Job ID = 6368570 SRX = SRX5020796 Genome = ce11 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-16T00:25:46 prefetch.2.10.7: 1) Downloading 'SRR8201419'... 2020-06-16T00:25:46 prefetch.2.10.7: Downloading via HTTPS... 2020-06-16T00:26:50 prefetch.2.10.7: HTTPS download succeed 2020-06-16T00:26:50 prefetch.2.10.7: 'SRR8201419' is valid 2020-06-16T00:26:50 prefetch.2.10.7: 1) 'SRR8201419' was downloaded successfully Read 5486215 spots for SRR8201419/SRR8201419.sra Written 5486215 spots for SRR8201419/SRR8201419.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: 00:00:56 5486215 reads; of these: 5486215 (100.00%) were unpaired; of these: 2330816 (42.48%) aligned 0 times 2655744 (48.41%) aligned exactly 1 time 499655 (9.11%) aligned >1 times 57.52% overall alignment rate Time searching: 00:00:56 Overall time: 00:00:56 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] 471935 / 3155399 = 0.1496 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 09:29:24: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX5020796/SRX5020796.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX5020796/SRX5020796.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX5020796/SRX5020796.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX5020796/SRX5020796.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 09:29:24: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:29:24: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:29:30: 1000000 INFO @ Tue, 16 Jun 2020 09:29:36: 2000000 INFO @ Tue, 16 Jun 2020 09:29:39: #1 tag size is determined as 51 bps INFO @ Tue, 16 Jun 2020 09:29:39: #1 tag size = 51 INFO @ Tue, 16 Jun 2020 09:29:39: #1 total tags in treatment: 2683464 INFO @ Tue, 16 Jun 2020 09:29:39: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:29:39: #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 09:29:40: #1 tags after filtering in treatment: 2683464 INFO @ Tue, 16 Jun 2020 09:29:40: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 09:29:40: #1 finished! INFO @ Tue, 16 Jun 2020 09:29:40: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:29:40: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:29:40: #2 number of paired peaks: 397 WARNING @ Tue, 16 Jun 2020 09:29:40: Fewer paired peaks (397) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 397 pairs to build model! INFO @ Tue, 16 Jun 2020 09:29:40: start model_add_line... INFO @ Tue, 16 Jun 2020 09:29:40: start X-correlation... INFO @ Tue, 16 Jun 2020 09:29:40: end of X-cor INFO @ Tue, 16 Jun 2020 09:29:40: #2 finished! INFO @ Tue, 16 Jun 2020 09:29:40: #2 predicted fragment length is 52 bps INFO @ Tue, 16 Jun 2020 09:29:40: #2 alternative fragment length(s) may be 52,548 bps INFO @ Tue, 16 Jun 2020 09:29:40: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX5020796/SRX5020796.05_model.r WARNING @ Tue, 16 Jun 2020 09:29:40: #2 Since the d (52) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 09:29:40: #2 You may need to consider one of the other alternative d(s): 52,548 WARNING @ Tue, 16 Jun 2020 09:29:40: #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 09:29:40: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:29:40: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 09:29:46: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 09:29:49: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX5020796/SRX5020796.05_peaks.xls INFO @ Tue, 16 Jun 2020 09:29:49: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX5020796/SRX5020796.05_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:29:49: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX5020796/SRX5020796.05_summits.bed INFO @ Tue, 16 Jun 2020 09:29:49: Done! pass1 - making usageList (7 chroms): 0 millis pass2 - checking and writing primary data (369 records, 4 fields): 2 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 09:29:55: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX5020796/SRX5020796.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX5020796/SRX5020796.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX5020796/SRX5020796.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX5020796/SRX5020796.