Job ID = 6626500 SRX = SRX7262212 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: 00:03:08 14003105 reads; of these: 14003105 (100.00%) were unpaired; of these: 1805137 (12.89%) aligned 0 times 9058063 (64.69%) aligned exactly 1 time 3139905 (22.42%) aligned >1 times 87.11% overall alignment rate Time searching: 00:03:08 Overall time: 00:03:08 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_sort_core] merging from 8 files... [bam_rmdupse_core] 9714837 / 12197968 = 0.7964 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 07:14:33: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX7262212/SRX7262212.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX7262212/SRX7262212.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX7262212/SRX7262212.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX7262212/SRX7262212.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 07:14:33: #1 read tag files... INFO @ Tue, 14 Jul 2020 07:14:33: #1 read treatment tags... INFO @ Tue, 14 Jul 2020 07:14:39: 1000000 INFO @ Tue, 14 Jul 2020 07:14:46: 2000000 INFO @ Tue, 14 Jul 2020 07:14:49: #1 tag size is determined as 50 bps INFO @ Tue, 14 Jul 2020 07:14:49: #1 tag size = 50 INFO @ Tue, 14 Jul 2020 07:14:49: #1 total tags in treatment: 2483131 INFO @ Tue, 14 Jul 2020 07:14:49: #1 user defined the maximum tags... INFO @ Tue, 14 Jul 2020 07:14:49: #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 07:14:49: #1 tags after filtering in treatment: 2483131 INFO @ Tue, 14 Jul 2020 07:14:49: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 14 Jul 2020 07:14:49: #1 finished! INFO @ Tue, 14 Jul 2020 07:14:49: #2 Build Peak Model... INFO @ Tue, 14 Jul 2020 07:14:49: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 14 Jul 2020 07:14:50: #2 number of paired peaks: 2077 INFO @ Tue, 14 Jul 2020 07:14:50: start model_add_line... INFO @ Tue, 14 Jul 2020 07:14:50: start X-correlation... INFO @ Tue, 14 Jul 2020 07:14:50: end of X-cor INFO @ Tue, 14 Jul 2020 07:14:50: #2 finished! INFO @ Tue, 14 Jul 2020 07:14:50: #2 predicted fragment length is 54 bps INFO @ Tue, 14 Jul 2020 07:14:50: #2 alternative fragment length(s) may be 4,54 bps INFO @ Tue, 14 Jul 2020 07:14:50: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX7262212/SRX7262212.05_model.r WARNING @ Tue, 14 Jul 2020 07:14:50: #2 Since the d (54) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 14 Jul 2020 07:14:50: #2 You may need to consider one of the other alternative d(s): 4,54 WARNING @ Tue, 14 Jul 2020 07:14:50: #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 07:14:50: #3 Call peaks... INFO @ Tue, 14 Jul 2020 07:14:50: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 14 Jul 2020 07:14:56: #3 Call peaks for each chromosome... INFO @ Tue, 14 Jul 2020 07:14:59: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX7262212/SRX7262212.05_peaks.xls INFO @ Tue, 14 Jul 2020 07:14:59: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX7262212/SRX7262212.05_peaks.narrowPeak INFO @ Tue, 14 Jul 2020 07:14:59: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX7262212/SRX7262212.05_summits.bed INFO @ Tue, 14 Jul 2020 07:14:59: Done! 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 pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (1256 records, 4 fields): 27 millis CompletedMACS2peakCalling INFO @ Tue, 14 Jul 2020 07:15:08: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX7262212/SRX7262212.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX7262212/SRX7262212.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX7262212/SRX7262212.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX7262212/SRX7262212.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 07:15:08: #1 read tag files... INFO @ Tue, 14 Jul 2020 07:15:08: #1 read treatment tags... INFO @ Tue, 14 Jul 2020 07:15:15: 1000000 INFO @ Tue, 14 Jul 2020 07:15:21: 2000000 INFO @ Tue, 14 Jul 2020 07:15:24: #1 tag size is determined as 50 bps INFO @ Tue, 14 Jul 2020 07:15:24: #1 tag size = 50 INFO @ Tue, 14 Jul 2020 07:15:24: #1 total tags in treatment: 2483131 INFO @ Tue, 14 Jul 2020 07:15:24: #1 user defined the maximum tags... INFO @ Tue, 14 Jul 2020 07:15:24: #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 07:15:24: #1 tags after filtering in treatment: 2483131 INFO @ Tue, 14 Jul 2020 07:15:24: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 14 Jul 2020 07:15:24: #1 finished! INFO @ Tue, 14 