Job ID = 6457106 SRX = SRX4375865 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T11:27:28 prefetch.2.10.7: 1) Downloading 'SRR7506519'... 2020-06-21T11:27:28 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T11:28:20 prefetch.2.10.7: HTTPS download succeed 2020-06-21T11:28:20 prefetch.2.10.7: 'SRR7506519' is valid 2020-06-21T11:28:20 prefetch.2.10.7: 1) 'SRR7506519' was downloaded successfully Read 3119660 spots for SRR7506519/SRR7506519.sra Written 3119660 spots for SRR7506519/SRR7506519.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: 00:00:01 Multiseed full-index search: 00:00:39 3119660 reads; of these: 3119660 (100.00%) were unpaired; of these: 1604690 (51.44%) aligned 0 times 1057215 (33.89%) aligned exactly 1 time 457755 (14.67%) aligned >1 times 48.56% overall alignment rate Time searching: 00:00:40 Overall time: 00:00:40 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] 234200 / 1514970 = 0.1546 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 20:30:05: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX4375865/SRX4375865.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX4375865/SRX4375865.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX4375865/SRX4375865.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX4375865/SRX4375865.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 20:30:05: #1 read tag files... INFO @ Sun, 21 Jun 2020 20:30:05: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 20:30:12: 1000000 INFO @ Sun, 21 Jun 2020 20:30:14: #1 tag size is determined as 51 bps INFO @ Sun, 21 Jun 2020 20:30:14: #1 tag size = 51 INFO @ Sun, 21 Jun 2020 20:30:14: #1 total tags in treatment: 1280770 INFO @ Sun, 21 Jun 2020 20:30:14: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 20:30:14: #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 20:30:14: #1 tags after filtering in treatment: 1280394 INFO @ Sun, 21 Jun 2020 20:30:14: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 20:30:14: #1 finished! INFO @ Sun, 21 Jun 2020 20:30:14: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 20:30:14: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 20:30:14: #2 number of paired peaks: 920 WARNING @ Sun, 21 Jun 2020 20:30:14: Fewer paired peaks (920) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 920 pairs to build model! INFO @ Sun, 21 Jun 2020 20:30:14: start model_add_line... INFO @ Sun, 21 Jun 2020 20:30:14: start X-correlation... INFO @ Sun, 21 Jun 2020 20:30:14: end of X-cor INFO @ Sun, 21 Jun 2020 20:30:14: #2 finished! INFO @ Sun, 21 Jun 2020 20:30:14: #2 predicted fragment length is 95 bps INFO @ Sun, 21 Jun 2020 20:30:14: #2 alternative fragment length(s) may be 95,588 bps INFO @ Sun, 21 Jun 2020 20:30:14: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX4375865/SRX4375865.05_model.r WARNING @ Sun, 21 Jun 2020 20:30:14: #2 Since the d (95) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 20:30:14: #2 You may need to consider one of the other alternative d(s): 95,588 WARNING @ Sun, 21 Jun 2020 20:30:14: #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 20:30:14: #3 Call peaks... INFO @ Sun, 21 Jun 2020 20:30:14: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 20:30:17: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 20:30:19: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX4375865/SRX4375865.05_peaks.xls INFO @ Sun, 21 Jun 2020 20:30:19: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX4375865/SRX4375865.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 20:30:19: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX4375865/SRX4375865.05_summits.bed INFO @ Sun, 21 Jun 2020 20:30:19: Done! pass1 - making usageList (228 chroms): 0 millis pass2 - checking and writing primary data (476 records, 4 fields): 7 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 20:30:35: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX4375865/SRX4375865.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX4375865/SRX4375865.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX4375865/SRX4375865.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX4375865/SRX4375865.