Job ID = 6456091 SRX = SRX3170973 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T10:31:21 prefetch.2.10.7: 1) Downloading 'SRR6019820'... 2020-06-21T10:31:21 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T10:32:23 prefetch.2.10.7: HTTPS download succeed 2020-06-21T10:32:24 prefetch.2.10.7: 'SRR6019820' is valid 2020-06-21T10:32:24 prefetch.2.10.7: 1) 'SRR6019820' was downloaded successfully 2020-06-21T10:32:24 prefetch.2.10.7: 'SRR6019820' has 0 unresolved dependencies Read 9881083 spots for SRR6019820/SRR6019820.sra Written 9881083 spots for SRR6019820/SRR6019820.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: 00:02:33 9881083 reads; of these: 9881083 (100.00%) were unpaired; of these: 415690 (4.21%) aligned 0 times 7218304 (73.05%) aligned exactly 1 time 2247089 (22.74%) aligned >1 times 95.79% overall alignment rate Time searching: 00:02:33 Overall time: 00:02:33 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] 1621060 / 9465393 = 0.1713 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 19:37:45: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX3170973/SRX3170973.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX3170973/SRX3170973.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX3170973/SRX3170973.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX3170973/SRX3170973.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 19:37:45: #1 read tag files... INFO @ Sun, 21 Jun 2020 19:37:45: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 19:37:51: 1000000 INFO @ Sun, 21 Jun 2020 19:37:56: 2000000 INFO @ Sun, 21 Jun 2020 19:38:02: 3000000 INFO @ Sun, 21 Jun 2020 19:38:07: 4000000 INFO @ Sun, 21 Jun 2020 19:38:13: 5000000 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 19:38:15: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX3170973/SRX3170973.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX3170973/SRX3170973.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX3170973/SRX3170973.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX3170973/SRX3170973.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 19:38:15: #1 read tag files... INFO @ Sun, 21 Jun 2020 19:38:15: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 19:38:19: 6000000 INFO @ Sun, 21 Jun 2020 19:38:23: 1000000 INFO @ Sun, 21 Jun 2020 19:38:26: 7000000 INFO @ Sun, 21 Jun 2020 19:38:31: 2000000 INFO @ Sun, 21 Jun 2020 19:38:32: #1 tag size is determined as 49 bps INFO @ Sun, 21 Jun 2020 19:38:32: #1 tag size = 49 INFO @ Sun, 21 Jun 2020 19:38:32: #1 total tags in treatment: 7844333 INFO @ Sun, 21 Jun 2020 19:38:32: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 19:38:32: #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 19:38:32: #1 tags after filtering in treatment: 7844146 INFO @ Sun, 21 Jun 2020 19:38:32: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 19:38:32: #1 finished! INFO @ Sun, 21 Jun 2020 19:38:32: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 19:38:32: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 19:38:32: #2 number of paired peaks: 707 WARNING @ Sun, 21 Jun 2020 19:38:32: Fewer paired peaks (707) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 707 pairs to build model! INFO @ Sun, 21 Jun 2020 19:38:32: start model_add_line... INFO @ Sun, 21 Jun 2020 19:38:32: start X-correlation... INFO @ Sun, 21 Jun 2020 19:38:33: end of X-cor INFO @ Sun, 21 Jun 2020 19:38:33: #2 finished! INFO @ Sun, 21 Jun 2020 19:38:33: #2 predicted fragment length is 73 bps INFO @ Sun, 21 Jun 2020 19:38:33: #2 alternative fragment length(s) may be 73 bps INFO @ Sun, 21 Jun 2020 19:38:33: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX3170973/SRX3170973.05_model.r WARNING @ Sun, 21 Jun 2020 19:38:33: #2 Since the d (73) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 19:38:33: #2 You may need to consider one of the other alternative d(s): 73 WARNING @ Sun, 21 Jun 2020 19:38:33: #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 19:38:33: #3 Call peaks... INFO @ Sun, 21 Jun 2020 19:38:33: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 19:38:37: 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 @ Sun, 21 Jun 2020 19:38:44: 4000000 INFO @ Sun, 21 Jun 2020 19:38:45: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX3170973/SRX3170973.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX3170973/SRX3170973.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX3170973/SRX3170973.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX3170973/SRX3170973.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 19:38:45: #1 read tag files... INFO @ Sun, 21 Jun 2020 19:38:45: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 19:38:49: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 19:38:52: 5000000 INFO @ Sun, 21 Jun 2020 19:38:53: 1000000 INFO @ Sun, 21 Jun 2020 19:38:57: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX3170973/SRX3170973.05_peaks.xls INFO @ Sun, 21 Jun 2020 19:38:57: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX3170973/SRX3170973.