Job ID = 6507949 SRX = SRX495109 Genome = ce11 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-26T14:23:13 prefetch.2.10.7: 1) Downloading 'SRR1198641'... 2020-06-26T14:23:13 prefetch.2.10.7: Downloading via HTTPS... 2020-06-26T14:24:42 prefetch.2.10.7: HTTPS download succeed 2020-06-26T14:24:43 prefetch.2.10.7: 'SRR1198641' is valid 2020-06-26T14:24:43 prefetch.2.10.7: 1) 'SRR1198641' was downloaded successfully Read 11975507 spots for SRR1198641/SRR1198641.sra Written 11975507 spots for SRR1198641/SRR1198641.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: 00:02:20 11975507 reads; of these: 11975507 (100.00%) were unpaired; of these: 60891 (0.51%) aligned 0 times 9739963 (81.33%) aligned exactly 1 time 2174653 (18.16%) aligned >1 times 99.49% overall alignment rate Time searching: 00:02:20 Overall time: 00:02:20 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] 1527675 / 11914616 = 0.1282 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 23:30:38: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX495109/SRX495109.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX495109/SRX495109.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX495109/SRX495109.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX495109/SRX495109.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 23:30:38: #1 read tag files... INFO @ Fri, 26 Jun 2020 23:30:38: #1 read treatment tags... INFO @ Fri, 26 Jun 2020 23:30:44: 1000000 INFO @ Fri, 26 Jun 2020 23:30:49: 2000000 INFO @ Fri, 26 Jun 2020 23:30:55: 3000000 INFO @ Fri, 26 Jun 2020 23:31:00: 4000000 INFO @ Fri, 26 Jun 2020 23:31:05: 5000000 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 23:31:08: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX495109/SRX495109.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX495109/SRX495109.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX495109/SRX495109.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX495109/SRX495109.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 23:31:08: #1 read tag files... INFO @ Fri, 26 Jun 2020 23:31:08: #1 read treatment tags... INFO @ Fri, 26 Jun 2020 23:31:11: 6000000 INFO @ Fri, 26 Jun 2020 23:31:15: 1000000 INFO @ Fri, 26 Jun 2020 23:31:17: 7000000 INFO @ Fri, 26 Jun 2020 23:31:23: 2000000 INFO @ Fri, 26 Jun 2020 23:31:23: 8000000 INFO @ Fri, 26 Jun 2020 23:31:29: 9000000 INFO @ Fri, 26 Jun 2020 23:31:29: 3000000 INFO @ Fri, 26 Jun 2020 23:31:35: 10000000 INFO @ Fri, 26 Jun 2020 23:31:36: 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 23:31:38: #1 tag size is determined as 42 bps INFO @ Fri, 26 Jun 2020 23:31:38: #1 tag size = 42 INFO @ Fri, 26 Jun 2020 23:31:38: #1 total tags in treatment: 10386941 INFO @ Fri, 26 Jun 2020 23:31:38: #1 user defined the maximum tags... INFO @ Fri, 26 Jun 2020 23:31:38: #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 23:31:38: #1 tags after filtering in treatment: 10386941 INFO @ Fri, 26 Jun 2020 23:31:38: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 26 Jun 2020 23:31:38: #1 finished! INFO @ Fri, 26 Jun 2020 23:31:38: #2 Build Peak Model... INFO @ Fri, 26 Jun 2020 23:31:38: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 26 Jun 2020 23:31:38: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX495109/SRX495109.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX495109/SRX495109.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX495109/SRX495109.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX495109/SRX495109.