Job ID = 6507756 SRX = SRX277033 Genome = ce11 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-26T12:44:16 prefetch.2.10.7: 1) Downloading 'SRR849701'... 2020-06-26T12:44:16 prefetch.2.10.7: Downloading via HTTPS... 2020-06-26T12:44:50 prefetch.2.10.7: HTTPS download succeed 2020-06-26T12:44:51 prefetch.2.10.7: 'SRR849701' is valid 2020-06-26T12:44:51 prefetch.2.10.7: 1) 'SRR849701' was downloaded successfully Read 5420872 spots for SRR849701/SRR849701.sra Written 5420872 spots for SRR849701/SRR849701.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: 00:00:53 5420872 reads; of these: 5420872 (100.00%) were unpaired; of these: 40991 (0.76%) aligned 0 times 4530599 (83.58%) aligned exactly 1 time 849282 (15.67%) aligned >1 times 99.24% overall alignment rate Time searching: 00:00:54 Overall time: 00:00:54 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] 411415 / 5379881 = 0.0765 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 21:47:49: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX277033/SRX277033.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX277033/SRX277033.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX277033/SRX277033.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX277033/SRX277033.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 21:47:49: #1 read tag files... INFO @ Fri, 26 Jun 2020 21:47:49: #1 read treatment tags... INFO @ Fri, 26 Jun 2020 21:47:55: 1000000 INFO @ Fri, 26 Jun 2020 21:48:01: 2000000 INFO @ Fri, 26 Jun 2020 21:48:07: 3000000 INFO @ Fri, 26 Jun 2020 21:48:13: 4000000 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 21:48:19: #1 tag size is determined as 32 bps INFO @ Fri, 26 Jun 2020 21:48:19: #1 tag size = 32 INFO @ Fri, 26 Jun 2020 21:48:19: #1 total tags in treatment: 4968466 INFO @ Fri, 26 Jun 2020 21:48:19: #1 user defined the maximum tags... INFO @ Fri, 26 Jun 2020 21:48:19: #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 21:48:19: #1 tags after filtering in treatment: 4968466 INFO @ Fri, 26 Jun 2020 21:48:19: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 26 Jun 2020 21:48:19: #1 finished! INFO @ Fri, 26 Jun 2020 21:48:19: #2 Build Peak Model... INFO @ Fri, 26 Jun 2020 21:48:19: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 26 Jun 2020 21:48:19: #2 number of paired peaks: 353 WARNING @ Fri, 26 Jun 2020 21:48:19: Fewer paired peaks (353) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 353 pairs to build model! INFO @ Fri, 26 Jun 2020 21:48:19: start model_add_line... INFO @ Fri, 26 Jun 2020 21:48:19: start X-correlation... INFO @ Fri, 26 Jun 2020 21:48:19: end of X-cor INFO @ Fri, 26 Jun 2020 21:48:19: #2 finished! INFO @ Fri, 26 Jun 2020 21:48:19: #2 predicted fragment length is 29 bps INFO @ Fri, 26 Jun 2020 21:48:19: #2 alternative fragment length(s) may be 2,29,162,244,453,575 bps INFO @ Fri, 26 Jun 2020 21:48:19: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX277033/SRX277033.05_model.r WARNING @ Fri, 26 Jun 2020 21:48:19: #2 Since the d (29) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 26 Jun 2020 21:48:19: #2 You may need to consider one of the other alternative d(s): 2,29,162,244,453,575 WARNING @ Fri, 26 Jun 2020 21:48:19: #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 21:48:19: #3 Call peaks... INFO @ Fri, 26 Jun 2020 21:48:19: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 26 Jun 2020 21:48:19: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX277033/SRX277033.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX277033/SRX277033.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX277033/SRX277033.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX277033/SRX277033.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 21:48:19: #1 read tag files... INFO @ Fri, 26 Jun 2020 21:48:19: #1 read treatment tags... INFO @ Fri, 26 Jun 2020 21:48:26: 1000000 INFO @ Fri, 26 Jun 2020 21:48:29: #3 Call peaks for each chromosome... INFO @ Fri, 26 Jun 2020 21:48:32: 2000000 INFO @ Fri, 26 Jun 2020 21:48:34: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX277033/SRX277033.05_peaks.xls INFO @ Fri, 26 Jun 2020 21:48:34: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX277033/SRX277033.05_peaks.narrowPeak INFO @ Fri, 26 Jun 2020 21:48:34: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX277033/SRX277033.05_summits.bed INFO @ Fri, 26 Jun 2020 21:48:34: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (372 records, 4 fields): 1 millis CompletedMACS2peakCalling INFO @ Fri, 26 Jun 2020 21:48:38: 3000000 INFO @ Fri, 26 Jun 2020 21:48:45: 4000000 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 @ Fri, 26 Jun 2020 21:48:49: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX277033/SRX277033.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX277033/SRX277033.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX277033/SRX277033.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX277033/SRX277033.