Job ID = 6529833 SRX = SRX495253 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: 00:00:28 2188064 reads; of these: 2188064 (100.00%) were unpaired; of these: 320010 (14.63%) aligned 0 times 1584242 (72.40%) aligned exactly 1 time 283812 (12.97%) aligned >1 times 85.37% overall alignment rate Time searching: 00:00:28 Overall time: 00:00:28 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] 199090 / 1868054 = 0.1066 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 02:58:14: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX495253/SRX495253.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX495253/SRX495253.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX495253/SRX495253.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX495253/SRX495253.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 02:58:14: #1 read tag files... INFO @ Tue, 30 Jun 2020 02:58:14: #1 read treatment tags... INFO @ Tue, 30 Jun 2020 02:58:19: 1000000 INFO @ Tue, 30 Jun 2020 02:58:22: #1 tag size is determined as 50 bps INFO @ Tue, 30 Jun 2020 02:58:22: #1 tag size = 50 INFO @ Tue, 30 Jun 2020 02:58:22: #1 total tags in treatment: 1668964 INFO @ Tue, 30 Jun 2020 02:58:22: #1 user defined the maximum tags... INFO @ Tue, 30 Jun 2020 02:58:22: #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 02:58:23: #1 tags after filtering in treatment: 1668609 INFO @ Tue, 30 Jun 2020 02:58:23: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 30 Jun 2020 02:58:23: #1 finished! INFO @ Tue, 30 Jun 2020 02:58:23: #2 Build Peak Model... INFO @ Tue, 30 Jun 2020 02:58:23: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 30 Jun 2020 02:58:23: #2 number of paired peaks: 111 WARNING @ Tue, 30 Jun 2020 02:58:23: Fewer paired peaks (111) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 111 pairs to build model! INFO @ Tue, 30 Jun 2020 02:58:23: start model_add_line... INFO @ Tue, 30 Jun 2020 02:58:23: start X-correlation... INFO @ Tue, 30 Jun 2020 02:58:23: end of X-cor INFO @ Tue, 30 Jun 2020 02:58:23: #2 finished! INFO @ Tue, 30 Jun 2020 02:58:23: #2 predicted fragment length is 61 bps INFO @ Tue, 30 Jun 2020 02:58:23: #2 alternative fragment length(s) may be 61,172,212,391,428,460,535 bps INFO @ Tue, 30 Jun 2020 02:58:23: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX495253/SRX495253.05_model.r WARNING @ Tue, 30 Jun 2020 02:58:23: #2 Since the d (61) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 30 Jun 2020 02:58:23: #2 You may need to consider one of the other alternative d(s): 61,172,212,391,428,460,535 WARNING @ Tue, 30 Jun 2020 02:58:23: #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 02:58:23: #3 Call peaks... INFO @ Tue, 30 Jun 2020 02:58:23: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 30 Jun 2020 02:58:27: #3 Call peaks for each chromosome... INFO @ Tue, 30 Jun 2020 02:58:29: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX495253/SRX495253.05_peaks.xls INFO @ Tue, 30 Jun 2020 02:58:29: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX495253/SRX495253.05_peaks.narrowPeak INFO @ Tue, 30 Jun 2020 02:58:29: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX495253/SRX495253.05_summits.bed INFO @ Tue, 30 Jun 2020 02:58:29: Done! pass1 - making usageList (71 chroms): 1 millis pass2 - checking and writing primary data (125 records, 4 fields): 2 millis CompletedMACS2peakCalling 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 02:58:44: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX495253/SRX495253.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX495253/SRX495253.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX495253/SRX495253.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX495253/SRX495253.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 02:58:44: #1 read tag files... INFO @ Tue, 30 Jun 2020 02:58:44: #1 read treatment tags... INFO @ Tue, 30 Jun 2020 02:58:49: 1000000 INFO @ Tue, 30 Jun 2020 02:58:53: #1 tag size is determined as 50 bps INFO @ Tue, 30 Jun 2020 02:58:53: #1 tag size = 50 INFO @ Tue, 30 Jun 2020 02:58:53: #1 total tags in treatment: 1668964 INFO @ Tue, 30 Jun 2020 02:58:53: #1 user defined the maximum tags... INFO @ Tue, 30 Jun 2020 02:58:53: #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 02:58:53: #1 tags after filtering in treatment: 1668609 INFO @ Tue, 30 Jun 2020 02:58:53: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 30 Jun 2020 02:58:53: #1 finished! INFO @ Tue, 30 Jun 2020 02:58:53: #2 Build Peak Model... INFO @ Tue, 30 Jun 2020 02:58:53: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 30 Jun 2020 02:58:53: #2 number of paired peaks: 111 WARNING @ Tue, 