Job ID = 16440077 SRX = SRX10987325 Genome = dm3 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... Read 39550014 spots for SRR14648800/SRR14648800.sra Written 39550014 spots for SRR14648800/SRR14648800.sra fastq に変換しました。 bowtie でマッピング中... Your job 16440120 ("srTdm6") has been submitted Time loading reference: 00:00:00 Time loading forward index: 00:00:00 Time loading mirror index: 00:00:01 Multiseed full-index search: 00:05:09 39550014 reads; of these: 39550014 (100.00%) were unpaired; of these: 39082894 (98.82%) aligned 0 times 356828 (0.90%) aligned exactly 1 time 110292 (0.28%) aligned >1 times 1.18% overall alignment rate Time searching: 00:05:10 Overall time: 00:05:10 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] 193914 / 467120 = 0.4151 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 17:11:48: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX10987325/SRX10987325.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX10987325/SRX10987325.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX10987325/SRX10987325.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX10987325/SRX10987325.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 17:11:48: #1 read tag files... INFO @ Tue, 02 Aug 2022 17:11:48: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 17:11:50: #1 tag size is determined as 76 bps INFO @ Tue, 02 Aug 2022 17:11:50: #1 tag size = 76 INFO @ Tue, 02 Aug 2022 17:11:50: #1 total tags in treatment: 273206 INFO @ Tue, 02 Aug 2022 17:11:50: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 17:11:50: #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 17:11:50: #1 tags after filtering in treatment: 273206 INFO @ Tue, 02 Aug 2022 17:11:50: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 02 Aug 2022 17:11:50: #1 finished! INFO @ Tue, 02 Aug 2022 17:11:50: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 17:11:50: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 17:11:50: #2 number of paired peaks: 1521 INFO @ Tue, 02 Aug 2022 17:11:50: start model_add_line... INFO @ Tue, 02 Aug 2022 17:11:50: start X-correlation... INFO @ Tue, 02 Aug 2022 17:11:50: end of X-cor INFO @ Tue, 02 Aug 2022 17:11:50: #2 finished! INFO @ Tue, 02 Aug 2022 17:11:50: #2 predicted fragment length is 74 bps INFO @ Tue, 02 Aug 2022 17:11:50: #2 alternative fragment length(s) may be 74,188,215,240,289,588 bps INFO @ Tue, 02 Aug 2022 17:11:50: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX10987325/SRX10987325.05_model.r WARNING @ Tue, 02 Aug 2022 17:11:50: #2 Since the d (74) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 02 Aug 2022 17:11:50: #2 You may need to consider one of the other alternative d(s): 74,188,215,240,289,588 WARNING @ Tue, 02 Aug 2022 17:11:50: #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 17:11:50: #3 Call peaks... INFO @ Tue, 02 Aug 2022 17:11:50: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 02 Aug 2022 17:11:50: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 17:11:51: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX10987325/SRX10987325.05_peaks.xls INFO @ Tue, 02 Aug 2022 17:11:51: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX10987325/SRX10987325.05_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 17:11:51: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX10987325/SRX10987325.05_summits.bed INFO @ Tue, 02 Aug 2022 17:11:51: Done! pass1 - making usageList (8 chroms): 0 millis pass2 - checking and writing primary data (119 records, 4 fields): 37 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 17:12:17: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX10987325/SRX10987325.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX10987325/SRX10987325.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX10987325/SRX10987325.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX10987325/SRX10987325.