Job ID = 16440825 SRX = SRX15369009 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: 00:11:26 16247852 reads; of these: 16247852 (100.00%) were unpaired; of these: 903322 (5.56%) aligned 0 times 10540252 (64.87%) aligned exactly 1 time 4804278 (29.57%) aligned >1 times 94.44% overall alignment rate Time searching: 00:11:26 Overall time: 00:11:26 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_sort_core] merging from 8 files... [bam_rmdupse_core] 13572851 / 15344530 = 0.8845 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 18:13:37: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX15369009/SRX15369009.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX15369009/SRX15369009.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX15369009/SRX15369009.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX15369009/SRX15369009.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 18:13:37: #1 read tag files... INFO @ Tue, 02 Aug 2022 18:13:37: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 18:13:50: 1000000 INFO @ Tue, 02 Aug 2022 18:14:00: #1 tag size is determined as 74 bps INFO @ Tue, 02 Aug 2022 18:14:00: #1 tag size = 74 INFO @ Tue, 02 Aug 2022 18:14:00: #1 total tags in treatment: 1771679 INFO @ Tue, 02 Aug 2022 18:14:00: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 18:14:00: #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 18:14:00: #1 tags after filtering in treatment: 1771488 INFO @ Tue, 02 Aug 2022 18:14:00: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 02 Aug 2022 18:14:00: #1 finished! INFO @ Tue, 02 Aug 2022 18:14:00: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 18:14:00: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 18:14:01: #2 number of paired peaks: 5007 INFO @ Tue, 02 Aug 2022 18:14:01: start model_add_line... INFO @ Tue, 02 Aug 2022 18:14:01: start X-correlation... INFO @ Tue, 02 Aug 2022 18:14:01: end of X-cor INFO @ Tue, 02 Aug 2022 18:14:01: #2 finished! INFO @ Tue, 02 Aug 2022 18:14:01: #2 predicted fragment length is 112 bps INFO @ Tue, 02 Aug 2022 18:14:01: #2 alternative fragment length(s) may be 112 bps INFO @ Tue, 02 Aug 2022 18:14:01: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX15369009/SRX15369009.05_model.r WARNING @ Tue, 02 Aug 2022 18:14:01: #2 Since the d (112) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 02 Aug 2022 18:14:01: #2 You may need to consider one of the other alternative d(s): 112 WARNING @ Tue, 02 Aug 2022 18:14:01: #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 18:14:01: #3 Call peaks... INFO @ Tue, 02 Aug 2022 18:14:01: #3 Pre-compute pvalue-qvalue table... 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 18:14:06: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX15369009/SRX15369009.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX15369009/SRX15369009.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX15369009/SRX15369009.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX15369009/SRX15369009.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 18:14:06: #1 read tag files... INFO @ Tue, 02 Aug 2022 18:14:06: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 18:14:08: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 18:14:11: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX15369009/SRX15369009.05_peaks.xls INFO @ Tue, 02 Aug 2022 18:14:11: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX15369009/SRX15369009.05_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 18:14:11: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX15369009/SRX15369009.05_summits.bed INFO @ Tue, 02 Aug 2022 18:14:11: Done! pass1 - making usageList (640 chroms): 2 millis pass2 - checking and writing primary data (1944 records, 4 fields): 49 millis CompletedMACS2peakCalling INFO @ Tue, 02 Aug 2022 18:14:16: 1000000 INFO @ Tue, 02 Aug 2022 18:14:24: #1 tag size is determined as 74 bps INFO @ Tue, 02 Aug 2022 18:14:24: #1 tag size = 74 INFO @ Tue, 02 Aug 2022 18:14:24: #1 total tags in treatment: 1771679 INFO @ Tue, 02 Aug 2022 18:14:24: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 18:14:24: #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 18:14:25: #1 tags after filtering in treatment: 1771488 INFO @ Tue, 02 Aug 2022 18:14:25: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 02 Aug 2022 18:14:25: #1 finished! INFO @ Tue, 02 Aug 2022 18:14:25: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 