Job ID = 16437427 SRX = SRX12764391 Genome = dm3 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... Read 23538655 spots for SRR16562267/SRR16562267.sra Written 23538655 spots for SRR16562267/SRR16562267.sra fastq に変換しました。 bowtie でマッピング中... Your job 16437458 ("srTdm6") has been submitted Time loading reference: 00:00:01 Time loading forward index: 00:00:00 Time loading mirror index: 00:00:00 Multiseed full-index search: 00:02:40 23538655 reads; of these: 23538655 (100.00%) were unpaired; of these: 22142073 (94.07%) aligned 0 times 975725 (4.15%) aligned exactly 1 time 420857 (1.79%) aligned >1 times 5.93% overall alignment rate Time searching: 00:02:41 Overall time: 00:02:41 マッピングが完了しました。 samtools でBAM に変換中... [samopen] SAM header is present: 15 sequences. [bam_rmdupse_core] 123683 / 1396582 = 0.0886 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 12:32:11: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX12764391/SRX12764391.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX12764391/SRX12764391.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX12764391/SRX12764391.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX12764391/SRX12764391.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 12:32:11: #1 read tag files... INFO @ Tue, 02 Aug 2022 12:32:11: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 12:32:17: 1000000 INFO @ Tue, 02 Aug 2022 12:32:19: #1 tag size is determined as 50 bps INFO @ Tue, 02 Aug 2022 12:32:19: #1 tag size = 50 INFO @ Tue, 02 Aug 2022 12:32:19: #1 total tags in treatment: 1272899 INFO @ Tue, 02 Aug 2022 12:32:19: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 12:32:19: #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 12:32:19: #1 tags after filtering in treatment: 1272899 INFO @ Tue, 02 Aug 2022 12:32:19: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 02 Aug 2022 12:32:19: #1 finished! INFO @ Tue, 02 Aug 2022 12:32:19: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 12:32:19: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 12:32:19: #2 number of paired peaks: 1015 INFO @ Tue, 02 Aug 2022 12:32:19: start model_add_line... INFO @ Tue, 02 Aug 2022 12:32:19: start X-correlation... INFO @ Tue, 02 Aug 2022 12:32:19: end of X-cor INFO @ Tue, 02 Aug 2022 12:32:19: #2 finished! INFO @ Tue, 02 Aug 2022 12:32:19: #2 predicted fragment length is 50 bps INFO @ Tue, 02 Aug 2022 12:32:19: #2 alternative fragment length(s) may be 50,476,574 bps INFO @ Tue, 02 Aug 2022 12:32:19: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX12764391/SRX12764391.05_model.r WARNING @ Tue, 02 Aug 2022 12:32:19: #2 Since the d (50) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 02 Aug 2022 12:32:19: #2 You may need to consider one of the other alternative d(s): 50,476,574 WARNING @ Tue, 02 Aug 2022 12:32:19: #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 12:32:19: #3 Call peaks... INFO @ Tue, 02 Aug 2022 12:32:19: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 02 Aug 2022 12:32:22: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 12:32:23: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX12764391/SRX12764391.05_peaks.xls INFO @ Tue, 02 Aug 2022 12:32:23: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX12764391/SRX12764391.05_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 12:32:23: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX12764391/SRX12764391.05_summits.bed INFO @ Tue, 02 Aug 2022 12:32:23: Done! pass1 - making usageList (12 chroms): 1 millis pass2 - checking and writing primary data (540 records, 4 fields): 14 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 12:32:41: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX12764391/SRX12764391.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX12764391/SRX12764391.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX12764391/SRX12764391.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX12764391/SRX12764391.