Job ID = 5790930 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 540,718 reads read : 1,081,436 reads written : 540,718 reads 0-length : 540,718 rm: cannot remove ‘[DSE]RR*’: No such file or directory 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: 00:00:06 540718 reads; of these: 540718 (100.00%) were unpaired; of these: 198 (0.04%) aligned 0 times 493080 (91.19%) aligned exactly 1 time 47440 (8.77%) aligned >1 times 99.96% overall alignment rate Time searching: 00:00:06 Overall time: 00:00:06 マッピングが完了しました。 samtools でBAM に変換中... [samopen] SAM header is present: 17 sequences. [bam_rmdupse_core] 32210 / 540520 = 0.0596 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 @ Wed, 22 Apr 2020 08:04:49: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX5550847/SRX5550847.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX5550847/SRX5550847.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX5550847/SRX5550847.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX5550847/SRX5550847.bam'] # control file = None # effective genome size = 1.21e+07 # 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 @ Wed, 22 Apr 2020 08:04:49: #1 read tag files... INFO @ Wed, 22 Apr 2020 08:04:49: #1 read treatment tags... INFO @ Wed, 22 Apr 2020 08:04:52: #1 tag size is determined as 76 bps INFO @ Wed, 22 Apr 2020 08:04:52: #1 tag size = 76 INFO @ Wed, 22 Apr 2020 08:04:52: #1 total tags in treatment: 508310 INFO @ Wed, 22 Apr 2020 08:04:52: #1 user defined the maximum tags... INFO @ Wed, 22 Apr 2020 08:04:52: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Wed, 22 Apr 2020 08:04:52: #1 tags after filtering in treatment: 508310 INFO @ Wed, 22 Apr 2020 08:04:52: #1 Redundant rate of treatment: 0.00 INFO @ Wed, 22 Apr 2020 08:04:52: #1 finished! INFO @ Wed, 22 Apr 2020 08:04:52: #2 Build Peak Model... INFO @ Wed, 22 Apr 2020 08:04:52: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 22 Apr 2020 08:04:52: #2 number of paired peaks: 104 WARNING @ Wed, 22 Apr 2020 08:04:52: Fewer paired peaks (104) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 104 pairs to build model! INFO @ Wed, 22 Apr 2020 08:04:52: start model_add_line... INFO @ Wed, 22 Apr 2020 08:04:52: start X-correlation... INFO @ Wed, 22 Apr 2020 08:04:53: end of X-cor INFO @ Wed, 22 Apr 2020 08:04:53: #2 finished! INFO @ Wed, 22 Apr 2020 08:04:53: #2 predicted fragment length is 124 bps INFO @ Wed, 22 Apr 2020 08:04:53: #2 alternative fragment length(s) may be 124,554 bps INFO @ Wed, 22 Apr 2020 08:04:53: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX5550847/SRX5550847.05_model.r WARNING @ Wed, 22 Apr 2020 08:04:53: #2 Since the d (124) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Wed, 22 Apr 2020 08:04:53: #2 You may need to consider one of the other alternative d(s): 124,554 WARNING @ Wed, 22 Apr 2020 08:04:53: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Wed, 22 Apr 2020 08:04:53: #3 Call peaks... INFO @ Wed, 22 Apr 2020 08:04:53: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 22 Apr 2020 08:04:54: #3 Call peaks for each chromosome... INFO @ Wed, 22 Apr 2020 08:04:54: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX5550847/SRX5550847.05_peaks.xls INFO @ Wed, 22 Apr 2020 08:04:54: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX5550847/SRX5550847.05_peaks.narrowPeak INFO @ Wed, 22 Apr 2020 08:04:54: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX5550847/SRX5550847.05_summits.bed INFO @ Wed, 22 Apr 2020 08:04:54: Done! pass1 - making usageList (16 chroms): 1 millis pass2 - checking and writing primary data (1034 records, 4 fields): 5 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 @ Wed, 22 Apr 2020 08:05:18: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX5550847/SRX5550847.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX5550847/SRX5550847.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX5550847/SRX5550847.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX5550847/SRX5550847.bam'] # control file = None # effective genome size = 1.21e+07 # 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 @ Wed, 22 Apr 2020 08:05:18: #1 read tag files... INFO @ Wed, 22 Apr 2020 08:05:18: #1 read treatment tags... INFO @ Wed, 22 Apr 2020 08:05:20: #1 tag size is determined as 76 bps INFO @ Wed, 22 Apr 2020 08:05:20: #1 tag size = 76 INFO @ Wed, 22 Apr 2020 08:05:20: #1 total tags in treatment: 508310 INFO @ Wed, 22 Apr 2020 08:05:20: #1 user defined the maximum tags... INFO @ Wed, 22 Apr 2020 08:05:20: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Wed, 22 Apr 2020 08:05:20: #1 tags after filtering in treatment: 508310 INFO @ Wed, 22 Apr 2020 08:05:20: #1 Redundant rate of treatment: 0.00 INFO @ Wed, 22 Apr 2020 08:05:20: #1 finished! INFO @ Wed, 22 Apr 2020 08:05:20: #2 Build