Job ID = 6626393 SRX = SRX7262201 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: 00:00:41 3444666 reads; of these: 3444666 (100.00%) were unpaired; of these: 147319 (4.28%) aligned 0 times 2410176 (69.97%) aligned exactly 1 time 887171 (25.75%) aligned >1 times 95.72% overall alignment rate Time searching: 00:00:41 Overall time: 00:00:41 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] 283827 / 3297347 = 0.0861 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 06:59:14: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX7262201/SRX7262201.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX7262201/SRX7262201.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX7262201/SRX7262201.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX7262201/SRX7262201.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 06:59:14: #1 read tag files... INFO @ Tue, 14 Jul 2020 06:59:14: #1 read treatment tags... INFO @ Tue, 14 Jul 2020 06:59:23: 1000000 INFO @ Tue, 14 Jul 2020 06:59:31: 2000000 INFO @ Tue, 14 Jul 2020 06:59:38: 3000000 INFO @ Tue, 14 Jul 2020 06:59:38: #1 tag size is determined as 50 bps INFO @ Tue, 14 Jul 2020 06:59:38: #1 tag size = 50 INFO @ Tue, 14 Jul 2020 06:59:38: #1 total tags in treatment: 3013520 INFO @ Tue, 14 Jul 2020 06:59:38: #1 user defined the maximum tags... INFO @ Tue, 14 Jul 2020 06:59:38: #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 06:59:38: #1 tags after filtering in treatment: 3013520 INFO @ Tue, 14 Jul 2020 06:59:38: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 14 Jul 2020 06:59:38: #1 finished! INFO @ Tue, 14 Jul 2020 06:59:38: #2 Build Peak Model... INFO @ Tue, 14 Jul 2020 06:59:38: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 14 Jul 2020 06:59:38: #2 number of paired peaks: 1636 INFO @ Tue, 14 Jul 2020 06:59:38: start model_add_line... INFO @ Tue, 14 Jul 2020 06:59:38: start X-correlation... INFO @ Tue, 14 Jul 2020 06:59:38: end of X-cor INFO @ Tue, 14 Jul 2020 06:59:38: #2 finished! INFO @ Tue, 14 Jul 2020 06:59:38: #2 predicted fragment length is 58 bps INFO @ Tue, 14 Jul 2020 06:59:38: #2 alternative fragment length(s) may be 4,58,564,590 bps INFO @ Tue, 14 Jul 2020 06:59:38: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX7262201/SRX7262201.05_model.r WARNING @ Tue, 14 Jul 2020 06:59:38: #2 Since the d (58) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 14 Jul 2020 06:59:38: #2 You may need to consider one of the other alternative d(s): 4,58,564,590 WARNING @ Tue, 14 Jul 2020 06:59:38: #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 06:59:38: #3 Call peaks... INFO @ Tue, 14 Jul 2020 06:59:38: #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, 14 Jul 2020 06:59:44: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX7262201/SRX7262201.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX7262201/SRX7262201.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX7262201/SRX7262201.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX7262201/SRX7262201.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 06:59:44: #1 read tag files... INFO @ Tue, 14 Jul 2020 06:59:44: #1 read treatment tags... INFO @ Tue, 14 Jul 2020 06:59:45: #3 Call peaks for each chromosome... INFO @ Tue, 14 Jul 2020 06:59:48: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX7262201/SRX7262201.05_peaks.xls INFO @ Tue, 14 Jul 2020 06:59:48: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX7262201/SRX7262201.05_peaks.narrowPeak INFO @ Tue, 14 Jul 2020 06:59:48: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX7262201/SRX7262201.05_summits.bed INFO @ Tue, 14 Jul 2020 06:59:48: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (462 records, 4 fields): 21 millis CompletedMACS2peakCalling INFO @ Tue, 14 Jul 2020 06:59:53: 1000000 INFO @ Tue, 14 Jul 2020 07:00:02: 2000000 INFO @ Tue, 14 Jul 2020 07:00:10: 3000000 INFO @ Tue, 14 Jul 2020 07:00:10: #1 tag size is determined as 50 bps INFO @ Tue, 14 Jul 2020 07:00:10: #1 tag size = 50 INFO @ Tue, 14 Jul 2020 07:00:10: #1 total tags in treatment: 3013520 INFO @ Tue, 14 Jul 2020 07:00:10: #1 user defined the maximum tags... INFO @ Tue, 14 Jul 2020 07:00:10: #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 07:00:10: #1 tags after filtering in treatment: 3013520 INFO @ Tue, 14 Jul 2020 07:00:10: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 14 Jul 2020 07:00:10: #1 finished! INFO @ Tue, 14 Jul 2020 07:00:10: #2 Build Peak Model... INFO @ Tue, 14 Jul 2020 07:00:10: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 14 Jul 2020 07:00:10: #2 number of paired peaks: 1636 INFO @ Tue, 14 Jul 2020 07:00:10: start model_add_line... INFO @ Tue, 14 Jul 2020 07:00:10: start X-correlation... INFO @ Tue, 14 Jul 2020 07:00:10: end of X-cor INFO @ Tue, 14 Jul 2020 07:00:10: #2 finished! INFO @ Tue, 14 Jul 2020 07:00:10: #2 predicted fragment length is 58 bps INFO @ Tue, 14 Jul 2020 07:00:10: #2 alternative fragment length(s) may be 4,58,564,590 bps INFO @ Tue, 14 Jul 2020 07:00:10: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX7262201/SRX7262201.10_model.r WARNING @ Tue, 14 Jul 2020 07:00:10: #2 Since the d (58) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 14 Jul 2020 07:00:10: #2 You may need to consider one of the other alternative d(s): 4,58,564,590 WARNING @ Tue, 14 Jul 2020 07:00:10: #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 07:00:10: #3 Call peaks... INFO @ Tue, 14 Jul 2020 07:00:10: #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, 14 Jul 2020 07:00:14: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX7262201/SRX7262201.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX7262201/SRX7262201.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX7262201/SRX7262201.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX7262201/SRX7262201.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 07:00:14: #1 read tag files... INFO @ Tue, 14 Jul 2020 07:00:14: #1 read treatment tags... INFO @ Tue, 14 Jul 2020 07:00:18: #3 Call peaks for each chromosome... INFO @ Tue, 14 Jul 2020 07:00:21: 1000000 INFO @ Tue, 14 Jul 2020 07:00:21: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX7262201/SRX7262201.10_peaks.xls INFO @ Tue, 14 Jul 2020 07:00:21: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX7262201/SRX7262201.10_peaks.narrowPeak INFO @ Tue, 14 Jul 2020 07:00:22: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX7262201/SRX7262201.10_summits.bed INFO @ Tue, 14 Jul 2020 07:00:22: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (274 records, 4 fields): 19 millis CompletedMACS2peakCalling INFO @ Tue, 14 Jul 2020 07:00:27: 2000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 14 Jul 2020 07:00:33: 3000000 INFO @ Tue, 14 Jul 2020 07:00:33: #1 tag size is determined as 50 bps INFO @ Tue, 14 Jul 2020 07:00:33: #1 tag size = 50 INFO @ Tue, 14 Jul 2020 07:00:33: #1 total tags in treatment: 3013520 INFO @ Tue, 14 Jul 2020 07:00:33: #1 user defined the maximum tags... INFO @ Tue, 14 Jul 2020 07:00:33: #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 07:00:33: #1 tags after filtering in treatment: 3013520 INFO @ Tue, 14 Jul 2020 07:00:33: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 14 Jul 2020 07:00:33: #1 finished! INFO @ Tue, 14 Jul 2020 07:00:33: #2 Build Peak Model... INFO @ Tue, 14 Jul 2020 07:00:33: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 14 Jul 2020 07:00:34: #2 number of paired peaks: 1636 INFO @ Tue, 14 Jul 2020 07:00:34: start model_add_line... INFO @ Tue, 14 Jul 2020 07:00:34: start X-correlation... INFO @ Tue, 14 Jul 2020 07:00:34: end of X-cor INFO @ Tue, 14 Jul 2020 07:00:34: #2 finished! INFO @ Tue, 14 Jul 2020 07:00:34: #2 predicted fragment length is 58 bps INFO @ Tue, 14 Jul 2020 07:00:34: #2 alternative fragment length(s) may be 4,58,564,590 bps INFO @ Tue, 14 Jul 2020 07:00:34: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX7262201/SRX7262201.20_model.r WARNING @ Tue, 14 Jul 2020 07:00:34: #2 Since the d (58) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 14 Jul 2020 07:00:34: #2 You may need to consider one of the other alternative d(s): 4,58,564,590 WARNING @ Tue, 14 Jul 2020 07:00:34: #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 07:00:34: #3 Call peaks... INFO @ Tue, 14 Jul 2020 07:00:34: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Tue, 14 Jul 2020 07:00:40: #3 Call peaks for each chromosome... INFO @ Tue, 14 Jul 2020 07:00:43: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX7262201/SRX7262201.20_peaks.xls INFO @ Tue, 14 Jul 2020 07:00:43: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX7262201/SRX7262201.20_peaks.narrowPeak INFO @ Tue, 14 Jul 2020 07:00:43: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX7262201/SRX7262201.20_summits.bed INFO @ Tue, 14 Jul 2020 07:00:43: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (111 records, 4 fields): 20 millis CompletedMACS2peakCalling