Job ID = 6458797 SRX = SRX5515083 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T12:46:11 prefetch.2.10.7: 1) Downloading 'SRR8721837'... 2020-06-21T12:46:11 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T12:46:31 prefetch.2.10.7: HTTPS download succeed 2020-06-21T12:46:31 prefetch.2.10.7: 'SRR8721837' is valid 2020-06-21T12:46:31 prefetch.2.10.7: 1) 'SRR8721837' was downloaded successfully 2020-06-21T12:46:31 prefetch.2.10.7: 'SRR8721837' has 0 unresolved dependencies Read 1698148 spots for SRR8721837/SRR8721837.sra Written 1698148 spots for SRR8721837/SRR8721837.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: 00:00:31 1698148 reads; of these: 1698148 (100.00%) were unpaired; of these: 294 (0.02%) aligned 0 times 1258062 (74.08%) aligned exactly 1 time 439792 (25.90%) aligned >1 times 99.98% overall alignment rate Time searching: 00:00:31 Overall time: 00:00:31 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] 55055 / 1697854 = 0.0324 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 21:48:09: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX5515083/SRX5515083.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX5515083/SRX5515083.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX5515083/SRX5515083.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX5515083/SRX5515083.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 21:48:09: #1 read tag files... INFO @ Sun, 21 Jun 2020 21:48:09: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 21:48:15: 1000000 INFO @ Sun, 21 Jun 2020 21:48:20: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 21:48:20: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 21:48:20: #1 total tags in treatment: 1642799 INFO @ Sun, 21 Jun 2020 21:48:20: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 21:48:20: #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 21:48:21: #1 tags after filtering in treatment: 1642465 INFO @ Sun, 21 Jun 2020 21:48:21: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 21:48:21: #1 finished! INFO @ Sun, 21 Jun 2020 21:48:21: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 21:48:21: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 21:48:21: #2 number of paired peaks: 760 WARNING @ Sun, 21 Jun 2020 21:48:21: Fewer paired peaks (760) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 760 pairs to build model! INFO @ Sun, 21 Jun 2020 21:48:21: start model_add_line... INFO @ Sun, 21 Jun 2020 21:48:21: start X-correlation... INFO @ Sun, 21 Jun 2020 21:48:21: end of X-cor INFO @ Sun, 21 Jun 2020 21:48:21: #2 finished! INFO @ Sun, 21 Jun 2020 21:48:21: #2 predicted fragment length is 54 bps INFO @ Sun, 21 Jun 2020 21:48:21: #2 alternative fragment length(s) may be 54,529 bps INFO @ Sun, 21 Jun 2020 21:48:21: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX5515083/SRX5515083.05_model.r WARNING @ Sun, 21 Jun 2020 21:48:21: #2 Since the d (54) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 21:48:21: #2 You may need to consider one of the other alternative d(s): 54,529 WARNING @ Sun, 21 Jun 2020 21:48:21: #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 21:48:21: #3 Call peaks... INFO @ Sun, 21 Jun 2020 21:48:21: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 21:48:24: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 21:48:26: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX5515083/SRX5515083.05_peaks.xls INFO @ Sun, 21 Jun 2020 21:48:26: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX5515083/SRX5515083.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 21:48:26: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX5515083/SRX5515083.05_summits.bed INFO @ Sun, 21 Jun 2020 21:48:26: Done! pass1 - making usageList (233 chroms): 1 millis pass2 - checking and writing primary data (402 records, 4 fields): 14 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 21:48:39: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX5515083/SRX5515083.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX5515083/SRX5515083.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX5515083/SRX5515083.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX5515083/SRX5515083.