Jul 2020 07:15:24: #2 Build Peak Model... INFO @ Tue, 14 Jul 2020 07:15:24: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 14 Jul 2020 07:15:24: #2 number of paired peaks: 2077 INFO @ Tue, 14 Jul 2020 07:15:24: start model_add_line... INFO @ Tue, 14 Jul 2020 07:15:24: start X-correlation... INFO @ Tue, 14 Jul 2020 07:15:24: end of X-cor INFO @ Tue, 14 Jul 2020 07:15:24: #2 finished! INFO @ Tue, 14 Jul 2020 07:15:24: #2 predicted fragment length is 54 bps INFO @ Tue, 14 Jul 2020 07:15:24: #2 alternative fragment length(s) may be 4,54 bps INFO @ Tue, 14 Jul 2020 07:15:24: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX7262212/SRX7262212.10_model.r WARNING @ Tue, 14 Jul 2020 07:15:24: #2 Since the d (54) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 14 Jul 2020 07:15:24: #2 You may need to consider one of the other alternative d(s): 4,54 WARNING @ Tue, 14 Jul 2020 07:15:24: #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 07:15:24: #3 Call peaks... INFO @ Tue, 14 Jul 2020 07:15:24: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 14 Jul 2020 07:15:30: #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 07:15:33: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX7262212/SRX7262212.10_peaks.xls INFO @ Tue, 14 Jul 2020 07:15:33: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX7262212/SRX7262212.10_peaks.narrowPeak INFO @ Tue, 14 Jul 2020 07:15:33: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX7262212/SRX7262212.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX7262212/SRX7262212.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX7262212/SRX7262212.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX7262212/SRX7262212.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 07:15:33: #1 read tag files... INFO @ Tue, 14 Jul 2020 07:15:33: #1 read treatment tags... INFO @ Tue, 14 Jul 2020 07:15:33: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX7262212/SRX7262212.10_summits.bed INFO @ Tue, 14 Jul 2020 07:15:33: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (610 records, 4 fields): 20 millis CompletedMACS2peakCalling INFO @ Tue, 14 Jul 2020 07:15:38: 1000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 14 Jul 2020 07:15:43: 2000000 INFO @ Tue, 14 Jul 2020 07:15:46: #1 tag size is determined as 50 bps INFO @ Tue, 14 Jul 2020 07:15:46: #1 tag size = 50 INFO @ Tue, 14 Jul 2020 07:15:46: #1 total tags in treatment: 2483131 INFO @ Tue, 14 Jul 2020 07:15:46: #1 user defined the maximum tags... INFO @ Tue, 14 Jul 2020 07:15:46: #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 07:15:46: #1 tags after filtering in treatment: 2483131 INFO @ Tue, 14 Jul 2020 07:15:46: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 14 Jul 2020 07:15:46: #1 finished! INFO @ Tue, 14 Jul 2020 07:15:46: #2 Build Peak Model... INFO @ Tue, 14 Jul 2020 07:15:46: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 14 Jul 2020 07:15:46: #2 number of paired peaks: 2077 INFO @ Tue, 14 Jul 2020 07:15:46: start model_add_line... INFO @ Tue, 14 Jul 2020 07:15:46: start X-correlation... INFO @ Tue, 14 Jul 2020 07:15:46: end of X-cor INFO @ Tue, 14 Jul 2020 07:15:46: #2 finished! INFO @ Tue, 14 Jul 2020 07:15:46: #2 predicted fragment length is 54 bps INFO @ Tue, 14 Jul 2020 07:15:46: #2 alternative fragment length(s) may be 4,54 bps INFO @ Tue, 14 Jul 2020 07:15:46: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX7262212/SRX7262212.20_model.r WARNING @ Tue, 14 Jul 2020 07:15:46: #2 Since the d (54) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 14 Jul 2020 07:15:46: #2 You may need to consider one of the other alternative d(s): 4,54 WARNING @ Tue, 14 Jul 2020 07:15:46: #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 07:15:46: #3 Call peaks... INFO @ Tue, 14 Jul 2020 07:15:46: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Tue, 14 Jul 2020 07:15:52: #3 Call peaks for each chromosome... INFO @ Tue, 14 Jul 2020 07:15:55: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX7262212/SRX7262212.20_peaks.xls INFO @ Tue, 14 Jul 2020 07:15:55: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX7262212/SRX7262212.20_peaks.narrowPeak INFO @ Tue, 14 Jul 2020 07:15:55: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX7262212/SRX7262212.20_summits.bed INFO @ Tue, 14 Jul 2020 07:15:55: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (266 records, 4 fields): 26 millis CompletedMACS2peakCalling