Job ID = 6456679 SRX = SRX3937200 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T11:05:54 prefetch.2.10.7: 1) Downloading 'SRR7004620'... 2020-06-21T11:05:54 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T11:06:46 prefetch.2.10.7: HTTPS download succeed 2020-06-21T11:06:46 prefetch.2.10.7: 'SRR7004620' is valid 2020-06-21T11:06:46 prefetch.2.10.7: 1) 'SRR7004620' was downloaded successfully 2020-06-21T11:06:46 prefetch.2.10.7: 'SRR7004620' has 0 unresolved dependencies Read 2383875 spots for SRR7004620/SRR7004620.sra Written 2383875 spots for SRR7004620/SRR7004620.sra 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 2383875 reads; of these: 2383875 (100.00%) were unpaired; of these: 370813 (15.56%) aligned 0 times 1462180 (61.34%) aligned exactly 1 time 550882 (23.11%) aligned >1 times 84.44% 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] 75981 / 2013062 = 0.0377 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 @ Sun, 21 Jun 2020 20:09:30: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX3937200/SRX3937200.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX3937200/SRX3937200.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX3937200/SRX3937200.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX3937200/SRX3937200.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 @ Sun, 21 Jun 2020 20:09:30: #1 read tag files... INFO @ Sun, 21 Jun 2020 20:09:30: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 20:09:38: 1000000 INFO @ Sun, 21 Jun 2020 20:09:45: #1 tag size is determined as 98 bps INFO @ Sun, 21 Jun 2020 20:09:45: #1 tag size = 98 INFO @ Sun, 21 Jun 2020 20:09:45: #1 total tags in treatment: 1937081 INFO @ Sun, 21 Jun 2020 20:09:45: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 20:09:45: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sun, 21 Jun 2020 20:09:46: #1 tags after filtering in treatment: 1937009 INFO @ Sun, 21 Jun 2020 20:09:46: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 20:09:46: #1 finished! INFO @ Sun, 21 Jun 2020 20:09:46: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 20:09:46: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 20:09:46: #2 number of paired peaks: 523 WARNING @ Sun, 21 Jun 2020 20:09:46: Fewer paired peaks (523) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 523 pairs to build model! INFO @ Sun, 21 Jun 2020 20:09:46: start model_add_line... INFO @ Sun, 21 Jun 2020 20:09:46: start X-correlation... INFO @ Sun, 21 Jun 2020 20:09:46: end of X-cor INFO @ Sun, 21 Jun 2020 20:09:46: #2 finished! INFO @ Sun, 21 Jun 2020 20:09:46: #2 predicted fragment length is 99 bps INFO @ Sun, 21 Jun 2020 20:09:46: #2 alternative fragment length(s) may be 99 bps INFO @ Sun, 21 Jun 2020 20:09:46: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX3937200/SRX3937200.05_model.r WARNING @ Sun, 21 Jun 2020 20:09:46: #2 Since the d (99) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 20:09:46: #2 You may need to consider one of the other alternative d(s): 99 WARNING @ Sun, 21 Jun 2020 20:09:46: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sun, 21 Jun 2020 20:09:46: #3 Call peaks... INFO @ Sun, 21 Jun 2020 20:09:46: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 20:09:51: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 20:09:54: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX3937200/SRX3937200.05_peaks.xls INFO @ Sun, 21 Jun 2020 20:09:54: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX3937200/SRX3937200.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 20:09:54: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX3937200/SRX3937200.05_summits.bed INFO @ Sun, 21 Jun 2020 20:09:54: Done! pass1 - making usageList (347 chroms): 1 millis pass2 - checking and writing primary data (596 records, 4 fields): 10 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 @ Sun, 21 Jun 2020 20:10:00: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX3937200/SRX3937200.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX3937200/SRX3937200.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX3937200/SRX3937200.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX3937200/SRX3937200.