Job ID = 16440096 SRX = SRX10987329 Genome = dm3 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... Read 30936773 spots for SRR14648804/SRR14648804.sra Written 30936773 spots for SRR14648804/SRR14648804.sra fastq に変換しました。 bowtie でマッピング中... Your job 16440125 ("srTdm6") has been submitted Time loading reference: 00:00:00 Time loading forward index: 00:00:00 Time loading mirror index: 00:00:00 Multiseed full-index search: 00:03:44 30936773 reads; of these: 30936773 (100.00%) were unpaired; of these: 30186654 (97.58%) aligned 0 times 611013 (1.98%) aligned exactly 1 time 139106 (0.45%) aligned >1 times 2.42% overall alignment rate Time searching: 00:03:44 Overall time: 00:03:44 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] 198045 / 750119 = 0.2640 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 17:13:00: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX10987329/SRX10987329.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX10987329/SRX10987329.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX10987329/SRX10987329.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX10987329/SRX10987329.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 17:13:00: #1 read tag files... INFO @ Tue, 02 Aug 2022 17:13:00: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 17:13:05: #1 tag size is determined as 76 bps INFO @ Tue, 02 Aug 2022 17:13:05: #1 tag size = 76 INFO @ Tue, 02 Aug 2022 17:13:05: #1 total tags in treatment: 552074 INFO @ Tue, 02 Aug 2022 17:13:05: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 17:13:05: #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 17:13:05: #1 tags after filtering in treatment: 552074 INFO @ Tue, 02 Aug 2022 17:13:05: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 02 Aug 2022 17:13:05: #1 finished! INFO @ Tue, 02 Aug 2022 17:13:05: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 17:13:05: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 17:13:05: #2 number of paired peaks: 1831 INFO @ Tue, 02 Aug 2022 17:13:05: start model_add_line... INFO @ Tue, 02 Aug 2022 17:13:05: start X-correlation... INFO @ Tue, 02 Aug 2022 17:13:05: end of X-cor INFO @ Tue, 02 Aug 2022 17:13:05: #2 finished! INFO @ Tue, 02 Aug 2022 17:13:05: #2 predicted fragment length is 84 bps INFO @ Tue, 02 Aug 2022 17:13:05: #2 alternative fragment length(s) may be 84 bps INFO @ Tue, 02 Aug 2022 17:13:05: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX10987329/SRX10987329.05_model.r WARNING @ Tue, 02 Aug 2022 17:13:05: #2 Since the d (84) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 02 Aug 2022 17:13:05: #2 You may need to consider one of the other alternative d(s): 84 WARNING @ Tue, 02 Aug 2022 17:13:05: #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 17:13:05: #3 Call peaks... INFO @ Tue, 02 Aug 2022 17:13:05: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 02 Aug 2022 17:13:06: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 17:13:07: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX10987329/SRX10987329.05_peaks.xls INFO @ Tue, 02 Aug 2022 17:13:07: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX10987329/SRX10987329.05_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 17:13:07: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX10987329/SRX10987329.05_summits.bed INFO @ Tue, 02 Aug 2022 17:13:07: Done! pass1 - making usageList (9 chroms): 0 millis pass2 - checking and writing primary data (121 records, 4 fields): 39 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 17:13:29: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX10987329/SRX10987329.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX10987329/SRX10987329.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX10987329/SRX10987329.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX10987329/SRX10987329.