Job ID = 6368788 SRX = SRX5702595 Genome = ce11 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-16T00:25:49 prefetch.2.10.7: 1) Downloading 'SRR8921272'... 2020-06-16T00:25:49 prefetch.2.10.7: Downloading via HTTPS... 2020-06-16T00:27:40 prefetch.2.10.7: HTTPS download succeed 2020-06-16T00:27:41 prefetch.2.10.7: 'SRR8921272' is valid 2020-06-16T00:27:41 prefetch.2.10.7: 1) 'SRR8921272' was downloaded successfully 2020-06-16T00:27:41 prefetch.2.10.7: 'SRR8921272' has 0 unresolved dependencies Read 19594831 spots for SRR8921272/SRR8921272.sra Written 19594831 spots for SRR8921272/SRR8921272.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: 00:03:57 19594831 reads; of these: 19594831 (100.00%) were unpaired; of these: 2951981 (15.07%) aligned 0 times 13725328 (70.05%) aligned exactly 1 time 2917522 (14.89%) aligned >1 times 84.93% overall alignment rate Time searching: 00:03:57 Overall time: 00:03:57 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] 12842437 / 16642850 = 0.7716 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 09:35:04: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX5702595/SRX5702595.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX5702595/SRX5702595.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX5702595/SRX5702595.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX5702595/SRX5702595.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 09:35:04: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:35:04: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:35:10: 1000000 INFO @ Tue, 16 Jun 2020 09:35:16: 2000000 INFO @ Tue, 16 Jun 2020 09:35:21: 3000000 INFO @ Tue, 16 Jun 2020 09:35:26: #1 tag size is determined as 50 bps INFO @ Tue, 16 Jun 2020 09:35:26: #1 tag size = 50 INFO @ Tue, 16 Jun 2020 09:35:26: #1 total tags in treatment: 3800413 INFO @ Tue, 16 Jun 2020 09:35:26: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:35:26: #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 09:35:26: #1 tags after filtering in treatment: 3800413 INFO @ Tue, 16 Jun 2020 09:35:26: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 09:35:26: #1 finished! INFO @ Tue, 16 Jun 2020 09:35:26: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:35:26: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:35:26: #2 number of paired peaks: 660 WARNING @ Tue, 16 Jun 2020 09:35:26: Fewer paired peaks (660) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 660 pairs to build model! INFO @ Tue, 16 Jun 2020 09:35:26: start model_add_line... INFO @ Tue, 16 Jun 2020 09:35:26: start X-correlation... INFO @ Tue, 16 Jun 2020 09:35:26: end of X-cor INFO @ Tue, 16 Jun 2020 09:35:26: #2 finished! INFO @ Tue, 16 Jun 2020 09:35:26: #2 predicted fragment length is 50 bps INFO @ Tue, 16 Jun 2020 09:35:26: #2 alternative fragment length(s) may be 4,50,544 bps INFO @ Tue, 16 Jun 2020 09:35:26: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX5702595/SRX5702595.05_model.r WARNING @ Tue, 16 Jun 2020 09:35:26: #2 Since the d (50) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 09:35:26: #2 You may need to consider one of the other alternative d(s): 4,50,544 WARNING @ Tue, 16 Jun 2020 09:35:26: #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 09:35:26: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:35:26: #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 09:35:34: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 09:35:35: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX5702595/SRX5702595.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX5702595/SRX5702595.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX5702595/SRX5702595.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX5702595/SRX5702595.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 09:35:35: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:35:35: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:35:38: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX5702595/SRX5702595.05_peaks.xls INFO @ Tue, 16 Jun 2020 09:35:38: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX5702595/SRX5702595.05_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:35:38: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX5702595/SRX5702595.05_summits.bed INFO @ Tue, 16 Jun 2020 09:35:38: Done! pass1 - making usageList (7 chroms): 0 millis pass2 - checking and writing primary data (744 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 09:35:41: 1000000 INFO @ Tue, 16 Jun 2020 09:35:48: 2000000 INFO @ Tue, 16 Jun 2020 09:35:55: 3000000 INFO @ Tue, 16 Jun 2020 09:36:00: #1 tag size is determined as 50 bps INFO @ Tue, 16 Jun 2020 09:36:00: #1 tag size = 50 INFO @ Tue, 16 Jun 2020 09:36:00: #1 total tags in treatment: 3800413 INFO @ Tue, 16 Jun 2020 09:36:00: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:36:00: #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 09:36:00: #1 tags