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 21:48:49: #1 read tag files... INFO @ Fri, 26 Jun 2020 21:48:49: #1 read treatment tags... INFO @ Fri, 26 Jun 2020 21:48:51: #1 tag size is determined as 32 bps INFO @ Fri, 26 Jun 2020 21:48:51: #1 tag size = 32 INFO @ Fri, 26 Jun 2020 21:48:51: #1 total tags in treatment: 4968466 INFO @ Fri, 26 Jun 2020 21:48:51: #1 user defined the maximum tags... INFO @ Fri, 26 Jun 2020 21:48:51: #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 21:48:51: #1 tags after filtering in treatment: 4968466 INFO @ Fri, 26 Jun 2020 21:48:51: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 26 Jun 2020 21:48:51: #1 finished! INFO @ Fri, 26 Jun 2020 21:48:51: #2 Build Peak Model... INFO @ Fri, 26 Jun 2020 21:48:51: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 26 Jun 2020 21:48:51: #2 number of paired peaks: 353 WARNING @ Fri, 26 Jun 2020 21:48:51: Fewer paired peaks (353) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 353 pairs to build model! INFO @ Fri, 26 Jun 2020 21:48:51: start model_add_line... INFO @ Fri, 26 Jun 2020 21:48:52: start X-correlation... INFO @ Fri, 26 Jun 2020 21:48:52: end of X-cor INFO @ Fri, 26 Jun 2020 21:48:52: #2 finished! INFO @ Fri, 26 Jun 2020 21:48:52: #2 predicted fragment length is 29 bps INFO @ Fri, 26 Jun 2020 21:48:52: #2 alternative fragment length(s) may be 2,29,162,244,453,575 bps INFO @ Fri, 26 Jun 2020 21:48:52: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX277033/SRX277033.10_model.r WARNING @ Fri, 26 Jun 2020 21:48:52: #2 Since the d (29) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 26 Jun 2020 21:48:52: #2 You may need to consider one of the other alternative d(s): 2,29,162,244,453,575 WARNING @ Fri, 26 Jun 2020 21:48:52: #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 21:48:52: #3 Call peaks... INFO @ Fri, 26 Jun 2020 21:48:52: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 26 Jun 2020 21:48:57: 1000000 INFO @ Fri, 26 Jun 2020 21:49:01: #3 Call peaks for each chromosome... INFO @ Fri, 26 Jun 2020 21:49:04: 2000000 INFO @ Fri, 26 Jun 2020 21:49:06: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX277033/SRX277033.10_peaks.xls INFO @ Fri, 26 Jun 2020 21:49:06: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX277033/SRX277033.10_peaks.narrowPeak INFO @ Fri, 26 Jun 2020 21:49:06: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX277033/SRX277033.10_summits.bed INFO @ Fri, 26 Jun 2020 21:49:06: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (149 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Fri, 26 Jun 2020 21:49:11: 3000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Fri, 26 Jun 2020 21:49:19: 4000000 INFO @ Fri, 26 Jun 2020 21:49:26: #1 tag size is determined as 32 bps INFO @ Fri, 26 Jun 2020 21:49:26: #1 tag size = 32 INFO @ Fri, 26 Jun 2020 21:49:26: #1 total tags in treatment: 4968466 INFO @ Fri, 26 Jun 2020 21:49:26: #1 user defined the maximum tags... INFO @ Fri, 26 Jun 2020 21:49:26: #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 21:49:26: #1 tags after filtering in treatment: 4968466 INFO @ Fri, 26 Jun 2020 21:49:26: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 26 Jun 2020 21:49:26: #1 finished! INFO @ Fri, 26 Jun 2020 21:49:26: #2 Build Peak Model... INFO @ Fri, 26 Jun 2020 21:49:26: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 26 Jun 2020 21:49:26: #2 number of paired peaks: 353 WARNING @ Fri, 26 Jun 2020 21:49:26: Fewer paired peaks (353) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 353 pairs to build model! INFO @ Fri, 26 Jun 2020 21:49:26: start model_add_line... INFO @ Fri, 26 Jun 2020 21:49:26: start X-correlation... INFO @ Fri, 26 Jun 2020 21:49:26: end of X-cor INFO @ Fri, 26 Jun 2020 21:49:26: #2 finished! INFO @ Fri, 26 Jun 2020 21:49:26: #2 predicted fragment length is 29 bps INFO @ Fri, 26 Jun 2020 21:49:26: #2 alternative fragment length(s) may be 2,29,162,244,453,575 bps INFO @ Fri, 26 Jun 2020 21:49:26: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX277033/SRX277033.20_model.r WARNING @ Fri, 26 Jun 2020 21:49:26: #2 Since the d (29) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 26 Jun 2020 21:49:26: #2 You may need to consider one of the other alternative d(s): 2,29,162,244,453,575 WARNING @ Fri, 26 Jun 2020 21:49:26: #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 21:49:26: #3 Call peaks... INFO @ Fri, 26 Jun 2020 21:49:26: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Fri, 26 Jun 2020 21:49:35: #3 Call peaks for each chromosome... INFO @ Fri, 26 Jun 2020 21:49:40: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX277033/SRX277033.20_peaks.xls INFO @ Fri, 26 Jun 2020 21:49:40: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX277033/SRX277033.20_peaks.narrowPeak INFO @ Fri, 26 Jun 2020 21:49:40: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX277033/SRX277033.20_summits.bed INFO @ Fri, 26 Jun 2020 21:49:40: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (24 records, 4 fields): 2 millis CompletedMACS2peakCalling