Job ID = 6367059 SRX = SRX276917 Genome = ce11 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-15T23:11:46 prefetch.2.10.7: 1) Downloading 'SRR849523'... 2020-06-15T23:11:46 prefetch.2.10.7: Downloading via HTTPS... 2020-06-15T23:12:10 prefetch.2.10.7: HTTPS download succeed 2020-06-15T23:12:10 prefetch.2.10.7: 'SRR849523' is valid 2020-06-15T23:12:10 prefetch.2.10.7: 1) 'SRR849523' was downloaded successfully Read 4752630 spots for SRR849523/SRR849523.sra Written 4752630 spots for SRR849523/SRR849523.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: 00:00:41 4752630 reads; of these: 4752630 (100.00%) were unpaired; of these: 568254 (11.96%) aligned 0 times 3496028 (73.56%) aligned exactly 1 time 688348 (14.48%) aligned >1 times 88.04% overall alignment rate Time searching: 00:00:41 Overall time: 00:00:41 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] 208792 / 4184376 = 0.0499 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 08:14:25: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX276917/SRX276917.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX276917/SRX276917.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX276917/SRX276917.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX276917/SRX276917.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 08:14:25: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:14:25: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:14:31: 1000000 INFO @ Tue, 16 Jun 2020 08:14:37: 2000000 INFO @ Tue, 16 Jun 2020 08:14:44: 3000000 INFO @ Tue, 16 Jun 2020 08:14:49: #1 tag size is determined as 32 bps INFO @ Tue, 16 Jun 2020 08:14:49: #1 tag size = 32 INFO @ Tue, 16 Jun 2020 08:14:49: #1 total tags in treatment: 3975584 INFO @ Tue, 16 Jun 2020 08:14:49: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:14:49: #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 08:14:49: #1 tags after filtering in treatment: 3975584 INFO @ Tue, 16 Jun 2020 08:14:49: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:14:49: #1 finished! INFO @ Tue, 16 Jun 2020 08:14:49: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:14:49: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:14:50: #2 number of paired peaks: 403 WARNING @ Tue, 16 Jun 2020 08:14:50: Fewer paired peaks (403) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 403 pairs to build model! INFO @ Tue, 16 Jun 2020 08:14:50: start model_add_line... INFO @ Tue, 16 Jun 2020 08:14:50: start X-correlation... INFO @ Tue, 16 Jun 2020 08:14:50: end of X-cor INFO @ Tue, 16 Jun 2020 08:14:50: #2 finished! INFO @ Tue, 16 Jun 2020 08:14:50: #2 predicted fragment length is 30 bps INFO @ Tue, 16 Jun 2020 08:14:50: #2 alternative fragment length(s) may be 4,30,494,574,592 bps INFO @ Tue, 16 Jun 2020 08:14:50: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX276917/SRX276917.05_model.r WARNING @ Tue, 16 Jun 2020 08:14:50: #2 Since the d (30) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 08:14:50: #2 You may need to consider one of the other alternative d(s): 4,30,494,574,592 WARNING @ Tue, 16 Jun 2020 08:14:50: #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 08:14:50: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:14:50: #3 Pre-compute pvalue-qvalue table... 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 08:14:55: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX276917/SRX276917.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX276917/SRX276917.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX276917/SRX276917.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX276917/SRX276917.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 08:14:55: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:14:55: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:14:58: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 08:15:01: 1000000 INFO @ Tue, 16 Jun 2020 08:15:02: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX276917/SRX276917.05_peaks.xls INFO @ Tue, 16 Jun 2020 08:15:02: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX276917/SRX276917.05_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:15:02: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX276917/SRX276917.05_summits.bed INFO @ Tue, 16 Jun 2020 08:15:02: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (373 records, 4 fields): 1 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 08:15:06: 2000000 INFO @ Tue, 16 Jun 2020 08:15:11: 3000000 INFO @ Tue, 16 Jun 2020 08:15:16: #1 tag size is determined as 32 bps INFO @ Tue, 16 Jun 2020 08:15:16: #1 tag size = 32 INFO @ Tue, 16 Jun 2020 08:15:16: #1 total tags in treatment: 3975584 INFO @ Tue, 16 Jun 2020 08:15:16: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:15:16: #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 08:15:16: #1 tags after filtering in treatment: 