Job ID = 16437563 SRX = SRX12764396 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: 00:00:01 Time loading forward index: 00:00:00 Time loading mirror index: 00:00:00 Multiseed full-index search: 00:05:20 41487088 reads; of these: 41487088 (100.00%) were unpaired; of these: 40205602 (96.91%) aligned 0 times 821266 (1.98%) aligned exactly 1 time 460220 (1.11%) aligned >1 times 3.09% overall alignment rate Time searching: 00:05:21 Overall time: 00:05:21 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] 285176 / 1281486 = 0.2225 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 12:50:02: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX12764396/SRX12764396.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX12764396/SRX12764396.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX12764396/SRX12764396.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX12764396/SRX12764396.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 12:50:02: #1 read tag files... INFO @ Tue, 02 Aug 2022 12:50:02: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 12:50:10: #1 tag size is determined as 51 bps INFO @ Tue, 02 Aug 2022 12:50:10: #1 tag size = 51 INFO @ Tue, 02 Aug 2022 12:50:10: #1 total tags in treatment: 996310 INFO @ Tue, 02 Aug 2022 12:50:10: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 12:50:10: #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 12:50:10: #1 tags after filtering in treatment: 995934 INFO @ Tue, 02 Aug 2022 12:50:10: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 02 Aug 2022 12:50:10: #1 finished! INFO @ Tue, 02 Aug 2022 12:50:10: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 12:50:10: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 12:50:11: #2 number of paired peaks: 2476 INFO @ Tue, 02 Aug 2022 12:50:11: start model_add_line... INFO @ Tue, 02 Aug 2022 12:50:11: start X-correlation... INFO @ Tue, 02 Aug 2022 12:50:11: end of X-cor INFO @ Tue, 02 Aug 2022 12:50:11: #2 finished! INFO @ Tue, 02 Aug 2022 12:50:11: #2 predicted fragment length is 51 bps INFO @ Tue, 02 Aug 2022 12:50:11: #2 alternative fragment length(s) may be 51,160,216,274,388,497,573 bps INFO @ Tue, 02 Aug 2022 12:50:11: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX12764396/SRX12764396.05_model.r WARNING @ Tue, 02 Aug 2022 12:50:11: #2 Since the d (51) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 02 Aug 2022 12:50:11: #2 You may need to consider one of the other alternative d(s): 51,160,216,274,388,497,573 WARNING @ Tue, 02 Aug 2022 12:50:11: #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 12:50:11: #3 Call peaks... INFO @ Tue, 02 Aug 2022 12:50:11: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 02 Aug 2022 12:50:13: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 12:50:15: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX12764396/SRX12764396.05_peaks.xls INFO @ Tue, 02 Aug 2022 12:50:15: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX12764396/SRX12764396.05_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 12:50:15: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX12764396/SRX12764396.05_summits.bed INFO @ Tue, 02 Aug 2022 12:50:15: Done! pass1 - making usageList (170 chroms): 1 millis pass2 - checking and writing primary data (659 records, 4 fields): 64 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 12:50:32: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX12764396/SRX12764396.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX12764396/SRX12764396.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX12764396/SRX12764396.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX12764396/SRX12764396.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 12:50:32: #1 read tag files... INFO @ Tue, 02 Aug 2022 12:50:32: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 12:50:38: #1 tag size is determined as 51 bps INFO @ Tue, 02 Aug 2022 12:50:38: #1 tag size = 51 INFO @ Tue, 02 Aug 2022 12:50:38: #1 total tags in treatment: 996310 INFO @ Tue, 02 Aug 2022 12:50:38: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 12:50:38: #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 12:50:39: #1 tags after filtering in treatment: 995934 INFO @ Tue, 02 Aug 2022 12:50:39: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 02 Aug 2022 12:50:39: #1 finished! INFO @ Tue, 02 Aug 2022 12:50:39: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 12:50:39: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 