Job ID = 6626439 SRX = SRX7262197 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: 00:02:08 9157221 reads; of these: 9157221 (100.00%) were unpaired; of these: 350527 (3.83%) aligned 0 times 7147169 (78.05%) aligned exactly 1 time 1659525 (18.12%) aligned >1 times 96.17% overall alignment rate Time searching: 00:02:08 Overall time: 00:02:08 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] 771982 / 8806694 = 0.0877 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, 14 Jul 2020 07:05:44: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX7262197/SRX7262197.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX7262197/SRX7262197.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX7262197/SRX7262197.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX7262197/SRX7262197.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, 14 Jul 2020 07:05:44: #1 read tag files... INFO @ Tue, 14 Jul 2020 07:05:44: #1 read treatment tags... INFO @ Tue, 14 Jul 2020 07:05:49: 1000000 INFO @ Tue, 14 Jul 2020 07:05:54: 2000000 INFO @ Tue, 14 Jul 2020 07:05:58: 3000000 INFO @ Tue, 14 Jul 2020 07:06:03: 4000000 INFO @ Tue, 14 Jul 2020 07:06:08: 5000000 INFO @ Tue, 14 Jul 2020 07:06:12: 6000000 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, 14 Jul 2020 07:06:14: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX7262197/SRX7262197.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX7262197/SRX7262197.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX7262197/SRX7262197.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX7262197/SRX7262197.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, 14 Jul 2020 07:06:14: #1 read tag files... INFO @ Tue, 14 Jul 2020 07:06:14: #1 read treatment tags... INFO @ Tue, 14 Jul 2020 07:06:17: 7000000 INFO @ Tue, 14 Jul 2020 07:06:19: 1000000 INFO @ Tue, 14 Jul 2020 07:06:22: 8000000 INFO @ Tue, 14 Jul 2020 07:06:22: #1 tag size is determined as 50 bps INFO @ Tue, 14 Jul 2020 07:06:22: #1 tag size = 50 INFO @ Tue, 14 Jul 2020 07:06:22: #1 total tags in treatment: 8034712 INFO @ Tue, 14 Jul 2020 07:06:22: #1 user defined the maximum tags... INFO @ Tue, 14 Jul 2020 07:06:22: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 14 Jul 2020 07:06:22: #1 tags after filtering in treatment: 8034712 INFO @ Tue, 14 Jul 2020 07:06:22: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 14 Jul 2020 07:06:22: #1 finished! INFO @ Tue, 14 Jul 2020 07:06:22: #2 Build Peak Model... INFO @ Tue, 14 Jul 2020 07:06:22: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 14 Jul 2020 07:06:23: #2 number of paired peaks: 304 WARNING @ Tue, 14 Jul 2020 07:06:23: Fewer paired peaks (304) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 304 pairs to build model! INFO @ Tue, 14 Jul 2020 07:06:23: start model_add_line... INFO @ Tue, 14 Jul 2020 07:06:23: start X-correlation... INFO @ Tue, 14 Jul 2020 07:06:23: end of X-cor INFO @ Tue, 14 Jul 2020 07:06:23: #2 finished! INFO @ Tue, 14 Jul 2020 07:06:23: #2 predicted fragment length is 46 bps INFO @ Tue, 14 Jul 2020 07:06:23: #2 alternative fragment length(s) may be 3,46 bps INFO @ Tue, 14 Jul 2020 07:06:23: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX7262197/SRX7262197.05_model.r WARNING @ Tue, 14 Jul 2020 07:06:23: #2 Since the d (46) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 14 Jul 2020 07:06:23: #2 You may need to consider one of the other alternative d(s): 3,46 WARNING @ Tue, 14 Jul 2020 07:06:23: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 14 Jul 2020 07:06:23: #3 Call peaks... INFO @ Tue, 14 Jul 2020 07:06:23: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 14 Jul 2020 07:06:24: 2000000 INFO @ Tue, 14 Jul 2020 07:06:29: 3000000 INFO @ Tue, 14 Jul 2020 07:06:34: 4000000 INFO @ Tue, 14 Jul 2020 07:06:39: 5000000 INFO @ Tue, 14 Jul 2020 07:06:39: #3 Call peaks for each chromosome... 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, 14 Jul 2020 07:06:43: 6000000 INFO @ Tue, 14 Jul 2020 07:06:44: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX7262197/SRX7262197.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX7262197/SRX7262197.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX7262197/SRX7262197.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX7262197/SRX7262197.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, 14 Jul 2020 07:06:44: #1 read tag files... INFO @ Tue, 14 Jul 2020 07:06:44: #1 read treatment tags... INFO @ Tue, 14 Jul 2020 07:06:46: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX7262197/SRX7262197.05_peaks.xls INFO @ Tue, 14 Jul 2020 07:06:46: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX7262197/SRX7262197.05_peaks.narrowPeak INFO @ Tue, 14 Jul 2020 07:06:46: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX7262197/SRX7262197.05_summits.bed INFO @ Tue, 14 Jul 2020 07:06:46: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (630 records, 4 fields): 14 millis CompletedMACS2peakCalling INFO @ Tue, 14 Jul 2020 07:06:48: 7000000 INFO @ Tue, 14 Jul 2020 07:06:49: 1000000 INFO @ Tue, 14 Jul 2020 