Job ID = 6367470 SRX = SRX331227 Genome = ce11 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-15T23:24:05 prefetch.2.10.7: 1) Downloading 'SRR947459'... 2020-06-15T23:24:05 prefetch.2.10.7: Downloading via HTTPS... 2020-06-15T23:24:30 prefetch.2.10.7: HTTPS download succeed 2020-06-15T23:24:30 prefetch.2.10.7: 'SRR947459' is valid 2020-06-15T23:24:30 prefetch.2.10.7: 1) 'SRR947459' was downloaded successfully Read 5252515 spots for SRR947459/SRR947459.sra Written 5252515 spots for SRR947459/SRR947459.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: 00:00:01 Time loading mirror index: 00:00:00 Multiseed full-index search: 00:00:49 5252515 reads; of these: 5252515 (100.00%) were unpaired; of these: 189080 (3.60%) aligned 0 times 4196785 (79.90%) aligned exactly 1 time 866650 (16.50%) aligned >1 times 96.40% overall alignment rate Time searching: 00:00:50 Overall time: 00:00:50 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] 263074 / 5063435 = 0.0520 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 08:27:00: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX331227/SRX331227.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX331227/SRX331227.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX331227/SRX331227.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX331227/SRX331227.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 08:27:00: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:27:00: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:27:04: 1000000 INFO @ Tue, 16 Jun 2020 08:27:09: 2000000 INFO @ Tue, 16 Jun 2020 08:27:14: 3000000 INFO @ Tue, 16 Jun 2020 08:27:19: 4000000 INFO @ Tue, 16 Jun 2020 08:27:22: #1 tag size is determined as 32 bps INFO @ Tue, 16 Jun 2020 08:27:22: #1 tag size = 32 INFO @ Tue, 16 Jun 2020 08:27:22: #1 total tags in treatment: 4800361 INFO @ Tue, 16 Jun 2020 08:27:22: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:27:22: #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 08:27:22: #1 tags after filtering in treatment: 4800361 INFO @ Tue, 16 Jun 2020 08:27:22: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:27:22: #1 finished! INFO @ Tue, 16 Jun 2020 08:27:22: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:27:22: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:27:23: #2 number of paired peaks: 459 WARNING @ Tue, 16 Jun 2020 08:27:23: Fewer paired peaks (459) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 459 pairs to build model! INFO @ Tue, 16 Jun 2020 08:27:23: start model_add_line... INFO @ Tue, 16 Jun 2020 08:27:23: start X-correlation... INFO @ Tue, 16 Jun 2020 08:27:23: end of X-cor INFO @ Tue, 16 Jun 2020 08:27:23: #2 finished! INFO @ Tue, 16 Jun 2020 08:27:23: #2 predicted fragment length is 32 bps INFO @ Tue, 16 Jun 2020 08:27:23: #2 alternative fragment length(s) may be 3,32,498 bps INFO @ Tue, 16 Jun 2020 08:27:23: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX331227/SRX331227.05_model.r WARNING @ Tue, 16 Jun 2020 08:27:23: #2 Since the d (32) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 08:27:23: #2 You may need to consider one of the other alternative d(s): 3,32,498 WARNING @ Tue, 16 Jun 2020 08:27:23: #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 08:27:23: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:27:23: #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 08:27:30: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX331227/SRX331227.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX331227/SRX331227.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX331227/SRX331227.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX331227/SRX331227.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 08:27:30: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:27:30: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:27:32: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 08:27:34: 1000000 INFO @ Tue, 16 Jun 2020 08:27:37: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX331227/SRX331227.05_peaks.xls INFO @ Tue, 16 Jun 2020 08:27:37: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX331227/SRX331227.05_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:27:37: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX331227/SRX331227.05_summits.bed INFO @ Tue, 16 Jun 2020 08:27:37: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (425 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 08:27:39: 2000000 INFO @ Tue, 16 Jun 2020 08:27:44: 3000000 INFO @ Tue, 16 Jun 2020 08:27:49: 4000000 INFO @ Tue, 16 Jun 2020 08:27:52: #1 tag size is determined as 32 bps INFO @ Tue, 16 Jun 2020 08:27:52: #1 tag size = 32 INFO @ Tue, 16 Jun 2020 08:27:52: #1 total tags in treatment: 4800361 INFO @ Tue, 16 Jun 2020 08:27:52: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:27:52: #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 08:27:52: #1 tags after filtering in treatment: 4800361 INFO @ Tue, 16 Jun 2020 08:27:52: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:27:52: #1 finished! INFO @ Tue, 16 Jun 2020 08:27:52: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:27:52: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:27:53: #2 number of paired peaks: 459 WARNING @ Tue, 16 Jun 2020 08:27:53: Fewer paired peaks (459) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 459 pairs to build model! INFO @ Tue, 16 Jun 2020 08:27:53: start model_add_line... INFO @ Tue, 16 Jun 2020 08:27:53: start X-correlation... INFO @ Tue, 16 Jun 2020 08:27:53: end of X-cor INFO @ Tue, 16 Jun 2020 08:27:53: #2 finished! INFO @ Tue, 16 Jun 2020 08:27:53: #2 predicted fragment length is 32 bps INFO @ Tue, 16 Jun 2020 08:27:53: #2 alternative fragment length(s) may be 3,32,498 bps INFO @ Tue, 16 Jun 2020 08:27:53: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX331227/SRX331227.10_model.r WARNING @ Tue, 16 Jun 2020 08:27:53: #2 Since the d (32) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 08:27:53: #2 You may need to consider one of the other alternative d(s): 3,32,498 WARNING @ Tue, 16 Jun 2020 08:27:53: #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 08:27:53: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:27:53: #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 08:28:00: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX331227/SRX331227.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX331227/SRX331227.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX331227/SRX331227.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX331227/SRX331227.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 08:28:00: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:28:00: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:28:03: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 08:28:05: 1000000 INFO @ Tue, 16 Jun 2020 08:28:08: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX331227/SRX331227.10_peaks.xls INFO @ Tue, 16 Jun 2020 08:28:08: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX331227/SRX331227.10_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:28:08: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX331227/SRX331227.10_summits.bed INFO @ Tue, 16 Jun 2020 08:28:08: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (212 records, 4 fields): 1 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 08:28:10: 2000000 INFO @ Tue, 16 Jun 2020 08:28:15: 3000000 INFO @ Tue, 16 Jun 2020 08:28:20: 4000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 16 Jun 2020 08:28:24: #1 tag size is determined as 32 bps INFO @ Tue, 16 Jun 2020 08:28:24: #1 tag size = 32 INFO @ Tue, 16 Jun 2020 08:28:24: #1 total tags in treatment: 4800361 INFO @ Tue, 16 Jun 2020 08:28:24: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:28:24: #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 08:28:24: #1 tags after filtering in treatment: 4800361 INFO @ Tue, 16 Jun 2020 08:28:24: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:28:24: #1 finished! INFO @ Tue, 16 Jun 2020 08:28:24: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:28:24: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:28:24: #2 number of paired peaks: 459 WARNING @ Tue, 16 Jun 2020 08:28:24: Fewer paired peaks (459) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 459 pairs to build model! INFO @ Tue, 16 Jun 2020 08:28:24: start model_add_line... INFO @ Tue, 16 Jun 2020 08:28:24: start X-correlation... INFO @ Tue, 16 Jun 2020 08:28:24: end of X-cor INFO @ Tue, 16 Jun 2020 08:28:24: #2 finished! INFO @ Tue, 16 Jun 2020 08:28:24: #2 predicted fragment length is 32 bps INFO @ Tue, 16 Jun 2020 08:28:24: #2 alternative fragment length(s) may be 3,32,498 bps INFO @ Tue, 16 Jun 2020 08:28:24: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX331227/SRX331227.20_model.r WARNING @ Tue, 16 Jun 2020 08:28:24: #2 Since the d (32) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 08:28:24: #2 You may need to consider one of the other alternative d(s): 3,32,498 WARNING @ Tue, 16 Jun 2020 08:28:24: #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 08:28:24: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:28:24: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Tue, 16 Jun 2020 08:28:34: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 08:28:38: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX331227/SRX331227.20_peaks.xls INFO @ Tue, 16 Jun 2020 08:28:38: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX331227/SRX331227.20_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:28:38: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX331227/SRX331227.20_summits.bed INFO @ Tue, 16 Jun 2020 08:28:38: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (74 records, 4 fields): 0 millis CompletedMACS2peakCalling