Job ID = 6529624 SRX = SRX3511963 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: 00:03:21 6880213 reads; of these: 6880213 (100.00%) were unpaired; of these: 673775 (9.79%) aligned 0 times 4416256 (64.19%) aligned exactly 1 time 1790182 (26.02%) aligned >1 times 90.21% overall alignment rate Time searching: 00:03:21 Overall time: 00:03:21 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] 769131 / 6206438 = 0.1239 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/3.5.2/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Tue, 30 Jun 2020 02:32:52: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX3511963/SRX3511963.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX3511963/SRX3511963.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX3511963/SRX3511963.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX3511963/SRX3511963.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, 30 Jun 2020 02:32:52: #1 read tag files... INFO @ Tue, 30 Jun 2020 02:32:52: #1 read treatment tags... INFO @ Tue, 30 Jun 2020 02:33:02: 1000000 INFO @ Tue, 30 Jun 2020 02:33:12: 2000000 WARNING: Skipping mount /opt/pkg/singularity/3.5.2/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Tue, 30 Jun 2020 02:33:22: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX3511963/SRX3511963.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX3511963/SRX3511963.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX3511963/SRX3511963.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX3511963/SRX3511963.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, 30 Jun 2020 02:33:22: #1 read tag files... INFO @ Tue, 30 Jun 2020 02:33:22: #1 read treatment tags... INFO @ Tue, 30 Jun 2020 02:33:23: 3000000 INFO @ Tue, 30 Jun 2020 02:33:34: 4000000 INFO @ Tue, 30 Jun 2020 02:33:35: 1000000 INFO @ Tue, 30 Jun 2020 02:33:47: 5000000 INFO @ Tue, 30 Jun 2020 02:33:48: 2000000 BedGraph に変換中... WARNING: Skipping mount /opt/pkg/singularity/3.5.2/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Tue, 30 Jun 2020 02:33:52: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX3511963/SRX3511963.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX3511963/SRX3511963.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX3511963/SRX3511963.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX3511963/SRX3511963.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, 30 Jun 2020 02:33:52: #1 read tag files... INFO @ Tue, 30 Jun 2020 02:33:52: #1 read treatment tags... INFO @ Tue, 30 Jun 2020 02:33:52: #1 tag size is determined as 91 bps INFO @ Tue, 30 Jun 2020 02:33:52: #1 tag size = 91 INFO @ Tue, 30 Jun 2020 02:33:52: #1 total tags in treatment: 5437307 INFO @ Tue, 30 Jun 2020 02:33:52: #1 user defined the maximum tags... INFO @ Tue, 30 Jun 2020 02:33:52: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 30 Jun 2020 02:33:52: #1 tags after filtering in treatment: 5437304 INFO @ Tue, 30 Jun 2020 02:33:52: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 30 Jun 2020 02:33:52: #1 finished! INFO @ Tue, 30 Jun 2020 02:33:52: #2 Build Peak Model... INFO @ Tue, 30 Jun 2020 02:33:52: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 30 Jun 2020 02:33:53: #2 number of paired peaks: 290 WARNING @ Tue, 30 Jun 2020 02:33:53: Fewer paired peaks (290) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 290 pairs to build model! INFO @ Tue, 30 Jun 2020 02:33:53: start model_add_line... INFO @ Tue, 30 Jun 2020 02:33:53: start X-correlation... INFO @ Tue, 30 Jun 2020 02:33:53: end of X-cor INFO @ Tue, 30 Jun 2020 02:33:53: #2 finished! INFO @ Tue, 30 Jun 2020 02:33:53: #2 predicted fragment length is 89 bps INFO @ Tue, 30 Jun 2020 02:33:53: #2 alternative fragment length(s) may be 89 bps INFO @ Tue, 30 Jun 2020 02:33:53: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX3511963/SRX3511963.05_model.r WARNING @ Tue, 30 Jun 2020 02:33:53: #2 Since the d (89) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 30 Jun 2020 02:33:53: #2 You may need to consider one of the other alternative d(s): 89 WARNING @ Tue, 30 Jun 2020 02:33:53: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 30 Jun 2020 02:33:53: #3 Call peaks... INFO @ Tue, 30 Jun 2020 02:33:53: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 30 Jun 2020 02:34:01: 3000000 INFO @ Tue, 30 Jun 2020 02:34:02: 1000000 INFO @ Tue, 30 Jun 2020 02:34:06: #3 Call peaks for each chromosome... INFO @ Tue, 30 Jun 2020 02:34:11: 2000000 INFO @ Tue, 30 Jun 2020 02:34:12: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX3511963/SRX3511963.05_peaks.xls INFO @ Tue, 30 Jun 2020 02:34:12: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX3511963/SRX3511963.05_peaks.narrowPeak INFO @ Tue, 30 Jun 2020 02:34:12: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX3511963/SRX3511963.05_summits.bed INFO @ Tue, 30 Jun 2020 02:34:12: Done! pass1 - making usageList (546 chroms): 1 millis pass2 - checking and writing primary data (1199 records, 4 fields): 18 millis CompletedMACS2peakCalling INFO @ Tue, 30 