Job ID = 6366184 SRX = SRX065709 Genome = ce11 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-15T23:06:08 prefetch.2.10.7: 1) Downloading 'SRR217415'... 2020-06-15T23:06:08 prefetch.2.10.7: Downloading via HTTPS... 2020-06-15T23:06:34 prefetch.2.10.7: HTTPS download succeed 2020-06-15T23:06:34 prefetch.2.10.7: 'SRR217415' is valid 2020-06-15T23:06:34 prefetch.2.10.7: 1) 'SRR217415' was downloaded successfully Read 5679829 spots for SRR217415/SRR217415.sra Written 5679829 spots for SRR217415/SRR217415.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: 00:00:01 Multiseed full-index search: 00:00:42 5679829 reads; of these: 5679829 (100.00%) were unpaired; of these: 2386262 (42.01%) aligned 0 times 2711599 (47.74%) aligned exactly 1 time 581968 (10.25%) aligned >1 times 57.99% overall alignment rate Time searching: 00:00:43 Overall time: 00:00:43 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] 235139 / 3293567 = 0.0714 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 08:08:42: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX065709/SRX065709.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX065709/SRX065709.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX065709/SRX065709.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX065709/SRX065709.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 08:08:42: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:08:42: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:08:47: 1000000 INFO @ Tue, 16 Jun 2020 08:08:52: 2000000 INFO @ Tue, 16 Jun 2020 08:08:56: 3000000 INFO @ Tue, 16 Jun 2020 08:08:56: #1 tag size is determined as 32 bps INFO @ Tue, 16 Jun 2020 08:08:56: #1 tag size = 32 INFO @ Tue, 16 Jun 2020 08:08:56: #1 total tags in treatment: 3058428 INFO @ Tue, 16 Jun 2020 08:08:56: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:08:56: #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 08:08:56: #1 tags after filtering in treatment: 3058428 INFO @ Tue, 16 Jun 2020 08:08:56: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:08:56: #1 finished! INFO @ Tue, 16 Jun 2020 08:08:56: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:08:56: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:08:57: #2 number of paired peaks: 714 WARNING @ Tue, 16 Jun 2020 08:08:57: Fewer paired peaks (714) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 714 pairs to build model! INFO @ Tue, 16 Jun 2020 08:08:57: start model_add_line... INFO @ Tue, 16 Jun 2020 08:08:57: start X-correlation... INFO @ Tue, 16 Jun 2020 08:08:57: end of X-cor INFO @ Tue, 16 Jun 2020 08:08:57: #2 finished! INFO @ Tue, 16 Jun 2020 08:08:57: #2 predicted fragment length is 47 bps INFO @ Tue, 16 Jun 2020 08:08:57: #2 alternative fragment length(s) may be 47,67,93,589,595 bps INFO @ Tue, 16 Jun 2020 08:08:57: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX065709/SRX065709.05_model.r WARNING @ Tue, 16 Jun 2020 08:08:57: #2 Since the d (47) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 08:08:57: #2 You may need to consider one of the other alternative d(s): 47,67,93,589,595 WARNING @ Tue, 16 Jun 2020 08:08:57: #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 08:08:57: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:08:57: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 08:09:03: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 08:09:07: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX065709/SRX065709.05_peaks.xls INFO @ Tue, 16 Jun 2020 08:09:07: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX065709/SRX065709.05_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:09:07: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX065709/SRX065709.05_summits.bed INFO @ Tue, 16 Jun 2020 08:09:07: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (902 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 08:09:12: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX065709/SRX065709.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX065709/SRX065709.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX065709/SRX065709.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX065709/SRX065709.