18:14:25: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 18:14:25: #2 number of paired peaks: 5007 INFO @ Tue, 02 Aug 2022 18:14:25: start model_add_line... INFO @ Tue, 02 Aug 2022 18:14:25: start X-correlation... INFO @ Tue, 02 Aug 2022 18:14:25: end of X-cor INFO @ Tue, 02 Aug 2022 18:14:25: #2 finished! INFO @ Tue, 02 Aug 2022 18:14:25: #2 predicted fragment length is 112 bps INFO @ Tue, 02 Aug 2022 18:14:25: #2 alternative fragment length(s) may be 112 bps INFO @ Tue, 02 Aug 2022 18:14:25: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX15369009/SRX15369009.10_model.r WARNING @ Tue, 02 Aug 2022 18:14:25: #2 Since the d (112) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 02 Aug 2022 18:14:25: #2 You may need to consider one of the other alternative d(s): 112 WARNING @ Tue, 02 Aug 2022 18:14:25: #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 18:14:25: #3 Call peaks... INFO @ Tue, 02 Aug 2022 18:14:25: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 02 Aug 2022 18:14:32: #3 Call peaks for each chromosome... 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 18:14:35: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX15369009/SRX15369009.10_peaks.xls INFO @ Tue, 02 Aug 2022 18:14:35: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX15369009/SRX15369009.10_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 18:14:35: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX15369009/SRX15369009.10_summits.bed INFO @ Tue, 02 Aug 2022 18:14:35: Done! INFO @ Tue, 02 Aug 2022 18:14:36: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX15369009/SRX15369009.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX15369009/SRX15369009.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX15369009/SRX15369009.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX15369009/SRX15369009.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 18:14:36: #1 read tag files... INFO @ Tue, 02 Aug 2022 18:14:36: #1 read treatment tags... pass1 - making usageList (501 chroms): 4 millis pass2 - checking and writing primary data (1257 records, 4 fields): 63 millis CompletedMACS2peakCalling INFO @ Tue, 02 Aug 2022 18:14:46: 1000000 INFO @ Tue, 02 Aug 2022 18:14:55: #1 tag size is determined as 74 bps INFO @ Tue, 02 Aug 2022 18:14:55: #1 tag size = 74 INFO @ Tue, 02 Aug 2022 18:14:55: #1 total tags in treatment: 1771679 INFO @ Tue, 02 Aug 2022 18:14:55: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 18:14:55: #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 18:14:55: #1 tags after filtering in treatment: 1771488 INFO @ Tue, 02 Aug 2022 18:14:55: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 02 Aug 2022 18:14:55: #1 finished! INFO @ Tue, 02 Aug 2022 18:14:55: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 18:14:55: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 18:14:55: #2 number of paired peaks: 5007 INFO @ Tue, 02 Aug 2022 18:14:55: start model_add_line... INFO @ Tue, 02 Aug 2022 18:14:55: start X-correlation... INFO @ Tue, 02 Aug 2022 18:14:55: end of X-cor INFO @ Tue, 02 Aug 2022 18:14:55: #2 finished! INFO @ Tue, 02 Aug 2022 18:14:55: #2 predicted fragment length is 112 bps INFO @ Tue, 02 Aug 2022 18:14:55: #2 alternative fragment length(s) may be 112 bps INFO @ Tue, 02 Aug 2022 18:14:55: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX15369009/SRX15369009.20_model.r WARNING @ Tue, 02 Aug 2022 18:14:55: #2 Since the d (112) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 02 Aug 2022 18:14:55: #2 You may need to consider one of the other alternative d(s): 112 WARNING @ Tue, 02 Aug 2022 18:14:55: #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 18:14:55: #3 Call peaks... INFO @ Tue, 02 Aug 2022 18:14:55: #3 Pre-compute pvalue-qvalue table... BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 02 Aug 2022 18:15:02: #3 Call peaks for each chromosome... BigWig に変換しました。 INFO @ Tue, 02 Aug 2022 18:15:05: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX15369009/SRX15369009.20_peaks.xls INFO @ Tue, 02 Aug 2022 18:15:05: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX15369009/SRX15369009.20_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 18:15:05: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX15369009/SRX15369009.20_summits.bed INFO @ Tue, 02 Aug 2022 18:15:05: Done! pass1 - making usageList (423 chroms): 2 millis pass2 - checking and writing primary data (938 records, 4 fields): 54 millis CompletedMACS2peakCalling