07:06:53: 8000000 INFO @ Tue, 14 Jul 2020 07:06:53: #1 tag size is determined as 50 bps INFO @ Tue, 14 Jul 2020 07:06:53: #1 tag size = 50 INFO @ Tue, 14 Jul 2020 07:06:53: #1 total tags in treatment: 8034712 INFO @ Tue, 14 Jul 2020 07:06:53: #1 user defined the maximum tags... INFO @ Tue, 14 Jul 2020 07:06:53: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 14 Jul 2020 07:06:53: #1 tags after filtering in treatment: 8034712 INFO @ Tue, 14 Jul 2020 07:06:53: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 14 Jul 2020 07:06:53: #1 finished! INFO @ Tue, 14 Jul 2020 07:06:53: #2 Build Peak Model... INFO @ Tue, 14 Jul 2020 07:06:53: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 14 Jul 2020 07:06:54: #2 number of paired peaks: 304 WARNING @ Tue, 14 Jul 2020 07:06:54: Fewer paired peaks (304) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 304 pairs to build model! INFO @ Tue, 14 Jul 2020 07:06:54: start model_add_line... INFO @ Tue, 14 Jul 2020 07:06:54: start X-correlation... INFO @ Tue, 14 Jul 2020 07:06:54: end of X-cor INFO @ Tue, 14 Jul 2020 07:06:54: #2 finished! INFO @ Tue, 14 Jul 2020 07:06:54: #2 predicted fragment length is 46 bps INFO @ Tue, 14 Jul 2020 07:06:54: #2 alternative fragment length(s) may be 3,46 bps INFO @ Tue, 14 Jul 2020 07:06:54: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX7262197/SRX7262197.10_model.r WARNING @ Tue, 14 Jul 2020 07:06:54: #2 Since the d (46) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 14 Jul 2020 07:06:54: #2 You may need to consider one of the other alternative d(s): 3,46 WARNING @ Tue, 14 Jul 2020 07:06:54: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 14 Jul 2020 07:06:54: #3 Call peaks... INFO @ Tue, 14 Jul 2020 07:06:54: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 14 Jul 2020 07:06:54: 2000000 INFO @ Tue, 14 Jul 2020 07:06:59: 3000000 INFO @ Tue, 14 Jul 2020 07:07:04: 4000000 INFO @ Tue, 14 Jul 2020 07:07:09: 5000000 INFO @ Tue, 14 Jul 2020 07:07:10: #3 Call peaks for each chromosome... INFO @ Tue, 14 Jul 2020 07:07:14: 6000000 INFO @ Tue, 14 Jul 2020 07:07:17: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX7262197/SRX7262197.10_peaks.xls INFO @ Tue, 14 Jul 2020 07:07:17: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX7262197/SRX7262197.10_peaks.narrowPeak INFO @ Tue, 14 Jul 2020 07:07:17: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX7262197/SRX7262197.10_summits.bed INFO @ Tue, 14 Jul 2020 07:07:17: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (405 records, 4 fields): 28 millis CompletedMACS2peakCalling INFO @ Tue, 14 Jul 2020 07:07:18: 7000000 INFO @ Tue, 14 Jul 2020 07:07:23: 8000000 INFO @ Tue, 14 Jul 2020 07:07:23: #1 tag size is determined as 50 bps INFO @ Tue, 14 Jul 2020 07:07:23: #1 tag size = 50 INFO @ Tue, 14 Jul 2020 07:07:23: #1 total tags in treatment: 8034712 INFO @ Tue, 14 Jul 2020 07:07:23: #1 user defined the maximum tags... INFO @ Tue, 14 Jul 2020 07:07:23: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 14 Jul 2020 07:07:23: #1 tags after filtering in treatment: 8034712 INFO @ Tue, 14 Jul 2020 07:07:23: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 14 Jul 2020 07:07:23: #1 finished! INFO @ Tue, 14 Jul 2020 07:07:23: #2 Build Peak Model... INFO @ Tue, 14 Jul 2020 07:07:23: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 14 Jul 2020 07:07:24: #2 number of paired peaks: 304 WARNING @ Tue, 14 Jul 2020 07:07:24: Fewer paired peaks (304) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 304 pairs to build model! INFO @ Tue, 14 Jul 2020 07:07:24: start model_add_line... INFO @ Tue, 14 Jul 2020 07:07:24: start X-correlation... INFO @ Tue, 14 Jul 2020 07:07:24: end of X-cor INFO @ Tue, 14 Jul 2020 07:07:24: #2 finished! INFO @ Tue, 14 Jul 2020 07:07:24: #2 predicted fragment length is 46 bps INFO @ Tue, 14 Jul 2020 07:07:24: #2 alternative fragment length(s) may be 3,46 bps INFO @ Tue, 14 Jul 2020 07:07:24: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX7262197/SRX7262197.20_model.r WARNING @ Tue, 14 Jul 2020 07:07:24: #2 Since the d (46) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 14 Jul 2020 07:07:24: #2 You may need to consider one of the other alternative d(s): 3,46 WARNING @ Tue, 14 Jul 2020 07:07:24: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 14 Jul 2020 07:07:24: #3 Call peaks... INFO @ Tue, 14 Jul 2020 07:07:24: #3 Pre-compute pvalue-qvalue table... BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 14 Jul 2020 07:07:40: #3 Call peaks for each chromosome... BigWig に変換しました。 INFO @ Tue, 14 Jul 2020 07:07:47: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX7262197/SRX7262197.20_peaks.xls INFO @ Tue, 14 Jul 2020 07:07:47: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX7262197/SRX7262197.20_peaks.narrowPeak INFO @ Tue, 14 Jul 2020 07:07:47: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX7262197/SRX7262197.20_summits.bed INFO @ Tue, 14 Jul 2020 07:07:47: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (164 records, 4 fields): 13 millis CompletedMACS2peakCalling