Job ID = 6529613 SRX = SRX3511941 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: 00:04:40 11826653 reads; of these: 11826653 (100.00%) were unpaired; of these: 3626720 (30.67%) aligned 0 times 6859279 (58.00%) aligned exactly 1 time 1340654 (11.34%) aligned >1 times 69.33% overall alignment rate Time searching: 00:04:41 Overall time: 00:04:41 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] 403182 / 8199933 = 0.0492 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 02:31:08: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX3511941/SRX3511941.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX3511941/SRX3511941.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX3511941/SRX3511941.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX3511941/SRX3511941.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 02:31:08: #1 read tag files... INFO @ Tue, 30 Jun 2020 02:31:08: #1 read treatment tags... INFO @ Tue, 30 Jun 2020 02:31:16: 1000000 INFO @ Tue, 30 Jun 2020 02:31:25: 2000000 INFO @ Tue, 30 Jun 2020 02:31:34: 3000000 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 02:31:36: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX3511941/SRX3511941.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX3511941/SRX3511941.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX3511941/SRX3511941.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX3511941/SRX3511941.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 02:31:36: #1 read tag files... INFO @ Tue, 30 Jun 2020 02:31:36: #1 read treatment tags... INFO @ Tue, 30 Jun 2020 02:31:43: 4000000 INFO @ Tue, 30 Jun 2020 02:31:45: 1000000 INFO @ Tue, 30 Jun 2020 02:31:52: 5000000 INFO @ Tue, 30 Jun 2020 02:31:53: 2000000 INFO @ Tue, 30 Jun 2020 02:32:01: 6000000 INFO @ Tue, 30 Jun 2020 02:32:01: 3000000 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 02:32:06: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX3511941/SRX3511941.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX3511941/SRX3511941.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX3511941/SRX3511941.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX3511941/SRX3511941.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 02:32:06: #1 read tag files... INFO @ Tue, 30 Jun 2020 02:32:06: #1 read treatment tags... INFO @ Tue, 30 Jun 2020 02:32:10: 4000000 INFO @ Tue, 30 Jun 2020 02:32:11: 7000000 INFO @ Tue, 30 Jun 2020 02:32:16: 1000000 INFO @ Tue, 30 Jun 2020 02:32:18: #1 tag size is determined as 100 bps INFO @ Tue, 30 Jun 2020 02:32:18: #1 tag size = 100 INFO @ Tue, 30 Jun 2020 02:32:18: #1 total tags in treatment: 7796751 INFO @ Tue, 30 Jun 2020 02:32:18: #1 user defined the maximum tags... INFO @ Tue, 30 Jun 2020 02:32:18: #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 02:32:19: #1 tags after filtering in treatment: 7796704 INFO @ Tue, 30 Jun 2020 02:32:19: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 30 Jun 2020 02:32:19: #1 finished! INFO @ Tue, 30 Jun 2020 02:32:19: #2 Build Peak Model... INFO @ Tue, 30 Jun 2020 02:32:19: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 30 Jun 2020 02:32:19: #2 number of paired peaks: 239 WARNING @ Tue, 30 Jun 2020 02:32:19: Fewer paired peaks (239) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 239 pairs to build model! INFO @ Tue, 30 Jun 2020 02:32:19: start model_add_line... INFO @ Tue, 30 Jun 2020 02:32:19: start X-correlation... INFO @ Tue, 30 Jun 2020 02:32:19: end of X-cor INFO @ Tue, 30 Jun 2020 02:32:19: #2 finished! INFO @ Tue, 30 Jun 2020 02:32:19: #2 predicted fragment length is 103 bps INFO @ Tue, 30 Jun 2020 02:32:19: #2 alternative fragment length(s) may be 103 bps INFO @ Tue, 30 Jun 2020 02:32:19: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX3511941/SRX3511941.05_model.r WARNING @ Tue, 30 Jun 2020 02:32:19: #2 Since the d (103) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 30 Jun 2020 02:32:19: #2 You may need to consider one of the other alternative d(s): 103 WARNING @ Tue, 30 Jun 2020 02:32:19: #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 02:32:19: #3 Call peaks... INFO @ Tue, 30 Jun 2020 02:32:19: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 30 Jun 2020 02:32:19: 5000000 INFO @ Tue, 30 Jun 2020 02:32:26: 2000000 INFO @ Tue, 30 Jun 2020 02:32:29: 6000000 INFO @ Tue, 30 Jun 2020 02:32:35: #3 Call peaks for each chromosome... INFO @ Tue, 30 Jun 2020 02:32:35: 3000000 INFO @ Tue, 30 Jun 2020 02:32:40: 7000000 INFO @ Tue, 30 Jun 2020 02:32:43: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX3511941/SRX3511941.05_peaks.xls INFO @ Tue, 30 Jun 2020 02:32:43: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX3511941/SRX3511941.05_peaks.narrowPeak INFO @ Tue, 30 Jun 2020 02:32:43: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX3511941/SRX3511941.05_summits.bed INFO @ Tue, 30 Jun 2020 02:32:43: Done! pass1 - making usageList (243 chroms): 2 millis pass2 - checking and writing primary data (538 records, 4 fields): 