Job ID = 6528330 SRX = SRX5360575 Genome = dm3 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-29T14:52:54 prefetch.2.10.7: 1) Downloading 'SRR8559081'... 2020-06-29T14:52:54 prefetch.2.10.7: Downloading via HTTPS... 2020-06-29T14:53:56 prefetch.2.10.7: HTTPS download succeed 2020-06-29T14:53:56 prefetch.2.10.7: 'SRR8559081' is valid 2020-06-29T14:53:56 prefetch.2.10.7: 1) 'SRR8559081' was downloaded successfully Read 10529961 spots for SRR8559081/SRR8559081.sra Written 10529961 spots for SRR8559081/SRR8559081.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: 00:01:57 10529961 reads; of these: 10529961 (100.00%) were unpaired; of these: 1961953 (18.63%) aligned 0 times 8302424 (78.85%) aligned exactly 1 time 265584 (2.52%) aligned >1 times 81.37% overall alignment rate Time searching: 00:01:57 Overall time: 00:01:57 マッピングが完了しました。 samtools でBAM に変換中... [samopen] SAM header is present: 15 sequences. [bam_rmdupse_core] 8395462 / 8568008 = 0.9799 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 @ Tue, 30 Jun 2020 00:01:05: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX5360575/SRX5360575.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX5360575/SRX5360575.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX5360575/SRX5360575.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX5360575/SRX5360575.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 @ Tue, 30 Jun 2020 00:01:05: #1 read tag files... INFO @ Tue, 30 Jun 2020 00:01:05: #1 read treatment tags... INFO @ Tue, 30 Jun 2020 00:01:05: #1 tag size is determined as 50 bps INFO @ Tue, 30 Jun 2020 00:01:05: #1 tag size = 50 INFO @ Tue, 30 Jun 2020 00:01:05: #1 total tags in treatment: 172546 INFO @ Tue, 30 Jun 2020 00:01:05: #1 user defined the maximum tags... INFO @ Tue, 30 Jun 2020 00:01:05: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 30 Jun 2020 00:01:05: #1 tags after filtering in treatment: 172546 INFO @ Tue, 30 Jun 2020 00:01:05: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 30 Jun 2020 00:01:05: #1 finished! INFO @ Tue, 30 Jun 2020 00:01:05: #2 Build Peak Model... INFO @ Tue, 30 Jun 2020 00:01:05: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 30 Jun 2020 00:01:05: #2 number of paired peaks: 298 WARNING @ Tue, 30 Jun 2020 00:01:05: Fewer paired peaks (298) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 298 pairs to build model! INFO @ Tue, 30 Jun 2020 00:01:05: start model_add_line... INFO @ Tue, 30 Jun 2020 00:01:05: start X-correlation... INFO @ Tue, 30 Jun 2020 00:01:06: end of X-cor INFO @ Tue, 30 Jun 2020 00:01:06: #2 finished! INFO @ Tue, 30 Jun 2020 00:01:06: #2 predicted fragment length is 49 bps INFO @ Tue, 30 Jun 2020 00:01:06: #2 alternative fragment length(s) may be 49,409,460 bps INFO @ Tue, 30 Jun 2020 00:01:06: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX5360575/SRX5360575.05_model.r WARNING @ Tue, 30 Jun 2020 00:01:06: #2 Since the d (49) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 30 Jun 2020 00:01:06: #2 You may need to consider one of the other alternative d(s): 49,409,460 WARNING @ Tue, 30 Jun 2020 00:01:06: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 30 Jun 2020 00:01:06: #3 Call peaks... INFO @ Tue, 30 Jun 2020 00:01:06: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 30 Jun 2020 00:01:06: #3 Call peaks for each chromosome... INFO @ Tue, 30 Jun 2020 00:01:06: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX5360575/SRX5360575.05_peaks.xls INFO @ Tue, 30 Jun 2020 00:01:06: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX5360575/SRX5360575.05_peaks.narrowPeak INFO @ Tue, 30 Jun 2020 00:01:06: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX5360575/SRX5360575.05_summits.bed INFO @ Tue, 30 Jun 2020 00:01:06: Done! pass1 - making usageList (4 chroms): 1 millis pass2 - checking and writing primary data (417 records, 4 fields): 1 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 @ Tue, 30 Jun 2020 00:01:35: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX5360575/SRX5360575.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX5360575/SRX5360575.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX5360575/SRX5360575.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX5360575/SRX5360575.