Job ID = 6366756 SRX = SRX2228909 Genome = ce11 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-15T23:34:20 prefetch.2.10.7: 1) Downloading 'SRR4380365'... 2020-06-15T23:34:20 prefetch.2.10.7: Downloading via HTTPS... 2020-06-15T23:36:18 prefetch.2.10.7: HTTPS download succeed 2020-06-15T23:36:19 prefetch.2.10.7: 'SRR4380365' is valid 2020-06-15T23:36:19 prefetch.2.10.7: 1) 'SRR4380365' was downloaded successfully 2020-06-15T23:36:19 prefetch.2.10.7: 'SRR4380365' has 0 unresolved dependencies Read 13551305 spots for SRR4380365/SRR4380365.sra Written 13551305 spots for SRR4380365/SRR4380365.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: 00:03:13 13551305 reads; of these: 13551305 (100.00%) were unpaired; of these: 162746 (1.20%) aligned 0 times 11066882 (81.67%) aligned exactly 1 time 2321677 (17.13%) aligned >1 times 98.80% overall alignment rate Time searching: 00:03:13 Overall time: 00:03:13 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_sort_core] merging from 8 files... [bam_rmdupse_core] 1166674 / 13388559 = 0.0871 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 08:43:38: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX2228909/SRX2228909.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX2228909/SRX2228909.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX2228909/SRX2228909.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX2228909/SRX2228909.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 08:43:38: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:43:38: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:43:45: 1000000 INFO @ Tue, 16 Jun 2020 08:43:52: 2000000 INFO @ Tue, 16 Jun 2020 08:43:59: 3000000 INFO @ Tue, 16 Jun 2020 08:44:05: 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 08:44:08: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX2228909/SRX2228909.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX2228909/SRX2228909.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX2228909/SRX2228909.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX2228909/SRX2228909.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 08:44:08: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:44:08: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:44:12: 5000000 INFO @ Tue, 16 Jun 2020 08:44:15: 1000000 INFO @ Tue, 16 Jun 2020 08:44:20: 6000000 INFO @ Tue, 16 Jun 2020 08:44:22: 2000000 INFO @ Tue, 16 Jun 2020 08:44:27: 7000000 INFO @ Tue, 16 Jun 2020 08:44:29: 3000000 INFO @ Tue, 16 Jun 2020 08:44:35: 8000000 INFO @ Tue, 16 Jun 2020 08:44:35: 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 08:44:38: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX2228909/SRX2228909.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX2228909/SRX2228909.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX2228909/SRX2228909.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX2228909/SRX2228909.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 08:44:38: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:44:38: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:44:42: 5000000 INFO @ Tue, 16 Jun 2020 08:44:42: 9000000 INFO @ Tue, 16 Jun 2020 08:44:46: 1000000 INFO @ Tue, 16 Jun 2020 08:44:50: 6000000 INFO @ Tue, 16 Jun 2020 08:44:50: 10000000 INFO @ Tue, 16 Jun 2020 08:44:53: 2000000 INFO @ Tue, 16 Jun 2020 08:44:57: 7000000 INFO @ Tue, 16 Jun 2020 08:44:57: 11000000 INFO @ Tue, 16 Jun 2020 08:45:00: 3000000 INFO @ Tue, 16 Jun 2020 08:45:04: 8000000 INFO @ Tue, 16 Jun 2020 08:45:05: 12000000 INFO @ Tue, 16 Jun 2020 08:45:06: #1 tag size is determined as 51 bps INFO @ Tue, 16 Jun 2020 08:45:06: #1 tag size = 51 INFO @ Tue, 16 Jun 2020 08:45:06: #1 total tags in treatment: 12221885 INFO @ Tue, 16 Jun 2020 08:45:06: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:45:06: #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 08:45:07: #1 tags after filtering in treatment: 12221885 INFO @ Tue, 16 Jun 2020 08:45:07: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:45:07: #1 finished! INFO @ Tue, 16 Jun 2020 08:45:07: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:45:07: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:45:07: 4000000 INFO @ Tue, 16 Jun 2020 08:45:07: #2 number of paired peaks: 300 WARNING @ Tue, 16 Jun 2020 08:45:07: Fewer paired peaks (300) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 300 pairs to build model! INFO @ Tue, 16 Jun 2020 08:45:07: start model_add_line... INFO @ Tue, 16 Jun 2020 08:45:07: start X-correlation... INFO @ Tue, 16 Jun 2020 08:45:07: end of X-cor INFO @ Tue, 16 Jun 2020 08:45:07: #2 finished! INFO @ Tue, 16 Jun 2020 08:45:07: #2 predicted fragment length is 52 bps INFO @ Tue, 16 Jun 2020 08:45:07: #2 alternative fragment length(s) may be 2,52,515 bps INFO @ Tue, 16 Jun 2020 08:45:07: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX2228909/SRX2228909.05_model.r WARNING @ Tue, 16 Jun 2020 08:45:07: #2 Since the d (52) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 08:45:07: #2 You may need to consider one of the other alternative d(s): 2,52,515 WARNING @ Tue, 16 Jun 2020 08:45:07: #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 08:45:07: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:45:07: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 08:45:11: 9000000 INFO @ Tue, 16 Jun 2020 08:45:14: 5000000 INFO @ Tue, 16 Jun 2020 08:45:17: 10000000 INFO @ Tue, 16 Jun 2020 08:45:21: 6000000 INFO @ Tue, 16 Jun 2020 08:45:24: 11000000 INFO @ Tue, 16 Jun 2020 08:45:28: 