Job ID = 6366549 SRX = SRX188615 Genome = ce11 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-15T22:47:11 prefetch.2.10.7: 1) Downloading 'SRR573721'... 2020-06-15T22:47:11 prefetch.2.10.7: Downloading via HTTPS... 2020-06-15T22:47:31 prefetch.2.10.7: HTTPS download succeed 2020-06-15T22:47:31 prefetch.2.10.7: 'SRR573721' is valid 2020-06-15T22:47:31 prefetch.2.10.7: 1) 'SRR573721' was downloaded successfully Read 3327294 spots for SRR573721/SRR573721.sra Written 3327294 spots for SRR573721/SRR573721.sra 2020-06-15T22:47:56 prefetch.2.10.7: 1) Downloading 'SRR573722'... 2020-06-15T22:47:56 prefetch.2.10.7: Downloading via HTTPS... 2020-06-15T22:48:23 prefetch.2.10.7: HTTPS download succeed 2020-06-15T22:48:23 prefetch.2.10.7: 'SRR573722' is valid 2020-06-15T22:48:23 prefetch.2.10.7: 1) 'SRR573722' was downloaded successfully Read 3564992 spots for SRR573722/SRR573722.sra Written 3564992 spots for SRR573722/SRR573722.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: 00:00:45 6892286 reads; of these: 6892286 (100.00%) were unpaired; of these: 5063885 (73.47%) aligned 0 times 1585148 (23.00%) aligned exactly 1 time 243253 (3.53%) aligned >1 times 26.53% overall alignment rate Time searching: 00:00:45 Overall time: 00:00:45 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] 86142 / 1828401 = 0.0471 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 07:50:25: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX188615/SRX188615.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX188615/SRX188615.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX188615/SRX188615.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX188615/SRX188615.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 07:50:25: #1 read tag files... INFO @ Tue, 16 Jun 2020 07:50:25: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 07:50:31: 1000000 INFO @ Tue, 16 Jun 2020 07:50:36: #1 tag size is determined as 34 bps INFO @ Tue, 16 Jun 2020 07:50:36: #1 tag size = 34 INFO @ Tue, 16 Jun 2020 07:50:36: #1 total tags in treatment: 1742259 INFO @ Tue, 16 Jun 2020 07:50:36: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 07:50:36: #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 07:50:36: #1 tags after filtering in treatment: 1742259 INFO @ Tue, 16 Jun 2020 07:50:36: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 07:50:36: #1 finished! INFO @ Tue, 16 Jun 2020 07:50:36: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 07:50:36: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 07:50:36: #2 number of paired peaks: 317 WARNING @ Tue, 16 Jun 2020 07:50:36: Fewer paired peaks (317) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 317 pairs to build model! INFO @ Tue, 16 Jun 2020 07:50:36: start model_add_line... INFO @ Tue, 16 Jun 2020 07:50:36: start X-correlation... INFO @ Tue, 16 Jun 2020 07:50:36: end of X-cor INFO @ Tue, 16 Jun 2020 07:50:36: #2 finished! INFO @ Tue, 16 Jun 2020 07:50:36: #2 predicted fragment length is 44 bps INFO @ Tue, 16 Jun 2020 07:50:36: #2 alternative fragment length(s) may be 44,190,515,543,564 bps INFO @ Tue, 16 Jun 2020 07:50:36: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX188615/SRX188615.05_model.r WARNING @ Tue, 16 Jun 2020 07:50:36: #2 Since the d (44) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 07:50:36: #2 You may need to consider one of the other alternative d(s): 44,190,515,543,564 WARNING @ Tue, 16 Jun 2020 07:50:36: #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 07:50:36: #3 Call peaks... INFO @ Tue, 16 Jun 2020 07:50:36: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 07:50:40: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 07:50:42: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX188615/SRX188615.05_peaks.xls INFO @ Tue, 16 Jun 2020 07:50:42: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX188615/SRX188615.05_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 07:50:42: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX188615/SRX188615.05_summits.bed INFO @ Tue, 16 Jun 2020 07:50:42: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (97 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 07:50:55: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX188615/SRX188615.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX188615/SRX188615.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX188615/SRX188615.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX188615/SRX188615.