Job ID = 6529374 SRX = SRX231914 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: 00:01:14 9708731 reads; of these: 9708731 (100.00%) were unpaired; of these: 5271118 (54.29%) aligned 0 times 3459013 (35.63%) aligned exactly 1 time 978600 (10.08%) aligned >1 times 45.71% overall alignment rate Time searching: 00:01:14 Overall time: 00:01:14 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] 182251 / 4437613 = 0.0411 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 01:58:07: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX231914/SRX231914.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX231914/SRX231914.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX231914/SRX231914.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX231914/SRX231914.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 01:58:07: #1 read tag files... INFO @ Tue, 30 Jun 2020 01:58:07: #1 read treatment tags... INFO @ Tue, 30 Jun 2020 01:58:12: 1000000 INFO @ Tue, 30 Jun 2020 01:58:17: 2000000 INFO @ Tue, 30 Jun 2020 01:58:22: 3000000 INFO @ Tue, 30 Jun 2020 01:58:27: 4000000 INFO @ Tue, 30 Jun 2020 01:58:29: #1 tag size is determined as 35 bps INFO @ Tue, 30 Jun 2020 01:58:29: #1 tag size = 35 INFO @ Tue, 30 Jun 2020 01:58:29: #1 total tags in treatment: 4255362 INFO @ Tue, 30 Jun 2020 01:58:29: #1 user defined the maximum tags... INFO @ Tue, 30 Jun 2020 01:58:29: #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 01:58:29: #1 tags after filtering in treatment: 4255352 INFO @ Tue, 30 Jun 2020 01:58:29: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 30 Jun 2020 01:58:29: #1 finished! INFO @ Tue, 30 Jun 2020 01:58:29: #2 Build Peak Model... INFO @ Tue, 30 Jun 2020 01:58:29: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 30 Jun 2020 01:58:30: #2 number of paired peaks: 234 WARNING @ Tue, 30 Jun 2020 01:58:30: Fewer paired peaks (234) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 234 pairs to build model! INFO @ Tue, 30 Jun 2020 01:58:30: start model_add_line... INFO @ Tue, 30 Jun 2020 01:58:30: start X-correlation... INFO @ Tue, 30 Jun 2020 01:58:30: end of X-cor INFO @ Tue, 30 Jun 2020 01:58:30: #2 finished! INFO @ Tue, 30 Jun 2020 01:58:30: #2 predicted fragment length is 41 bps INFO @ Tue, 30 Jun 2020 01:58:30: #2 alternative fragment length(s) may be 41 bps INFO @ Tue, 30 Jun 2020 01:58:30: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX231914/SRX231914.05_model.r WARNING @ Tue, 30 Jun 2020 01:58:30: #2 Since the d (41) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 30 Jun 2020 01:58:30: #2 You may need to consider one of the other alternative d(s): 41 WARNING @ Tue, 30 Jun 2020 01:58:30: #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 01:58:30: #3 Call peaks... INFO @ Tue, 30 Jun 2020 01:58:30: #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 01:58:37: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX231914/SRX231914.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX231914/SRX231914.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX231914/SRX231914.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX231914/SRX231914.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 01:58:37: #1 read tag files... INFO @ Tue, 30 Jun 2020 01:58:37: #1 read treatment tags... INFO @ Tue, 30 Jun 2020 01:58:41: #3 Call peaks for each chromosome... INFO @ Tue, 30 Jun 2020 01:58:42: 1000000 INFO @ Tue, 30 Jun 2020 01:58:46: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX231914/SRX231914.05_peaks.xls INFO @ Tue, 30 Jun 2020 01:58:46: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX231914/SRX231914.05_peaks.narrowPeak INFO @ Tue, 30 Jun 2020 01:58:46: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX231914/SRX231914.05_summits.bed INFO @ Tue, 30 Jun 2020 01:58:46: Done! pass1 - making usageList (205 chroms): 1 millis pass2 - checking and writing primary data (471 records, 4 fields): 9 millis CompletedMACS2peakCalling INFO @ Tue, 30 Jun 2020 01:58:47: 2000000 INFO @ Tue, 30 Jun 2020 01:58:53: 3000000 INFO @ Tue, 30 Jun 2020 01:58:58: 4000000 INFO @ Tue, 30 Jun 2020 01:59:00: #1 tag size is determined as 35 bps INFO @ Tue, 30 Jun 2020 01:59:00: #1 tag size = 35 INFO @ Tue, 30 Jun 2020 01:59:00: #1 total tags in treatment: 4255362 INFO @ Tue, 30 Jun 2020 01:59:00: #1 user defined the maximum tags... INFO @ Tue, 30 Jun 2020 01:59:00: #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 01:59:00: #1 tags after filtering in treatment: 4255352 INFO @ Tue, 30 Jun 2020 01:59:00: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 30 Jun 2020 01:59:00: #1 finished! INFO @ Tue, 30 Jun 2020 01:59:00: #2 Build Peak Model... INFO @ Tue, 30 Jun 2020 01:59:00: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 