Job ID = 6366435 SRX = SRX146499 Genome = ce11 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-15T22:49:52 prefetch.2.10.7: 1) Downloading 'SRR494664'... 2020-06-15T22:49:52 prefetch.2.10.7: Downloading via HTTPS... 2020-06-15T22:50:16 prefetch.2.10.7: HTTPS download succeed 2020-06-15T22:50:16 prefetch.2.10.7: 'SRR494664' is valid 2020-06-15T22:50:16 prefetch.2.10.7: 1) 'SRR494664' was downloaded successfully Read 3175883 spots for SRR494664/SRR494664.sra Written 3175883 spots for SRR494664/SRR494664.sra 2020-06-15T22:50:35 prefetch.2.10.7: 1) Downloading 'SRR494665'... 2020-06-15T22:50:35 prefetch.2.10.7: Downloading via HTTPS... 2020-06-15T22:51:01 prefetch.2.10.7: HTTPS download succeed 2020-06-15T22:51:01 prefetch.2.10.7: 'SRR494665' is valid 2020-06-15T22:51:01 prefetch.2.10.7: 1) 'SRR494665' was downloaded successfully Read 4085478 spots for SRR494665/SRR494665.sra Written 4085478 spots for SRR494665/SRR494665.sra fastq に変換しました。 bowtie でマッピング中... Time loading reference: 00:00:01 Time loading forward index: 00:00:00 Time loading mirror index: 00:00:00 Multiseed full-index search: 00:00:33 7261361 reads; of these: 7261361 (100.00%) were unpaired; of these: 5933680 (81.72%) aligned 0 times 1180352 (16.26%) aligned exactly 1 time 147329 (2.03%) aligned >1 times 18.28% overall alignment rate Time searching: 00:00:34 Overall time: 00:00:34 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] 77361 / 1327681 = 0.0583 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 07:52:40: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX146499/SRX146499.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX146499/SRX146499.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX146499/SRX146499.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX146499/SRX146499.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 07:52:40: #1 read tag files... INFO @ Tue, 16 Jun 2020 07:52:40: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 07:52:46: 1000000 INFO @ Tue, 16 Jun 2020 07:52:48: #1 tag size is determined as 34 bps INFO @ Tue, 16 Jun 2020 07:52:48: #1 tag size = 34 INFO @ Tue, 16 Jun 2020 07:52:48: #1 total tags in treatment: 1250320 INFO @ Tue, 16 Jun 2020 07:52:48: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 07:52:48: #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 07:52:48: #1 tags after filtering in treatment: 1250320 INFO @ Tue, 16 Jun 2020 07:52:48: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 07:52:48: #1 finished! INFO @ Tue, 16 Jun 2020 07:52:48: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 07:52:48: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 07:52:48: #2 number of paired peaks: 250 WARNING @ Tue, 16 Jun 2020 07:52:48: Fewer paired peaks (250) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 250 pairs to build model! INFO @ Tue, 16 Jun 2020 07:52:48: start model_add_line... INFO @ Tue, 16 Jun 2020 07:52:48: start X-correlation... INFO @ Tue, 16 Jun 2020 07:52:48: end of X-cor INFO @ Tue, 16 Jun 2020 07:52:48: #2 finished! INFO @ Tue, 16 Jun 2020 07:52:48: #2 predicted fragment length is 38 bps INFO @ Tue, 16 Jun 2020 07:52:48: #2 alternative fragment length(s) may be 38,57,81,114,138,187,241,291,443,461,521,589 bps INFO @ Tue, 16 Jun 2020 07:52:48: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX146499/SRX146499.05_model.r WARNING @ Tue, 16 Jun 2020 07:52:48: #2 Since the d (38) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 07:52:48: #2 You may need to consider one of the other alternative d(s): 38,57,81,114,138,187,241,291,443,461,521,589 WARNING @ Tue, 16 Jun 2020 07:52:48: #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 07:52:48: #3 Call peaks... INFO @ Tue, 16 Jun 2020 07:52:48: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 07:52:50: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 07:52:52: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX146499/SRX146499.05_peaks.xls INFO @ Tue, 16 Jun 2020 07:52:52: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX146499/SRX146499.05_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 07:52:52: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX146499/SRX146499.05_summits.bed INFO @ Tue, 16 Jun 2020 07:52:52: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (51 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 07:53:10: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX146499/SRX146499.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX146499/SRX146499.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX146499/SRX146499.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX146499/SRX146499.