Job ID = 6456670 SRX = SRX3937196 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T11:03:16 prefetch.2.10.7: 1) Downloading 'SRR7004616'... 2020-06-21T11:03:16 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T11:03:52 prefetch.2.10.7: HTTPS download succeed 2020-06-21T11:03:52 prefetch.2.10.7: 'SRR7004616' is valid 2020-06-21T11:03:52 prefetch.2.10.7: 1) 'SRR7004616' was downloaded successfully 2020-06-21T11:03:52 prefetch.2.10.7: 'SRR7004616' has 0 unresolved dependencies Read 2053778 spots for SRR7004616/SRR7004616.sra Written 2053778 spots for SRR7004616/SRR7004616.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: 00:00:54 2053778 reads; of these: 2053778 (100.00%) were unpaired; of these: 109788 (5.35%) aligned 0 times 1498444 (72.96%) aligned exactly 1 time 445546 (21.69%) aligned >1 times 94.65% overall alignment rate Time searching: 00:00:54 Overall time: 00:00:54 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] 33542 / 1943990 = 0.0173 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 20:06:10: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX3937196/SRX3937196.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX3937196/SRX3937196.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX3937196/SRX3937196.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX3937196/SRX3937196.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 20:06:10: #1 read tag files... INFO @ Sun, 21 Jun 2020 20:06:10: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 20:06:17: 1000000 INFO @ Sun, 21 Jun 2020 20:06:25: #1 tag size is determined as 100 bps INFO @ Sun, 21 Jun 2020 20:06:25: #1 tag size = 100 INFO @ Sun, 21 Jun 2020 20:06:25: #1 total tags in treatment: 1910448 INFO @ Sun, 21 Jun 2020 20:06:25: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 20:06:25: #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 20:06:25: #1 tags after filtering in treatment: 1910339 INFO @ Sun, 21 Jun 2020 20:06:25: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 20:06:25: #1 finished! INFO @ Sun, 21 Jun 2020 20:06:25: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 20:06:25: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 20:06:25: #2 number of paired peaks: 736 WARNING @ Sun, 21 Jun 2020 20:06:25: Fewer paired peaks (736) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 736 pairs to build model! INFO @ Sun, 21 Jun 2020 20:06:25: start model_add_line... INFO @ Sun, 21 Jun 2020 20:06:25: start X-correlation... INFO @ Sun, 21 Jun 2020 20:06:25: end of X-cor INFO @ Sun, 21 Jun 2020 20:06:25: #2 finished! INFO @ Sun, 21 Jun 2020 20:06:25: #2 predicted fragment length is 109 bps INFO @ Sun, 21 Jun 2020 20:06:25: #2 alternative fragment length(s) may be 109 bps INFO @ Sun, 21 Jun 2020 20:06:25: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX3937196/SRX3937196.05_model.r WARNING @ Sun, 21 Jun 2020 20:06:25: #2 Since the d (109) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 20:06:25: #2 You may need to consider one of the other alternative d(s): 109 WARNING @ Sun, 21 Jun 2020 20:06:25: #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 20:06:25: #3 Call peaks... INFO @ Sun, 21 Jun 2020 20:06:25: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 20:06:30: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 20:06:32: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX3937196/SRX3937196.05_peaks.xls INFO @ Sun, 21 Jun 2020 20:06:32: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX3937196/SRX3937196.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 20:06:32: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX3937196/SRX3937196.05_summits.bed INFO @ Sun, 21 Jun 2020 20:06:32: Done! pass1 - making usageList (188 chroms): 1 millis pass2 - checking and writing primary data (342 records, 4 fields): 6 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 20:06:40: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX3937196/SRX3937196.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX3937196/SRX3937196.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX3937196/SRX3937196.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX3937196/SRX3937196.