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 07:50:55: #1 read tag files... INFO @ Tue, 16 Jun 2020 07:50:55: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 07:51:02: 1000000 INFO @ Tue, 16 Jun 2020 07:51:06: #1 tag size is determined as 34 bps INFO @ Tue, 16 Jun 2020 07:51:06: #1 tag size = 34 INFO @ Tue, 16 Jun 2020 07:51:06: #1 total tags in treatment: 1742259 INFO @ Tue, 16 Jun 2020 07:51:06: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 07:51:06: #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 07:51:06: #1 tags after filtering in treatment: 1742259 INFO @ Tue, 16 Jun 2020 07:51:06: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 07:51:06: #1 finished! INFO @ Tue, 16 Jun 2020 07:51:06: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 07:51:06: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 07:51:07: #2 number of paired peaks: 317 WARNING @ Tue, 16 Jun 2020 07:51:07: Fewer paired peaks (317) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 317 pairs to build model! INFO @ Tue, 16 Jun 2020 07:51:07: start model_add_line... INFO @ Tue, 16 Jun 2020 07:51:07: start X-correlation... INFO @ Tue, 16 Jun 2020 07:51:07: end of X-cor INFO @ Tue, 16 Jun 2020 07:51:07: #2 finished! INFO @ Tue, 16 Jun 2020 07:51:07: #2 predicted fragment length is 44 bps INFO @ Tue, 16 Jun 2020 07:51:07: #2 alternative fragment length(s) may be 44,190,515,543,564 bps INFO @ Tue, 16 Jun 2020 07:51:07: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX188615/SRX188615.10_model.r WARNING @ Tue, 16 Jun 2020 07:51:07: #2 Since the d (44) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 07:51:07: #2 You may need to consider one of the other alternative d(s): 44,190,515,543,564 WARNING @ Tue, 16 Jun 2020 07:51:07: #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 07:51:07: #3 Call peaks... INFO @ Tue, 16 Jun 2020 07:51:07: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 07:51:11: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 07:51:13: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX188615/SRX188615.10_peaks.xls INFO @ Tue, 16 Jun 2020 07:51:13: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX188615/SRX188615.10_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 07:51:13: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX188615/SRX188615.10_summits.bed INFO @ Tue, 16 Jun 2020 07:51:13: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (35 records, 4 fields): 2 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 07:51:25: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX188615/SRX188615.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX188615/SRX188615.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX188615/SRX188615.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX188615/SRX188615.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 07:51:25: #1 read tag files... INFO @ Tue, 16 Jun 2020 07:51:25: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 07:51:32: 1000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 16 Jun 2020 07:51:36: #1 tag size is determined as 34 bps INFO @ Tue, 16 Jun 2020 07:51:36: #1 tag size = 34 INFO @ Tue, 16 Jun 2020 07:51:36: #1 total tags in treatment: 1742259 INFO @ Tue, 16 Jun 2020 07:51:36: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 07:51:36: #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 07:51:36: #1 tags after filtering in treatment: 1742259 INFO @ Tue, 16 Jun 2020 07:51:36: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 07:51:36: #1 finished! INFO @ Tue, 16 Jun 2020 07:51:36: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 07:51:36: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 07:51:36: #2 number of paired peaks: 317 WARNING @ Tue, 16 Jun 2020 07:51:36: Fewer paired peaks (317) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 317 pairs to build model! INFO @ Tue, 16 Jun 2020 07:51:36: start model_add_line... INFO @ Tue, 16 Jun 2020 07:51:36: start X-correlation... INFO @ Tue, 16 Jun 2020 07:51:36: end of X-cor INFO @ Tue, 16 Jun 2020 07:51:36: #2 finished! INFO @ Tue, 16 Jun 2020 07:51:36: #2 predicted fragment length is 44 bps INFO @ Tue, 16 Jun 2020 07:51:36: #2 alternative fragment length(s) may be 44,190,515,543,564 bps INFO @ Tue, 16 Jun 2020 07:51:36: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX188615/SRX188615.20_model.r WARNING @ Tue, 16 Jun 2020 07:51:36: #2 Since the d (44) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 07:51:36: #2 You may need to consider one of the other alternative d(s): 44,190,515,543,564 WARNING @ Tue, 16 Jun 2020 07:51:36: #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 07:51:36: #3 Call peaks... INFO @ Tue, 16 Jun 2020 07:51:36: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Tue, 16 Jun 2020 07:51:41: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 07:51:43: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX188615/SRX188615.20_peaks.xls INFO @ Tue, 16 Jun 2020 07:51:43: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX188615/SRX188615.20_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 07:51:43: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX188615/SRX188615.20_summits.bed INFO @ Tue, 16 Jun 2020 07:51:43: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (8 records, 4 fields): 1 millis CompletedMACS2peakCalling