Job ID = 16439134 SRX = SRX15206435 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: 00:02:55 6992229 reads; of these: 6992229 (100.00%) were unpaired; of these: 138683 (1.98%) aligned 0 times 2985680 (42.70%) aligned exactly 1 time 3867866 (55.32%) aligned >1 times 98.02% overall alignment rate Time searching: 00:02:55 Overall time: 00:02:55 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] 858442 / 6853546 = 0.1253 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 14:40:53: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX15206435/SRX15206435.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX15206435/SRX15206435.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX15206435/SRX15206435.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX15206435/SRX15206435.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 14:40:53: #1 read tag files... INFO @ Tue, 02 Aug 2022 14:40:53: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 14:40:59: 1000000 INFO @ Tue, 02 Aug 2022 14:41:05: 2000000 INFO @ Tue, 02 Aug 2022 14:41:12: 3000000 INFO @ Tue, 02 Aug 2022 14:41:18: 4000000 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 14:41:22: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX15206435/SRX15206435.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX15206435/SRX15206435.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX15206435/SRX15206435.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX15206435/SRX15206435.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 14:41:22: #1 read tag files... INFO @ Tue, 02 Aug 2022 14:41:22: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 14:41:25: 5000000 INFO @ Tue, 02 Aug 2022 14:41:31: 1000000 INFO @ Tue, 02 Aug 2022 14:41:33: #1 tag size is determined as 74 bps INFO @ Tue, 02 Aug 2022 14:41:33: #1 tag size = 74 INFO @ Tue, 02 Aug 2022 14:41:33: #1 total tags in treatment: 5995104 INFO @ Tue, 02 Aug 2022 14:41:33: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 14:41:33: #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 14:41:34: #1 tags after filtering in treatment: 5994981 INFO @ Tue, 02 Aug 2022 14:41:34: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 02 Aug 2022 14:41:34: #1 finished! INFO @ Tue, 02 Aug 2022 14:41:34: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 14:41:34: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 14:41:34: #2 number of paired peaks: 3195 INFO @ Tue, 02 Aug 2022 14:41:34: start model_add_line... INFO @ Tue, 02 Aug 2022 14:41:34: start X-correlation... INFO @ Tue, 02 Aug 2022 14:41:34: end of X-cor INFO @ Tue, 02 Aug 2022 14:41:34: #2 finished! INFO @ Tue, 02 Aug 2022 14:41:34: #2 predicted fragment length is 83 bps INFO @ Tue, 02 Aug 2022 14:41:34: #2 alternative fragment length(s) may be 4,83 bps INFO @ Tue, 02 Aug 2022 14:41:34: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX15206435/SRX15206435.05_model.r WARNING @ Tue, 02 Aug 2022 14:41:34: #2 Since the d (83) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 02 Aug 2022 14:41:34: #2 You may need to consider one of the other alternative d(s): 4,83 WARNING @ Tue, 02 Aug 2022 14:41:34: #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 14:41:34: #3 Call peaks... INFO @ Tue, 02 Aug 2022 14:41:34: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 02 Aug 2022 14:41:38: 2000000 INFO @ Tue, 02 Aug 2022 14:41:46: 3000000 INFO @ Tue, 02 Aug 2022 14:41:47: #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 14:41:52: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX15206435/SRX15206435.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX15206435/SRX15206435.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX15206435/SRX15206435.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX15206435/SRX15206435.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 14:41:52: #1 read tag files... INFO @ Tue, 02 Aug 2022 14:41:52: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 14:41:53: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX15206435/SRX15206435.05_peaks.xls INFO @ Tue, 02 Aug 2022 14:41:53: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX15206435/SRX15206435.05_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 14:41:53: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX15206435/SRX15206435.05_summits.bed INFO @ Tue, 02 Aug 2022 14:41:53: Done! pass1 - making usageList (741 chroms): 2 millis pass2 - checking and writing primary data (2802 records, 4 fields): 110 millis CompletedMACS2peakCalling INFO @ Tue, 02 Aug 2022 14:41:54: 4000000 INFO @ Tue, 02 Aug 2022 14:42:01: 1000000 INFO @ Tue, 02 Aug 2022 14:42:03: 5000000 INFO @ Tue, 02 Aug 2022 