Job ID = 6367141 SRX = SRX277099 Genome = ce11 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-15T23:17:16 prefetch.2.10.7: 1) Downloading 'SRR849775'... 2020-06-15T23:17:16 prefetch.2.10.7: Downloading via HTTPS... 2020-06-15T23:17:44 prefetch.2.10.7: HTTPS download succeed 2020-06-15T23:17:44 prefetch.2.10.7: 'SRR849775' is valid 2020-06-15T23:17:44 prefetch.2.10.7: 1) 'SRR849775' was downloaded successfully Read 4246825 spots for SRR849775/SRR849775.sra Written 4246825 spots for SRR849775/SRR849775.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: 00:00:40 4246825 reads; of these: 4246825 (100.00%) were unpaired; of these: 103281 (2.43%) aligned 0 times 3483695 (82.03%) aligned exactly 1 time 659849 (15.54%) aligned >1 times 97.57% 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: 7 sequences. [bam_rmdupse_core] 240522 / 4143544 = 0.0580 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, 16 Jun 2020 08:19:53: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX277099/SRX277099.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX277099/SRX277099.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX277099/SRX277099.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX277099/SRX277099.bam'] # control file = None # effective genome size = 9.00e+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 @ Tue, 16 Jun 2020 08:19:53: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:19:53: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:19:58: 1000000 INFO @ Tue, 16 Jun 2020 08:20:03: 2000000 INFO @ Tue, 16 Jun 2020 08:20:08: 3000000 INFO @ Tue, 16 Jun 2020 08:20:12: #1 tag size is determined as 32 bps INFO @ Tue, 16 Jun 2020 08:20:12: #1 tag size = 32 INFO @ Tue, 16 Jun 2020 08:20:12: #1 total tags in treatment: 3903022 INFO @ Tue, 16 Jun 2020 08:20:12: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:20:12: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 16 Jun 2020 08:20:12: #1 tags after filtering in treatment: 3903022 INFO @ Tue, 16 Jun 2020 08:20:12: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:20:12: #1 finished! INFO @ Tue, 16 Jun 2020 08:20:12: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:20:12: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:20:13: #2 number of paired peaks: 384 WARNING @ Tue, 16 Jun 2020 08:20:13: Fewer paired peaks (384) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 384 pairs to build model! INFO @ Tue, 16 Jun 2020 08:20:13: start model_add_line... INFO @ Tue, 16 Jun 2020 08:20:13: start X-correlation... INFO @ Tue, 16 Jun 2020 08:20:13: end of X-cor INFO @ Tue, 16 Jun 2020 08:20:13: #2 finished! INFO @ Tue, 16 Jun 2020 08:20:13: #2 predicted fragment length is 31 bps INFO @ Tue, 16 Jun 2020 08:20:13: #2 alternative fragment length(s) may be 4,31,479,483,488,597 bps INFO @ Tue, 16 Jun 2020 08:20:13: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX277099/SRX277099.05_model.r WARNING @ Tue, 16 Jun 2020 08:20:13: #2 Since the d (31) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 08:20:13: #2 You may need to consider one of the other alternative d(s): 4,31,479,483,488,597 WARNING @ Tue, 16 Jun 2020 08:20:13: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 16 Jun 2020 08:20:13: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:20:13: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 08:20:21: #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 @ Tue, 16 Jun 2020 08:20:23: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX277099/SRX277099.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX277099/SRX277099.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX277099/SRX277099.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX277099/SRX277099.bam'] # control file = None # effective genome size = 9.00e+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 @ Tue, 16 Jun 2020 08:20:23: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:20:23: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:20:25: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX277099/SRX277099.05_peaks.xls INFO @ Tue, 16 Jun 2020 08:20:25: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX277099/SRX277099.05_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:20:25: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX277099/SRX277099.05_summits.bed INFO @ Tue, 16 Jun 2020 08:20:25: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (343 records, 4 fields): 1 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 08:20:28: 1000000 INFO @ Tue, 16 Jun 2020 08:20:33: 2000000 INFO @ Tue, 16 Jun 2020 08:20:39: 3000000 INFO @ Tue, 16 Jun 2020 08:20:43: #1 tag size is determined as 32 bps INFO @ Tue, 16 Jun 2020 08:20:43: #1 tag size = 32 INFO @ Tue, 16 Jun 2020 08:20:43: #1 total tags in treatment: 3903022 INFO @ Tue, 16 Jun 2020 08:20:43: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:20:43: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 16 Jun 2020 08:20:43: #1 tags after filtering in treatment: 3903022 INFO @ Tue, 16 Jun 2020 08:20:43: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:20:43: #1 finished! INFO @ Tue, 16 Jun 2020 08:20:43: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:20:43: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:20:44: #2 number of paired peaks: 384 WARNING @ Tue, 16 Jun 2020 08:20:44: Fewer paired peaks (384) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 384 pairs to build model! INFO @ Tue, 16 Jun 2020 08:20:44: start model_add_line... INFO @ Tue, 16 Jun 2020 08:20:44: start X-correlation... INFO @ Tue, 16 Jun 2020 08:20:44: end of X-cor INFO @ Tue, 16 Jun 2020 08:20:44: #2 finished! INFO @ Tue, 16 Jun 2020 08:20:44: #2 predicted fragment length is 31 bps INFO @ Tue, 16 Jun 2020 08:20:44: #2 alternative fragment length(s) may be 4,31,479,483,488,597 bps INFO @ Tue, 16 Jun 2020 08:20:44: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX277099/SRX277099.10_model.r WARNING @ Tue, 16 Jun 2020 08:20:44: #2 Since the d (31) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 08:20:44: #2 You may need to consider one of the other alternative d(s): 4,31,479,483,488,597 WARNING @ Tue, 16 Jun 2020 08:20:44: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 16 Jun 2020 08:20:44: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:20:44: #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 @ Tue, 16 Jun 2020 08:20:52: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 08:20:53: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX277099/SRX277099.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX277099/SRX277099.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX277099/SRX277099.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX277099/SRX277099.bam'] # control file = None # effective genome size = 9.00e+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 @ Tue, 16 Jun 2020 08:20:53: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:20:53: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:20:56: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX277099/SRX277099.10_peaks.xls INFO @ Tue, 16 Jun 2020 08:20:56: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX277099/SRX277099.10_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:20:56: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX277099/SRX277099.10_summits.bed INFO @ Tue, 16 Jun 2020 08:20:56: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (168 records, 4 fields): 1 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 08:20:59: 1000000 INFO @ Tue, 16 Jun 2020 08:21:06: 2000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 16 Jun 2020 08:21:12: 3000000 INFO @ Tue, 16 Jun 2020 08:21:18: #1 tag size is determined as 32 bps INFO @ Tue, 16 Jun 2020 08:21:18: #1 tag size = 32 INFO @ Tue, 16 Jun 2020 08:21:18: #1 total tags in treatment: 3903022 INFO @ Tue, 16 Jun 2020 08:21:18: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:21:18: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 16 Jun 2020 08:21:18: #1 tags after filtering in treatment: 3903022 INFO @ Tue, 16 Jun 2020 08:21:18: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:21:18: #1 finished! INFO @ Tue, 16 Jun 2020 08:21:18: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:21:18: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:21:18: #2 number of paired peaks: 384 WARNING @ Tue, 16 Jun 2020 08:21:18: Fewer paired peaks (384) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 384 pairs to build model! INFO @ Tue, 16 Jun 2020 08:21:18: start model_add_line... INFO @ Tue, 16 Jun 2020 08:21:18: start X-correlation... INFO @ Tue, 16 Jun 2020 08:21:18: end of X-cor INFO @ Tue, 16 Jun 2020 08:21:18: #2 finished! INFO @ Tue, 16 Jun 2020 08:21:18: #2 predicted fragment length is 31 bps INFO @ Tue, 16 Jun 2020 08:21:18: #2 alternative fragment length(s) may be 4,31,479,483,488,597 bps INFO @ Tue, 16 Jun 2020 08:21:18: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX277099/SRX277099.20_model.r WARNING @ Tue, 16 Jun 2020 08:21:18: #2 Since the d (31) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 08:21:18: #2 You may need to consider one of the other alternative d(s): 4,31,479,483,488,597 WARNING @ Tue, 16 Jun 2020 08:21:18: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 16 Jun 2020 08:21:18: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:21:18: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Tue, 16 Jun 2020 08:21:26: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 08:21:31: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX277099/SRX277099.20_peaks.xls INFO @ Tue, 16 Jun 2020 08:21:31: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX277099/SRX277099.20_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:21:31: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX277099/SRX277099.20_summits.bed INFO @ Tue, 16 Jun 2020 08:21:31: Done! pass1 - making usageList (6 chroms): 2 millis pass2 - checking and writing primary data (56 records, 4 fields): 1 millis CompletedMACS2peakCalling