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 07:53:10: #1 read tag files... INFO @ Tue, 16 Jun 2020 07:53:10: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 07:53:16: 1000000 INFO @ Tue, 16 Jun 2020 07:53:17: #1 tag size is determined as 34 bps INFO @ Tue, 16 Jun 2020 07:53:17: #1 tag size = 34 INFO @ Tue, 16 Jun 2020 07:53:17: #1 total tags in treatment: 1250320 INFO @ Tue, 16 Jun 2020 07:53:17: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 07:53:17: #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 07:53:17: #1 tags after filtering in treatment: 1250320 INFO @ Tue, 16 Jun 2020 07:53:17: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 07:53:17: #1 finished! INFO @ Tue, 16 Jun 2020 07:53:17: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 07:53:17: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 07:53:17: #2 number of paired peaks: 250 WARNING @ Tue, 16 Jun 2020 07:53:17: Fewer paired peaks (250) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 250 pairs to build model! INFO @ Tue, 16 Jun 2020 07:53:17: start model_add_line... INFO @ Tue, 16 Jun 2020 07:53:17: start X-correlation... INFO @ Tue, 16 Jun 2020 07:53:17: end of X-cor INFO @ Tue, 16 Jun 2020 07:53:17: #2 finished! INFO @ Tue, 16 Jun 2020 07:53:17: #2 predicted fragment length is 38 bps INFO @ Tue, 16 Jun 2020 07:53:17: #2 alternative fragment length(s) may be 38,57,81,114,138,187,241,291,443,461,521,589 bps INFO @ Tue, 16 Jun 2020 07:53:17: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX146499/SRX146499.10_model.r WARNING @ Tue, 16 Jun 2020 07:53:17: #2 Since the d (38) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 07:53:17: #2 You may need to consider one of the other alternative d(s): 38,57,81,114,138,187,241,291,443,461,521,589 WARNING @ Tue, 16 Jun 2020 07:53:17: #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 07:53:17: #3 Call peaks... INFO @ Tue, 16 Jun 2020 07:53:17: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 07:53:20: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 07:53:21: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX146499/SRX146499.10_peaks.xls INFO @ Tue, 16 Jun 2020 07:53:21: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX146499/SRX146499.10_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 07:53:21: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX146499/SRX146499.10_summits.bed INFO @ Tue, 16 Jun 2020 07:53:21: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (17 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 07:53:40: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX146499/SRX146499.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX146499/SRX146499.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX146499/SRX146499.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX146499/SRX146499.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 07:53:40: #1 read tag files... INFO @ Tue, 16 Jun 2020 07:53:40: #1 read treatment tags... BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 16 Jun 2020 07:53:46: 1000000 BigWig に変換しました。 INFO @ Tue, 16 Jun 2020 07:53:48: #1 tag size is determined as 34 bps INFO @ Tue, 16 Jun 2020 07:53:48: #1 tag size = 34 INFO @ Tue, 16 Jun 2020 07:53:48: #1 total tags in treatment: 1250320 INFO @ Tue, 16 Jun 2020 07:53:48: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 07:53:48: #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 07:53:48: #1 tags after filtering in treatment: 1250320 INFO @ Tue, 16 Jun 2020 07:53:48: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 07:53:48: #1 finished! INFO @ Tue, 16 Jun 2020 07:53:48: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 07:53:48: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 07:53:48: #2 number of paired peaks: 250 WARNING @ Tue, 16 Jun 2020 07:53:48: Fewer paired peaks (250) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 250 pairs to build model! INFO @ Tue, 16 Jun 2020 07:53:48: start model_add_line... INFO @ Tue, 16 Jun 2020 07:53:48: start X-correlation... INFO @ Tue, 16 Jun 2020 07:53:48: end of X-cor INFO @ Tue, 16 Jun 2020 07:53:48: #2 finished! INFO @ Tue, 16 Jun 2020 07:53:48: #2 predicted fragment length is 38 bps INFO @ Tue, 16 Jun 2020 07:53:48: #2 alternative fragment length(s) may be 38,57,81,114,138,187,241,291,443,461,521,589 bps INFO @ Tue, 16 Jun 2020 07:53:48: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX146499/SRX146499.20_model.r WARNING @ Tue, 16 Jun 2020 07:53:48: #2 Since the d (38) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 07:53:48: #2 You may need to consider one of the other alternative d(s): 38,57,81,114,138,187,241,291,443,461,521,589 WARNING @ Tue, 16 Jun 2020 07:53:48: #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 07:53:48: #3 Call peaks... INFO @ Tue, 16 Jun 2020 07:53:48: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 07:53:51: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 07:53:52: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX146499/SRX146499.20_peaks.xls INFO @ Tue, 16 Jun 2020 07:53:52: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX146499/SRX146499.20_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 07:53:52: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX146499/SRX146499.20_summits.bed INFO @ Tue, 16 Jun 2020 07:53:52: Done! pass1 - making usageList (3 chroms): 0 millis pass2 - checking and writing primary data (4 records, 4 fields): 1 millis CompletedMACS2peakCalling