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 23:31:38: #1 read tag files... INFO @ Fri, 26 Jun 2020 23:31:38: #1 read treatment tags... INFO @ Fri, 26 Jun 2020 23:31:38: #2 number of paired peaks: 344 WARNING @ Fri, 26 Jun 2020 23:31:38: Fewer paired peaks (344) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 344 pairs to build model! INFO @ Fri, 26 Jun 2020 23:31:38: start model_add_line... INFO @ Fri, 26 Jun 2020 23:31:38: start X-correlation... INFO @ Fri, 26 Jun 2020 23:31:38: end of X-cor INFO @ Fri, 26 Jun 2020 23:31:38: #2 finished! INFO @ Fri, 26 Jun 2020 23:31:38: #2 predicted fragment length is 49 bps INFO @ Fri, 26 Jun 2020 23:31:38: #2 alternative fragment length(s) may be 4,49,563 bps INFO @ Fri, 26 Jun 2020 23:31:38: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX495109/SRX495109.05_model.r WARNING @ Fri, 26 Jun 2020 23:31:38: #2 Since the d (49) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 26 Jun 2020 23:31:38: #2 You may need to consider one of the other alternative d(s): 4,49,563 WARNING @ Fri, 26 Jun 2020 23:31:38: #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 23:31:38: #3 Call peaks... INFO @ Fri, 26 Jun 2020 23:31:38: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 26 Jun 2020 23:31:43: 5000000 INFO @ Fri, 26 Jun 2020 23:31:45: 1000000 INFO @ Fri, 26 Jun 2020 23:31:50: 6000000 INFO @ Fri, 26 Jun 2020 23:31:52: 2000000 INFO @ Fri, 26 Jun 2020 23:31:57: 7000000 INFO @ Fri, 26 Jun 2020 23:31:59: 3000000 INFO @ Fri, 26 Jun 2020 23:32:00: #3 Call peaks for each chromosome... INFO @ Fri, 26 Jun 2020 23:32:03: 8000000 INFO @ Fri, 26 Jun 2020 23:32:06: 4000000 INFO @ Fri, 26 Jun 2020 23:32:10: 9000000 INFO @ Fri, 26 Jun 2020 23:32:11: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX495109/SRX495109.05_peaks.xls INFO @ Fri, 26 Jun 2020 23:32:11: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX495109/SRX495109.05_peaks.narrowPeak INFO @ Fri, 26 Jun 2020 23:32:11: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX495109/SRX495109.05_summits.bed INFO @ Fri, 26 Jun 2020 23:32:11: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (6410 records, 4 fields): 8 millis CompletedMACS2peakCalling INFO @ Fri, 26 Jun 2020 23:32:13: 5000000 INFO @ Fri, 26 Jun 2020 23:32:17: 10000000 INFO @ Fri, 26 Jun 2020 23:32:19: 6000000 INFO @ Fri, 26 Jun 2020 23:32:20: #1 tag size is determined as 42 bps INFO @ Fri, 26 Jun 2020 23:32:20: #1 tag size = 42 INFO @ Fri, 26 Jun 2020 23:32:20: #1 total tags in treatment: 10386941 INFO @ Fri, 26 Jun 2020 23:32:20: #1 user defined the maximum tags... INFO @ Fri, 26 Jun 2020 23:32:20: #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 23:32:20: #1 tags after filtering in treatment: 10386941 INFO @ Fri, 26 Jun 2020 23:32:20: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 26 Jun 2020 23:32:20: #1 finished! INFO @ Fri, 26 Jun 2020 23:32:20: #2 Build Peak Model... INFO @ Fri, 26 Jun 2020 23:32:20: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 26 Jun 2020 23:32:21: #2 number of paired peaks: 344 WARNING @ Fri, 26 Jun 2020 23:32:21: Fewer paired peaks (344) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 344 pairs to build model! INFO @ Fri, 26 Jun 2020 23:32:21: start model_add_line... INFO @ Fri, 26 Jun 2020 23:32:21: start X-correlation... INFO @ Fri, 26 Jun 2020 23:32:21: end of X-cor INFO @ Fri, 26 Jun 2020 23:32:21: #2 finished! INFO @ Fri, 26 Jun 2020 23:32:21: #2 predicted fragment length is 49 bps INFO @ Fri, 26 Jun 2020 23:32:21: #2 alternative fragment length(s) may be 4,49,563 bps INFO @ Fri, 26 Jun 2020 23:32:21: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX495109/SRX495109.10_model.r