Job ID = 6367048 SRX = SRX276906 Genome = ce11 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-15T23:11:01 prefetch.2.10.7: 1) Downloading 'SRR849512'... 2020-06-15T23:11:01 prefetch.2.10.7: Downloading via HTTPS... 2020-06-15T23:11:30 prefetch.2.10.7: HTTPS download succeed 2020-06-15T23:11:30 prefetch.2.10.7: 'SRR849512' is valid 2020-06-15T23:11:30 prefetch.2.10.7: 1) 'SRR849512' was downloaded successfully Read 3393973 spots for SRR849512/SRR849512.sra Written 3393973 spots for SRR849512/SRR849512.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: 00:00:24 3393973 reads; of these: 3393973 (100.00%) were unpaired; of these: 1149922 (33.88%) aligned 0 times 1871154 (55.13%) aligned exactly 1 time 372897 (10.99%) aligned >1 times 66.12% overall alignment rate Time searching: 00:00:24 Overall time: 00:00:24 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] 68021 / 2244051 = 0.0303 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 08:13:01: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX276906/SRX276906.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX276906/SRX276906.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX276906/SRX276906.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX276906/SRX276906.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 08:13:01: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:13:01: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:13:06: 1000000 INFO @ Tue, 16 Jun 2020 08:13:12: 2000000 INFO @ Tue, 16 Jun 2020 08:13:13: #1 tag size is determined as 32 bps INFO @ Tue, 16 Jun 2020 08:13:13: #1 tag size = 32 INFO @ Tue, 16 Jun 2020 08:13:13: #1 total tags in treatment: 2176030 INFO @ Tue, 16 Jun 2020 08:13:13: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:13:13: #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 08:13:13: #1 tags after filtering in treatment: 2176030 INFO @ Tue, 16 Jun 2020 08:13:13: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:13:13: #1 finished! INFO @ Tue, 16 Jun 2020 08:13:13: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:13:13: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:13:13: #2 number of paired peaks: 390 WARNING @ Tue, 16 Jun 2020 08:13:13: Fewer paired peaks (390) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 390 pairs to build model! INFO @ Tue, 16 Jun 2020 08:13:13: start model_add_line... INFO @ Tue, 16 Jun 2020 08:13:13: start X-correlation... INFO @ Tue, 16 Jun 2020 08:13:13: end of X-cor INFO @ Tue, 16 Jun 2020 08:13:13: #2 finished! INFO @ Tue, 16 Jun 2020 08:13:13: #2 predicted fragment length is 33 bps INFO @ Tue, 16 Jun 2020 08:13:13: #2 alternative fragment length(s) may be 33,448,493,528 bps INFO @ Tue, 16 Jun 2020 08:13:13: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX276906/SRX276906.05_model.r WARNING @ Tue, 16 Jun 2020 08:13:13: #2 Since the d (33) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 08:13:13: #2 You may need to consider one of the other alternative d(s): 33,448,493,528 WARNING @ Tue, 16 Jun 2020 08:13:13: #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 08:13:13: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:13:13: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 08:13:18: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 08:13:20: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX276906/SRX276906.05_peaks.xls INFO @ Tue, 16 Jun 2020 08:13:20: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX276906/SRX276906.05_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:13:20: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX276906/SRX276906.05_summits.bed INFO @ Tue, 16 Jun 2020 08:13:20: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (274 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, 16 Jun 2020 08:13:31: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX276906/SRX276906.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX276906/SRX276906.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX276906/SRX276906.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX276906/SRX276906.