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 17:13:29: #1 read tag files... INFO @ Tue, 02 Aug 2022 17:13:29: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 17:13:33: #1 tag size is determined as 76 bps INFO @ Tue, 02 Aug 2022 17:13:33: #1 tag size = 76 INFO @ Tue, 02 Aug 2022 17:13:33: #1 total tags in treatment: 552074 INFO @ Tue, 02 Aug 2022 17:13:33: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 17:13:33: #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 17:13:33: #1 tags after filtering in treatment: 552074 INFO @ Tue, 02 Aug 2022 17:13:33: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 02 Aug 2022 17:13:33: #1 finished! INFO @ Tue, 02 Aug 2022 17:13:33: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 17:13:33: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 17:13:33: #2 number of paired peaks: 1831 INFO @ Tue, 02 Aug 2022 17:13:33: start model_add_line... INFO @ Tue, 02 Aug 2022 17:13:33: start X-correlation... INFO @ Tue, 02 Aug 2022 17:13:33: end of X-cor INFO @ Tue, 02 Aug 2022 17:13:33: #2 finished! INFO @ Tue, 02 Aug 2022 17:13:33: #2 predicted fragment length is 84 bps INFO @ Tue, 02 Aug 2022 17:13:33: #2 alternative fragment length(s) may be 84 bps INFO @ Tue, 02 Aug 2022 17:13:33: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX10987329/SRX10987329.10_model.r WARNING @ Tue, 02 Aug 2022 17:13:33: #2 Since the d (84) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 02 Aug 2022 17:13:33: #2 You may need to consider one of the other alternative d(s): 84 WARNING @ Tue, 02 Aug 2022 17:13:33: #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 17:13:33: #3 Call peaks... INFO @ Tue, 02 Aug 2022 17:13:33: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 02 Aug 2022 17:13:34: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 17:13:35: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX10987329/SRX10987329.10_peaks.xls INFO @ Tue, 02 Aug 2022 17:13:35: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX10987329/SRX10987329.10_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 17:13:35: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX10987329/SRX10987329.10_summits.bed INFO @ Tue, 02 Aug 2022 17:13:35: Done! pass1 - making usageList (4 chroms): 1 millis pass2 - checking and writing primary data (71 records, 4 fields): 32 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 17:14:00: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX10987329/SRX10987329.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX10987329/SRX10987329.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX10987329/SRX10987329.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX10987329/SRX10987329.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 17:14:00: #1 read tag files... INFO @ Tue, 02 Aug 2022 17:14:00: #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 17:14:04: #1 tag size is determined as 76 bps INFO @ Tue, 02 Aug 2022 17:14:04: #1 tag size = 76 INFO @ Tue, 02 Aug 2022 17:14:04: #1 total tags in treatment: 552074 INFO @ Tue, 02 Aug 2022 17:14:04: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 17:14:04: #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 17:14:04: #1 tags after filtering in treatment: 552074 INFO @ Tue, 02 Aug 2022 17:14:04: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 02 Aug 2022 17:14:04: #1 finished! INFO @ Tue, 02 Aug 2022 17:14:04: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 17:14:04: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 17:14:04: #2 number of paired peaks: 1831 INFO @ Tue, 02 Aug 2022 17:14:04: start model_add_line... INFO @ Tue, 02 Aug 2022 17:14:04: start X-correlation... INFO @ Tue, 02 Aug 2022 17:14:04: end of X-cor INFO @ Tue, 02 Aug 2022 17:14:04: #2 finished! INFO @ Tue, 02 Aug 2022 17:14:04: #2 predicted fragment length is 84 bps INFO @ Tue, 02 Aug 2022 17:14:04: #2 alternative fragment length(s) may be 84 bps INFO @ Tue, 02 Aug 2022 17:14:04: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX10987329/SRX10987329.20_model.r WARNING @ Tue, 02 Aug 2022 17:14:04: #2 Since the d (84) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 02 Aug 2022 17:14:04: #2 You may need to consider one of the other alternative d(s): 84 WARNING @ Tue, 02 Aug 2022 17:14:04: #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 17:14:04: #3 Call peaks... INFO @ Tue, 02 Aug 2022 17:14:04: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 02 Aug 2022 17:14:05: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 17:14:06: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX10987329/SRX10987329.20_peaks.xls INFO @ Tue, 02 Aug 2022 17:14:06: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX10987329/SRX10987329.20_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 17:14:06: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX10987329/SRX10987329.20_summits.bed INFO @ Tue, 02 Aug 2022 17:14:06: Done! pass1 - making usageList (3 chroms): 1 millis pass2 - checking and writing primary data (55 records, 4 fields): 33 millis CompletedMACS2peakCalling