Job ID = 6368387 SRX = SRX495066 Genome = ce11 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-16T00:13:20 prefetch.2.10.7: 1) Downloading 'SRR1198598'... 2020-06-16T00:13:20 prefetch.2.10.7: Downloading via HTTPS... 2020-06-16T00:15:41 prefetch.2.10.7: HTTPS download succeed 2020-06-16T00:15:41 prefetch.2.10.7: 1) 'SRR1198598' was downloaded successfully Read 10727987 spots for SRR1198598/SRR1198598.sra Written 10727987 spots for SRR1198598/SRR1198598.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: 00:01:48 10727987 reads; of these: 10727987 (100.00%) were unpaired; of these: 2099476 (19.57%) aligned 0 times 7380313 (68.79%) aligned exactly 1 time 1248198 (11.63%) aligned >1 times 80.43% overall alignment rate Time searching: 00:01:48 Overall time: 00:01:48 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] 1364465 / 8628511 = 0.1581 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 09:20:21: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX495066/SRX495066.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX495066/SRX495066.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX495066/SRX495066.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX495066/SRX495066.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 09:20:21: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:20:21: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:20:27: 1000000 INFO @ Tue, 16 Jun 2020 09:20:33: 2000000 INFO @ Tue, 16 Jun 2020 09:20:39: 3000000 INFO @ Tue, 16 Jun 2020 09:20:45: 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 @ Tue, 16 Jun 2020 09:20:51: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX495066/SRX495066.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX495066/SRX495066.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX495066/SRX495066.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX495066/SRX495066.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 09:20:51: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:20:51: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:20:52: 5000000 INFO @ Tue, 16 Jun 2020 09:20:58: 1000000 INFO @ Tue, 16 Jun 2020 09:20:58: 6000000 INFO @ Tue, 16 Jun 2020 09:21:04: 2000000 INFO @ Tue, 16 Jun 2020 09:21:04: 7000000 INFO @ Tue, 16 Jun 2020 09:21:06: #1 tag size is determined as 42 bps INFO @ Tue, 16 Jun 2020 09:21:06: #1 tag size = 42 INFO @ Tue, 16 Jun 2020 09:21:06: #1 total tags in treatment: 7264046 INFO @ Tue, 16 Jun 2020 09:21:06: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:21:06: #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 09:21:06: #1 tags after filtering in treatment: 7264046 INFO @ Tue, 16 Jun 2020 09:21:06: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 09:21:06: #1 finished! INFO @ Tue, 16 Jun 2020 09:21:06: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:21:06: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:21:07: #2 number of paired peaks: 278 WARNING @ Tue, 16 Jun 2020 09:21:07: Fewer paired peaks (278) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 278 pairs to build model! INFO @ Tue, 16 Jun 2020 09:21:07: start model_add_line... INFO @ Tue, 16 Jun 2020 09:21:07: start X-correlation... INFO @ Tue, 16 Jun 2020 09:21:07: end of X-cor INFO @ Tue, 16 Jun 2020 09:21:07: #2 finished! INFO @ Tue, 16 Jun 2020 09:21:07: #2 predicted fragment length is 38 bps INFO @ Tue, 16 Jun 2020 09:21:07: #2 alternative fragment length(s) may be 4,38,462,485,520,578 bps INFO @ Tue, 16 Jun 2020 09:21:07: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX495066/SRX495066.05_model.r WARNING @ Tue, 16 Jun 2020 09:21:07: #2 Since the d (38) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 09:21:07: #2 You may need to consider one of the other alternative d(s): 4,38,462,485,520,578 WARNING @ Tue, 16 Jun 2020 09:21:07: #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 09:21:07: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:21:07: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 09:21:11: 3000000 INFO @ Tue, 16 Jun 2020 09:21:17: 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 @ Tue, 16 Jun 2020 09:21:21: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX495066/SRX495066.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX495066/SRX495066.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX495066/SRX495066.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX495066/SRX495066.