Job ID = 14167069 SRX = SRX7434140 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: 00:00:01 Time loading forward index: 00:00:00 Time loading mirror index: 00:00:00 Multiseed full-index search: 00:02:44 8687260 reads; of these: 8687260 (100.00%) were unpaired; of these: 2495426 (28.73%) aligned 0 times 4630120 (53.30%) aligned exactly 1 time 1561714 (17.98%) aligned >1 times 71.27% overall alignment rate Time searching: 00:02:45 Overall time: 00:02:46 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] 1268654 / 6191834 = 0.2049 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/3.8.3/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Fri, 10 Dec 2021 09:34:57: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX7434140/SRX7434140.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX7434140/SRX7434140.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX7434140/SRX7434140.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX7434140/SRX7434140.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 @ Fri, 10 Dec 2021 09:34:57: #1 read tag files... INFO @ Fri, 10 Dec 2021 09:34:57: #1 read treatment tags... INFO @ Fri, 10 Dec 2021 09:35:04: 1000000 INFO @ Fri, 10 Dec 2021 09:35:11: 2000000 INFO @ Fri, 10 Dec 2021 09:35:18: 3000000 WARNING: Skipping mount /opt/pkg/singularity/3.8.3/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Fri, 10 Dec 2021 09:35:26: 4000000 INFO @ Fri, 10 Dec 2021 09:35:26: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX7434140/SRX7434140.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX7434140/SRX7434140.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX7434140/SRX7434140.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX7434140/SRX7434140.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 @ Fri, 10 Dec 2021 09:35:26: #1 read tag files... INFO @ Fri, 10 Dec 2021 09:35:26: #1 read treatment tags... INFO @ Fri, 10 Dec 2021 09:35:32: 1000000 INFO @ Fri, 10 Dec 2021 09:35:33: #1 tag size is determined as 51 bps INFO @ Fri, 10 Dec 2021 09:35:33: #1 tag size = 51 INFO @ Fri, 10 Dec 2021 09:35:33: #1 total tags in treatment: 4923180 INFO @ Fri, 10 Dec 2021 09:35:33: #1 user defined the maximum tags... INFO @ Fri, 10 Dec 2021 09:35:33: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 10 Dec 2021 09:35:33: #1 tags after filtering in treatment: 4922980 INFO @ Fri, 10 Dec 2021 09:35:33: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 10 Dec 2021 09:35:33: #1 finished! INFO @ Fri, 10 Dec 2021 09:35:33: #2 Build Peak Model... INFO @ Fri, 10 Dec 2021 09:35:33: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Dec 2021 09:35:33: #2 number of paired peaks: 720 WARNING @ Fri, 10 Dec 2021 09:35:33: Fewer paired peaks (720) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 720 pairs to build model! INFO @ Fri, 10 Dec 2021 09:35:33: start model_add_line... INFO @ Fri, 10 Dec 2021 09:35:34: start X-correlation... INFO @ Fri, 10 Dec 2021 09:35:34: end of X-cor INFO @ Fri, 10 Dec 2021 09:35:34: #2 finished! INFO @ Fri, 10 Dec 2021 09:35:34: #2 predicted fragment length is 59 bps INFO @ Fri, 10 Dec 2021 09:35:34: #2 alternative fragment length(s) may be 59 bps INFO @ Fri, 10 Dec 2021 09:35:34: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX7434140/SRX7434140.05_model.r WARNING @ Fri, 10 Dec 2021 09:35:34: #2 Since the d (59) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 10 Dec 2021 09:35:34: #2 You may need to consider one of the other alternative d(s): 59 WARNING @ Fri, 10 Dec 2021 09:35:34: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Fri, 10 Dec 2021 09:35:34: #3 Call peaks... INFO @ Fri, 10 Dec 2021 09:35:34: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 10 Dec 2021 09:35:37: 2000000 INFO @ Fri, 10 Dec 2021 09:35:42: 3000000 INFO @ Fri, 10 Dec 2021 09:35:47: #3 Call peaks for each chromosome... INFO @ Fri, 10 Dec 2021 09:35:47: 4000000 INFO @ Fri, 10 Dec 2021 09:35:52: #1 tag size is determined as 51 bps INFO @ Fri, 10 Dec 2021 09:35:52: #1 tag size = 51 INFO @ Fri, 10 Dec 2021 09:35:52: #1 total tags in treatment: 4923180 INFO @ Fri, 10 Dec 2021 09:35:52: #1 user defined the maximum tags... INFO @ Fri, 10 Dec 2021 09:35:52: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 10 Dec 2021 09:35:53: #1 tags after filtering in treatment: 4922980 INFO @ Fri, 10 Dec 2021 09:35:53: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 10 Dec 2021 09:35:53: #1 finished! INFO @ Fri, 10 Dec 2021 09:35:53: #2 Build Peak Model... INFO @ Fri, 10 Dec 2021 09:35:53: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Dec 2021 09:35:53: #2 number of paired peaks: 720 WARNING @ Fri, 10 Dec 2021 09:35:53: Fewer paired peaks (720) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 720 pairs to build model! INFO @ Fri, 10 Dec 2021 09:35:53: start model_add_line... INFO @ Fri, 10 Dec 2021 09:35:53: start X-correlation... INFO @ Fri, 10 Dec 2021 09:35:53: end of X-cor INFO @ Fri, 10 Dec 2021 09:35:53: #2 finished! INFO @ Fri, 10 Dec 2021 09:35:53: #2 predicted fragment