Jun 2020 02:34:13: 4000000 INFO @ Tue, 30 Jun 2020 02:34:21: 3000000 INFO @ Tue, 30 Jun 2020 02:34:25: 5000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 30 Jun 2020 02:34:31: 4000000 INFO @ Tue, 30 Jun 2020 02:34:31: #1 tag size is determined as 91 bps INFO @ Tue, 30 Jun 2020 02:34:31: #1 tag size = 91 INFO @ Tue, 30 Jun 2020 02:34:31: #1 total tags in treatment: 5437307 INFO @ Tue, 30 Jun 2020 02:34:31: #1 user defined the maximum tags... INFO @ Tue, 30 Jun 2020 02:34:31: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 30 Jun 2020 02:34:31: #1 tags after filtering in treatment: 5437304 INFO @ Tue, 30 Jun 2020 02:34:31: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 30 Jun 2020 02:34:31: #1 finished! INFO @ Tue, 30 Jun 2020 02:34:31: #2 Build Peak Model... INFO @ Tue, 30 Jun 2020 02:34:31: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 30 Jun 2020 02:34:32: #2 number of paired peaks: 290 WARNING @ Tue, 30 Jun 2020 02:34:32: Fewer paired peaks (290) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 290 pairs to build model! INFO @ Tue, 30 Jun 2020 02:34:32: start model_add_line... INFO @ Tue, 30 Jun 2020 02:34:32: start X-correlation... INFO @ Tue, 30 Jun 2020 02:34:32: end of X-cor INFO @ Tue, 30 Jun 2020 02:34:32: #2 finished! INFO @ Tue, 30 Jun 2020 02:34:32: #2 predicted fragment length is 89 bps INFO @ Tue, 30 Jun 2020 02:34:32: #2 alternative fragment length(s) may be 89 bps INFO @ Tue, 30 Jun 2020 02:34:32: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX3511963/SRX3511963.10_model.r WARNING @ Tue, 30 Jun 2020 02:34:32: #2 Since the d (89) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 30 Jun 2020 02:34:32: #2 You may need to consider one of the other alternative d(s): 89 WARNING @ Tue, 30 Jun 2020 02:34:32: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 30 Jun 2020 02:34:32: #3 Call peaks... INFO @ Tue, 30 Jun 2020 02:34:32: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 30 Jun 2020 02:34:39: 5000000 BigWig に変換しました。 INFO @ Tue, 30 Jun 2020 02:34:43: #1 tag size is determined as 91 bps INFO @ Tue, 30 Jun 2020 02:34:43: #1 tag size = 91 INFO @ Tue, 30 Jun 2020 02:34:43: #1 total tags in treatment: 5437307 INFO @ Tue, 30 Jun 2020 02:34:43: #1 user defined the maximum tags... INFO @ Tue, 30 Jun 2020 02:34:43: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 30 Jun 2020 02:34:43: #1 tags after filtering in treatment: 5437304 INFO @ Tue, 30 Jun 2020 02:34:43: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 30 Jun 2020 02:34:43: #1 finished! INFO @ Tue, 30 Jun 2020 02:34:43: #2 Build Peak Model... INFO @ Tue, 30 Jun 2020 02:34:43: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 30 Jun 2020 02:34:44: #2 number of paired peaks: 290 WARNING @ Tue, 30 Jun 2020 02:34:44: Fewer paired peaks (290) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 290 pairs to build model! INFO @ Tue, 30 Jun 2020 02:34:44: start model_add_line... INFO @ Tue, 30 Jun 2020 02:34:44: start X-correlation... INFO @ Tue, 30 Jun 2020 02:34:44: end of X-cor INFO @ Tue, 30 Jun 2020 02:34:44: #2 finished! INFO @ Tue, 30 Jun 2020 02:34:44: #2 predicted fragment length is 89 bps INFO @ Tue, 30 Jun 2020 02:34:44: #2 alternative fragment length(s) may be 89 bps INFO @ Tue, 30 Jun 2020 02:34:44: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX3511963/SRX3511963.20_model.r WARNING @ Tue, 30 Jun 2020 02:34:44: #2 Since the d (89) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 30 Jun 2020 02:34:44: #2 You may need to consider one of the other alternative d(s): 89 WARNING @ Tue, 30 Jun 2020 02:34:44: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 30 Jun 2020 02:34:44: #3 Call peaks... INFO @ Tue, 30 Jun 2020 02:34:44: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 30 Jun 2020 02:34:45: #3 Call peaks for each chromosome... INFO @ Tue, 30 Jun 2020 02:34:51: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX3511963/SRX3511963.10_peaks.xls INFO @ Tue, 30 Jun 2020 02:34:51: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX3511963/SRX3511963.10_peaks.narrowPeak INFO @ Tue, 30 Jun 2020 02:34:51: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX3511963/SRX3511963.10_summits.bed INFO @ Tue, 30 Jun 2020 02:34:51: Done! pass1 - making usageList (344 chroms): 2 millis pass2 - checking and writing primary data (593 records, 4 fields): 13 millis CompletedMACS2peakCalling INFO @ Tue, 30 Jun 2020 02:34:56: #3 Call peaks for each chromosome... INFO @ Tue, 30 Jun 2020 02:35:02: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX3511963/SRX3511963.20_peaks.xls INFO @ Tue, 30 Jun 2020 02:35:02: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX3511963/SRX3511963.20_peaks.narrowPeak INFO @ Tue, 30 Jun 2020 02:35:02: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX3511963/SRX3511963.20_summits.bed INFO @ Tue, 30 Jun 2020 02:35:02: Done! pass1 - making usageList (153 chroms): 1 millis pass2 - checking and writing primary data (230 records, 4 fields): 6 millis CompletedMACS2peakCalling