14:42:09: 2000000 INFO @ Tue, 02 Aug 2022 14:42:11: #1 tag size is determined as 74 bps INFO @ Tue, 02 Aug 2022 14:42:11: #1 tag size = 74 INFO @ Tue, 02 Aug 2022 14:42:11: #1 total tags in treatment: 5995104 INFO @ Tue, 02 Aug 2022 14:42:11: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 14:42:11: #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 14:42:11: #1 tags after filtering in treatment: 5994981 INFO @ Tue, 02 Aug 2022 14:42:11: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 02 Aug 2022 14:42:11: #1 finished! INFO @ Tue, 02 Aug 2022 14:42:11: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 14:42:11: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 14:42:12: #2 number of paired peaks: 3195 INFO @ Tue, 02 Aug 2022 14:42:12: start model_add_line... INFO @ Tue, 02 Aug 2022 14:42:12: start X-correlation... INFO @ Tue, 02 Aug 2022 14:42:12: end of X-cor INFO @ Tue, 02 Aug 2022 14:42:12: #2 finished! INFO @ Tue, 02 Aug 2022 14:42:12: #2 predicted fragment length is 83 bps INFO @ Tue, 02 Aug 2022 14:42:12: #2 alternative fragment length(s) may be 4,83 bps INFO @ Tue, 02 Aug 2022 14:42:12: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX15206435/SRX15206435.10_model.r WARNING @ Tue, 02 Aug 2022 14:42:12: #2 Since the d (83) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 02 Aug 2022 14:42:12: #2 You may need to consider one of the other alternative d(s): 4,83 WARNING @ Tue, 02 Aug 2022 14:42:12: #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 14:42:12: #3 Call peaks... INFO @ Tue, 02 Aug 2022 14:42:12: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 02 Aug 2022 14:42:17: 3000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 02 Aug 2022 14:42:24: 4000000 INFO @ Tue, 02 Aug 2022 14:42:24: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 14:42:30: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX15206435/SRX15206435.10_peaks.xls INFO @ Tue, 02 Aug 2022 14:42:30: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX15206435/SRX15206435.10_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 14:42:30: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX15206435/SRX15206435.10_summits.bed INFO @ Tue, 02 Aug 2022 14:42:30: Done! pass1 - making usageList (631 chroms): 2 millis pass2 - checking and writing primary data (1793 records, 4 fields): 311 millis CompletedMACS2peakCalling BigWig に変換しました。 INFO @ Tue, 02 Aug 2022 14:42:32: 5000000 INFO @ Tue, 02 Aug 2022 14:42:39: #1 tag size is determined as 74 bps INFO @ Tue, 02 Aug 2022 14:42:39: #1 tag size = 74 INFO @ Tue, 02 Aug 2022 14:42:39: #1 total tags in treatment: 5995104 INFO @ Tue, 02 Aug 2022 14:42:39: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 14:42:39: #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 14:42:40: #1 tags after filtering in treatment: 5994981 INFO @ Tue, 02 Aug 2022 14:42:40: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 02 Aug 2022 14:42:40: #1 finished! INFO @ Tue, 02 Aug 2022 14:42:40: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 14:42:40: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 14:42:40: #2 number of paired peaks: 3195 INFO @ Tue, 02 Aug 2022 14:42:40: start model_add_line... INFO @ Tue, 02 Aug 2022 14:42:40: start X-correlation... INFO @ Tue, 02 Aug 2022 14:42:40: end of X-cor INFO @ Tue, 02 Aug 2022 14:42:40: #2 finished! INFO @ Tue, 02 Aug 2022 14:42:40: #2 predicted fragment length is 83 bps INFO @ Tue, 02 Aug 2022 14:42:40: #2 alternative fragment length(s) may be 4,83 bps INFO @ Tue, 02 Aug 2022 14:42:40: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX15206435/SRX15206435.20_model.r WARNING @ Tue, 02 Aug 2022 14:42:40: #2 Since the d (83) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 02 Aug 2022 14:42:40: #2 You may need to consider one of the other alternative d(s): 4,83 WARNING @ Tue, 02 Aug 2022 14:42:40: #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 14:42:40: #3 Call peaks... INFO @ Tue, 02 Aug 2022 14:42:40: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 02 Aug 2022 14:42:53: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 14:42:59: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX15206435/SRX15206435.20_peaks.xls INFO @ Tue, 02 Aug 2022 14:42:59: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX15206435/SRX15206435.20_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 14:42:59: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX15206435/SRX15206435.20_summits.bed INFO @ Tue, 02 Aug 2022 14:43:00: Done! pass1 - making usageList (489 chroms): 1 millis pass2 - checking and writing primary data (1031 records, 4 fields): 44 millis CompletedMACS2peakCalling