Job ID = 16436573 SRX = SRX12764410 Genome = dm6 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: 00:08:22 45767373 reads; of these: 45767373 (100.00%) were unpaired; of these: 44698850 (97.67%) aligned 0 times 791866 (1.73%) aligned exactly 1 time 276657 (0.60%) aligned >1 times 2.33% overall alignment rate Time searching: 00:08:22 Overall time: 00:08:22 マッピングが完了しました。 samtools でBAM に変換中... [samopen] SAM header is present: 1870 sequences. [bam_rmdupse_core] 101022 / 1068523 = 0.0945 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/3.8.7/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Tue, 02 Aug 2022 11:51:57: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX12764410/SRX12764410.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX12764410/SRX12764410.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX12764410/SRX12764410.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX12764410/SRX12764410.bam'] # control file = None # effective genome size = 1.20e+08 # 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, 02 Aug 2022 11:51:57: #1 read tag files... INFO @ Tue, 02 Aug 2022 11:51:57: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 11:52:04: #1 tag size is determined as 101 bps INFO @ Tue, 02 Aug 2022 11:52:04: #1 tag size = 101 INFO @ Tue, 02 Aug 2022 11:52:04: #1 total tags in treatment: 967501 INFO @ Tue, 02 Aug 2022 11:52:04: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 11:52:04: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 02 Aug 2022 11:52:04: #1 tags after filtering in treatment: 967059 INFO @ Tue, 02 Aug 2022 11:52:04: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 02 Aug 2022 11:52:04: #1 finished! INFO @ Tue, 02 Aug 2022 11:52:04: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 11:52:04: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 11:52:04: #2 number of paired peaks: 2162 INFO @ Tue, 02 Aug 2022 11:52:04: start model_add_line... INFO @ Tue, 02 Aug 2022 11:52:04: start X-correlation... INFO @ Tue, 02 Aug 2022 11:52:04: end of X-cor INFO @ Tue, 02 Aug 2022 11:52:04: #2 finished! INFO @ Tue, 02 Aug 2022 11:52:04: #2 predicted fragment length is 109 bps INFO @ Tue, 02 Aug 2022 11:52:04: #2 alternative fragment length(s) may be 109 bps INFO @ Tue, 02 Aug 2022 11:52:04: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX12764410/SRX12764410.05_model.r WARNING @ Tue, 02 Aug 2022 11:52:04: #2 Since the d (109) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 02 Aug 2022 11:52:04: #2 You may need to consider one of the other alternative d(s): 109 WARNING @ Tue, 02 Aug 2022 11:52:04: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 02 Aug 2022 11:52:04: #3 Call peaks... INFO @ Tue, 02 Aug 2022 11:52:04: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 02 Aug 2022 11:52:06: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 11:52:08: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX12764410/SRX12764410.05_peaks.xls INFO @ Tue, 02 Aug 2022 11:52:08: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX12764410/SRX12764410.05_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 11:52:08: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX12764410/SRX12764410.05_summits.bed INFO @ Tue, 02 Aug 2022 11:52:08: Done! pass1 - making usageList (123 chroms): 1 millis pass2 - checking and writing primary data (324 records, 4 fields): 77 millis CompletedMACS2peakCalling WARNING: Skipping mount /opt/pkg/singularity/3.8.7/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Tue, 02 Aug 2022 11:52:26: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX12764410/SRX12764410.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX12764410/SRX12764410.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX12764410/SRX12764410.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX12764410/SRX12764410.bam'] # control file = None # effective genome size = 1.20e+08 # 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, 02 Aug 2022 11:52:26: #1 read tag files... INFO @ Tue, 02 Aug 2022 11:52:26: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 11:52:33: #1 tag size is determined as 101 bps INFO @ Tue, 02 Aug 2022 11:52:33: #1 tag size = 101 INFO @ Tue, 02 Aug 2022 11:52:33: #1 total tags in treatment: 967501 INFO @ Tue, 02 Aug 2022 11:52:33: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 11:52:33: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 02 Aug 2022 11:52:33: #1 tags after filtering in treatment: 967059 INFO @ Tue, 02 Aug 2022 11:52:33: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 02 Aug 2022 11:52:33: #1 finished! INFO @ Tue, 02 Aug 2022 