Job ID = 16439438 SRX = SRX15206442 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: 00:45:11 32790098 reads; of these: 32790098 (100.00%) were unpaired; of these: 2081186 (6.35%) aligned 0 times 16180940 (49.35%) aligned exactly 1 time 14527972 (44.31%) aligned >1 times 93.65% overall alignment rate Time searching: 00:45:11 Overall time: 00:45:11 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_sort_core] merging from 24 files... [bam_rmdupse_core] 22254583 / 30708912 = 0.7247 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 16:12:02: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX15206442/SRX15206442.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX15206442/SRX15206442.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX15206442/SRX15206442.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX15206442/SRX15206442.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 16:12:02: #1 read tag files... INFO @ Tue, 02 Aug 2022 16:12:02: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 16:12:20: 1000000 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 16:12:30: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX15206442/SRX15206442.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX15206442/SRX15206442.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX15206442/SRX15206442.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX15206442/SRX15206442.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 16:12:30: #1 read tag files... INFO @ Tue, 02 Aug 2022 16:12:30: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 16:12:37: 2000000 INFO @ Tue, 02 Aug 2022 16:12:48: 1000000 INFO @ Tue, 02 Aug 2022 16:12:55: 3000000 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 16:13:00: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX15206442/SRX15206442.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX15206442/SRX15206442.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX15206442/SRX15206442.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX15206442/SRX15206442.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 16:13:00: #1 read tag files... INFO @ Tue, 02 Aug 2022 16:13:00: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 16:13:06: 2000000 INFO @ Tue, 02 Aug 2022 16:13:12: 4000000 INFO @ Tue, 02 Aug 2022 16:13:20: 1000000 INFO @ Tue, 02 Aug 2022 16:13:24: 3000000 INFO @ Tue, 02 Aug 2022 16:13:31: 5000000 INFO @ Tue, 02 Aug 2022 16:13:38: 2000000 INFO @ Tue, 02 Aug 2022 16:13:43: 4000000 INFO @ Tue, 02 Aug 2022 16:13:49: 6000000 INFO @ Tue, 02 Aug 2022 16:13:58: 3000000 INFO @ Tue, 02 Aug 2022 16:14:00: 5000000 INFO @ Tue, 02 Aug 2022 16:14:07: 7000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 02 Aug 2022 16:14:18: 4000000 INFO @ Tue, 02 Aug 2022 16:14:18: 6000000 INFO @ Tue, 02 Aug 2022 16:14:26: 8000000 INFO @ Tue, 02 Aug 2022 16:14:34: #1 tag size is determined as 150 bps INFO @ Tue, 02 Aug 2022 16:14:34: #1 tag size = 150 INFO @ Tue, 02 Aug 2022 16:14:34: #1 total tags in treatment: 8454329 INFO @ Tue, 02 Aug 2022 16:14:34: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 16:14:34: #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 16:14:34: #1 tags after filtering in treatment: 8454170 INFO @ Tue, 02 Aug 2022 16:14:34: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 02 Aug 2022 16:14:34: #1 finished! INFO @ Tue, 02 Aug 2022 16:14:34: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 16:14:34: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 16:14:36: #2 number of paired peaks: 7343 INFO @ Tue, 02 Aug 2022 16:14:36: start model_add_line... INFO @ Tue, 02 Aug 2022 16:14:36: start X-correlation... INFO @ Tue, 02 Aug 2022 16:14:37: end of X-cor INFO @ Tue, 02 Aug 2022 16:14:37: #2 finished! INFO @ Tue, 02 Aug 2022 16:14:37: #2 predicted fragment length is 185 bps INFO @ Tue, 02 Aug 2022 16:14:37: #2 alternative fragment length(s) may be 185 bps INFO @ Tue, 02 Aug 2022 16:14:37: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX15206442/SRX15206442.05_model.r WARNING @ Tue, 02 Aug 2022 16:14:37: #2 Since the d (185) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 02 Aug 2022 16:14:37: #2 You may need to consider one of the other alternative d(s): 185 WARNING @ Tue, 02 Aug 2022 16:14:37: #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 16:14:37: #3 Call peaks... INFO @ Tue, 02 Aug 2022 16:14:37: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 02 Aug 2022 16:14:37: 7000000 INFO @ Tue, 02 Aug 2022 16:14:37: 5000000 BigWig に変換しました。 