21 millis CompletedMACS2peakCalling INFO @ Tue, 30 Jun 2020 02:32:45: 4000000 INFO @ Tue, 30 Jun 2020 02:32:48: #1 tag size is determined as 100 bps INFO @ Tue, 30 Jun 2020 02:32:48: #1 tag size = 100 INFO @ Tue, 30 Jun 2020 02:32:48: #1 total tags in treatment: 7796751 INFO @ Tue, 30 Jun 2020 02:32:48: #1 user defined the maximum tags... INFO @ Tue, 30 Jun 2020 02:32:48: #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 02:32:49: #1 tags after filtering in treatment: 7796704 INFO @ Tue, 30 Jun 2020 02:32:49: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 30 Jun 2020 02:32:49: #1 finished! INFO @ Tue, 30 Jun 2020 02:32:49: #2 Build Peak Model... INFO @ Tue, 30 Jun 2020 02:32:49: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 30 Jun 2020 02:32:49: #2 number of paired peaks: 239 WARNING @ Tue, 30 Jun 2020 02:32:49: Fewer paired peaks (239) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 239 pairs to build model! INFO @ Tue, 30 Jun 2020 02:32:49: start model_add_line... INFO @ Tue, 30 Jun 2020 02:32:50: start X-correlation... INFO @ Tue, 30 Jun 2020 02:32:50: end of X-cor INFO @ Tue, 30 Jun 2020 02:32:50: #2 finished! INFO @ Tue, 30 Jun 2020 02:32:50: #2 predicted fragment length is 103 bps INFO @ Tue, 30 Jun 2020 02:32:50: #2 alternative fragment length(s) may be 103 bps INFO @ Tue, 30 Jun 2020 02:32:50: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX3511941/SRX3511941.10_model.r WARNING @ Tue, 30 Jun 2020 02:32:50: #2 Since the d (103) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 30 Jun 2020 02:32:50: #2 You may need to consider one of the other alternative d(s): 103 WARNING @ Tue, 30 Jun 2020 02:32:50: #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 02:32:50: #3 Call peaks... INFO @ Tue, 30 Jun 2020 02:32:50: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 30 Jun 2020 02:32:55: 5000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 30 Jun 2020 02:33:04: 6000000 INFO @ Tue, 30 Jun 2020 02:33:06: #3 Call peaks for each chromosome... INFO @ Tue, 30 Jun 2020 02:33:14: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX3511941/SRX3511941.10_peaks.xls INFO @ Tue, 30 Jun 2020 02:33:14: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX3511941/SRX3511941.10_peaks.narrowPeak INFO @ Tue, 30 Jun 2020 02:33:14: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX3511941/SRX3511941.10_summits.bed INFO @ Tue, 30 Jun 2020 02:33:14: Done! INFO @ Tue, 30 Jun 2020 02:33:14: 7000000 pass1 - making usageList (129 chroms): 1 millis pass2 - checking and writing primary data (263 records, 4 fields): 9 millis CompletedMACS2peakCalling INFO @ Tue, 30 Jun 2020 02:33:22: #1 tag size is determined as 100 bps INFO @ Tue, 30 Jun 2020 02:33:22: #1 tag size = 100 INFO @ Tue, 30 Jun 2020 02:33:22: #1 total tags in treatment: 7796751 INFO @ Tue, 30 Jun 2020 02:33:22: #1 user defined the maximum tags... INFO @ Tue, 30 Jun 2020 02:33:22: #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 02:33:23: #1 tags after filtering in treatment: 7796704 INFO @ Tue, 30 Jun 2020 02:33:23: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 30 Jun 2020 02:33:23: #1 finished! INFO @ Tue, 30 Jun 2020 02:33:23: #2 Build Peak Model... INFO @ Tue, 30 Jun 2020 02:33:23: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 30 Jun 2020 02:33:23: #2 number of paired peaks: 239 WARNING @ Tue, 30 Jun 2020 02:33:23: Fewer paired peaks (239) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 239 pairs to build model! INFO @ Tue, 30 Jun 2020 02:33:23: start model_add_line... INFO @ Tue, 30 Jun 2020 02:33:23: start X-correlation... INFO @ Tue, 30 Jun 2020 02:33:23: end of X-cor INFO @ Tue, 30 Jun 2020 02:33:23: #2 finished! INFO @ Tue, 30 Jun 2020 02:33:23: #2 predicted fragment length is 103 bps INFO @ Tue, 30 Jun 2020 02:33:23: #2 alternative fragment length(s) may be 103 bps INFO @ Tue, 30 Jun 2020 02:33:23: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX3511941/SRX3511941.20_model.r WARNING @ Tue, 30 Jun 2020 02:33:23: #2 Since the d (103) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 30 Jun 2020 02:33:23: #2 You may need to consider one of the other alternative d(s): 103 WARNING @ Tue, 30 Jun 2020 02:33:23: #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 02:33:23: #3 Call peaks... INFO @ Tue, 30 Jun 2020 02:33:23: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Tue, 30 Jun 2020 02:33:39: #3 Call peaks for each chromosome... INFO @ Tue, 30 Jun 2020 02:33:47: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX3511941/SRX3511941.20_peaks.xls INFO @ Tue, 30 Jun 2020 02:33:47: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX3511941/SRX3511941.20_peaks.narrowPeak INFO @ Tue, 30 Jun 2020 02:33:47: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX3511941/SRX3511941.20_summits.bed INFO @ Tue, 30 Jun 2020 02:33:47: Done! pass1 - making usageList (80 chroms): 1 millis pass2 - checking and writing primary data (144 records, 4 fields): 6 millis CompletedMACS2peakCalling