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 19:38:57: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX3170973/SRX3170973.05_summits.bed INFO @ Sun, 21 Jun 2020 19:38:57: Done! pass1 - making usageList (288 chroms): 1 millis pass2 - checking and writing primary data (1411 records, 4 fields): 9 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 19:39:00: 6000000 INFO @ Sun, 21 Jun 2020 19:39:00: 2000000 INFO @ Sun, 21 Jun 2020 19:39:07: 3000000 INFO @ Sun, 21 Jun 2020 19:39:08: 7000000 INFO @ Sun, 21 Jun 2020 19:39:14: #1 tag size is determined as 49 bps INFO @ Sun, 21 Jun 2020 19:39:14: #1 tag size = 49 INFO @ Sun, 21 Jun 2020 19:39:14: #1 total tags in treatment: 7844333 INFO @ Sun, 21 Jun 2020 19:39:14: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 19:39:14: #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 19:39:14: 4000000 INFO @ Sun, 21 Jun 2020 19:39:14: #1 tags after filtering in treatment: 7844146 INFO @ Sun, 21 Jun 2020 19:39:14: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 19:39:14: #1 finished! INFO @ Sun, 21 Jun 2020 19:39:14: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 19:39:14: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 19:39:15: #2 number of paired peaks: 707 WARNING @ Sun, 21 Jun 2020 19:39:15: Fewer paired peaks (707) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 707 pairs to build model! INFO @ Sun, 21 Jun 2020 19:39:15: start model_add_line... INFO @ Sun, 21 Jun 2020 19:39:15: start X-correlation... INFO @ Sun, 21 Jun 2020 19:39:15: end of X-cor INFO @ Sun, 21 Jun 2020 19:39:15: #2 finished! INFO @ Sun, 21 Jun 2020 19:39:15: #2 predicted fragment length is 73 bps INFO @ Sun, 21 Jun 2020 19:39:15: #2 alternative fragment length(s) may be 73 bps INFO @ Sun, 21 Jun 2020 19:39:15: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX3170973/SRX3170973.10_model.r WARNING @ Sun, 21 Jun 2020 19:39:15: #2 Since the d (73) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 19:39:15: #2 You may need to consider one of the other alternative d(s): 73 WARNING @ Sun, 21 Jun 2020 19:39:15: #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 19:39:15: #3 Call peaks... INFO @ Sun, 21 Jun 2020 19:39:15: #3 Pre-compute pvalue-qvalue table... BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 19:39:21: 5000000 INFO @ Sun, 21 Jun 2020 19:39:28: 6000000 INFO @ Sun, 21 Jun 2020 19:39:32: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 19:39:35: 7000000 BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 19:39:41: #1 tag size is determined as 49 bps INFO @ Sun, 21 Jun 2020 19:39:41: #1 tag size = 49 INFO @ Sun, 21 Jun 2020 19:39:41: #1 total tags in treatment: 7844333 INFO @ Sun, 21 Jun 2020 19:39:41: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 19:39:41: #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 19:39:41: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX3170973/SRX3170973.10_peaks.xls INFO @ Sun, 21 Jun 2020 19:39:41: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX3170973/SRX3170973.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 19:39:41: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX3170973/SRX3170973.10_summits.bed INFO @ Sun, 21 Jun 2020 19:39:41: Done! INFO @ Sun, 21 Jun 2020 19:39:41: #1 tags after filtering in treatment: 7844146 INFO @ Sun, 21 Jun 2020 19:39:41: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 19:39:41: #1 finished! INFO @ Sun, 21 Jun 2020 19:39:41: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 19:39:41: #2 looking for paired plus/minus strand peaks... pass1 - making usageList (188 chroms): 1 millis pass2 - checking and writing primary data (616 records, 4 fields): 6 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 19:39:42: #2 number of paired peaks: 707 WARNING @ Sun, 21 Jun 2020 19:39:42: Fewer paired peaks (707) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 707 pairs to build model! INFO @ Sun, 21 Jun 2020 19:39:42: start model_add_line... INFO @ Sun, 21 Jun 2020 19:39:42: start X-correlation... INFO @ Sun, 21 Jun 2020 19:39:42: end of X-cor INFO @ Sun, 21 Jun 2020 19:39:42: #2 finished! INFO @ Sun, 21 Jun 2020 19:39:42: #2 predicted fragment length is 73 bps INFO @ Sun, 21 Jun 2020 19:39:42: #2 alternative fragment length(s) may be 73 bps INFO @ Sun, 21 Jun 2020 19:39:42: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX3170973/SRX3170973.20_model.r WARNING @ Sun, 21 Jun 2020 19:39:42: #2 Since the d (73) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 19:39:42: #2 You may need to consider one of the other alternative d(s): 73 WARNING @ Sun, 21 Jun 2020 19:39:42: #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 19:39:42: #3 Call peaks... INFO @ Sun, 21 Jun 2020 19:39:42: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 19:39:59: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 19:40:07: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX3170973/SRX3170973.20_peaks.xls INFO @ Sun, 21 Jun 2020 19:40:07: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX3170973/SRX3170973.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 19:40:07: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX3170973/SRX3170973.20_summits.bed INFO @ Sun, 21 Jun 2020 19:40:07: Done! pass1 - making usageList (120 chroms): 1 millis pass2 - checking and writing primary data (269 records, 4 fields): 4 millis CompletedMACS2peakCalling