Job ID = 6455051 SRX = SRX2642398 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T09:43:25 prefetch.2.10.7: 1) Downloading 'SRR5345738'... 2020-06-21T09:43:25 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T09:44:34 prefetch.2.10.7: HTTPS download succeed 2020-06-21T09:44:34 prefetch.2.10.7: 'SRR5345738' is valid 2020-06-21T09:44:34 prefetch.2.10.7: 1) 'SRR5345738' was downloaded successfully 2020-06-21T09:44:34 prefetch.2.10.7: 'SRR5345738' has 0 unresolved dependencies Read 4134223 spots for SRR5345738/SRR5345738.sra Written 4134223 spots for SRR5345738/SRR5345738.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: 00:01:51 4134223 reads; of these: 4134223 (100.00%) were unpaired; of these: 863312 (20.88%) aligned 0 times 2455085 (59.38%) aligned exactly 1 time 815826 (19.73%) aligned >1 times 79.12% overall alignment rate Time searching: 00:01:51 Overall time: 00:01:51 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] 130315 / 3270911 = 0.0398 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 18:48:25: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX2642398/SRX2642398.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX2642398/SRX2642398.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX2642398/SRX2642398.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX2642398/SRX2642398.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 18:48:25: #1 read tag files... INFO @ Sun, 21 Jun 2020 18:48:25: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 18:48:32: 1000000 INFO @ Sun, 21 Jun 2020 18:48:38: 2000000 INFO @ Sun, 21 Jun 2020 18:48:44: 3000000 INFO @ Sun, 21 Jun 2020 18:48:45: #1 tag size is determined as 99 bps INFO @ Sun, 21 Jun 2020 18:48:45: #1 tag size = 99 INFO @ Sun, 21 Jun 2020 18:48:45: #1 total tags in treatment: 3140596 INFO @ Sun, 21 Jun 2020 18:48:45: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 18:48:45: #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 18:48:45: #1 tags after filtering in treatment: 3140569 INFO @ Sun, 21 Jun 2020 18:48:45: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 18:48:45: #1 finished! INFO @ Sun, 21 Jun 2020 18:48:45: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 18:48:45: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 18:48:46: #2 number of paired peaks: 403 WARNING @ Sun, 21 Jun 2020 18:48:46: Fewer paired peaks (403) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 403 pairs to build model! INFO @ Sun, 21 Jun 2020 18:48:46: start model_add_line... INFO @ Sun, 21 Jun 2020 18:48:46: start X-correlation... INFO @ Sun, 21 Jun 2020 18:48:46: end of X-cor INFO @ Sun, 21 Jun 2020 18:48:46: #2 finished! INFO @ Sun, 21 Jun 2020 18:48:46: #2 predicted fragment length is 93 bps INFO @ Sun, 21 Jun 2020 18:48:46: #2 alternative fragment length(s) may be 93 bps INFO @ Sun, 21 Jun 2020 18:48:46: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX2642398/SRX2642398.05_model.r WARNING @ Sun, 21 Jun 2020 18:48:46: #2 Since the d (93) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 18:48:46: #2 You may need to consider one of the other alternative d(s): 93 WARNING @ Sun, 21 Jun 2020 18:48:46: #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 18:48:46: #3 Call peaks... INFO @ Sun, 21 Jun 2020 18:48:46: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 18:48:53: #3 Call peaks for each chromosome... 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 18:48:55: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX2642398/SRX2642398.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX2642398/SRX2642398.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX2642398/SRX2642398.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX2642398/SRX2642398.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 18:48:55: #1 read tag files... INFO @ Sun, 21 Jun 2020 18:48:55: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 18:48:56: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX2642398/SRX2642398.05_peaks.xls INFO @ Sun, 21 Jun 2020 18:48:56: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX2642398/SRX2642398.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 18:48:56: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX2642398/SRX2642398.05_summits.bed INFO @ Sun, 21 Jun 2020 18:48:56: Done! pass1 - making usageList (398 chroms): 1 millis pass2 - checking and writing primary data (744 records, 4 fields): 12 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 18:49:03: 1000000 INFO @ Sun, 21 Jun 2020 18:49:11: 2000000 INFO @ Sun, 21 Jun 2020 18:49:19: 3000000 INFO @ Sun, 21 Jun 2020 18:49:20: #1 tag size is determined as 99 bps INFO @ Sun, 21 Jun 2020 18:49:20: #1 tag size = 99 INFO @ Sun, 21 Jun 2020 18:49:20: #1 total tags in treatment: 3140596 INFO @ Sun, 21 Jun 2020 18:49:20: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 18:49:20: #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 18:49:20: #1 tags after