30 Jun 2020 01:59:01: #2 number of paired peaks: 234 WARNING @ Tue, 30 Jun 2020 01:59:01: Fewer paired peaks (234) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 234 pairs to build model! INFO @ Tue, 30 Jun 2020 01:59:01: start model_add_line... INFO @ Tue, 30 Jun 2020 01:59:01: start X-correlation... INFO @ Tue, 30 Jun 2020 01:59:01: end of X-cor INFO @ Tue, 30 Jun 2020 01:59:01: #2 finished! INFO @ Tue, 30 Jun 2020 01:59:01: #2 predicted fragment length is 41 bps INFO @ Tue, 30 Jun 2020 01:59:01: #2 alternative fragment length(s) may be 41 bps INFO @ Tue, 30 Jun 2020 01:59:01: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX231914/SRX231914.10_model.r WARNING @ Tue, 30 Jun 2020 01:59:01: #2 Since the d (41) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 30 Jun 2020 01:59:01: #2 You may need to consider one of the other alternative d(s): 41 WARNING @ Tue, 30 Jun 2020 01:59:01: #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 01:59:01: #3 Call peaks... INFO @ Tue, 30 Jun 2020 01:59:01: #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 01:59:07: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX231914/SRX231914.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX231914/SRX231914.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX231914/SRX231914.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX231914/SRX231914.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 01:59:07: #1 read tag files... INFO @ Tue, 30 Jun 2020 01:59:07: #1 read treatment tags... INFO @ Tue, 30 Jun 2020 01:59:12: #3 Call peaks for each chromosome... INFO @ Tue, 30 Jun 2020 01:59:12: 1000000 INFO @ Tue, 30 Jun 2020 01:59:17: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX231914/SRX231914.10_peaks.xls INFO @ Tue, 30 Jun 2020 01:59:17: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX231914/SRX231914.10_peaks.narrowPeak INFO @ Tue, 30 Jun 2020 01:59:17: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX231914/SRX231914.10_summits.bed INFO @ Tue, 30 Jun 2020 01:59:17: Done! pass1 - making usageList (96 chroms): 1 millis pass2 - checking and writing primary data (217 records, 4 fields): 4 millis INFO @ Tue, 30 Jun 2020 01:59:17: 2000000 CompletedMACS2peakCalling INFO @ Tue, 30 Jun 2020 01:59:23: 3000000 INFO @ Tue, 30 Jun 2020 01:59:28: 4000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 30 Jun 2020 01:59:30: #1 tag size is determined as 35 bps INFO @ Tue, 30 Jun 2020 01:59:30: #1 tag size = 35 INFO @ Tue, 30 Jun 2020 01:59:30: #1 total tags in treatment: 4255362 INFO @ Tue, 30 Jun 2020 01:59:30: #1 user defined the maximum tags... INFO @ Tue, 30 Jun 2020 01:59:30: #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 01:59:30: #1 tags after filtering in treatment: 4255352 INFO @ Tue, 30 Jun 2020 01:59:30: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 30 Jun 2020 01:59:30: #1 finished! INFO @ Tue, 30 Jun 2020 01:59:30: #2 Build Peak Model... INFO @ Tue, 30 Jun 2020 01:59:30: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 30 Jun 2020 01:59:31: #2 number of paired peaks: 234 WARNING @ Tue, 30 Jun 2020 01:59:31: Fewer paired peaks (234) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 234 pairs to build model! INFO @ Tue, 30 Jun 2020 01:59:31: start model_add_line... INFO @ Tue, 30 Jun 2020 01:59:31: start X-correlation... INFO @ Tue, 30 Jun 2020 01:59:31: end of X-cor INFO @ Tue, 30 Jun 2020 01:59:31: #2 finished! INFO @ Tue, 30 Jun 2020 01:59:31: #2 predicted fragment length is 41 bps INFO @ Tue, 30 Jun 2020 01:59:31: #2 alternative fragment length(s) may be 41 bps INFO @ Tue, 30 Jun 2020 01:59:31: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX231914/SRX231914.20_model.r WARNING @ Tue, 30 Jun 2020 01:59:31: #2 Since the d (41) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 30 Jun 2020 01:59:31: #2 You may need to consider one of the other alternative d(s): 41 WARNING @ Tue, 30 Jun 2020 01:59:31: #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 01:59:31: #3 Call peaks... INFO @ Tue, 30 Jun 2020 01:59:31: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Tue, 30 Jun 2020 01:59:42: #3 Call peaks for each chromosome... INFO @ Tue, 30 Jun 2020 01:59:47: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX231914/SRX231914.20_peaks.xls INFO @ Tue, 30 Jun 2020 01:59:47: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX231914/SRX231914.20_peaks.narrowPeak INFO @ Tue, 30 Jun 2020 01:59:47: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX231914/SRX231914.20_summits.bed INFO @ Tue, 30 Jun 2020 01:59:47: Done! pass1 - making usageList (50 chroms): 2 millis pass2 - checking and writing primary data (76 records, 4 fields): 5 millis CompletedMACS2peakCalling