after filtering in treatment: 3800413 INFO @ Tue, 16 Jun 2020 09:36:00: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 09:36:00: #1 finished! INFO @ Tue, 16 Jun 2020 09:36:00: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:36:00: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:36:00: #2 number of paired peaks: 660 WARNING @ Tue, 16 Jun 2020 09:36:00: Fewer paired peaks (660) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 660 pairs to build model! INFO @ Tue, 16 Jun 2020 09:36:00: start model_add_line... INFO @ Tue, 16 Jun 2020 09:36:00: start X-correlation... INFO @ Tue, 16 Jun 2020 09:36:00: end of X-cor INFO @ Tue, 16 Jun 2020 09:36:00: #2 finished! INFO @ Tue, 16 Jun 2020 09:36:00: #2 predicted fragment length is 50 bps INFO @ Tue, 16 Jun 2020 09:36:00: #2 alternative fragment length(s) may be 4,50,544 bps INFO @ Tue, 16 Jun 2020 09:36:00: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX5702595/SRX5702595.10_model.r WARNING @ Tue, 16 Jun 2020 09:36:00: #2 Since the d (50) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 09:36:00: #2 You may need to consider one of the other alternative d(s): 4,50,544 WARNING @ Tue, 16 Jun 2020 09:36:00: #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 09:36:00: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:36:00: #3 Pre-compute pvalue-qvalue table... 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 09:36:04: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX5702595/SRX5702595.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX5702595/SRX5702595.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX5702595/SRX5702595.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX5702595/SRX5702595.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 09:36:04: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:36:04: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:36:08: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 09:36:11: 1000000 INFO @ Tue, 16 Jun 2020 09:36:12: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX5702595/SRX5702595.10_peaks.xls INFO @ Tue, 16 Jun 2020 09:36:12: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX5702595/SRX5702595.10_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:36:12: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX5702595/SRX5702595.10_summits.bed INFO @ Tue, 16 Jun 2020 09:36:12: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (481 records, 4 fields): 1 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 09:36:17: 2000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 16 Jun 2020 09:36:24: 3000000 INFO @ Tue, 16 Jun 2020 09:36:29: #1 tag size is determined as 50 bps INFO @ Tue, 16 Jun 2020 09:36:29: #1 tag size = 50 INFO @ Tue, 16 Jun 2020 09:36:29: #1 total tags in treatment: 3800413 INFO @ Tue, 16 Jun 2020 09:36:29: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:36:29: #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 09:36:29: #1 tags after filtering in treatment: 3800413 INFO @ Tue, 16 Jun 2020 09:36:29: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 09:36:29: #1 finished! INFO @ Tue, 16 Jun 2020 09:36:29: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:36:29: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:36:29: #2 number of paired peaks: 660 WARNING @ Tue, 16 Jun 2020 09:36:29: Fewer paired peaks (660) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 660 pairs to build model! INFO @ Tue, 16 Jun 2020 09:36:29: start model_add_line... INFO @ Tue, 16 Jun 2020 09:36:29: start X-correlation... INFO @ Tue, 16 Jun 2020 09:36:29: end of X-cor INFO @ Tue, 16 Jun 2020 09:36:29: #2 finished! INFO @ Tue, 16 Jun 2020 09:36:29: #2 predicted fragment length is 50 bps INFO @ Tue, 16 Jun 2020 09:36:29: #2 alternative fragment length(s) may be 4,50,544 bps INFO @ Tue, 16 Jun 2020 09:36:29: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX5702595/SRX5702595.20_model.r WARNING @ Tue, 16 Jun 2020 09:36:29: #2 Since the d (50) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 09:36:29: #2 You may need to consider one of the other alternative d(s): 4,50,544 WARNING @ Tue, 16 Jun 2020 09:36:29: #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 09:36:29: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:36:29: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Tue, 16 Jun 2020 09:36:37: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 09:36:42: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX5702595/SRX5702595.20_peaks.xls INFO @ Tue, 16 Jun 2020 09:36:42: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX5702595/SRX5702595.20_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:36:42: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX5702595/SRX5702595.20_summits.bed INFO @ Tue, 16 Jun 2020 09:36:42: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (209 records, 4 fields): 1 millis CompletedMACS2peakCalling