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 17:12:17: #1 read tag files... INFO @ Tue, 02 Aug 2022 17:12:17: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 17:12:19: #1 tag size is determined as 76 bps INFO @ Tue, 02 Aug 2022 17:12:19: #1 tag size = 76 INFO @ Tue, 02 Aug 2022 17:12:19: #1 total tags in treatment: 273206 INFO @ Tue, 02 Aug 2022 17:12:19: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 17:12:19: #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 17:12:19: #1 tags after filtering in treatment: 273206 INFO @ Tue, 02 Aug 2022 17:12:19: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 02 Aug 2022 17:12:19: #1 finished! INFO @ Tue, 02 Aug 2022 17:12:19: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 17:12:19: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 17:12:19: #2 number of paired peaks: 1521 INFO @ Tue, 02 Aug 2022 17:12:19: start model_add_line... INFO @ Tue, 02 Aug 2022 17:12:19: start X-correlation... INFO @ Tue, 02 Aug 2022 17:12:19: end of X-cor INFO @ Tue, 02 Aug 2022 17:12:19: #2 finished! INFO @ Tue, 02 Aug 2022 17:12:19: #2 predicted fragment length is 74 bps INFO @ Tue, 02 Aug 2022 17:12:19: #2 alternative fragment length(s) may be 74,188,215,240,289,588 bps INFO @ Tue, 02 Aug 2022 17:12:19: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX10987325/SRX10987325.10_model.r WARNING @ Tue, 02 Aug 2022 17:12:19: #2 Since the d (74) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 02 Aug 2022 17:12:19: #2 You may need to consider one of the other alternative d(s): 74,188,215,240,289,588 WARNING @ Tue, 02 Aug 2022 17:12:19: #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 17:12:19: #3 Call peaks... INFO @ Tue, 02 Aug 2022 17:12:19: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 02 Aug 2022 17:12:19: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 17:12:20: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX10987325/SRX10987325.10_peaks.xls INFO @ Tue, 02 Aug 2022 17:12:20: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX10987325/SRX10987325.10_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 17:12:20: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX10987325/SRX10987325.10_summits.bed INFO @ Tue, 02 Aug 2022 17:12:20: Done! pass1 - making usageList (5 chroms): 0 millis pass2 - checking and writing primary data (78 records, 4 fields): 48 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 17:12:47: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX10987325/SRX10987325.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX10987325/SRX10987325.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX10987325/SRX10987325.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX10987325/SRX10987325.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 BedGraph に変換しました。 INFO @ Tue, 02 Aug 2022 17:12:47: #1 read tag files... INFO @ Tue, 02 Aug 2022 17:12:47: #1 read treatment tags... BigWig に変換中... BigWig に変換しました。 INFO @ Tue, 02 Aug 2022 17:12:49: #1 tag size is determined as 76 bps INFO @ Tue, 02 Aug 2022 17:12:49: #1 tag size = 76 INFO @ Tue, 02 Aug 2022 17:12:49: #1 total tags in treatment: 273206 INFO @ Tue, 02 Aug 2022 17:12:49: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 17:12:49: #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 17:12:49: #1 tags after filtering in treatment: 273206 INFO @ Tue, 02 Aug 2022 17:12:49: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 02 Aug 2022 17:12:49: #1 finished! INFO @ Tue, 02 Aug 2022 17:12:49: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 17:12:49: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 17:12:49: #2 number of paired peaks: 1521 INFO @ Tue, 02 Aug 2022 17:12:49: start model_add_line... INFO @ Tue, 02 Aug 2022 17:12:49: start X-correlation... INFO @ Tue, 02 Aug 2022 17:12:49: end of X-cor INFO @ Tue, 02 Aug 2022 17:12:49: #2 finished! INFO @ Tue, 02 Aug 2022 17:12:49: #2 predicted fragment length is 74 bps INFO @ Tue, 02 Aug 2022 17:12:49: #2 alternative fragment length(s) may be 74,188,215,240,289,588 bps INFO @ Tue, 02 Aug 2022 17:12:49: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX10987325/SRX10987325.20_model.r WARNING @ Tue, 02 Aug 2022 17:12:49: #2 Since the d (74) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 02 Aug 2022 17:12:49: #2 You may need to consider one of the other alternative d(s): 74,188,215,240,289,588 WARNING @ Tue, 02 Aug 2022 17:12:49: #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 17:12:49: #3 Call peaks... INFO @ Tue, 02 Aug 2022 17:12:49: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 02 Aug 2022 17:12:49: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 17:12:50: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX10987325/SRX10987325.20_peaks.xls INFO @ Tue, 02 Aug 2022 17:12:50: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX10987325/SRX10987325.20_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 17:12:50: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX10987325/SRX10987325.20_summits.bed INFO @ Tue, 02 Aug 2022 17:12:50: Done! pass1 - making usageList (2 chroms): 1 millis pass2 - checking and writing primary data (59 records, 4 fields): 20 millis CompletedMACS2peakCalling