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 08:09:12: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:09:12: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:09:17: 1000000 INFO @ Tue, 16 Jun 2020 08:09:22: 2000000 INFO @ Tue, 16 Jun 2020 08:09:26: 3000000 INFO @ Tue, 16 Jun 2020 08:09:27: #1 tag size is determined as 32 bps INFO @ Tue, 16 Jun 2020 08:09:27: #1 tag size = 32 INFO @ Tue, 16 Jun 2020 08:09:27: #1 total tags in treatment: 3058428 INFO @ Tue, 16 Jun 2020 08:09:27: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:09:27: #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 08:09:27: #1 tags after filtering in treatment: 3058428 INFO @ Tue, 16 Jun 2020 08:09:27: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:09:27: #1 finished! INFO @ Tue, 16 Jun 2020 08:09:27: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:09:27: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:09:27: #2 number of paired peaks: 714 WARNING @ Tue, 16 Jun 2020 08:09:27: Fewer paired peaks (714) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 714 pairs to build model! INFO @ Tue, 16 Jun 2020 08:09:27: start model_add_line... INFO @ Tue, 16 Jun 2020 08:09:27: start X-correlation... INFO @ Tue, 16 Jun 2020 08:09:27: end of X-cor INFO @ Tue, 16 Jun 2020 08:09:27: #2 finished! INFO @ Tue, 16 Jun 2020 08:09:27: #2 predicted fragment length is 47 bps INFO @ Tue, 16 Jun 2020 08:09:27: #2 alternative fragment length(s) may be 47,67,93,589,595 bps INFO @ Tue, 16 Jun 2020 08:09:27: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX065709/SRX065709.10_model.r WARNING @ Tue, 16 Jun 2020 08:09:27: #2 Since the d (47) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 08:09:27: #2 You may need to consider one of the other alternative d(s): 47,67,93,589,595 WARNING @ Tue, 16 Jun 2020 08:09:27: #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 08:09:27: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:09:27: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 08:09:34: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 08:09:38: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX065709/SRX065709.10_peaks.xls INFO @ Tue, 16 Jun 2020 08:09:38: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX065709/SRX065709.10_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:09:38: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX065709/SRX065709.10_summits.bed INFO @ Tue, 16 Jun 2020 08:09:38: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (348 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 08:09:42: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX065709/SRX065709.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX065709/SRX065709.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX065709/SRX065709.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX065709/SRX065709.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 08:09:42: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:09:42: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:09:47: 1000000 INFO @ Tue, 16 Jun 2020 08:09:52: 2000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 16 Jun 2020 08:09:57: 3000000 INFO @ Tue, 16 Jun 2020 08:09:57: #1 tag size is determined as 32 bps INFO @ Tue, 16 Jun 2020 08:09:57: #1 tag size = 32 INFO @ Tue, 16 Jun 2020 08:09:57: #1 total tags in treatment: 3058428 INFO @ Tue, 16 Jun 2020 08:09:57: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:09:57: #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 08:09:57: #1 tags after filtering in treatment: 3058428 INFO @ Tue, 16 Jun 2020 08:09:57: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:09:57: #1 finished! INFO @ Tue, 16 Jun 2020 08:09:57: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:09:57: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:09:58: #2 number of paired peaks: 714 WARNING @ Tue, 16 Jun 2020 08:09:58: Fewer paired peaks (714) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 714 pairs to build model! INFO @ Tue, 16 Jun 2020 08:09:58: start model_add_line... INFO @ Tue, 16 Jun 2020 08:09:58: start X-correlation... INFO @ Tue, 16 Jun 2020 08:09:58: end of X-cor INFO @ Tue, 16 Jun 2020 08:09:58: #2 finished! INFO @ Tue, 16 Jun 2020 08:09:58: #2 predicted fragment length is 47 bps INFO @ Tue, 16 Jun 2020 08:09:58: #2 alternative fragment length(s) may be 47,67,93,589,595 bps INFO @ Tue, 16 Jun 2020 08:09:58: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX065709/SRX065709.20_model.r WARNING @ Tue, 16 Jun 2020 08:09:58: #2 Since the d (47) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 08:09:58: #2 You may need to consider one of the other alternative d(s): 47,67,93,589,595 WARNING @ Tue, 16 Jun 2020 08:09:58: #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 08:09:58: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:09:58: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Tue, 16 Jun 2020 08:10:05: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 08:10:09: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX065709/SRX065709.20_peaks.xls INFO @ Tue, 16 Jun 2020 08:10:09: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX065709/SRX065709.20_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:10:09: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX065709/SRX065709.20_summits.bed INFO @ Tue, 16 Jun 2020 08:10:09: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (84 records, 4 fields): 1 millis CompletedMACS2peakCalling