Job ID = 6368125 SRX = SRX466588 Genome = ce11 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-16T00:14:05 prefetch.2.10.7: 1) Downloading 'SRR1163654'... 2020-06-16T00:14:05 prefetch.2.10.7: Downloading via HTTPS... 2020-06-16T00:15:36 prefetch.2.10.7: HTTPS download succeed 2020-06-16T00:15:37 prefetch.2.10.7: 'SRR1163654' is valid 2020-06-16T00:15:37 prefetch.2.10.7: 1) 'SRR1163654' was downloaded successfully Read 8287219 spots for SRR1163654/SRR1163654.sra Written 8287219 spots for SRR1163654/SRR1163654.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: 00:01:38 8287219 reads; of these: 8287219 (100.00%) were unpaired; of these: 529835 (6.39%) aligned 0 times 6501859 (78.46%) aligned exactly 1 time 1255525 (15.15%) aligned >1 times 93.61% overall alignment rate Time searching: 00:01:38 Overall time: 00:01:38 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] 3358519 / 7757384 = 0.4329 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 09:19:42: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX466588/SRX466588.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX466588/SRX466588.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX466588/SRX466588.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX466588/SRX466588.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 09:19:42: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:19:42: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:19:48: 1000000 INFO @ Tue, 16 Jun 2020 09:19:54: 2000000 INFO @ Tue, 16 Jun 2020 09:20:01: 3000000 INFO @ Tue, 16 Jun 2020 09:20:07: 4000000 INFO @ Tue, 16 Jun 2020 09:20:09: #1 tag size is determined as 42 bps INFO @ Tue, 16 Jun 2020 09:20:09: #1 tag size = 42 INFO @ Tue, 16 Jun 2020 09:20:09: #1 total tags in treatment: 4398865 INFO @ Tue, 16 Jun 2020 09:20:09: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:20:09: #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 09:20:09: #1 tags after filtering in treatment: 4398865 INFO @ Tue, 16 Jun 2020 09:20:09: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 09:20:09: #1 finished! INFO @ Tue, 16 Jun 2020 09:20:09: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:20:09: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:20:09: #2 number of paired peaks: 486 WARNING @ Tue, 16 Jun 2020 09:20:09: Fewer paired peaks (486) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 486 pairs to build model! INFO @ Tue, 16 Jun 2020 09:20:09: start model_add_line... INFO @ Tue, 16 Jun 2020 09:20:09: start X-correlation... INFO @ Tue, 16 Jun 2020 09:20:09: end of X-cor INFO @ Tue, 16 Jun 2020 09:20:09: #2 finished! INFO @ Tue, 16 Jun 2020 09:20:09: #2 predicted fragment length is 42 bps INFO @ Tue, 16 Jun 2020 09:20:09: #2 alternative fragment length(s) may be 3,42,552,568 bps INFO @ Tue, 16 Jun 2020 09:20:09: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX466588/SRX466588.05_model.r WARNING @ Tue, 16 Jun 2020 09:20:09: #2 Since the d (42) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 09:20:09: #2 You may need to consider one of the other alternative d(s): 3,42,552,568 WARNING @ Tue, 16 Jun 2020 09:20:09: #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 09:20:09: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:20:09: #3 Pre-compute pvalue-qvalue table... 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 09:20:13: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX466588/SRX466588.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX466588/SRX466588.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX466588/SRX466588.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX466588/SRX466588.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 09:20:13: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:20:13: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:20:19: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 09:20:20: 1000000 INFO @ Tue, 16 Jun 2020 09:20:23: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX466588/SRX466588.05_peaks.xls INFO @ Tue, 16 Jun 2020 09:20:23: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX466588/SRX466588.05_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:20:23: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX466588/SRX466588.05_summits.bed INFO @ Tue, 16 Jun 2020 09:20:23: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (595 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 09:20:28: 2000000 INFO @ Tue, 16 Jun 2020 09:20:35: 3000000 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 09:20:42: 4000000 INFO @ Tue, 16 Jun 2020 09:20:43: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX466588/SRX466588.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX466588/SRX466588.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX466588/SRX466588.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX466588/SRX466588.