12:50:39: #2 number of paired peaks: 2476 INFO @ Tue, 02 Aug 2022 12:50:39: start model_add_line... INFO @ Tue, 02 Aug 2022 12:50:39: start X-correlation... INFO @ Tue, 02 Aug 2022 12:50:39: end of X-cor INFO @ Tue, 02 Aug 2022 12:50:39: #2 finished! INFO @ Tue, 02 Aug 2022 12:50:39: #2 predicted fragment length is 51 bps INFO @ Tue, 02 Aug 2022 12:50:39: #2 alternative fragment length(s) may be 51,160,216,274,388,497,573 bps INFO @ Tue, 02 Aug 2022 12:50:39: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX12764396/SRX12764396.10_model.r WARNING @ Tue, 02 Aug 2022 12:50:39: #2 Since the d (51) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 02 Aug 2022 12:50:39: #2 You may need to consider one of the other alternative d(s): 51,160,216,274,388,497,573 WARNING @ Tue, 02 Aug 2022 12:50:39: #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 12:50:39: #3 Call peaks... INFO @ Tue, 02 Aug 2022 12:50:39: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 02 Aug 2022 12:50:42: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 12:50:43: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX12764396/SRX12764396.10_peaks.xls INFO @ Tue, 02 Aug 2022 12:50:43: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX12764396/SRX12764396.10_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 12:50:43: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX12764396/SRX12764396.10_summits.bed INFO @ Tue, 02 Aug 2022 12:50:43: Done! pass1 - making usageList (56 chroms): 1 millis pass2 - checking and writing primary data (321 records, 4 fields): 75 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 12:51:02: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX12764396/SRX12764396.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX12764396/SRX12764396.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX12764396/SRX12764396.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX12764396/SRX12764396.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 12:51:02: #1 read tag files... INFO @ Tue, 02 Aug 2022 12:51:02: #1 read treatment tags... BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 02 Aug 2022 12:51:10: #1 tag size is determined as 51 bps INFO @ Tue, 02 Aug 2022 12:51:10: #1 tag size = 51 INFO @ Tue, 02 Aug 2022 12:51:10: #1 total tags in treatment: 996310 INFO @ Tue, 02 Aug 2022 12:51:10: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 12:51:10: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) BigWig に変換しました。 INFO @ Tue, 02 Aug 2022 12:51:10: #1 tags after filtering in treatment: 995934 INFO @ Tue, 02 Aug 2022 12:51:10: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 02 Aug 2022 12:51:10: #1 finished! INFO @ Tue, 02 Aug 2022 12:51:10: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 12:51:10: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 12:51:10: #2 number of paired peaks: 2476 INFO @ Tue, 02 Aug 2022 12:51:10: start model_add_line... INFO @ Tue, 02 Aug 2022 12:51:10: start X-correlation... INFO @ Tue, 02 Aug 2022 12:51:11: end of X-cor INFO @ Tue, 02 Aug 2022 12:51:11: #2 finished! INFO @ Tue, 02 Aug 2022 12:51:11: #2 predicted fragment length is 51 bps INFO @ Tue, 02 Aug 2022 12:51:11: #2 alternative fragment length(s) may be 51,160,216,274,388,497,573 bps INFO @ Tue, 02 Aug 2022 12:51:11: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX12764396/SRX12764396.20_model.r WARNING @ Tue, 02 Aug 2022 12:51:11: #2 Since the d (51) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 02 Aug 2022 12:51:11: #2 You may need to consider one of the other alternative d(s): 51,160,216,274,388,497,573 WARNING @ Tue, 02 Aug 2022 12:51:11: #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 12:51:11: #3 Call peaks... INFO @ Tue, 02 Aug 2022 12:51:11: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 02 Aug 2022 12:51:13: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 12:51:15: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX12764396/SRX12764396.20_peaks.xls INFO @ Tue, 02 Aug 2022 12:51:15: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX12764396/SRX12764396.20_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 12:51:15: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX12764396/SRX12764396.20_summits.bed INFO @ Tue, 02 Aug 2022 12:51:15: Done! pass1 - making usageList (24 chroms): 3 millis pass2 - checking and writing primary data (162 records, 4 fields): 31 millis CompletedMACS2peakCalling