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 20:06:40: #1 read tag files... INFO @ Sun, 21 Jun 2020 20:06:40: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 20:06:48: 1000000 INFO @ Sun, 21 Jun 2020 20:06:55: #1 tag size is determined as 100 bps INFO @ Sun, 21 Jun 2020 20:06:55: #1 tag size = 100 INFO @ Sun, 21 Jun 2020 20:06:55: #1 total tags in treatment: 1910448 INFO @ Sun, 21 Jun 2020 20:06:55: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 20:06:55: #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 20:06:55: #1 tags after filtering in treatment: 1910339 INFO @ Sun, 21 Jun 2020 20:06:55: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 20:06:55: #1 finished! INFO @ Sun, 21 Jun 2020 20:06:55: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 20:06:55: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 20:06:55: #2 number of paired peaks: 736 WARNING @ Sun, 21 Jun 2020 20:06:55: Fewer paired peaks (736) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 736 pairs to build model! INFO @ Sun, 21 Jun 2020 20:06:55: start model_add_line... INFO @ Sun, 21 Jun 2020 20:06:55: start X-correlation... INFO @ Sun, 21 Jun 2020 20:06:55: end of X-cor INFO @ Sun, 21 Jun 2020 20:06:55: #2 finished! INFO @ Sun, 21 Jun 2020 20:06:55: #2 predicted fragment length is 109 bps INFO @ Sun, 21 Jun 2020 20:06:55: #2 alternative fragment length(s) may be 109 bps INFO @ Sun, 21 Jun 2020 20:06:55: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX3937196/SRX3937196.10_model.r WARNING @ Sun, 21 Jun 2020 20:06:55: #2 Since the d (109) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 20:06:55: #2 You may need to consider one of the other alternative d(s): 109 WARNING @ Sun, 21 Jun 2020 20:06:55: #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 20:06:55: #3 Call peaks... INFO @ Sun, 21 Jun 2020 20:06:55: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 20:07:00: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 20:07:02: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX3937196/SRX3937196.10_peaks.xls INFO @ Sun, 21 Jun 2020 20:07:02: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX3937196/SRX3937196.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 20:07:02: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX3937196/SRX3937196.10_summits.bed INFO @ Sun, 21 Jun 2020 20:07:02: Done! pass1 - making usageList (121 chroms): 1 millis pass2 - checking and writing primary data (195 records, 4 fields): 5 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 20:07:10: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX3937196/SRX3937196.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX3937196/SRX3937196.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX3937196/SRX3937196.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX3937196/SRX3937196.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 20:07:10: #1 read tag files... INFO @ Sun, 21 Jun 2020 20:07:10: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 20:07:18: 1000000 BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 20:07:26: #1 tag size is determined as 100 bps INFO @ Sun, 21 Jun 2020 20:07:26: #1 tag size = 100 INFO @ Sun, 21 Jun 2020 20:07:26: #1 total tags in treatment: 1910448 INFO @ Sun, 21 Jun 2020 20:07:26: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 20:07:26: #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 20:07:26: #1 tags after filtering in treatment: 1910339 INFO @ Sun, 21 Jun 2020 20:07:26: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 20:07:26: #1 finished! INFO @ Sun, 21 Jun 2020 20:07:26: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 20:07:26: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 20:07:26: #2 number of paired peaks: 736 WARNING @ Sun, 21 Jun 2020 20:07:26: Fewer paired peaks (736) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 736 pairs to build model! INFO @ Sun, 21 Jun 2020 20:07:26: start model_add_line... INFO @ Sun, 21 Jun 2020 20:07:26: start X-correlation... INFO @ Sun, 21 Jun 2020 20:07:26: end of X-cor INFO @ Sun, 21 Jun 2020 20:07:26: #2 finished! INFO @ Sun, 21 Jun 2020 20:07:26: #2 predicted fragment length is 109 bps INFO @ Sun, 21 Jun 2020 20:07:26: #2 alternative fragment length(s) may be 109 bps INFO @ Sun, 21 Jun 2020 20:07:26: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX3937196/SRX3937196.20_model.r WARNING @ Sun, 21 Jun 2020 20:07:26: #2 Since the d (109) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 20:07:26: #2 You may need to consider one of the other alternative d(s): 109 WARNING @ Sun, 21 Jun 2020 20:07:26: #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 20:07:26: #3 Call peaks... INFO @ Sun, 21 Jun 2020 20:07:26: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 20:07:31: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 20:07:33: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX3937196/SRX3937196.20_peaks.xls INFO @ Sun, 21 Jun 2020 20:07:33: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX3937196/SRX3937196.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 20:07:33: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX3937196/SRX3937196.20_summits.bed INFO @ Sun, 21 Jun 2020 20:07:33: Done! pass1 - making usageList (70 chroms): 1 millis pass2 - checking and writing primary data (93 records, 4 fields): 3 millis CompletedMACS2peakCalling