Job ID = 6497372 SRX = SRX331183 Genome = ce10 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-25T21:43:26 prefetch.2.10.7: 1) Downloading 'SRR947415'... 2020-06-25T21:43:26 prefetch.2.10.7: Downloading via HTTPS... 2020-06-25T21:43:59 prefetch.2.10.7: HTTPS download succeed 2020-06-25T21:44:00 prefetch.2.10.7: 'SRR947415' is valid 2020-06-25T21:44:00 prefetch.2.10.7: 1) 'SRR947415' was downloaded successfully Read 6014854 spots for SRR947415/SRR947415.sra Written 6014854 spots for SRR947415/SRR947415.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: 00:00:39 6014854 reads; of these: 6014854 (100.00%) were unpaired; of these: 2926676 (48.66%) aligned 0 times 2604508 (43.30%) aligned exactly 1 time 483670 (8.04%) aligned >1 times 51.34% overall alignment rate Time searching: 00:00:39 Overall time: 00:00:39 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] 206886 / 3088178 = 0.0670 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 @ Fri, 26 Jun 2020 06:46:32: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX331183/SRX331183.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX331183/SRX331183.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX331183/SRX331183.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX331183/SRX331183.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 @ Fri, 26 Jun 2020 06:46:32: #1 read tag files... INFO @ Fri, 26 Jun 2020 06:46:32: #1 read treatment tags... INFO @ Fri, 26 Jun 2020 06:46:37: 1000000 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 @ Fri, 26 Jun 2020 06:46:42: 2000000 INFO @ Fri, 26 Jun 2020 06:46:43: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX331183/SRX331183.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX331183/SRX331183.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX331183/SRX331183.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX331183/SRX331183.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 @ Fri, 26 Jun 2020 06:46:43: #1 read tag files... INFO @ Fri, 26 Jun 2020 06:46:43: #1 read treatment tags... INFO @ Fri, 26 Jun 2020 06:46:46: #1 tag size is determined as 32 bps INFO @ Fri, 26 Jun 2020 06:46:46: #1 tag size = 32 INFO @ Fri, 26 Jun 2020 06:46:46: #1 total tags in treatment: 2881292 INFO @ Fri, 26 Jun 2020 06:46:46: #1 user defined the maximum tags... INFO @ Fri, 26 Jun 2020 06:46:46: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 26 Jun 2020 06:46:46: #1 tags after filtering in treatment: 2881292 INFO @ Fri, 26 Jun 2020 06:46:46: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 26 Jun 2020 06:46:46: #1 finished! INFO @ Fri, 26 Jun 2020 06:46:46: #2 Build Peak Model... INFO @ Fri, 26 Jun 2020 06:46:46: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 26 Jun 2020 06:46:46: #2 number of paired peaks: 408 WARNING @ Fri, 26 Jun 2020 06:46:46: Fewer paired peaks (408) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 408 pairs to build model! INFO @ Fri, 26 Jun 2020 06:46:46: start model_add_line... INFO @ Fri, 26 Jun 2020 06:46:46: start X-correlation... INFO @ Fri, 26 Jun 2020 06:46:47: end of X-cor INFO @ Fri, 26 Jun 2020 06:46:47: #2 finished! INFO @ Fri, 26 Jun 2020 06:46:47: #2 predicted fragment length is 34 bps INFO @ Fri, 26 Jun 2020 06:46:47: #2 alternative fragment length(s) may be 4,34,97,574,592 bps INFO @ Fri, 26 Jun 2020 06:46:47: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX331183/SRX331183.05_model.r WARNING @ Fri, 26 Jun 2020 06:46:47: #2 Since the d (34) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 26 Jun 2020 06:46:47: #2 You may need to consider one of the other alternative d(s): 4,34,97,574,592 WARNING @ Fri, 26 Jun 2020 06:46:47: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Fri, 26 Jun 2020 06:46:47: #3 Call peaks... INFO @ Fri, 26 Jun 2020 06:46:47: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 26 Jun 2020 06:46:49: 1000000 INFO @ Fri, 26 Jun 2020 06:46:53: #3 Call peaks for each chromosome... INFO @ Fri, 26 Jun 2020 06:46:54: 2000000 INFO @ Fri, 26 Jun 2020 06:46:56: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX331183/SRX331183.05_peaks.xls INFO @ Fri, 26 Jun 2020 06:46:58: #1 tag size is determined as 32 bps INFO @ Fri, 26 Jun 2020 06:46:58: #1 tag size = 32 INFO @ Fri, 26 Jun 2020 06:46:58: #1 total tags in treatment: 2881292 INFO @ Fri, 26 Jun 2020 06:46:58: #1 user defined the maximum tags... INFO @ Fri, 26 Jun 2020 06:46:58: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 26 Jun 2020 06:46:58: #1 tags after filtering in treatment: 2881292 INFO @ Fri, 26 Jun 2020 06:46:58: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 26 Jun 2020 06:46:58: #1 finished! INFO @ Fri, 26 Jun 2020 06:46:58: #2 Build Peak Model... INFO @ Fri, 26 Jun 2020 06:46:58: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 26 Jun 2020 06:46:58: #2 number of paired peaks: 408 WARNING @ Fri, 26 Jun 2020 06:46:58: Fewer paired peaks (408) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 