Job ID = 6529371 SRX = SRX231893 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: 00:01:10 9830247 reads; of these: 9830247 (100.00%) were unpaired; of these: 4991642 (50.78%) aligned 0 times 3792751 (38.58%) aligned exactly 1 time 1045854 (10.64%) aligned >1 times 49.22% overall alignment rate Time searching: 00:01:10 Overall time: 00:01:10 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] 199355 / 4838605 = 0.0412 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 01:55:21: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX231893/SRX231893.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX231893/SRX231893.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX231893/SRX231893.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX231893/SRX231893.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 01:55:21: #1 read tag files... INFO @ Tue, 30 Jun 2020 01:55:21: #1 read treatment tags... INFO @ Tue, 30 Jun 2020 01:55:26: 1000000 INFO @ Tue, 30 Jun 2020 01:55:32: 2000000 INFO @ Tue, 30 Jun 2020 01:55:37: 3000000 INFO @ Tue, 30 Jun 2020 01:55:43: 4000000 INFO @ Tue, 30 Jun 2020 01:55:46: #1 tag size is determined as 35 bps INFO @ Tue, 30 Jun 2020 01:55:46: #1 tag size = 35 INFO @ Tue, 30 Jun 2020 01:55:46: #1 total tags in treatment: 4639250 INFO @ Tue, 30 Jun 2020 01:55:46: #1 user defined the maximum tags... INFO @ Tue, 30 Jun 2020 01:55:46: #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 01:55:47: #1 tags after filtering in treatment: 4639241 INFO @ Tue, 30 Jun 2020 01:55:47: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 30 Jun 2020 01:55:47: #1 finished! INFO @ Tue, 30 Jun 2020 01:55:47: #2 Build Peak Model... INFO @ Tue, 30 Jun 2020 01:55:47: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 30 Jun 2020 01:55:47: #2 number of paired peaks: 271 WARNING @ Tue, 30 Jun 2020 01:55:47: Fewer paired peaks (271) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 271 pairs to build model! INFO @ Tue, 30 Jun 2020 01:55:47: start model_add_line... INFO @ Tue, 30 Jun 2020 01:55:47: start X-correlation... INFO @ Tue, 30 Jun 2020 01:55:47: end of X-cor INFO @ Tue, 30 Jun 2020 01:55:47: #2 finished! INFO @ Tue, 30 Jun 2020 01:55:47: #2 predicted fragment length is 46 bps INFO @ Tue, 30 Jun 2020 01:55:47: #2 alternative fragment length(s) may be 46,497,546 bps INFO @ Tue, 30 Jun 2020 01:55:47: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX231893/SRX231893.05_model.r WARNING @ Tue, 30 Jun 2020 01:55:47: #2 Since the d (46) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 30 Jun 2020 01:55:47: #2 You may need to consider one of the other alternative d(s): 46,497,546 WARNING @ Tue, 30 Jun 2020 01:55:47: #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 01:55:47: #3 Call peaks... INFO @ Tue, 30 Jun 2020 01:55:47: #3 Pre-compute pvalue-qvalue table... 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 01:55:50: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX231893/SRX231893.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX231893/SRX231893.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX231893/SRX231893.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX231893/SRX231893.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 01:55:50: #1 read tag files... INFO @ Tue, 30 Jun 2020 01:55:50: #1 read treatment tags... INFO @ Tue, 30 Jun 2020 01:55:56: 1000000 INFO @ Tue, 30 Jun 2020 01:55:57: #3 Call peaks for each chromosome... INFO @ Tue, 30 Jun 2020 01:56:01: 2000000 INFO @ Tue, 30 Jun 2020 01:56:02: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX231893/SRX231893.05_peaks.xls INFO @ Tue, 30 Jun 2020 01:56:02: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX231893/SRX231893.05_peaks.narrowPeak INFO @ Tue, 30 Jun 2020 01:56:02: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX231893/SRX231893.05_summits.bed INFO @ Tue, 30 Jun 2020 01:56:02: Done! pass1 - making usageList (410 chroms): 1 millis pass2 - checking and writing primary data (1110 records, 4 fields): 12 millis CompletedMACS2peakCalling INFO @ Tue, 30 Jun 2020 01:56:06: 3000000 INFO @ Tue, 30 Jun 2020 01:56:11: 4000000 INFO @ Tue, 30 Jun 2020 01:56:14: #1 tag size is determined as 35 bps INFO @ Tue, 30 Jun 2020 01:56:14: #1 tag size = 35 INFO @ Tue, 30 Jun 2020 01:56:14: #1 total tags in treatment: 4639250 INFO @ Tue, 30 Jun 2020 01:56:14: #1 user defined the maximum tags... INFO @ Tue, 30 Jun 2020 01:56:14: #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 01:56:14: #1 tags after filtering in treatment: 4639241 INFO @ Tue, 30 Jun 2020 01:56:14: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 30 Jun 2020 01:56:14: #1 finished! INFO @ Tue, 30 Jun 2020 01:56:14: #2 Build Peak Model... INFO @ Tue, 30 Jun 2020 01:56:14: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 