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 @ Tue, 30 Jun 2020 00:01:35: #1 read tag files... INFO @ Tue, 30 Jun 2020 00:01:35: #1 read treatment tags... INFO @ Tue, 30 Jun 2020 00:01:35: #1 tag size is determined as 50 bps INFO @ Tue, 30 Jun 2020 00:01:35: #1 tag size = 50 INFO @ Tue, 30 Jun 2020 00:01:35: #1 total tags in treatment: 172546 INFO @ Tue, 30 Jun 2020 00:01:35: #1 user defined the maximum tags... INFO @ Tue, 30 Jun 2020 00:01:35: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 30 Jun 2020 00:01:35: #1 tags after filtering in treatment: 172546 INFO @ Tue, 30 Jun 2020 00:01:35: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 30 Jun 2020 00:01:35: #1 finished! INFO @ Tue, 30 Jun 2020 00:01:35: #2 Build Peak Model... INFO @ Tue, 30 Jun 2020 00:01:35: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 30 Jun 2020 00:01:35: #2 number of paired peaks: 298 WARNING @ Tue, 30 Jun 2020 00:01:35: Fewer paired peaks (298) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 298 pairs to build model! INFO @ Tue, 30 Jun 2020 00:01:35: start model_add_line... INFO @ Tue, 30 Jun 2020 00:01:35: start X-correlation... INFO @ Tue, 30 Jun 2020 00:01:36: end of X-cor INFO @ Tue, 30 Jun 2020 00:01:36: #2 finished! INFO @ Tue, 30 Jun 2020 00:01:36: #2 predicted fragment length is 49 bps INFO @ Tue, 30 Jun 2020 00:01:36: #2 alternative fragment length(s) may be 49,409,460 bps INFO @ Tue, 30 Jun 2020 00:01:36: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX5360575/SRX5360575.10_model.r WARNING @ Tue, 30 Jun 2020 00:01:36: #2 Since the d (49) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 30 Jun 2020 00:01:36: #2 You may need to consider one of the other alternative d(s): 49,409,460 WARNING @ Tue, 30 Jun 2020 00:01:36: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 30 Jun 2020 00:01:36: #3 Call peaks... INFO @ Tue, 30 Jun 2020 00:01:36: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 30 Jun 2020 00:01:36: #3 Call peaks for each chromosome... INFO @ Tue, 30 Jun 2020 00:01:36: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX5360575/SRX5360575.10_peaks.xls INFO @ Tue, 30 Jun 2020 00:01:36: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX5360575/SRX5360575.10_peaks.narrowPeak INFO @ Tue, 30 Jun 2020 00:01:36: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX5360575/SRX5360575.10_summits.bed INFO @ Tue, 30 Jun 2020 00:01:36: Done! pass1 - making usageList (3 chroms): 1 millis pass2 - checking and writing primary data (299 records, 4 fields): 1 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 BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。 INFO @ Tue, 30 Jun 2020 00:02:05: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX5360575/SRX5360575.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX5360575/SRX5360575.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX5360575/SRX5360575.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX5360575/SRX5360575.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 @ Tue, 30 Jun 2020 00:02:05: #1 read tag files... INFO @ Tue, 30 Jun 2020 00:02:05: #1 read treatment tags... INFO @ Tue, 30 Jun 2020 00:02:06: #1 tag size is determined as 50 bps INFO @ Tue, 30 Jun 2020 00:02:06: #1 tag size = 50 INFO @ Tue, 30 Jun 2020 00:02:06: #1 total tags in treatment: 172546 INFO @ Tue, 30 Jun 2020 00:02:06: #1 user defined the maximum tags... INFO @ Tue, 30 Jun 2020 00:02:06: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 30 Jun 2020 00:02:06: #1 tags after filtering in treatment: 172546 INFO @ Tue, 30 Jun 2020 00:02:06: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 30 Jun 2020 00:02:06: #1 finished! INFO @ Tue, 30 Jun 2020 00:02:06: #2 Build Peak Model... INFO @ Tue, 30 Jun 2020 00:02:06: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 30 Jun 2020 00:02:06: #2 number of paired peaks: 298 WARNING @ Tue, 30 Jun 2020 00:02:06: Fewer paired peaks (298) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 298 pairs to build model! INFO @ Tue, 30 Jun 2020 00:02:06: start model_add_line... INFO @ Tue, 30 Jun 2020 00:02:06: start X-correlation... INFO @ Tue, 30 Jun 2020 00:02:06: end of X-cor INFO @ Tue, 30 Jun 2020 00:02:06: #2 finished! INFO @ Tue, 30 Jun 2020 00:02:06: #2 predicted fragment length is 49 bps INFO @ Tue, 30 Jun 2020 00:02:06: #2 alternative fragment length(s) may be 49,409,460 bps INFO @ Tue, 30 Jun 2020 00:02:06: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX5360575/SRX5360575.20_model.r WARNING @ Tue, 30 Jun 2020 00:02:06: #2 Since the d (49) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 30 Jun 2020 00:02:06: #2 You may need to consider one of the other alternative d(s): 49,409,460 WARNING @ Tue, 30 Jun 2020 00:02:06: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 30 Jun 2020 00:02:06: #3 Call peaks... INFO @ Tue, 30 Jun 2020 00:02:06: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 30 Jun 2020 00:02:06: #3 Call peaks for each chromosome... INFO @ Tue, 30 Jun 2020 00:02:06: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX5360575/SRX5360575.20_peaks.xls INFO @ Tue, 30 Jun 2020 00:02:06: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX5360575/SRX5360575.20_peaks.narrowPeak INFO @ Tue, 30 Jun 2020 00:02:06: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX5360575/SRX5360575.20_summits.bed INFO @ Tue, 30 Jun 2020 00:02:06: Done! pass1 - making usageList (3 chroms): 1 millis pass2 - checking and writing primary data (193 records, 4 fields): 1 millis CompletedMACS2peakCalling