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 09:29:55: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:29:55: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:30:01: 1000000 INFO @ Tue, 16 Jun 2020 09:30:07: 2000000 INFO @ Tue, 16 Jun 2020 09:30:11: #1 tag size is determined as 51 bps INFO @ Tue, 16 Jun 2020 09:30:11: #1 tag size = 51 INFO @ Tue, 16 Jun 2020 09:30:11: #1 total tags in treatment: 2683464 INFO @ Tue, 16 Jun 2020 09:30:11: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:30:11: #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 09:30:11: #1 tags after filtering in treatment: 2683464 INFO @ Tue, 16 Jun 2020 09:30:11: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 09:30:11: #1 finished! INFO @ Tue, 16 Jun 2020 09:30:11: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:30:11: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:30:11: #2 number of paired peaks: 397 WARNING @ Tue, 16 Jun 2020 09:30:11: Fewer paired peaks (397) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 397 pairs to build model! INFO @ Tue, 16 Jun 2020 09:30:11: start model_add_line... INFO @ Tue, 16 Jun 2020 09:30:11: start X-correlation... INFO @ Tue, 16 Jun 2020 09:30:11: end of X-cor INFO @ Tue, 16 Jun 2020 09:30:11: #2 finished! INFO @ Tue, 16 Jun 2020 09:30:11: #2 predicted fragment length is 52 bps INFO @ Tue, 16 Jun 2020 09:30:11: #2 alternative fragment length(s) may be 52,548 bps INFO @ Tue, 16 Jun 2020 09:30:11: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX5020796/SRX5020796.10_model.r WARNING @ Tue, 16 Jun 2020 09:30:11: #2 Since the d (52) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 09:30:11: #2 You may need to consider one of the other alternative d(s): 52,548 WARNING @ Tue, 16 Jun 2020 09:30:11: #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 09:30:11: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:30:11: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 09:30:18: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 09:30:21: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX5020796/SRX5020796.10_peaks.xls INFO @ Tue, 16 Jun 2020 09:30:21: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX5020796/SRX5020796.10_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:30:21: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX5020796/SRX5020796.10_summits.bed INFO @ Tue, 16 Jun 2020 09:30:21: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (197 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 09:30:24: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX5020796/SRX5020796.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX5020796/SRX5020796.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX5020796/SRX5020796.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX5020796/SRX5020796.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 09:30:24: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:30:24: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:30:30: 1000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 16 Jun 2020 09:30:36: 2000000 INFO @ Tue, 16 Jun 2020 09:30:40: #1 tag size is determined as 51 bps INFO @ Tue, 16 Jun 2020 09:30:40: #1 tag size = 51 INFO @ Tue, 16 Jun 2020 09:30:40: #1 total tags in treatment: 2683464 INFO @ Tue, 16 Jun 2020 09:30:40: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:30:40: #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 09:30:40: #1 tags after filtering in treatment: 2683464 INFO @ Tue, 16 Jun 2020 09:30:40: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 09:30:40: #1 finished! INFO @ Tue, 16 Jun 2020 09:30:40: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:30:40: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:30:41: #2 number of paired peaks: 397 WARNING @ Tue, 16 Jun 2020 09:30:41: Fewer paired peaks (397) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 397 pairs to build model! INFO @ Tue, 16 Jun 2020 09:30:41: start model_add_line... INFO @ Tue, 16 Jun 2020 09:30:41: start X-correlation... INFO @ Tue, 16 Jun 2020 09:30:41: end of X-cor INFO @ Tue, 16 Jun 2020 09:30:41: #2 finished! INFO @ Tue, 16 Jun 2020 09:30:41: #2 predicted fragment length is 52 bps INFO @ Tue, 16 Jun 2020 09:30:41: #2 alternative fragment length(s) may be 52,548 bps INFO @ Tue, 16 Jun 2020 09:30:41: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX5020796/SRX5020796.20_model.r WARNING @ Tue, 16 Jun 2020 09:30:41: #2 Since the d (52) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 09:30:41: #2 You may need to consider one of the other alternative d(s): 52,548 WARNING @ Tue, 16 Jun 2020 09:30:41: #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 09:30:41: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:30:41: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Tue, 16 Jun 2020 09:30:46: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 09:30:49: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX5020796/SRX5020796.20_peaks.xls INFO @ Tue, 16 Jun 2020 09:30:49: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX5020796/SRX5020796.20_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:30:49: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX5020796/SRX5020796.20_summits.bed INFO @ Tue, 16 Jun 2020 09:30:49: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (87 records, 4 fields): 1 millis CompletedMACS2peakCalling