30 Jun 2020 01:56:15: #2 number of paired peaks: 271 WARNING @ Tue, 30 Jun 2020 01:56:15: Fewer paired peaks (271) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 271 pairs to build model! INFO @ Tue, 30 Jun 2020 01:56:15: start model_add_line... INFO @ Tue, 30 Jun 2020 01:56:15: start X-correlation... INFO @ Tue, 30 Jun 2020 01:56:15: end of X-cor INFO @ Tue, 30 Jun 2020 01:56:15: #2 finished! INFO @ Tue, 30 Jun 2020 01:56:15: #2 predicted fragment length is 46 bps INFO @ Tue, 30 Jun 2020 01:56:15: #2 alternative fragment length(s) may be 46,497,546 bps INFO @ Tue, 30 Jun 2020 01:56:15: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX231893/SRX231893.10_model.r WARNING @ Tue, 30 Jun 2020 01:56:15: #2 Since the d (46) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 30 Jun 2020 01:56:15: #2 You may need to consider one of the other alternative d(s): 46,497,546 WARNING @ Tue, 30 Jun 2020 01:56:15: #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 01:56:15: #3 Call peaks... INFO @ Tue, 30 Jun 2020 01:56:15: #3 Pre-compute pvalue-qvalue table... 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 01:56:20: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX231893/SRX231893.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX231893/SRX231893.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX231893/SRX231893.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX231893/SRX231893.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 01:56:20: #1 read tag files... INFO @ Tue, 30 Jun 2020 01:56:20: #1 read treatment tags... INFO @ Tue, 30 Jun 2020 01:56:25: #3 Call peaks for each chromosome... INFO @ Tue, 30 Jun 2020 01:56:26: 1000000 INFO @ Tue, 30 Jun 2020 01:56:30: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX231893/SRX231893.10_peaks.xls INFO @ Tue, 30 Jun 2020 01:56:30: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX231893/SRX231893.10_peaks.narrowPeak INFO @ Tue, 30 Jun 2020 01:56:30: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX231893/SRX231893.10_summits.bed INFO @ Tue, 30 Jun 2020 01:56:30: Done! pass1 - making usageList (202 chroms): 0 millis pass2 - checking and writing primary data (389 records, 4 fields): 7 millis CompletedMACS2peakCalling INFO @ Tue, 30 Jun 2020 01:56:31: 2000000 INFO @ Tue, 30 Jun 2020 01:56:37: 3000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 30 Jun 2020 01:56:43: 4000000 INFO @ Tue, 30 Jun 2020 01:56:46: #1 tag size is determined as 35 bps INFO @ Tue, 30 Jun 2020 01:56:46: #1 tag size = 35 INFO @ Tue, 30 Jun 2020 01:56:46: #1 total tags in treatment: 4639250 INFO @ Tue, 30 Jun 2020 01:56:46: #1 user defined the maximum tags... INFO @ Tue, 30 Jun 2020 01:56:46: #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 01:56:47: #1 tags after filtering in treatment: 4639241 INFO @ Tue, 30 Jun 2020 01:56:47: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 30 Jun 2020 01:56:47: #1 finished! INFO @ Tue, 30 Jun 2020 01:56:47: #2 Build Peak Model... INFO @ Tue, 30 Jun 2020 01:56:47: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 30 Jun 2020 01:56:47: #2 number of paired peaks: 271 WARNING @ Tue, 30 Jun 2020 01:56:47: Fewer paired peaks (271) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 271 pairs to build model! INFO @ Tue, 30 Jun 2020 01:56:47: start model_add_line... INFO @ Tue, 30 Jun 2020 01:56:47: start X-correlation... INFO @ Tue, 30 Jun 2020 01:56:47: end of X-cor INFO @ Tue, 30 Jun 2020 01:56:47: #2 finished! INFO @ Tue, 30 Jun 2020 01:56:47: #2 predicted fragment length is 46 bps INFO @ Tue, 30 Jun 2020 01:56:47: #2 alternative fragment length(s) may be 46,497,546 bps INFO @ Tue, 30 Jun 2020 01:56:47: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX231893/SRX231893.20_model.r WARNING @ Tue, 30 Jun 2020 01:56:47: #2 Since the d (46) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 30 Jun 2020 01:56:47: #2 You may need to consider one of the other alternative d(s): 46,497,546 WARNING @ Tue, 30 Jun 2020 01:56:47: #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 01:56:47: #3 Call peaks... INFO @ Tue, 30 Jun 2020 01:56:47: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Tue, 30 Jun 2020 01:56:57: #3 Call peaks for each chromosome... INFO @ Tue, 30 Jun 2020 01:57:02: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX231893/SRX231893.20_peaks.xls INFO @ Tue, 30 Jun 2020 01:57:02: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX231893/SRX231893.20_peaks.narrowPeak INFO @ Tue, 30 Jun 2020 01:57:02: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX231893/SRX231893.20_summits.bed INFO @ Tue, 30 Jun 2020 01:57:02: Done! pass1 - making usageList (81 chroms): 0 millis pass2 - checking and writing primary data (132 records, 4 fields): 4 millis CompletedMACS2peakCalling