11:52:33: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 11:52:33: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 11:52:33: #2 number of paired peaks: 2162 INFO @ Tue, 02 Aug 2022 11:52:33: start model_add_line... INFO @ Tue, 02 Aug 2022 11:52:33: start X-correlation... INFO @ Tue, 02 Aug 2022 11:52:33: end of X-cor INFO @ Tue, 02 Aug 2022 11:52:33: #2 finished! INFO @ Tue, 02 Aug 2022 11:52:33: #2 predicted fragment length is 109 bps INFO @ Tue, 02 Aug 2022 11:52:33: #2 alternative fragment length(s) may be 109 bps INFO @ Tue, 02 Aug 2022 11:52:33: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX12764410/SRX12764410.10_model.r WARNING @ Tue, 02 Aug 2022 11:52:33: #2 Since the d (109) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 02 Aug 2022 11:52:33: #2 You may need to consider one of the other alternative d(s): 109 WARNING @ Tue, 02 Aug 2022 11:52:33: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 02 Aug 2022 11:52:33: #3 Call peaks... INFO @ Tue, 02 Aug 2022 11:52:33: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 02 Aug 2022 11:52:35: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 11:52:36: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX12764410/SRX12764410.10_peaks.xls INFO @ Tue, 02 Aug 2022 11:52:36: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX12764410/SRX12764410.10_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 11:52:36: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX12764410/SRX12764410.10_summits.bed INFO @ Tue, 02 Aug 2022 11:52:37: Done! pass1 - making usageList (75 chroms): 0 millis pass2 - checking and writing primary data (170 records, 4 fields): 37 millis CompletedMACS2peakCalling BedGraph に変換中... WARNING: Skipping mount /opt/pkg/singularity/3.8.7/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Tue, 02 Aug 2022 11:52:56: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX12764410/SRX12764410.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX12764410/SRX12764410.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX12764410/SRX12764410.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX12764410/SRX12764410.bam'] # control file = None # effective genome size = 1.20e+08 # 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, 02 Aug 2022 11:52:56: #1 read tag files... INFO @ Tue, 02 Aug 2022 11:52:56: #1 read treatment tags... BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。 INFO @ Tue, 02 Aug 2022 11:53:03: #1 tag size is determined as 101 bps INFO @ Tue, 02 Aug 2022 11:53:03: #1 tag size = 101 INFO @ Tue, 02 Aug 2022 11:53:03: #1 total tags in treatment: 967501 INFO @ Tue, 02 Aug 2022 11:53:03: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 11:53:03: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 02 Aug 2022 11:53:03: #1 tags after filtering in treatment: 967059 INFO @ Tue, 02 Aug 2022 11:53:03: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 02 Aug 2022 11:53:03: #1 finished! INFO @ Tue, 02 Aug 2022 11:53:03: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 11:53:03: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 11:53:03: #2 number of paired peaks: 2162 INFO @ Tue, 02 Aug 2022 11:53:03: start model_add_line... INFO @ Tue, 02 Aug 2022 11:53:03: start X-correlation... INFO @ Tue, 02 Aug 2022 11:53:03: end of X-cor INFO @ Tue, 02 Aug 2022 11:53:03: #2 finished! INFO @ Tue, 02 Aug 2022 11:53:03: #2 predicted fragment length is 109 bps INFO @ Tue, 02 Aug 2022 11:53:03: #2 alternative fragment length(s) may be 109 bps INFO @ Tue, 02 Aug 2022 11:53:03: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX12764410/SRX12764410.20_model.r WARNING @ Tue, 02 Aug 2022 11:53:03: #2 Since the d (109) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 02 Aug 2022 11:53:03: #2 You may need to consider one of the other alternative d(s): 109 WARNING @ Tue, 02 Aug 2022 11:53:03: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 02 Aug 2022 11:53:03: #3 Call peaks... INFO @ Tue, 02 Aug 2022 11:53:03: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 02 Aug 2022 11:53:06: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 11:53:07: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX12764410/SRX12764410.20_peaks.xls INFO @ Tue, 02 Aug 2022 11:53:07: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX12764410/SRX12764410.20_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 11:53:07: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX12764410/SRX12764410.20_summits.bed INFO @ Tue, 02 Aug 2022 11:53:07: Done! pass1 - making usageList (49 chroms): 1 millis pass2 - checking and writing primary data (86 records, 4 fields): 165 millis CompletedMACS2peakCalling