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 09:20:43: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:20:43: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:20:45: #1 tag size is determined as 42 bps INFO @ Tue, 16 Jun 2020 09:20:45: #1 tag size = 42 INFO @ Tue, 16 Jun 2020 09:20:45: #1 total tags in treatment: 4398865 INFO @ Tue, 16 Jun 2020 09:20:45: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:20:45: #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 09:20:46: #1 tags after filtering in treatment: 4398865 INFO @ Tue, 16 Jun 2020 09:20:46: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 09:20:46: #1 finished! INFO @ Tue, 16 Jun 2020 09:20:46: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:20:46: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:20:46: #2 number of paired peaks: 486 WARNING @ Tue, 16 Jun 2020 09:20:46: Fewer paired peaks (486) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 486 pairs to build model! INFO @ Tue, 16 Jun 2020 09:20:46: start model_add_line... INFO @ Tue, 16 Jun 2020 09:20:46: start X-correlation... INFO @ Tue, 16 Jun 2020 09:20:46: end of X-cor INFO @ Tue, 16 Jun 2020 09:20:46: #2 finished! INFO @ Tue, 16 Jun 2020 09:20:46: #2 predicted fragment length is 42 bps INFO @ Tue, 16 Jun 2020 09:20:46: #2 alternative fragment length(s) may be 3,42,552,568 bps INFO @ Tue, 16 Jun 2020 09:20:46: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX466588/SRX466588.10_model.r WARNING @ Tue, 16 Jun 2020 09:20:46: #2 Since the d (42) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 09:20:46: #2 You may need to consider one of the other alternative d(s): 3,42,552,568 WARNING @ Tue, 16 Jun 2020 09:20:46: #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 09:20:46: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:20:46: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 09:20:50: 1000000 INFO @ Tue, 16 Jun 2020 09:20:56: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 09:20:58: 2000000 INFO @ Tue, 16 Jun 2020 09:21:01: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX466588/SRX466588.10_peaks.xls INFO @ Tue, 16 Jun 2020 09:21:01: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX466588/SRX466588.10_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:21:01: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX466588/SRX466588.10_summits.bed INFO @ Tue, 16 Jun 2020 09:21:01: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (318 records, 4 fields): 1 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 16 Jun 2020 09:21:05: 3000000 BigWig に変換しました。 INFO @ Tue, 16 Jun 2020 09:21:12: 4000000 INFO @ Tue, 16 Jun 2020 09:21:15: #1 tag size is determined as 42 bps INFO @ Tue, 16 Jun 2020 09:21:15: #1 tag size = 42 INFO @ Tue, 16 Jun 2020 09:21:15: #1 total tags in treatment: 4398865 INFO @ Tue, 16 Jun 2020 09:21:15: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:21:15: #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 09:21:15: #1 tags after filtering in treatment: 4398865 INFO @ Tue, 16 Jun 2020 09:21:15: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 09:21:15: #1 finished! INFO @ Tue, 16 Jun 2020 09:21:15: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:21:15: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:21:16: #2 number of paired peaks: 486 WARNING @ Tue, 16 Jun 2020 09:21:16: Fewer paired peaks (486) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 486 pairs to build model! INFO @ Tue, 16 Jun 2020 09:21:16: start model_add_line... INFO @ Tue, 16 Jun 2020 09:21:16: start X-correlation... INFO @ Tue, 16 Jun 2020 09:21:16: end of X-cor INFO @ Tue, 16 Jun 2020 09:21:16: #2 finished! INFO @ Tue, 16 Jun 2020 09:21:16: #2 predicted fragment length is 42 bps INFO @ Tue, 16 Jun 2020 09:21:16: #2 alternative fragment length(s) may be 3,42,552,568 bps INFO @ Tue, 16 Jun 2020 09:21:16: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX466588/SRX466588.20_model.r WARNING @ Tue, 16 Jun 2020 09:21:16: #2 Since the d (42) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 09:21:16: #2 You may need to consider one of the other alternative d(s): 3,42,552,568 WARNING @ Tue, 16 Jun 2020 09:21:16: #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 09:21:16: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:21:16: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 09:21:26: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 09:21:30: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX466588/SRX466588.20_peaks.xls INFO @ Tue, 16 Jun 2020 09:21:30: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX466588/SRX466588.20_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:21:30: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX466588/SRX466588.20_summits.bed INFO @ Tue, 16 Jun 2020 09:21:30: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (120 records, 4 fields): 2 millis CompletedMACS2peakCalling