length is 59 bps INFO @ Fri, 10 Dec 2021 09:35:53: #2 alternative fragment length(s) may be 59 bps INFO @ Fri, 10 Dec 2021 09:35:53: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX7434140/SRX7434140.10_model.r WARNING @ Fri, 10 Dec 2021 09:35:53: #2 Since the d (59) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 10 Dec 2021 09:35:53: #2 You may need to consider one of the other alternative d(s): 59 WARNING @ Fri, 10 Dec 2021 09:35:53: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Fri, 10 Dec 2021 09:35:53: #3 Call peaks... INFO @ Fri, 10 Dec 2021 09:35:53: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 10 Dec 2021 09:35:54: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX7434140/SRX7434140.05_peaks.xls INFO @ Fri, 10 Dec 2021 09:35:54: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX7434140/SRX7434140.05_peaks.narrowPeak INFO @ Fri, 10 Dec 2021 09:35:54: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX7434140/SRX7434140.05_summits.bed INFO @ Fri, 10 Dec 2021 09:35:54: Done! BedGraph に変換中... pass1 - making usageList (480 chroms): 2 millis pass2 - checking and writing primary data (1895 records, 4 fields): 20 millis WARNING: Skipping mount /opt/pkg/singularity/3.8.3/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container CompletedMACS2peakCalling INFO @ Fri, 10 Dec 2021 09:35:57: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX7434140/SRX7434140.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX7434140/SRX7434140.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX7434140/SRX7434140.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX7434140/SRX7434140.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 @ Fri, 10 Dec 2021 09:35:57: #1 read tag files... INFO @ Fri, 10 Dec 2021 09:35:57: #1 read treatment tags... INFO @ Fri, 10 Dec 2021 09:36:04: 1000000 INFO @ Fri, 10 Dec 2021 09:36:04: #3 Call peaks for each chromosome... INFO @ Fri, 10 Dec 2021 09:36:10: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX7434140/SRX7434140.10_peaks.xls INFO @ Fri, 10 Dec 2021 09:36:10: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX7434140/SRX7434140.10_peaks.narrowPeak INFO @ Fri, 10 Dec 2021 09:36:10: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX7434140/SRX7434140.10_summits.bed INFO @ Fri, 10 Dec 2021 09:36:10: Done! pass1 - making usageList (328 chroms): 1 millis pass2 - checking and writing primary data (775 records, 4 fields): 27 millis CompletedMACS2peakCalling INFO @ Fri, 10 Dec 2021 09:36:11: 2000000 INFO @ Fri, 10 Dec 2021 09:36:18: 3000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Fri, 10 Dec 2021 09:36:26: 4000000 INFO @ Fri, 10 Dec 2021 09:36:32: #1 tag size is determined as 51 bps INFO @ Fri, 10 Dec 2021 09:36:32: #1 tag size = 51 INFO @ Fri, 10 Dec 2021 09:36:32: #1 total tags in treatment: 4923180 INFO @ Fri, 10 Dec 2021 09:36:32: #1 user defined the maximum tags... INFO @ Fri, 10 Dec 2021 09:36:32: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 10 Dec 2021 09:36:33: #1 tags after filtering in treatment: 4922980 INFO @ Fri, 10 Dec 2021 09:36:33: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 10 Dec 2021 09:36:33: #1 finished! INFO @ Fri, 10 Dec 2021 09:36:33: #2 Build Peak Model... INFO @ Fri, 10 Dec 2021 09:36:33: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Dec 2021 09:36:33: #2 number of paired peaks: 720 WARNING @ Fri, 10 Dec 2021 09:36:33: Fewer paired peaks (720) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 720 pairs to build model! INFO @ Fri, 10 Dec 2021 09:36:33: start model_add_line... INFO @ Fri, 10 Dec 2021 09:36:33: start X-correlation... INFO @ Fri, 10 Dec 2021 09:36:33: end of X-cor INFO @ Fri, 10 Dec 2021 09:36:33: #2 finished! INFO @ Fri, 10 Dec 2021 09:36:33: #2 predicted fragment length is 59 bps INFO @ Fri, 10 Dec 2021 09:36:33: #2 alternative fragment length(s) may be 59 bps INFO @ Fri, 10 Dec 2021 09:36:33: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX7434140/SRX7434140.20_model.r WARNING @ Fri, 10 Dec 2021 09:36:33: #2 Since the d (59) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 10 Dec 2021 09:36:33: #2 You may need to consider one of the other alternative d(s): 59 WARNING @ Fri, 10 Dec 2021 09:36:33: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Fri, 10 Dec 2021 09:36:33: #3 Call peaks... INFO @ Fri, 10 Dec 2021 09:36:33: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Fri, 10 Dec 2021 09:36:47: #3 Call peaks for each chromosome... INFO @ Fri, 10 Dec 2021 09:36:55: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX7434140/SRX7434140.20_peaks.xls INFO @ Fri, 10 Dec 2021 09:36:55: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX7434140/SRX7434140.20_peaks.narrowPeak INFO @ Fri, 10 Dec 2021 09:36:55: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX7434140/SRX7434140.20_summits.bed INFO @ Fri, 10 Dec 2021 09:36:55: Done! pass1 - making usageList (113 chroms): 1 millis pass2 - checking and writing primary data (183 records, 4 fields): 7 millis CompletedMACS2peakCalling