >1 times 92.56% overall alignment rate Time searching: 00:08:25 Overall time: 00:08:25 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] 27989209 / 38324335 = 0.7303 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/3.7.1/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Sat, 03 Apr 2021 06:25:47: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX2969573/SRX2969573.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX2969573/SRX2969573.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX2969573/SRX2969573.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX2969573/SRX2969573.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 @ Sat, 03 Apr 2021 06:25:47: #1 read tag files... INFO @ Sat, 03 Apr 2021 06:25:47: #1 read treatment tags... INFO @ Sat, 03 Apr 2021 06:25:52: 1000000 INFO @ Sat, 03 Apr 2021 06:25:57: 2000000 INFO @ Sat, 03 Apr 2021 06:26:02: 3000000 INFO @ Sat, 03 Apr 2021 06:26:07: 4000000 INFO @ Sat, 03 Apr 2021 06:26:12: 5000000 WARNING: Skipping mount /opt/pkg/singularity/3.7.1/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Sat, 03 Apr 2021 06:26:17: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX2969573/SRX2969573.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX2969573/SRX2969573.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX2969573/SRX2969573.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX2969573/SRX2969573.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 @ Sat, 03 Apr 2021 06:26:17: #1 read tag files... INFO @ Sat, 03 Apr 2021 06:26:17: #1 read treatment tags... INFO @ Sat, 03 Apr 2021 06:26:17: 6000000 INFO @ Sat, 03 Apr 2021 06:26:22: 1000000 INFO @ Sat, 03 Apr 2021 06:26:22: 7000000 INFO @ Sat, 03 Apr 2021 06:26:28: 2000000 INFO @ Sat, 03 Apr 2021 06:26:28: 8000000 INFO @ Sat, 03 Apr 2021 06:26:33: 3000000 INFO @ Sat, 03 Apr 2021 06:26:33: 9000000 INFO @ Sat, 03 Apr 2021 06:26:38: 4000000 INFO @ Sat, 03 Apr 2021 06:26:38: 10000000 INFO @ Sat, 03 Apr 2021 06:26:40: #1 tag size is determined as 51 bps INFO @ Sat, 03 Apr 2021 06:26:40: #1 tag size = 51 INFO @ Sat, 03 Apr 2021 06:26:40: #1 total tags in treatment: 10335126 INFO @ Sat, 03 Apr 2021 06:26:40: #1 user defined the maximum tags... INFO @ Sat, 03 Apr 2021 06:26:40: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 03 Apr 2021 06:26:40: #1 tags after filtering in treatment: 10335126 INFO @ Sat, 03 Apr 2021 06:26:40: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 03 Apr 2021 06:26:40: #1 finished! INFO @ Sat, 03 Apr 2021 06:26:40: #2 Build Peak Model... INFO @ Sat, 03 Apr 2021 06:26:40: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 03 Apr 2021 06:26:41: #2 number of paired peaks: 524 WARNING @ Sat, 03 Apr 2021 06:26:41: Fewer paired peaks (524) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 524 pairs to build model! INFO @ Sat, 03 Apr 2021 06:26:41: start model_add_line... INFO @ Sat, 03 Apr 2021 06:26:41: start X-correlation... INFO @ Sat, 03 Apr 2021 06:26:41: end of X-cor INFO @ Sat, 03 Apr 2021 06:26:41: #2 finished! INFO @ Sat, 03 Apr 2021 06:26:41: #2 predicted fragment length is 68 bps INFO @ Sat, 03 Apr 2021 06:26:41: #2 alternative fragment length(s) may be 68 bps INFO @ Sat, 03 Apr 2021 06:26:41: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX2969573/SRX2969573.05_model.r WARNING @ Sat, 03 Apr 2021 06:26:41: #2 Since the d (68) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 03 Apr 2021 06:26:41: #2 You may need to consider one of the other alternative d(s): 68 WARNING @ Sat, 03 Apr 2021 06:26:41: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sat, 03 Apr 2021 06:26:41: #3 Call peaks... INFO @ Sat, 03 Apr 2021 06:26:41: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Apr 2021 06:26:44: 5000000 BedGraph に変換中... WARNING: Skipping mount /opt/pkg/singularity/3.7.1/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Sat, 03 Apr 2021 06:26:47: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX2969573/SRX2969573.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX2969573/SRX2969573.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX2969573/SRX2969573.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX2969573/SRX2969573.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 @ Sat, 03 Apr 2021 06:26:47: #1 read tag files... INFO @ Sat, 03 Apr 2021 06:26:47: #1 read treatment tags... INFO @ Sat, 03 Apr 2021 06:26:49: 6000000 INFO @ Sat, 03 Apr 2021 06:26:53: 1000000 INFO @ Sat, 03 Apr 2021 06:26:55: 7000000 INFO @ Sat, 03 Apr 2021 06:26:59: 2000000 INFO @ Sat, 03 Apr 2021 06:27:00: 8000000 INFO @ Sat, 03 Apr 2021 06:27:01: #3 Call peaks for each chromosome... INFO @ Sat, 03 Apr 2021 06:27:05: 3000000 INFO @ Sat, 03 Apr 2021 06:27:06: 9000000 INFO @ Sat, 03 Apr 2021 06:27:11: 10000000 INFO @ Sat, 03 Apr 2021 06:27:12: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX2969573/SRX2969573.05_peaks.xls INFO @ Sat, 03 Apr 2021 06:27:12: 4000000 INFO @ Sat, 03 Apr 2021 06:27:12: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX2969573/SRX2969573.05_peaks.narrowPeak INFO @ Sat, 03 Apr 2021 06:27:12: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX2969573/SRX2969573.05_summits.bed