Job ID = 6368994 SRX = SRX982060 Genome = ce11 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-16T01:16:06 prefetch.2.10.7: 1) Downloading 'SRR1956536'... 2020-06-16T01:16:06 prefetch.2.10.7: Downloading via HTTPS... 2020-06-16T01:19:46 prefetch.2.10.7: HTTPS download succeed 2020-06-16T01:19:46 prefetch.2.10.7: 1) 'SRR1956536' was downloaded successfully Read 18405815 spots for SRR1956536/SRR1956536.sra Written 18405815 spots for SRR1956536/SRR1956536.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: 00:04:54 18405815 reads; of these: 18405815 (100.00%) were unpaired; of these: 4539909 (24.67%) aligned 0 times 11616405 (63.11%) aligned exactly 1 time 2249501 (12.22%) aligned >1 times 75.33% overall alignment rate Time searching: 00:04:54 Overall time: 00:04:54 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_sort_core] merging from 8 files... [bam_rmdupse_core] 3679519 / 13865906 = 0.2654 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 10:30:16: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX982060/SRX982060.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX982060/SRX982060.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX982060/SRX982060.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX982060/SRX982060.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 10:30:16: #1 read tag files... INFO @ Tue, 16 Jun 2020 10:30:16: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 10:30:23: 1000000 INFO @ Tue, 16 Jun 2020 10:30:30: 2000000 INFO @ Tue, 16 Jun 2020 10:30:37: 3000000 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 10:30:44: 4000000 INFO @ Tue, 16 Jun 2020 10:30:46: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX982060/SRX982060.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX982060/SRX982060.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX982060/SRX982060.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX982060/SRX982060.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 10:30:46: #1 read tag files... INFO @ Tue, 16 Jun 2020 10:30:46: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 10:30:52: 5000000 INFO @ Tue, 16 Jun 2020 10:30:54: 1000000 INFO @ Tue, 16 Jun 2020 10:31:00: 6000000 INFO @ Tue, 16 Jun 2020 10:31:02: 2000000 INFO @ Tue, 16 Jun 2020 10:31:08: 7000000 INFO @ Tue, 16 Jun 2020 10:31:10: 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 10:31:16: 8000000 INFO @ Tue, 16 Jun 2020 10:31:16: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX982060/SRX982060.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX982060/SRX982060.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX982060/SRX982060.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX982060/SRX982060.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 10:31:16: #1 read tag files... INFO @ Tue, 16 Jun 2020 10:31:16: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 10:31:19: 4000000 INFO @ Tue, 16 Jun 2020 10:31:24: 9000000 INFO @ Tue, 16 Jun 2020 10:31:24: 1000000 INFO @ Tue, 16 Jun 2020 10:31:27: 5000000 INFO @ Tue, 16 Jun 2020 10:31:32: 10000000 INFO @ Tue, 16 Jun 2020 10:31:33: 2000000 INFO @ Tue, 16 Jun 2020 10:31:33: #1 tag size is determined as 76 bps INFO @ Tue, 16 Jun 2020 10:31:33: #1 tag size = 76 INFO @ Tue, 16 Jun 2020 10:31:33: #1 total tags in treatment: 10186387 INFO @ Tue, 16 Jun 2020 10:31:33: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 10:31:33: #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 10:31:33: #1 tags after filtering in treatment: 10186387 INFO @ Tue, 16 Jun 2020 10:31:33: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 10:31:33: #1 finished! INFO @ Tue, 16 Jun 2020 10:31:33: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 10:31:33: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 10:31:34: #2 number of paired peaks: 497 WARNING @ Tue, 16 Jun 2020 10:31:34: Fewer paired peaks (497) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 497 pairs to build model! INFO @ Tue, 16 Jun 2020 10:31:34: start model_add_line... INFO @ Tue, 16 Jun 2020 10:31:34: start X-correlation... INFO @ Tue, 16 Jun 2020 10:31:34: end of X-cor INFO @ Tue, 16 Jun 2020 10:31:34: #2 finished! INFO @ Tue, 16 Jun 2020 10:31:34: #2 predicted fragment length is 89 bps INFO @ Tue, 16 Jun 2020 10:31:34: #2 alternative fragment length(s) may be 89 bps INFO @ Tue, 16 Jun 2020 10:31:34: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX982060/SRX982060.05_model.r WARNING @ Tue, 16 Jun 2020 10:31:34: #2 Since the d (89) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 10:31:34: #2 You may need to consider one of the other alternative d(s): 89 WARNING @ Tue, 16 Jun 2020 10:31:34: #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 10:31:34: #3 Call peaks... INFO @ Tue, 16 Jun 2020 10:31:34: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 10:31:36: 6000000 INFO @ Tue, 16 Jun 2020 10:31:41: 3000000 INFO @ Tue, 16 Jun 2020 10:31:44: 7000000 INFO @ Tue, 16 Jun 2020 10:31:49: 4000000 INFO @ Tue, 16 Jun 2020 10:31:52: 8000000 INFO @ Tue, 16 Jun 2020 10:31:56: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 10:31:57: 5000000 INFO @ Tue, 16 Jun 2020 10:31:59: 9000000 INFO @ Tue, 16 Jun 2020 10:32:05: 6000000 INFO @ Tue, 16 Jun 2020 