408 pairs to build model! INFO @ Fri, 26 Jun 2020 06:46:58: start model_add_line... INFO @ Fri, 26 Jun 2020 06:46:58: start X-correlation... INFO @ Fri, 26 Jun 2020 06:46:58: end of X-cor INFO @ Fri, 26 Jun 2020 06:46:58: #2 finished! INFO @ Fri, 26 Jun 2020 06:46:58: #2 predicted fragment length is 34 bps INFO @ Fri, 26 Jun 2020 06:46:58: #2 alternative fragment length(s) may be 4,34,97,574,592 bps INFO @ Fri, 26 Jun 2020 06:46:58: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX331183/SRX331183.10_model.r BedGraph に変換中... WARNING @ Fri, 26 Jun 2020 06:47:32: #2 Since the d (34) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 26 Jun 2020 06:47:32: #2 You may need to consider one of the other alternative d(s): 4,34,97,574,592 WARNING @ Fri, 26 Jun 2020 06:47:32: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Fri, 26 Jun 2020 06:47:32: #3 Call peaks... INFO @ Fri, 26 Jun 2020 06:47:32: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 26 Jun 2020 06:47:32: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX331183/SRX331183.05_peaks.narrowPeak INFO @ Fri, 26 Jun 2020 06:47:32: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX331183/SRX331183.05_summits.bed 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 @ Fri, 26 Jun 2020 06:47:32: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (328 records, 4 fields): 5 millis CompletedMACS2peakCalling INFO @ Fri, 26 Jun 2020 06:47:34: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX331183/SRX331183.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX331183/SRX331183.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX331183/SRX331183.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX331183/SRX331183.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 @ Fri, 26 Jun 2020 06:47:34: #1 read tag files... INFO @ Fri, 26 Jun 2020 06:47:34: #1 read treatment tags... INFO @ Fri, 26 Jun 2020 06:47:38: #3 Call peaks for each chromosome... INFO @ Fri, 26 Jun 2020 06:47:39: 1000000 INFO @ Fri, 26 Jun 2020 06:47:41: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX331183/SRX331183.10_peaks.xls INFO @ Fri, 26 Jun 2020 06:47:41: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX331183/SRX331183.10_peaks.narrowPeak INFO @ Fri, 26 Jun 2020 06:47:41: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX331183/SRX331183.10_summits.bed INFO @ Fri, 26 Jun 2020 06:47:41: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (120 records, 4 fields): 1 millis CompletedMACS2peakCalling INFO @ Fri, 26 Jun 2020 06:47:44: 2000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Fri, 26 Jun 2020 06:47:49: #1 tag size is determined as 32 bps INFO @ Fri, 26 Jun 2020 06:47:49: #1 tag size = 32 INFO @ Fri, 26 Jun 2020 06:47:49: #1 total tags in treatment: 2881292 INFO @ Fri, 26 Jun 2020 06:47:49: #1 user defined the maximum tags... INFO @ Fri, 26 Jun 2020 06:47:49: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 26 Jun 2020 06:47:49: #1 tags after filtering in treatment: 2881292 INFO @ Fri, 26 Jun 2020 06:47:49: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 26 Jun 2020 06:47:49: #1 finished! INFO @ Fri, 26 Jun 2020 06:47:49: #2 Build Peak Model... INFO @ Fri, 26 Jun 2020 06:47:49: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 26 Jun 2020 06:47:49: #2 number of paired peaks: 408 WARNING @ Fri, 26 Jun 2020 06:47:49: Fewer paired peaks (408) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 408 pairs to build model! INFO @ Fri, 26 Jun 2020 06:47:49: start model_add_line... INFO @ Fri, 26 Jun 2020 06:47:49: start X-correlation... INFO @ Fri, 26 Jun 2020 06:47:49: end of X-cor INFO @ Fri, 26 Jun 2020 06:47:49: #2 finished! INFO @ Fri, 26 Jun 2020 06:47:49: #2 predicted fragment length is 34 bps INFO @ Fri, 26 Jun 2020 06:47:49: #2 alternative fragment length(s) may be 4,34,97,574,592 bps INFO @ Fri, 26 Jun 2020 06:47:49: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX331183/SRX331183.20_model.r WARNING @ Fri, 26 Jun 2020 06:47:49: #2 Since the d (34) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 26 Jun 2020 06:47:49: #2 You may need to consider one of the other alternative d(s): 4,34,97,574,592 WARNING @ Fri, 26 Jun 2020 06:47:49: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Fri, 26 Jun 2020 06:47:49: #3 Call peaks... INFO @ Fri, 26 Jun 2020 06:47:49: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Fri, 26 Jun 2020 06:47:56: #3 Call peaks for each chromosome... INFO @ Fri, 26 Jun 2020 06:47:59: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX331183/SRX331183.20_peaks.xls INFO @ Fri, 26 Jun 2020 06:47:59: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX331183/SRX331183.20_peaks.narrowPeak INFO @ Fri, 26 Jun 2020 06:47:59: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX331183/SRX331183.20_summits.bed INFO @ Fri, 26 Jun 2020 06:47:59: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (26 records, 4 fields): 2 millis CompletedMACS2peakCalling