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 09:21:21: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:21:21: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:21:21: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 09:21:23: 5000000 INFO @ Tue, 16 Jun 2020 09:21:28: 1000000 INFO @ Tue, 16 Jun 2020 09:21:29: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX495066/SRX495066.05_peaks.xls INFO @ Tue, 16 Jun 2020 09:21:29: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX495066/SRX495066.05_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:21:29: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX495066/SRX495066.05_summits.bed INFO @ Tue, 16 Jun 2020 09:21:29: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (495 records, 4 fields): 1 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 09:21:30: 6000000 INFO @ Tue, 16 Jun 2020 09:21:34: 2000000 INFO @ Tue, 16 Jun 2020 09:21:37: 7000000 INFO @ Tue, 16 Jun 2020 09:21:38: #1 tag size is determined as 42 bps INFO @ Tue, 16 Jun 2020 09:21:38: #1 tag size = 42 INFO @ Tue, 16 Jun 2020 09:21:38: #1 total tags in treatment: 7264046 INFO @ Tue, 16 Jun 2020 09:21:38: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:21:38: #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 09:21:38: #1 tags after filtering in treatment: 7264046 INFO @ Tue, 16 Jun 2020 09:21:38: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 09:21:39: #1 finished! INFO @ Tue, 16 Jun 2020 09:21:39: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:21:39: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:21:39: #2 number of paired peaks: 278 WARNING @ Tue, 16 Jun 2020 09:21:39: Fewer paired peaks (278) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 278 pairs to build model! INFO @ Tue, 16 Jun 2020 09:21:39: start model_add_line... INFO @ Tue, 16 Jun 2020 09:21:39: start X-correlation... INFO @ Tue, 16 Jun 2020 09:21:39: end of X-cor INFO @ Tue, 16 Jun 2020 09:21:39: #2 finished! INFO @ Tue, 16 Jun 2020 09:21:39: #2 predicted fragment length is 38 bps INFO @ Tue, 16 Jun 2020 09:21:39: #2 alternative fragment length(s) may be 4,38,462,485,520,578 bps INFO @ Tue, 16 Jun 2020 09:21:39: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX495066/SRX495066.10_model.r WARNING @ Tue, 16 Jun 2020 09:21:39: #2 Since the d (38) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 09:21:39: #2 You may need to consider one of the other alternative d(s): 4,38,462,485,520,578 WARNING @ Tue, 16 Jun 2020 09:21:39: #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 09:21:39: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:21:39: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 09:21:40: 3000000 INFO @ Tue, 16 Jun 2020 09:21:46: 4000000 INFO @ Tue, 16 Jun 2020 09:21:52: 5000000 INFO @ Tue, 16 Jun 2020 09:21:53: #3 Call peaks for each chromosome... BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 16 Jun 2020 09:21:58: 6000000 INFO @ Tue, 16 Jun 2020 09:22:00: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX495066/SRX495066.10_peaks.xls INFO @ Tue, 16 Jun 2020 09:22:00: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX495066/SRX495066.10_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:22:01: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX495066/SRX495066.10_summits.bed INFO @ Tue, 16 Jun 2020 09:22:01: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (265 records, 4 fields): 1 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 09:22:04: 7000000 INFO @ Tue, 16 Jun 2020 09:22:05: #1 tag size is determined as 42 bps INFO @ Tue, 16 Jun 2020 09:22:05: #1 tag size = 42 INFO @ Tue, 16 Jun 2020 09:22:05: #1 total tags in treatment: 7264046 INFO @ Tue, 16 Jun 2020 09:22:05: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:22:05: #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 09:22:06: #1 tags after filtering in treatment: 7264046 INFO @ Tue, 16 Jun 2020 09:22:06: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 09:22:06: #1 finished! INFO @ Tue, 16 Jun 2020 09:22:06: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:22:06: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:22:06: #2 number of paired peaks: 278 WARNING @ Tue, 16 Jun 2020 09:22:06: Fewer paired peaks (278) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 278 pairs to build model! INFO @ Tue, 16 Jun 2020 09:22:06: start model_add_line... INFO @ Tue, 16 Jun 2020 09:22:06: start X-correlation... INFO @ Tue, 16 Jun 2020 09:22:06: end of X-cor INFO @ Tue, 16 Jun 2020 09:22:06: #2 finished! INFO @ Tue, 16 Jun 2020 09:22:06: #2 predicted fragment length is 38 bps INFO @ Tue, 16 Jun 2020 09:22:06: #2 alternative fragment length(s) may be 4,38,462,485,520,578 bps INFO @ Tue, 16 Jun 2020 09:22:06: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX495066/SRX495066.20_model.r WARNING @ Tue, 16 Jun 2020 09:22:06: #2 Since the d (38) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 09:22:06: #2 You may need to consider one of the other alternative d(s): 4,38,462,485,520,578 WARNING @ Tue, 16 Jun 2020 09:22:06: #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 09:22:06: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:22:06: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Tue, 16 Jun 2020 09:22:20: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 09:22:27: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX495066/SRX495066.20_peaks.xls INFO @ Tue, 16 Jun 2020 09:22:27: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX495066/SRX495066.20_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:22:27: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX495066/SRX495066.20_summits.bed INFO @ Tue, 16 Jun 2020 09:22:27: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (82 records, 4 fields): 1 millis CompletedMACS2peakCalling