10:32:06: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX982060/SRX982060.05_peaks.xls INFO @ Tue, 16 Jun 2020 10:32:06: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX982060/SRX982060.05_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 10:32:06: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX982060/SRX982060.05_summits.bed INFO @ Tue, 16 Jun 2020 10:32:06: Done! pass1 - making usageList (7 chroms): 0 millis pass2 - checking and writing primary data (1291 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 10:32:07: 10000000 INFO @ Tue, 16 Jun 2020 10:32:09: #1 tag size is determined as 76 bps INFO @ Tue, 16 Jun 2020 10:32:09: #1 tag size = 76 INFO @ Tue, 16 Jun 2020 10:32:09: #1 total tags in treatment: 10186387 INFO @ Tue, 16 Jun 2020 10:32:09: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 10:32:09: #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 10:32:09: #1 tags after filtering in treatment: 10186387 INFO @ Tue, 16 Jun 2020 10:32:09: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 10:32:09: #1 finished! INFO @ Tue, 16 Jun 2020 10:32:09: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 10:32:09: #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 10:32:09: #2 number of paired peaks: 497 WARNING @ Tue, 16 Jun 2020 10:32:09: Fewer paired peaks (497) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 497 pairs to build model! INFO @ Tue, 16 Jun 2020 10:32:09: start model_add_line... INFO @ Tue, 16 Jun 2020 10:32:10: start X-correlation... INFO @ Tue, 16 Jun 2020 10:32:10: end of X-cor INFO @ Tue, 16 Jun 2020 10:32:10: #2 finished! INFO @ Tue, 16 Jun 2020 10:32:10: #2 predicted fragment length is 89 bps INFO @ Tue, 16 Jun 2020 10:32:10: #2 alternative fragment length(s) may be 89 bps INFO @ Tue, 16 Jun 2020 10:32:10: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX982060/SRX982060.10_model.r WARNING @ Tue, 16 Jun 2020 10:32:10: #2 Since the d (89) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 10:32:10: #2 You may need to consider one of the other alternative d(s): 89 WARNING @ Tue, 16 Jun 2020 10:32:10: #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 10:32:10: #3 Call peaks... INFO @ Tue, 16 Jun 2020 10:32:10: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 10:32:12: 7000000 INFO @ Tue, 16 Jun 2020 10:32:19: 8000000 INFO @ Tue, 16 Jun 2020 10:32:26: 9000000 INFO @ Tue, 16 Jun 2020 10:32:31: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 10:32:33: 10000000 BigWig に変換しました。 INFO @ Tue, 16 Jun 2020 10:32:34: #1 tag size is determined as 76 bps INFO @ Tue, 16 Jun 2020 10:32:34: #1 tag size = 76 INFO @ Tue, 16 Jun 2020 10:32:34: #1 total tags in treatment: 10186387 INFO @ Tue, 16 Jun 2020 10:32:34: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 10:32:34: #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 10:32:34: #1 tags after filtering in treatment: 10186387 INFO @ Tue, 16 Jun 2020 10:32:34: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 10:32:34: #1 finished! INFO @ Tue, 16 Jun 2020 10:32:34: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 10:32:34: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 10:32:35: #2 number of paired peaks: 497 WARNING @ Tue, 16 Jun 2020 10:32:35: Fewer paired peaks (497) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 497 pairs to build model! INFO @ Tue, 16 Jun 2020 10:32:35: start model_add_line... INFO @ Tue, 16 Jun 2020 10:32:35: start X-correlation... INFO @ Tue, 16 Jun 2020 10:32:35: end of X-cor INFO @ Tue, 16 Jun 2020 10:32:35: #2 finished! INFO @ Tue, 16 Jun 2020 10:32:35: #2 predicted fragment length is 89 bps INFO @ Tue, 16 Jun 2020 10:32:35: #2 alternative fragment length(s) may be 89 bps INFO @ Tue, 16 Jun 2020 10:32:35: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX982060/SRX982060.20_model.r WARNING @ Tue, 16 Jun 2020 10:32:35: #2 Since the d (89) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 10:32:35: #2 You may need to consider one of the other alternative d(s): 89 WARNING @ Tue, 16 Jun 2020 10:32:35: #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 10:32:35: #3 Call peaks... INFO @ Tue, 16 Jun 2020 10:32:35: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 10:32:41: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX982060/SRX982060.10_peaks.xls INFO @ Tue, 16 Jun 2020 10:32:41: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX982060/SRX982060.10_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 10:32:41: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX982060/SRX982060.10_summits.bed INFO @ Tue, 16 Jun 2020 10:32:41: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (854 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 10:32:55: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 10:33:05: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX982060/SRX982060.20_peaks.xls INFO @ Tue, 16 Jun 2020 10:33:05: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX982060/SRX982060.20_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 10:33:05: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX982060/SRX982060.20_summits.bed INFO @ Tue, 16 Jun 2020 10:33:05: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (446 records, 4 fields): 1 millis CompletedMACS2peakCalling