Peak Model... INFO @ Wed, 22 Apr 2020 08:05:20: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 22 Apr 2020 08:05:20: #2 number of paired peaks: 104 WARNING @ Wed, 22 Apr 2020 08:05:20: Fewer paired peaks (104) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 104 pairs to build model! INFO @ Wed, 22 Apr 2020 08:05:20: start model_add_line... INFO @ Wed, 22 Apr 2020 08:05:20: start X-correlation... INFO @ Wed, 22 Apr 2020 08:05:20: end of X-cor INFO @ Wed, 22 Apr 2020 08:05:20: #2 finished! INFO @ Wed, 22 Apr 2020 08:05:20: #2 predicted fragment length is 124 bps INFO @ Wed, 22 Apr 2020 08:05:20: #2 alternative fragment length(s) may be 124,554 bps INFO @ Wed, 22 Apr 2020 08:05:20: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX5550847/SRX5550847.10_model.r WARNING @ Wed, 22 Apr 2020 08:05:20: #2 Since the d (124) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Wed, 22 Apr 2020 08:05:20: #2 You may need to consider one of the other alternative d(s): 124,554 WARNING @ Wed, 22 Apr 2020 08:05:20: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Wed, 22 Apr 2020 08:05:20: #3 Call peaks... INFO @ Wed, 22 Apr 2020 08:05:20: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 22 Apr 2020 08:05:22: #3 Call peaks for each chromosome... INFO @ Wed, 22 Apr 2020 08:05:22: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX5550847/SRX5550847.10_peaks.xls INFO @ Wed, 22 Apr 2020 08:05:22: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX5550847/SRX5550847.10_peaks.narrowPeak INFO @ Wed, 22 Apr 2020 08:05:22: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX5550847/SRX5550847.10_summits.bed INFO @ Wed, 22 Apr 2020 08:05:22: Done! pass1 - making usageList (16 chroms): 1 millis pass2 - checking and writing primary data (307 records, 4 fields): 2 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 @ Wed, 22 Apr 2020 08:05:48: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX5550847/SRX5550847.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX5550847/SRX5550847.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX5550847/SRX5550847.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX5550847/SRX5550847.bam'] # control file = None # effective genome size = 1.21e+07 # 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 @ Wed, 22 Apr 2020 08:05:48: #1 read tag files... INFO @ Wed, 22 Apr 2020 08:05:48: #1 read treatment tags... BedGraph に変換しました。 BigWig に変換中... INFO @ Wed, 22 Apr 2020 08:05:51: #1 tag size is determined as 76 bps INFO @ Wed, 22 Apr 2020 08:05:51: #1 tag size = 76 INFO @ Wed, 22 Apr 2020 08:05:51: #1 total tags in treatment: 508310 INFO @ Wed, 22 Apr 2020 08:05:51: #1 user defined the maximum tags... INFO @ Wed, 22 Apr 2020 08:05:51: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Wed, 22 Apr 2020 08:05:51: #1 tags after filtering in treatment: 508310 INFO @ Wed, 22 Apr 2020 08:05:51: #1 Redundant rate of treatment: 0.00 INFO @ Wed, 22 Apr 2020 08:05:51: #1 finished! INFO @ Wed, 22 Apr 2020 08:05:51: #2 Build Peak Model... INFO @ Wed, 22 Apr 2020 08:05:51: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 22 Apr 2020 08:05:51: #2 number of paired peaks: 104 WARNING @ Wed, 22 Apr 2020 08:05:51: Fewer paired peaks (104) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 104 pairs to build model! INFO @ Wed, 22 Apr 2020 08:05:51: start model_add_line... INFO @ Wed, 22 Apr 2020 08:05:51: start X-correlation... INFO @ Wed, 22 Apr 2020 08:05:51: end of X-cor INFO @ Wed, 22 Apr 2020 08:05:51: #2 finished! INFO @ Wed, 22 Apr 2020 08:05:51: #2 predicted fragment length is 124 bps INFO @ Wed, 22 Apr 2020 08:05:51: #2 alternative fragment length(s) may be 124,554 bps INFO @ Wed, 22 Apr 2020 08:05:51: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX5550847/SRX5550847.20_model.r WARNING @ Wed, 22 Apr 2020 08:05:51: #2 Since the d (124) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Wed, 22 Apr 2020 08:05:51: #2 You may need to consider one of the other alternative d(s): 124,554 WARNING @ Wed, 22 Apr 2020 08:05:51: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Wed, 22 Apr 2020 08:05:51: #3 Call peaks... INFO @ Wed, 22 Apr 2020 08:05:51: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Wed, 22 Apr 2020 08:05:53: #3 Call peaks for each chromosome... INFO @ Wed, 22 Apr 2020 08:05:53: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX5550847/SRX5550847.20_peaks.xls INFO @ Wed, 22 Apr 2020 08:05:53: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX5550847/SRX5550847.20_peaks.narrowPeak INFO @ Wed, 22 Apr 2020 08:05:53: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX5550847/SRX5550847.20_summits.bed INFO @ Wed, 22 Apr 2020 08:05:53: Done! pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (60 records, 4 fields): 1 millis CompletedMACS2peakCalling