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 08:13:31: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:13:31: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:13:36: 1000000 INFO @ Tue, 16 Jun 2020 08:13:42: 2000000 INFO @ Tue, 16 Jun 2020 08:13:43: #1 tag size is determined as 32 bps INFO @ Tue, 16 Jun 2020 08:13:43: #1 tag size = 32 INFO @ Tue, 16 Jun 2020 08:13:43: #1 total tags in treatment: 2176030 INFO @ Tue, 16 Jun 2020 08:13:43: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:13:43: #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 08:13:43: #1 tags after filtering in treatment: 2176030 INFO @ Tue, 16 Jun 2020 08:13:43: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:13:43: #1 finished! INFO @ Tue, 16 Jun 2020 08:13:43: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:13:43: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:13:43: #2 number of paired peaks: 390 WARNING @ Tue, 16 Jun 2020 08:13:43: Fewer paired peaks (390) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 390 pairs to build model! INFO @ Tue, 16 Jun 2020 08:13:43: start model_add_line... INFO @ Tue, 16 Jun 2020 08:13:43: start X-correlation... INFO @ Tue, 16 Jun 2020 08:13:43: end of X-cor INFO @ Tue, 16 Jun 2020 08:13:43: #2 finished! INFO @ Tue, 16 Jun 2020 08:13:43: #2 predicted fragment length is 33 bps INFO @ Tue, 16 Jun 2020 08:13:43: #2 alternative fragment length(s) may be 33,448,493,528 bps INFO @ Tue, 16 Jun 2020 08:13:43: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX276906/SRX276906.10_model.r WARNING @ Tue, 16 Jun 2020 08:13:43: #2 Since the d (33) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 08:13:43: #2 You may need to consider one of the other alternative d(s): 33,448,493,528 WARNING @ Tue, 16 Jun 2020 08:13:43: #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 08:13:43: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:13:43: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 08:13:48: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 08:13:50: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX276906/SRX276906.10_peaks.xls INFO @ Tue, 16 Jun 2020 08:13:50: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX276906/SRX276906.10_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:13:50: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX276906/SRX276906.10_summits.bed INFO @ Tue, 16 Jun 2020 08:13:50: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (127 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 INFO @ Tue, 16 Jun 2020 08:14:01: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX276906/SRX276906.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX276906/SRX276906.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX276906/SRX276906.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX276906/SRX276906.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 08:14:01: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:14:01: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:14:06: 1000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 16 Jun 2020 08:14:12: 2000000 INFO @ Tue, 16 Jun 2020 08:14:13: #1 tag size is determined as 32 bps INFO @ Tue, 16 Jun 2020 08:14:13: #1 tag size = 32 INFO @ Tue, 16 Jun 2020 08:14:13: #1 total tags in treatment: 2176030 INFO @ Tue, 16 Jun 2020 08:14:13: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:14:13: #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 08:14:13: #1 tags after filtering in treatment: 2176030 INFO @ Tue, 16 Jun 2020 08:14:13: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:14:13: #1 finished! INFO @ Tue, 16 Jun 2020 08:14:13: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:14:13: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:14:13: #2 number of paired peaks: 390 WARNING @ Tue, 16 Jun 2020 08:14:13: Fewer paired peaks (390) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 390 pairs to build model! INFO @ Tue, 16 Jun 2020 08:14:13: start model_add_line... INFO @ Tue, 16 Jun 2020 08:14:13: start X-correlation... INFO @ Tue, 16 Jun 2020 08:14:13: end of X-cor INFO @ Tue, 16 Jun 2020 08:14:13: #2 finished! INFO @ Tue, 16 Jun 2020 08:14:13: #2 predicted fragment length is 33 bps INFO @ Tue, 16 Jun 2020 08:14:13: #2 alternative fragment length(s) may be 33,448,493,528 bps INFO @ Tue, 16 Jun 2020 08:14:13: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX276906/SRX276906.20_model.r WARNING @ Tue, 16 Jun 2020 08:14:13: #2 Since the d (33) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 08:14:13: #2 You may need to consider one of the other alternative d(s): 33,448,493,528 WARNING @ Tue, 16 Jun 2020 08:14:13: #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 08:14:13: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:14:13: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Tue, 16 Jun 2020 08:14:18: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 08:14:20: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX276906/SRX276906.20_peaks.xls INFO @ Tue, 16 Jun 2020 08:14:20: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX276906/SRX276906.20_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:14:20: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX276906/SRX276906.20_summits.bed INFO @ Tue, 16 Jun 2020 08:14:20: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (37 records, 4 fields): 0 millis CompletedMACS2peakCalling