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 12:32:41: #1 read tag files... INFO @ Tue, 02 Aug 2022 12:32:41: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 12:32:47: 1000000 INFO @ Tue, 02 Aug 2022 12:32:48: #1 tag size is determined as 50 bps INFO @ Tue, 02 Aug 2022 12:32:48: #1 tag size = 50 INFO @ Tue, 02 Aug 2022 12:32:48: #1 total tags in treatment: 1272899 INFO @ Tue, 02 Aug 2022 12:32:48: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 12:32:48: #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 12:32:48: #1 tags after filtering in treatment: 1272899 INFO @ Tue, 02 Aug 2022 12:32:48: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 02 Aug 2022 12:32:48: #1 finished! INFO @ Tue, 02 Aug 2022 12:32:48: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 12:32:48: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 12:32:49: #2 number of paired peaks: 1015 INFO @ Tue, 02 Aug 2022 12:32:49: start model_add_line... INFO @ Tue, 02 Aug 2022 12:32:49: start X-correlation... INFO @ Tue, 02 Aug 2022 12:32:49: end of X-cor INFO @ Tue, 02 Aug 2022 12:32:49: #2 finished! INFO @ Tue, 02 Aug 2022 12:32:49: #2 predicted fragment length is 50 bps INFO @ Tue, 02 Aug 2022 12:32:49: #2 alternative fragment length(s) may be 50,476,574 bps INFO @ Tue, 02 Aug 2022 12:32:49: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX12764391/SRX12764391.10_model.r WARNING @ Tue, 02 Aug 2022 12:32:49: #2 Since the d (50) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 02 Aug 2022 12:32:49: #2 You may need to consider one of the other alternative d(s): 50,476,574 WARNING @ Tue, 02 Aug 2022 12:32:49: #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 12:32:49: #3 Call peaks... INFO @ Tue, 02 Aug 2022 12:32:49: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 02 Aug 2022 12:32:51: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 12:32:53: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX12764391/SRX12764391.10_peaks.xls INFO @ Tue, 02 Aug 2022 12:32:53: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX12764391/SRX12764391.10_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 12:32:53: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX12764391/SRX12764391.10_summits.bed INFO @ Tue, 02 Aug 2022 12:32:53: Done! pass1 - making usageList (9 chroms): 1 millis pass2 - checking and writing primary data (320 records, 4 fields): 18 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 12:33:11: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX12764391/SRX12764391.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX12764391/SRX12764391.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX12764391/SRX12764391.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX12764391/SRX12764391.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 12:33:11: #1 read tag files... INFO @ Tue, 02 Aug 2022 12:33:11: #1 read treatment tags... BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 02 Aug 2022 12:33:17: 1000000 INFO @ Tue, 02 Aug 2022 12:33:18: #1 tag size is determined as 50 bps INFO @ Tue, 02 Aug 2022 12:33:18: #1 tag size = 50 INFO @ Tue, 02 Aug 2022 12:33:18: #1 total tags in treatment: 1272899 INFO @ Tue, 02 Aug 2022 12:33:18: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 12:33:18: #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 12:33:18: #1 tags after filtering in treatment: 1272899 INFO @ Tue, 02 Aug 2022 12:33:18: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 02 Aug 2022 12:33:18: #1 finished! INFO @ Tue, 02 Aug 2022 12:33:18: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 12:33:18: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 12:33:19: #2 number of paired peaks: 1015 INFO @ Tue, 02 Aug 2022 12:33:19: start model_add_line... INFO @ Tue, 02 Aug 2022 12:33:19: start X-correlation... INFO @ Tue, 02 Aug 2022 12:33:19: end of X-cor INFO @ Tue, 02 Aug 2022 12:33:19: #2 finished! INFO @ Tue, 02 Aug 2022 12:33:19: #2 predicted fragment length is 50 bps INFO @ Tue, 02 Aug 2022 12:33:19: #2 alternative fragment length(s) may be 50,476,574 bps INFO @ Tue, 02 Aug 2022 12:33:19: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX12764391/SRX12764391.20_model.r WARNING @ Tue, 02 Aug 2022 12:33:19: #2 Since the d (50) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 02 Aug 2022 12:33:19: #2 You may need to consider one of the other alternative d(s): 50,476,574 WARNING @ Tue, 02 Aug 2022 12:33:19: #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 12:33:19: #3 Call peaks... INFO @ Tue, 02 Aug 2022 12:33:19: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Tue, 02 Aug 2022 12:33:21: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 12:33:23: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX12764391/SRX12764391.20_peaks.xls INFO @ Tue, 02 Aug 2022 12:33:23: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX12764391/SRX12764391.20_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 12:33:23: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX12764391/SRX12764391.20_summits.bed INFO @ Tue, 02 Aug 2022 12:33:23: Done! pass1 - making usageList (8 chroms): 0 millis pass2 - checking and writing primary data (147 records, 4 fields): 106 millis CompletedMACS2peakCalling