INFO @ Sat, 03 Apr 2021 06:27:12: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (8394 records, 4 fields): 15 millis CompletedMACS2peakCalling INFO @ Sat, 03 Apr 2021 06:27:13: #1 tag size is determined as 51 bps INFO @ Sat, 03 Apr 2021 06:27:13: #1 tag size = 51 INFO @ Sat, 03 Apr 2021 06:27:13: #1 total tags in treatment: 10335126 INFO @ Sat, 03 Apr 2021 06:27:13: #1 user defined the maximum tags... INFO @ Sat, 03 Apr 2021 06:27:13: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 03 Apr 2021 06:27:13: #1 tags after filtering in treatment: 10335126 INFO @ Sat, 03 Apr 2021 06:27:13: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 03 Apr 2021 06:27:13: #1 finished! INFO @ Sat, 03 Apr 2021 06:27:13: #2 Build Peak Model... INFO @ Sat, 03 Apr 2021 06:27:13: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 03 Apr 2021 06:27:14: #2 number of paired peaks: 524 WARNING @ Sat, 03 Apr 2021 06:27:14: Fewer paired peaks (524) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 524 pairs to build model! INFO @ Sat, 03 Apr 2021 06:27:14: start model_add_line... INFO @ Sat, 03 Apr 2021 06:27:14: start X-correlation... INFO @ Sat, 03 Apr 2021 06:27:14: end of X-cor INFO @ Sat, 03 Apr 2021 06:27:14: #2 finished! INFO @ Sat, 03 Apr 2021 06:27:14: #2 predicted fragment length is 68 bps INFO @ Sat, 03 Apr 2021 06:27:14: #2 alternative fragment length(s) may be 68 bps INFO @ Sat, 03 Apr 2021 06:27:14: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX2969573/SRX2969573.10_model.r WARNING @ Sat, 03 Apr 2021 06:27:14: #2 Since the d (68) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 03 Apr 2021 06:27:14: #2 You may need to consider one of the other alternative d(s): 68 WARNING @ Sat, 03 Apr 2021 06:27:14: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sat, 03 Apr 2021 06:27:14: #3 Call peaks... INFO @ Sat, 03 Apr 2021 06:27:14: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Apr 2021 06:27:18: 5000000 INFO @ Sat, 03 Apr 2021 06:27:24: 6000000 INFO @ Sat, 03 Apr 2021 06:27:30: 7000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 03 Apr 2021 06:27:36: 8000000 INFO @ Sat, 03 Apr 2021 06:27:36: #3 Call peaks for each chromosome... INFO @ Sat, 03 Apr 2021 06:27:42: 9000000 INFO @ Sat, 03 Apr 2021 06:27:48: 10000000 INFO @ Sat, 03 Apr 2021 06:27:48: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX2969573/SRX2969573.10_peaks.xls INFO @ Sat, 03 Apr 2021 06:27:48: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX2969573/SRX2969573.10_peaks.narrowPeak INFO @ Sat, 03 Apr 2021 06:27:48: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX2969573/SRX2969573.10_summits.bed INFO @ Sat, 03 Apr 2021 06:27:48: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (5132 records, 4 fields): 6 millis CompletedMACS2peakCalling INFO @ Sat, 03 Apr 2021 06:27:50: #1 tag size is determined as 51 bps INFO @ Sat, 03 Apr 2021 06:27:50: #1 tag size = 51 INFO @ Sat, 03 Apr 2021 06:27:50: #1 total tags in treatment: 10335126 INFO @ Sat, 03 Apr 2021 06:27:50: #1 user defined the maximum tags... INFO @ Sat, 03 Apr 2021 06:27:50: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 03 Apr 2021 06:27:50: #1 tags after filtering in treatment: 10335126 INFO @ Sat, 03 Apr 2021 06:27:50: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 03 Apr 2021 06:27:50: #1 finished! INFO @ Sat, 03 Apr 2021 06:27:50: #2 Build Peak Model... INFO @ Sat, 03 Apr 2021 06:27:50: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 03 Apr 2021 06:27:50: #2 number of paired peaks: 524 WARNING @ Sat, 03 Apr 2021 06:27:50: Fewer paired peaks (524) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 524 pairs to build model! INFO @ Sat, 03 Apr 2021 06:27:50: start model_add_line... INFO @ Sat, 03 Apr 2021 06:27:50: start X-correlation... INFO @ Sat, 03 Apr 2021 06:27:51: end of X-cor INFO @ Sat, 03 Apr 2021 06:27:51: #2 finished! INFO @ Sat, 03 Apr 2021 06:27:51: #2 predicted fragment length is 68 bps INFO @ Sat, 03 Apr 2021 06:27:51: #2 alternative fragment length(s) may be 68 bps INFO @ Sat, 03 Apr 2021 06:27:51: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX2969573/SRX2969573.20_model.r WARNING @ Sat, 03 Apr 2021 06:27:51: #2 Since the d (68) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 03 Apr 2021 06:27:51: #2 You may need to consider one of the other alternative d(s): 68 WARNING @ Sat, 03 Apr 2021 06:27:51: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sat, 03 Apr 2021 06:27:51: #3 Call peaks... INFO @ Sat, 03 Apr 2021 06:27:51: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Sat, 03 Apr 2021 06:28:13: #3 Call peaks for each chromosome... INFO @ Sat, 03 Apr 2021 06:28:26: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX2969573/SRX2969573.20_peaks.xls INFO @ Sat, 03 Apr 2021 06:28:26: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX2969573/SRX2969573.20_peaks.narrowPeak INFO @ Sat, 03 Apr 2021 06:28:26: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX2969573/SRX2969573.20_summits.bed INFO @ Sat, 03 Apr 2021 06:28:26: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (2354 records, 4 fields): 3 millis CompletedMACS2peakCalling