7000000 INFO @ Tue, 16 Jun 2020 08:45:29: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 08:45:31: 12000000 INFO @ Tue, 16 Jun 2020 08:45:32: #1 tag size is determined as 51 bps INFO @ Tue, 16 Jun 2020 08:45:32: #1 tag size = 51 INFO @ Tue, 16 Jun 2020 08:45:32: #1 total tags in treatment: 12221885 INFO @ Tue, 16 Jun 2020 08:45:32: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:45:32: #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 08:45:33: #1 tags after filtering in treatment: 12221885 INFO @ Tue, 16 Jun 2020 08:45:33: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:45:33: #1 finished! INFO @ Tue, 16 Jun 2020 08:45:33: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:45:33: #2 looking for paired plus/minus strand peaks... BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 16 Jun 2020 08:45:33: #2 number of paired peaks: 300 WARNING @ Tue, 16 Jun 2020 08:45:33: Fewer paired peaks (300) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 300 pairs to build model! INFO @ Tue, 16 Jun 2020 08:45:33: start model_add_line... INFO @ Tue, 16 Jun 2020 08:45:33: start X-correlation... INFO @ Tue, 16 Jun 2020 08:45:33: end of X-cor INFO @ Tue, 16 Jun 2020 08:45:33: #2 finished! INFO @ Tue, 16 Jun 2020 08:45:33: #2 predicted fragment length is 52 bps INFO @ Tue, 16 Jun 2020 08:45:33: #2 alternative fragment length(s) may be 2,52,515 bps INFO @ Tue, 16 Jun 2020 08:45:33: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX2228909/SRX2228909.10_model.r WARNING @ Tue, 16 Jun 2020 08:45:33: #2 Since the d (52) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 08:45:33: #2 You may need to consider one of the other alternative d(s): 2,52,515 WARNING @ Tue, 16 Jun 2020 08:45:33: #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 08:45:33: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:45:33: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 08:45:34: 8000000 INFO @ Tue, 16 Jun 2020 08:45:40: 9000000 INFO @ Tue, 16 Jun 2020 08:45:41: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX2228909/SRX2228909.05_peaks.xls INFO @ Tue, 16 Jun 2020 08:45:41: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX2228909/SRX2228909.05_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:45:41: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX2228909/SRX2228909.05_summits.bed INFO @ Tue, 16 Jun 2020 08:45:41: Done! pass1 - making usageList (7 chroms): 2 millis pass2 - checking and writing primary data (616 records, 4 fields): 1 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 08:45:46: 10000000 INFO @ Tue, 16 Jun 2020 08:45:52: 11000000 INFO @ Tue, 16 Jun 2020 08:45:55: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 08:45:57: 12000000 INFO @ Tue, 16 Jun 2020 08:45:59: #1 tag size is determined as 51 bps INFO @ Tue, 16 Jun 2020 08:45:59: #1 tag size = 51 INFO @ Tue, 16 Jun 2020 08:45:59: #1 total tags in treatment: 12221885 INFO @ Tue, 16 Jun 2020 08:45:59: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:45:59: #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 08:45:59: #1 tags after filtering in treatment: 12221885 INFO @ Tue, 16 Jun 2020 08:45:59: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:45:59: #1 finished! INFO @ Tue, 16 Jun 2020 08:45:59: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:45:59: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:46:00: #2 number of paired peaks: 300 WARNING @ Tue, 16 Jun 2020 08:46:00: Fewer paired peaks (300) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 300 pairs to build model! INFO @ Tue, 16 Jun 2020 08:46:00: start model_add_line... INFO @ Tue, 16 Jun 2020 08:46:00: start X-correlation... INFO @ Tue, 16 Jun 2020 08:46:00: end of X-cor INFO @ Tue, 16 Jun 2020 08:46:00: #2 finished! INFO @ Tue, 16 Jun 2020 08:46:00: #2 predicted fragment length is 52 bps INFO @ Tue, 16 Jun 2020 08:46:00: #2 alternative fragment length(s) may be 2,52,515 bps INFO @ Tue, 16 Jun 2020 08:46:00: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX2228909/SRX2228909.20_model.r WARNING @ Tue, 16 Jun 2020 08:46:00: #2 Since the d (52) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 08:46:00: #2 You may need to consider one of the other alternative d(s): 2,52,515 WARNING @ Tue, 16 Jun 2020 08:46:00: #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 08:46:00: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:46:00: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Tue, 16 Jun 2020 08:46:06: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX2228909/SRX2228909.10_peaks.xls INFO @ Tue, 16 Jun 2020 08:46:06: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX2228909/SRX2228909.10_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:46:06: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX2228909/SRX2228909.10_summits.bed INFO @ Tue, 16 Jun 2020 08:46:06: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (411 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 08:46:21: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 08:46:32: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX2228909/SRX2228909.20_peaks.xls INFO @ Tue, 16 Jun 2020 08:46:32: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX2228909/SRX2228909.20_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:46:32: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX2228909/SRX2228909.20_summits.bed INFO @ Tue, 16 Jun 2020 08:46:32: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (181 records, 4 fields): 1 millis CompletedMACS2peakCalling