3975584 INFO @ Tue, 16 Jun 2020 08:15:16: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:15:16: #1 finished! INFO @ Tue, 16 Jun 2020 08:15:16: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:15:16: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:15:16: #2 number of paired peaks: 403 WARNING @ Tue, 16 Jun 2020 08:15:16: Fewer paired peaks (403) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 403 pairs to build model! INFO @ Tue, 16 Jun 2020 08:15:16: start model_add_line... INFO @ Tue, 16 Jun 2020 08:15:16: start X-correlation... INFO @ Tue, 16 Jun 2020 08:15:16: end of X-cor INFO @ Tue, 16 Jun 2020 08:15:16: #2 finished! INFO @ Tue, 16 Jun 2020 08:15:16: #2 predicted fragment length is 30 bps INFO @ Tue, 16 Jun 2020 08:15:16: #2 alternative fragment length(s) may be 4,30,494,574,592 bps INFO @ Tue, 16 Jun 2020 08:15:16: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX276917/SRX276917.10_model.r WARNING @ Tue, 16 Jun 2020 08:15:16: #2 Since the d (30) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 08:15:16: #2 You may need to consider one of the other alternative d(s): 4,30,494,574,592 WARNING @ Tue, 16 Jun 2020 08:15:16: #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 08:15:16: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:15:16: #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 08:15:24: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 08:15:25: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX276917/SRX276917.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX276917/SRX276917.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX276917/SRX276917.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX276917/SRX276917.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 08:15:25: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:15:25: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:15:29: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX276917/SRX276917.10_peaks.xls INFO @ Tue, 16 Jun 2020 08:15:29: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX276917/SRX276917.10_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:15:29: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX276917/SRX276917.10_summits.bed INFO @ Tue, 16 Jun 2020 08:15:29: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (189 records, 4 fields): 1 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 08:15:31: 1000000 INFO @ Tue, 16 Jun 2020 08:15:37: 2000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 16 Jun 2020 08:15:43: 3000000 INFO @ Tue, 16 Jun 2020 08:15:49: #1 tag size is determined as 32 bps INFO @ Tue, 16 Jun 2020 08:15:49: #1 tag size = 32 INFO @ Tue, 16 Jun 2020 08:15:49: #1 total tags in treatment: 3975584 INFO @ Tue, 16 Jun 2020 08:15:49: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:15:49: #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 08:15:49: #1 tags after filtering in treatment: 3975584 INFO @ Tue, 16 Jun 2020 08:15:49: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:15:49: #1 finished! INFO @ Tue, 16 Jun 2020 08:15:49: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:15:49: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:15:50: #2 number of paired peaks: 403 WARNING @ Tue, 16 Jun 2020 08:15:50: Fewer paired peaks (403) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 403 pairs to build model! INFO @ Tue, 16 Jun 2020 08:15:50: start model_add_line... BigWig に変換しました。 INFO @ Tue, 16 Jun 2020 08:15:50: start X-correlation... INFO @ Tue, 16 Jun 2020 08:15:50: end of X-cor INFO @ Tue, 16 Jun 2020 08:15:50: #2 finished! INFO @ Tue, 16 Jun 2020 08:15:50: #2 predicted fragment length is 30 bps INFO @ Tue, 16 Jun 2020 08:15:50: #2 alternative fragment length(s) may be 4,30,494,574,592 bps INFO @ Tue, 16 Jun 2020 08:15:50: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX276917/SRX276917.20_model.r WARNING @ Tue, 16 Jun 2020 08:15:50: #2 Since the d (30) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 08:15:50: #2 You may need to consider one of the other alternative d(s): 4,30,494,574,592 WARNING @ Tue, 16 Jun 2020 08:15:50: #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 08:15:50: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:15:50: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 08:15:58: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 08:16:03: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX276917/SRX276917.20_peaks.xls INFO @ Tue, 16 Jun 2020 08:16:03: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX276917/SRX276917.20_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:16:03: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX276917/SRX276917.20_summits.bed INFO @ Tue, 16 Jun 2020 08:16:03: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (58 records, 4 fields): 0 millis CompletedMACS2peakCalling