30 Jun 2020 02:58:53: Fewer paired peaks (111) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 111 pairs to build model! INFO @ Tue, 30 Jun 2020 02:58:53: start model_add_line... INFO @ Tue, 30 Jun 2020 02:58:53: start X-correlation... INFO @ Tue, 30 Jun 2020 02:58:53: end of X-cor INFO @ Tue, 30 Jun 2020 02:58:53: #2 finished! INFO @ Tue, 30 Jun 2020 02:58:53: #2 predicted fragment length is 61 bps INFO @ Tue, 30 Jun 2020 02:58:53: #2 alternative fragment length(s) may be 61,172,212,391,428,460,535 bps INFO @ Tue, 30 Jun 2020 02:58:53: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX495253/SRX495253.10_model.r WARNING @ Tue, 30 Jun 2020 02:58:53: #2 Since the d (61) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 30 Jun 2020 02:58:53: #2 You may need to consider one of the other alternative d(s): 61,172,212,391,428,460,535 WARNING @ Tue, 30 Jun 2020 02:58:53: #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 02:58:53: #3 Call peaks... INFO @ Tue, 30 Jun 2020 02:58:53: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 30 Jun 2020 02:58:57: #3 Call peaks for each chromosome... INFO @ Tue, 30 Jun 2020 02:58:59: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX495253/SRX495253.10_peaks.xls INFO @ Tue, 30 Jun 2020 02:58:59: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX495253/SRX495253.10_peaks.narrowPeak INFO @ Tue, 30 Jun 2020 02:58:59: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX495253/SRX495253.10_summits.bed INFO @ Tue, 30 Jun 2020 02:58:59: Done! pass1 - making usageList (46 chroms): 1 millis pass2 - checking and writing primary data (80 records, 4 fields): 2 millis CompletedMACS2peakCalling 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 02:59:14: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX495253/SRX495253.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX495253/SRX495253.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX495253/SRX495253.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX495253/SRX495253.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 02:59:14: #1 read tag files... INFO @ Tue, 30 Jun 2020 02:59:14: #1 read treatment tags... INFO @ Tue, 30 Jun 2020 02:59:19: 1000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 30 Jun 2020 02:59:23: #1 tag size is determined as 50 bps INFO @ Tue, 30 Jun 2020 02:59:23: #1 tag size = 50 INFO @ Tue, 30 Jun 2020 02:59:23: #1 total tags in treatment: 1668964 INFO @ Tue, 30 Jun 2020 02:59:23: #1 user defined the maximum tags... INFO @ Tue, 30 Jun 2020 02:59:23: #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 02:59:23: #1 tags after filtering in treatment: 1668609 INFO @ Tue, 30 Jun 2020 02:59:23: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 30 Jun 2020 02:59:23: #1 finished! INFO @ Tue, 30 Jun 2020 02:59:23: #2 Build Peak Model... INFO @ Tue, 30 Jun 2020 02:59:23: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 30 Jun 2020 02:59:23: #2 number of paired peaks: 111 WARNING @ Tue, 30 Jun 2020 02:59:23: Fewer paired peaks (111) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 111 pairs to build model! INFO @ Tue, 30 Jun 2020 02:59:23: start model_add_line... INFO @ Tue, 30 Jun 2020 02:59:23: start X-correlation... INFO @ Tue, 30 Jun 2020 02:59:23: end of X-cor INFO @ Tue, 30 Jun 2020 02:59:23: #2 finished! INFO @ Tue, 30 Jun 2020 02:59:23: #2 predicted fragment length is 61 bps INFO @ Tue, 30 Jun 2020 02:59:23: #2 alternative fragment length(s) may be 61,172,212,391,428,460,535 bps INFO @ Tue, 30 Jun 2020 02:59:23: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX495253/SRX495253.20_model.r WARNING @ Tue, 30 Jun 2020 02:59:23: #2 Since the d (61) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 30 Jun 2020 02:59:23: #2 You may need to consider one of the other alternative d(s): 61,172,212,391,428,460,535 WARNING @ Tue, 30 Jun 2020 02:59:23: #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 02:59:23: #3 Call peaks... INFO @ Tue, 30 Jun 2020 02:59:23: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Tue, 30 Jun 2020 02:59:27: #3 Call peaks for each chromosome... INFO @ Tue, 30 Jun 2020 02:59:29: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX495253/SRX495253.20_peaks.xls INFO @ Tue, 30 Jun 2020 02:59:29: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX495253/SRX495253.20_peaks.narrowPeak INFO @ Tue, 30 Jun 2020 02:59:29: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX495253/SRX495253.20_summits.bed INFO @ Tue, 30 Jun 2020 02:59:29: Done! pass1 - making usageList (27 chroms): 0 millis pass2 - checking and writing primary data (41 records, 4 fields): 2 millis CompletedMACS2peakCalling