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 21:48:39: #1 read tag files... INFO @ Sun, 21 Jun 2020 21:48:39: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 21:48:45: 1000000 INFO @ Sun, 21 Jun 2020 21:48:50: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 21:48:50: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 21:48:50: #1 total tags in treatment: 1642799 INFO @ Sun, 21 Jun 2020 21:48:50: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 21:48:50: #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 21:48:50: #1 tags after filtering in treatment: 1642465 INFO @ Sun, 21 Jun 2020 21:48:50: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 21:48:50: #1 finished! INFO @ Sun, 21 Jun 2020 21:48:50: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 21:48:50: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 21:48:51: #2 number of paired peaks: 760 WARNING @ Sun, 21 Jun 2020 21:48:51: Fewer paired peaks (760) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 760 pairs to build model! INFO @ Sun, 21 Jun 2020 21:48:51: start model_add_line... INFO @ Sun, 21 Jun 2020 21:48:51: start X-correlation... INFO @ Sun, 21 Jun 2020 21:48:51: end of X-cor INFO @ Sun, 21 Jun 2020 21:48:51: #2 finished! INFO @ Sun, 21 Jun 2020 21:48:51: #2 predicted fragment length is 54 bps INFO @ Sun, 21 Jun 2020 21:48:51: #2 alternative fragment length(s) may be 54,529 bps INFO @ Sun, 21 Jun 2020 21:48:51: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX5515083/SRX5515083.10_model.r WARNING @ Sun, 21 Jun 2020 21:48:51: #2 Since the d (54) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 21:48:51: #2 You may need to consider one of the other alternative d(s): 54,529 WARNING @ Sun, 21 Jun 2020 21:48:51: #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 21:48:51: #3 Call peaks... INFO @ Sun, 21 Jun 2020 21:48:51: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 21:48:54: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 21:48:56: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX5515083/SRX5515083.10_peaks.xls INFO @ Sun, 21 Jun 2020 21:48:56: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX5515083/SRX5515083.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 21:48:56: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX5515083/SRX5515083.10_summits.bed INFO @ Sun, 21 Jun 2020 21:48:56: Done! pass1 - making usageList (50 chroms): 1 millis pass2 - checking and writing primary data (68 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 21:49:09: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX5515083/SRX5515083.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX5515083/SRX5515083.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX5515083/SRX5515083.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX5515083/SRX5515083.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 21:49:09: #1 read tag files... INFO @ Sun, 21 Jun 2020 21:49:09: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 21:49:15: 1000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 21:49:21: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 21:49:21: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 21:49:21: #1 total tags in treatment: 1642799 INFO @ Sun, 21 Jun 2020 21:49:21: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 21:49:21: #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 21:49:21: #1 tags after filtering in treatment: 1642465 INFO @ Sun, 21 Jun 2020 21:49:21: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 21:49:21: #1 finished! INFO @ Sun, 21 Jun 2020 21:49:21: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 21:49:21: #2 looking for paired plus/minus strand peaks... BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 21:49:22: #2 number of paired peaks: 760 WARNING @ Sun, 21 Jun 2020 21:49:22: Fewer paired peaks (760) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 760 pairs to build model! INFO @ Sun, 21 Jun 2020 21:49:22: start model_add_line... INFO @ Sun, 21 Jun 2020 21:49:22: start X-correlation... INFO @ Sun, 21 Jun 2020 21:49:22: end of X-cor INFO @ Sun, 21 Jun 2020 21:49:22: #2 finished! INFO @ Sun, 21 Jun 2020 21:49:22: #2 predicted fragment length is 54 bps INFO @ Sun, 21 Jun 2020 21:49:22: #2 alternative fragment length(s) may be 54,529 bps INFO @ Sun, 21 Jun 2020 21:49:22: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX5515083/SRX5515083.20_model.r WARNING @ Sun, 21 Jun 2020 21:49:22: #2 Since the d (54) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 21:49:22: #2 You may need to consider one of the other alternative d(s): 54,529 WARNING @ Sun, 21 Jun 2020 21:49:22: #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 21:49:22: #3 Call peaks... INFO @ Sun, 21 Jun 2020 21:49:22: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 21:49:25: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 21:49:27: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX5515083/SRX5515083.20_peaks.xls INFO @ Sun, 21 Jun 2020 21:49:27: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX5515083/SRX5515083.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 21:49:27: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX5515083/SRX5515083.20_summits.bed INFO @ Sun, 21 Jun 2020 21:49:27: Done! pass1 - making usageList (17 chroms): 1 millis pass2 - checking and writing primary data (22 records, 4 fields): 2 millis CompletedMACS2peakCalling