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 20:30:35: #1 read tag files... INFO @ Sun, 21 Jun 2020 20:30:35: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 20:30:41: 1000000 INFO @ Sun, 21 Jun 2020 20:30:43: #1 tag size is determined as 51 bps INFO @ Sun, 21 Jun 2020 20:30:43: #1 tag size = 51 INFO @ Sun, 21 Jun 2020 20:30:43: #1 total tags in treatment: 1280770 INFO @ Sun, 21 Jun 2020 20:30:43: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 20:30:43: #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 20:30:43: #1 tags after filtering in treatment: 1280394 INFO @ Sun, 21 Jun 2020 20:30:43: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 20:30:43: #1 finished! INFO @ Sun, 21 Jun 2020 20:30:43: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 20:30:43: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 20:30:43: #2 number of paired peaks: 920 WARNING @ Sun, 21 Jun 2020 20:30:43: Fewer paired peaks (920) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 920 pairs to build model! INFO @ Sun, 21 Jun 2020 20:30:43: start model_add_line... INFO @ Sun, 21 Jun 2020 20:30:43: start X-correlation... INFO @ Sun, 21 Jun 2020 20:30:43: end of X-cor INFO @ Sun, 21 Jun 2020 20:30:43: #2 finished! INFO @ Sun, 21 Jun 2020 20:30:43: #2 predicted fragment length is 95 bps INFO @ Sun, 21 Jun 2020 20:30:43: #2 alternative fragment length(s) may be 95,588 bps INFO @ Sun, 21 Jun 2020 20:30:43: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX4375865/SRX4375865.10_model.r WARNING @ Sun, 21 Jun 2020 20:30:43: #2 Since the d (95) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 20:30:43: #2 You may need to consider one of the other alternative d(s): 95,588 WARNING @ Sun, 21 Jun 2020 20:30:43: #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 20:30:43: #3 Call peaks... INFO @ Sun, 21 Jun 2020 20:30:43: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 20:30:47: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 20:30:48: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX4375865/SRX4375865.10_peaks.xls INFO @ Sun, 21 Jun 2020 20:30:48: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX4375865/SRX4375865.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 20:30:48: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX4375865/SRX4375865.10_summits.bed INFO @ Sun, 21 Jun 2020 20:30:48: Done! pass1 - making usageList (94 chroms): 0 millis pass2 - checking and writing primary data (160 records, 4 fields): 4 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 20:31:05: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX4375865/SRX4375865.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX4375865/SRX4375865.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX4375865/SRX4375865.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX4375865/SRX4375865.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 20:31:05: #1 read tag files... INFO @ Sun, 21 Jun 2020 20:31:05: #1 read treatment tags... BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 20:31:11: 1000000 BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 20:31:13: #1 tag size is determined as 51 bps INFO @ Sun, 21 Jun 2020 20:31:13: #1 tag size = 51 INFO @ Sun, 21 Jun 2020 20:31:13: #1 total tags in treatment: 1280770 INFO @ Sun, 21 Jun 2020 20:31:13: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 20:31:13: #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 20:31:13: #1 tags after filtering in treatment: 1280394 INFO @ Sun, 21 Jun 2020 20:31:13: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 20:31:13: #1 finished! INFO @ Sun, 21 Jun 2020 20:31:13: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 20:31:13: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 20:31:14: #2 number of paired peaks: 920 WARNING @ Sun, 21 Jun 2020 20:31:14: Fewer paired peaks (920) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 920 pairs to build model! INFO @ Sun, 21 Jun 2020 20:31:14: start model_add_line... INFO @ Sun, 21 Jun 2020 20:31:14: start X-correlation... INFO @ Sun, 21 Jun 2020 20:31:14: end of X-cor INFO @ Sun, 21 Jun 2020 20:31:14: #2 finished! INFO @ Sun, 21 Jun 2020 20:31:14: #2 predicted fragment length is 95 bps INFO @ Sun, 21 Jun 2020 20:31:14: #2 alternative fragment length(s) may be 95,588 bps INFO @ Sun, 21 Jun 2020 20:31:14: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX4375865/SRX4375865.20_model.r WARNING @ Sun, 21 Jun 2020 20:31:14: #2 Since the d (95) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 20:31:14: #2 You may need to consider one of the other alternative d(s): 95,588 WARNING @ Sun, 21 Jun 2020 20:31:14: #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 20:31:14: #3 Call peaks... INFO @ Sun, 21 Jun 2020 20:31:14: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 20:31:17: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 20:31:18: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX4375865/SRX4375865.20_peaks.xls INFO @ Sun, 21 Jun 2020 20:31:18: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX4375865/SRX4375865.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 20:31:18: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX4375865/SRX4375865.20_summits.bed INFO @ Sun, 21 Jun 2020 20:31:18: Done! pass1 - making usageList (37 chroms): 0 millis pass2 - checking and writing primary data (60 records, 4 fields): 2 millis CompletedMACS2peakCalling