filtering in treatment: 3140569 INFO @ Sun, 21 Jun 2020 18:49:20: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 18:49:20: #1 finished! INFO @ Sun, 21 Jun 2020 18:49:20: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 18:49:20: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 18:49:20: #2 number of paired peaks: 403 WARNING @ Sun, 21 Jun 2020 18:49:20: Fewer paired peaks (403) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 403 pairs to build model! INFO @ Sun, 21 Jun 2020 18:49:20: start model_add_line... INFO @ Sun, 21 Jun 2020 18:49:20: start X-correlation... INFO @ Sun, 21 Jun 2020 18:49:20: end of X-cor INFO @ Sun, 21 Jun 2020 18:49:20: #2 finished! INFO @ Sun, 21 Jun 2020 18:49:20: #2 predicted fragment length is 93 bps INFO @ Sun, 21 Jun 2020 18:49:20: #2 alternative fragment length(s) may be 93 bps INFO @ Sun, 21 Jun 2020 18:49:20: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX2642398/SRX2642398.10_model.r WARNING @ Sun, 21 Jun 2020 18:49:20: #2 Since the d (93) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 18:49:20: #2 You may need to consider one of the other alternative d(s): 93 WARNING @ Sun, 21 Jun 2020 18:49:20: #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 18:49:20: #3 Call peaks... INFO @ Sun, 21 Jun 2020 18:49:20: #3 Pre-compute pvalue-qvalue table... 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 18:49:25: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX2642398/SRX2642398.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX2642398/SRX2642398.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX2642398/SRX2642398.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX2642398/SRX2642398.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 18:49:25: #1 read tag files... INFO @ Sun, 21 Jun 2020 18:49:25: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 18:49:27: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 18:49:31: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX2642398/SRX2642398.10_peaks.xls INFO @ Sun, 21 Jun 2020 18:49:31: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX2642398/SRX2642398.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 18:49:31: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX2642398/SRX2642398.10_summits.bed INFO @ Sun, 21 Jun 2020 18:49:31: Done! pass1 - making usageList (211 chroms): 0 millis pass2 - checking and writing primary data (358 records, 4 fields): 7 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 18:49:32: 1000000 INFO @ Sun, 21 Jun 2020 18:49:38: 2000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 18:49:44: 3000000 INFO @ Sun, 21 Jun 2020 18:49:45: #1 tag size is determined as 99 bps INFO @ Sun, 21 Jun 2020 18:49:45: #1 tag size = 99 INFO @ Sun, 21 Jun 2020 18:49:45: #1 total tags in treatment: 3140596 INFO @ Sun, 21 Jun 2020 18:49:45: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 18:49:45: #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 18:49:45: #1 tags after filtering in treatment: 3140569 INFO @ Sun, 21 Jun 2020 18:49:45: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 18:49:45: #1 finished! INFO @ Sun, 21 Jun 2020 18:49:45: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 18:49:45: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 18:49:46: #2 number of paired peaks: 403 WARNING @ Sun, 21 Jun 2020 18:49:46: Fewer paired peaks (403) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 403 pairs to build model! INFO @ Sun, 21 Jun 2020 18:49:46: start model_add_line... INFO @ Sun, 21 Jun 2020 18:49:46: start X-correlation... INFO @ Sun, 21 Jun 2020 18:49:46: end of X-cor INFO @ Sun, 21 Jun 2020 18:49:46: #2 finished! INFO @ Sun, 21 Jun 2020 18:49:46: #2 predicted fragment length is 93 bps INFO @ Sun, 21 Jun 2020 18:49:46: #2 alternative fragment length(s) may be 93 bps INFO @ Sun, 21 Jun 2020 18:49:46: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX2642398/SRX2642398.20_model.r WARNING @ Sun, 21 Jun 2020 18:49:46: #2 Since the d (93) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 18:49:46: #2 You may need to consider one of the other alternative d(s): 93 WARNING @ Sun, 21 Jun 2020 18:49:46: #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 18:49:46: #3 Call peaks... INFO @ Sun, 21 Jun 2020 18:49:46: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 18:49:53: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 18:49:57: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX2642398/SRX2642398.20_peaks.xls INFO @ Sun, 21 Jun 2020 18:49:57: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX2642398/SRX2642398.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 18:49:57: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX2642398/SRX2642398.20_summits.bed INFO @ Sun, 21 Jun 2020 18:49:57: Done! pass1 - making usageList (107 chroms): 0 millis pass2 - checking and writing primary data (175 records, 4 fields): 4 millis CompletedMACS2peakCalling