WARNING @ Fri, 26 Jun 2020 23:32:21: #2 Since the d (49) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 26 Jun 2020 23:32:21: #2 You may need to consider one of the other alternative d(s): 4,49,563 WARNING @ Fri, 26 Jun 2020 23:32:21: #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 23:32:21: #3 Call peaks... INFO @ Fri, 26 Jun 2020 23:32:21: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 26 Jun 2020 23:32:26: 7000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Fri, 26 Jun 2020 23:32:32: 8000000 INFO @ Fri, 26 Jun 2020 23:32:39: 9000000 INFO @ Fri, 26 Jun 2020 23:32:44: #3 Call peaks for each chromosome... INFO @ Fri, 26 Jun 2020 23:32:45: 10000000 INFO @ Fri, 26 Jun 2020 23:32:48: #1 tag size is determined as 42 bps INFO @ Fri, 26 Jun 2020 23:32:48: #1 tag size = 42 INFO @ Fri, 26 Jun 2020 23:32:48: #1 total tags in treatment: 10386941 INFO @ Fri, 26 Jun 2020 23:32:48: #1 user defined the maximum tags... INFO @ Fri, 26 Jun 2020 23:32:48: #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 23:32:48: #1 tags after filtering in treatment: 10386941 INFO @ Fri, 26 Jun 2020 23:32:48: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 26 Jun 2020 23:32:48: #1 finished! INFO @ Fri, 26 Jun 2020 23:32:48: #2 Build Peak Model... INFO @ Fri, 26 Jun 2020 23:32:48: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 26 Jun 2020 23:32:49: #2 number of paired peaks: 344 WARNING @ Fri, 26 Jun 2020 23:32:49: Fewer paired peaks (344) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 344 pairs to build model! INFO @ Fri, 26 Jun 2020 23:32:49: start model_add_line... BigWig に変換しました。 INFO @ Fri, 26 Jun 2020 23:32:49: start X-correlation... INFO @ Fri, 26 Jun 2020 23:32:49: end of X-cor INFO @ Fri, 26 Jun 2020 23:32:49: #2 finished! INFO @ Fri, 26 Jun 2020 23:32:49: #2 predicted fragment length is 49 bps INFO @ Fri, 26 Jun 2020 23:32:49: #2 alternative fragment length(s) may be 4,49,563 bps INFO @ Fri, 26 Jun 2020 23:32:49: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX495109/SRX495109.20_model.r WARNING @ Fri, 26 Jun 2020 23:32:49: #2 Since the d (49) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 26 Jun 2020 23:32:49: #2 You may need to consider one of the other alternative d(s): 4,49,563 WARNING @ Fri, 26 Jun 2020 23:32:49: #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 23:32:49: #3 Call peaks... INFO @ Fri, 26 Jun 2020 23:32:49: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 26 Jun 2020 23:32:56: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX495109/SRX495109.10_peaks.xls INFO @ Fri, 26 Jun 2020 23:32:56: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX495109/SRX495109.10_peaks.narrowPeak INFO @ Fri, 26 Jun 2020 23:32:56: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX495109/SRX495109.10_summits.bed INFO @ Fri, 26 Jun 2020 23:32:56: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (1244 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Fri, 26 Jun 2020 23:33:12: #3 Call peaks for each chromosome... INFO @ Fri, 26 Jun 2020 23:33:24: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX495109/SRX495109.20_peaks.xls INFO @ Fri, 26 Jun 2020 23:33:24: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX495109/SRX495109.20_peaks.narrowPeak INFO @ Fri, 26 Jun 2020 23:33:24: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX495109/SRX495109.20_summits.bed INFO @ Fri, 26 Jun 2020 23:33:24: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (235 records, 4 fields): 1 millis CompletedMACS2peakCalling