INFO @ Tue, 02 Aug 2022 16:14:56: 6000000 INFO @ Tue, 02 Aug 2022 16:14:56: 8000000 INFO @ Tue, 02 Aug 2022 16:15:05: #1 tag size is determined as 150 bps INFO @ Tue, 02 Aug 2022 16:15:05: #1 tag size = 150 INFO @ Tue, 02 Aug 2022 16:15:05: #1 total tags in treatment: 8454329 INFO @ Tue, 02 Aug 2022 16:15:05: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 16:15:05: #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 16:15:05: #1 tags after filtering in treatment: 8454170 INFO @ Tue, 02 Aug 2022 16:15:05: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 02 Aug 2022 16:15:05: #1 finished! INFO @ Tue, 02 Aug 2022 16:15:05: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 16:15:05: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 16:15:07: #2 number of paired peaks: 7343 INFO @ Tue, 02 Aug 2022 16:15:07: start model_add_line... INFO @ Tue, 02 Aug 2022 16:15:07: start X-correlation... INFO @ Tue, 02 Aug 2022 16:15:07: end of X-cor INFO @ Tue, 02 Aug 2022 16:15:07: #2 finished! INFO @ Tue, 02 Aug 2022 16:15:07: #2 predicted fragment length is 185 bps INFO @ Tue, 02 Aug 2022 16:15:07: #2 alternative fragment length(s) may be 185 bps INFO @ Tue, 02 Aug 2022 16:15:07: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX15206442/SRX15206442.10_model.r WARNING @ Tue, 02 Aug 2022 16:15:07: #2 Since the d (185) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 02 Aug 2022 16:15:07: #2 You may need to consider one of the other alternative d(s): 185 WARNING @ Tue, 02 Aug 2022 16:15:07: #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 16:15:07: #3 Call peaks... INFO @ Tue, 02 Aug 2022 16:15:07: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 02 Aug 2022 16:15:14: 7000000 INFO @ Tue, 02 Aug 2022 16:15:16: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 16:15:28: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX15206442/SRX15206442.05_peaks.xls INFO @ Tue, 02 Aug 2022 16:15:28: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX15206442/SRX15206442.05_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 16:15:29: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX15206442/SRX15206442.05_summits.bed INFO @ Tue, 02 Aug 2022 16:15:29: Done! pass1 - making usageList (693 chroms): 2 millis pass2 - checking and writing primary data (6178 records, 4 fields): 57 millis CompletedMACS2peakCalling INFO @ Tue, 02 Aug 2022 16:15:32: 8000000 INFO @ Tue, 02 Aug 2022 16:15:41: #1 tag size is determined as 150 bps INFO @ Tue, 02 Aug 2022 16:15:41: #1 tag size = 150 INFO @ Tue, 02 Aug 2022 16:15:41: #1 total tags in treatment: 8454329 INFO @ Tue, 02 Aug 2022 16:15:41: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 16:15:41: #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 16:15:41: #1 tags after filtering in treatment: 8454170 INFO @ Tue, 02 Aug 2022 16:15:41: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 02 Aug 2022 16:15:41: #1 finished! INFO @ Tue, 02 Aug 2022 16:15:41: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 16:15:41: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 16:15:43: #2 number of paired peaks: 7343 INFO @ Tue, 02 Aug 2022 16:15:43: start model_add_line... INFO @ Tue, 02 Aug 2022 16:15:43: start X-correlation... INFO @ Tue, 02 Aug 2022 16:15:43: end of X-cor INFO @ Tue, 02 Aug 2022 16:15:43: #2 finished! INFO @ Tue, 02 Aug 2022 16:15:43: #2 predicted fragment length is 185 bps INFO @ Tue, 02 Aug 2022 16:15:43: #2 alternative fragment length(s) may be 185 bps INFO @ Tue, 02 Aug 2022 16:15:43: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX15206442/SRX15206442.20_model.r WARNING @ Tue, 02 Aug 2022 16:15:43: #2 Since the d (185) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 02 Aug 2022 16:15:43: #2 You may need to consider one of the other alternative d(s): 185 WARNING @ Tue, 02 Aug 2022 16:15:43: #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 16:15:43: #3 Call peaks... INFO @ Tue, 02 Aug 2022 16:15:43: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 02 Aug 2022 16:15:47: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 16:16:00: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX15206442/SRX15206442.10_peaks.xls INFO @ Tue, 02 Aug 2022 16:16:00: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX15206442/SRX15206442.10_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 16:16:00: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX15206442/SRX15206442.10_summits.bed INFO @ Tue, 02 Aug 2022 16:16:00: Done! pass1 - making usageList (576 chroms): 2 millis pass2 - checking and writing primary data (4178 records, 4 fields): 77 millis CompletedMACS2peakCalling INFO @ Tue, 02 Aug 2022 16:16:26: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 16:16:39: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX15206442/SRX15206442.20_peaks.xls INFO @ Tue, 02 Aug 2022 16:16:39: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX15206442/SRX15206442.20_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 16:16:39: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX15206442/SRX15206442.20_summits.bed INFO @ Tue, 02 Aug 2022 16:16:39: Done! pass1 - making usageList (428 chroms): 3 millis pass2 - checking and writing primary data (2227 records, 4 fields): 83 millis CompletedMACS2peakCalling