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 @ Sun, 21 Jun 2020 20:10:00: #1 read tag files... INFO @ Sun, 21 Jun 2020 20:10:00: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 20:10:07: 1000000 INFO @ Sun, 21 Jun 2020 20:10:14: #1 tag size is determined as 98 bps INFO @ Sun, 21 Jun 2020 20:10:14: #1 tag size = 98 INFO @ Sun, 21 Jun 2020 20:10:14: #1 total tags in treatment: 1937081 INFO @ Sun, 21 Jun 2020 20:10:14: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 20:10:14: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sun, 21 Jun 2020 20:10:15: #1 tags after filtering in treatment: 1937009 INFO @ Sun, 21 Jun 2020 20:10:15: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 20:10:15: #1 finished! INFO @ Sun, 21 Jun 2020 20:10:15: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 20:10:15: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 20:10:15: #2 number of paired peaks: 523 WARNING @ Sun, 21 Jun 2020 20:10:15: Fewer paired peaks (523) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 523 pairs to build model! INFO @ Sun, 21 Jun 2020 20:10:15: start model_add_line... INFO @ Sun, 21 Jun 2020 20:10:15: start X-correlation... INFO @ Sun, 21 Jun 2020 20:10:15: end of X-cor INFO @ Sun, 21 Jun 2020 20:10:15: #2 finished! INFO @ Sun, 21 Jun 2020 20:10:15: #2 predicted fragment length is 99 bps INFO @ Sun, 21 Jun 2020 20:10:15: #2 alternative fragment length(s) may be 99 bps INFO @ Sun, 21 Jun 2020 20:10:15: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX3937200/SRX3937200.10_model.r WARNING @ Sun, 21 Jun 2020 20:10:15: #2 Since the d (99) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 20:10:15: #2 You may need to consider one of the other alternative d(s): 99 WARNING @ Sun, 21 Jun 2020 20:10:15: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sun, 21 Jun 2020 20:10:15: #3 Call peaks... INFO @ Sun, 21 Jun 2020 20:10:15: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 20:10:20: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 20:10:22: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX3937200/SRX3937200.10_peaks.xls INFO @ Sun, 21 Jun 2020 20:10:22: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX3937200/SRX3937200.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 20:10:22: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX3937200/SRX3937200.10_summits.bed INFO @ Sun, 21 Jun 2020 20:10:22: Done! pass1 - making usageList (188 chroms): 1 millis pass2 - checking and writing primary data (287 records, 4 fields): 7 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 @ Sun, 21 Jun 2020 20:10:30: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX3937200/SRX3937200.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX3937200/SRX3937200.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX3937200/SRX3937200.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX3937200/SRX3937200.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 @ Sun, 21 Jun 2020 20:10:30: #1 read tag files... INFO @ Sun, 21 Jun 2020 20:10:30: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 20:10:37: 1000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 20:10:44: #1 tag size is determined as 98 bps INFO @ Sun, 21 Jun 2020 20:10:44: #1 tag size = 98 INFO @ Sun, 21 Jun 2020 20:10:44: #1 total tags in treatment: 1937081 INFO @ Sun, 21 Jun 2020 20:10:44: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 20:10:44: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sun, 21 Jun 2020 20:10:45: #1 tags after filtering in treatment: 1937009 INFO @ Sun, 21 Jun 2020 20:10:45: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 20:10:45: #1 finished! INFO @ Sun, 21 Jun 2020 20:10:45: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 20:10:45: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 20:10:45: #2 number of paired peaks: 523 WARNING @ Sun, 21 Jun 2020 20:10:45: Fewer paired peaks (523) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 523 pairs to build model! INFO @ Sun, 21 Jun 2020 20:10:45: start model_add_line... INFO @ Sun, 21 Jun 2020 20:10:45: start X-correlation... INFO @ Sun, 21 Jun 2020 20:10:45: end of X-cor INFO @ Sun, 21 Jun 2020 20:10:45: #2 finished! INFO @ Sun, 21 Jun 2020 20:10:45: #2 predicted fragment length is 99 bps INFO @ Sun, 21 Jun 2020 20:10:45: #2 alternative fragment length(s) may be 99 bps INFO @ Sun, 21 Jun 2020 20:10:45: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX3937200/SRX3937200.20_model.r WARNING @ Sun, 21 Jun 2020 20:10:45: #2 Since the d (99) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 20:10:45: #2 You may need to consider one of the other alternative d(s): 99 WARNING @ Sun, 21 Jun 2020 20:10:45: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sun, 21 Jun 2020 20:10:45: #3 Call peaks... INFO @ Sun, 21 Jun 2020 20:10:45: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 20:10:50: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 20:10:53: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX3937200/SRX3937200.20_peaks.xls INFO @ Sun, 21 Jun 2020 20:10:53: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX3937200/SRX3937200.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 20:10:53: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX3937200/SRX3937200.20_summits.bed INFO @ Sun, 21 Jun 2020 20:10:53: Done! pass1 - making usageList (91 chroms): 1 millis pass2 - checking and writing primary data (130 records, 4 fields): 4 millis CompletedMACS2peakCalling