Job ID = 12531490 SRX = SRX8142331 Genome = rn6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... Read 7675320 spots for SRR11574133/SRR11574133.sra Written 7675320 spots for SRR11574133/SRR11574133.sra Read 7517382 spots for SRR11574134/SRR11574134.sra Written 7517382 spots for SRR11574134/SRR11574134.sra Read 7645914 spots for SRR11574135/SRR11574135.sra Written 7645914 spots for SRR11574135/SRR11574135.sra Read 7431478 spots for SRR11574136/SRR11574136.sra Written 7431478 spots for SRR11574136/SRR11574136.sra fastq に変換しました。 bowtie でマッピング中... Time loading reference: 00:00:01 Time loading forward index: 00:00:02 Time loading mirror index: 00:00:01 Multiseed full-index search: 00:18:26 30270094 reads; of these: 30270094 (100.00%) were unpaired; of these: 15432815 (50.98%) aligned 0 times 10098644 (33.36%) aligned exactly 1 time 4738635 (15.65%) aligned >1 times 49.02% overall alignment rate Time searching: 00:18:30 Overall time: 00:18:30 マッピングが完了しました。 samtools でBAM に変換中... [samopen] SAM header is present: 953 sequences. [bam_sort_core] merging from 8 files... [bam_rmdupse_core] 7477127 / 14837279 = 0.5039 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/3.7.1/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Sat, 17 Apr 2021 08:11:38: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/SRX8142331/SRX8142331.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/SRX8142331/SRX8142331.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/SRX8142331/SRX8142331.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/SRX8142331/SRX8142331.bam'] # control file = None # effective genome size = 2.15e+09 # 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 @ Sat, 17 Apr 2021 08:11:38: #1 read tag files... INFO @ Sat, 17 Apr 2021 08:11:38: #1 read treatment tags... INFO @ Sat, 17 Apr 2021 08:11:45: 1000000 INFO @ Sat, 17 Apr 2021 08:11:52: 2000000 INFO @ Sat, 17 Apr 2021 08:11:59: 3000000 WARNING: Skipping mount /opt/pkg/singularity/3.7.1/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Sat, 17 Apr 2021 08:12:06: 4000000 INFO @ Sat, 17 Apr 2021 08:12:08: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/SRX8142331/SRX8142331.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/SRX8142331/SRX8142331.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/SRX8142331/SRX8142331.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/SRX8142331/SRX8142331.bam'] # control file = None # effective genome size = 2.15e+09 # 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 @ Sat, 17 Apr 2021 08:12:08: #1 read tag files... INFO @ Sat, 17 Apr 2021 08:12:08: #1 read treatment tags... INFO @ Sat, 17 Apr 2021 08:12:14: 5000000 INFO @ Sat, 17 Apr 2021 08:12:16: 1000000 INFO @ Sat, 17 Apr 2021 08:12:22: 6000000 INFO @ Sat, 17 Apr 2021 08:12:24: 2000000 INFO @ Sat, 17 Apr 2021 08:12:30: 7000000 INFO @ Sat, 17 Apr 2021 08:12:31: 3000000 INFO @ Sat, 17 Apr 2021 08:12:32: #1 tag size is determined as 84 bps INFO @ Sat, 17 Apr 2021 08:12:32: #1 tag size = 84 INFO @ Sat, 17 Apr 2021 08:12:32: #1 total tags in treatment: 7360152 INFO @ Sat, 17 Apr 2021 08:12:32: #1 user defined the maximum tags... INFO @ Sat, 17 Apr 2021 08:12:32: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 17 Apr 2021 08:12:33: #1 tags after filtering in treatment: 7359943 INFO @ Sat, 17 Apr 2021 08:12:33: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 17 Apr 2021 08:12:33: #1 finished! INFO @ Sat, 17 Apr 2021 08:12:33: #2 Build Peak Model... INFO @ Sat, 17 Apr 2021 08:12:33: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 17 Apr 2021 08:12:34: #2 number of paired peaks: 7932 INFO @ Sat, 17 Apr 2021 08:12:34: start model_add_line... INFO @ Sat, 17 Apr 2021 08:12:34: start X-correlation... INFO @ Sat, 17 Apr 2021 08:12:34: end of X-cor INFO @ Sat, 17 Apr 2021 08:12:34: #2 finished! INFO @ Sat, 17 Apr 2021 08:12:34: #2 predicted fragment length is 86 bps INFO @ Sat, 17 Apr 2021 08:12:34: #2 alternative fragment length(s) may be 86 bps INFO @ Sat, 17 Apr 2021 08:12:34: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/SRX8142331/SRX8142331.05_model.r WARNING @ Sat, 17 Apr 2021 08:12:34: #2 Since the d (86) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 17 Apr 2021 08:12:34: #2 You may need to consider one of the other alternative d(s): 86 WARNING @ Sat, 17 Apr 2021 08:12:34: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sat, 17 Apr 2021 08:12:34: #3 Call peaks... INFO @ Sat, 17 Apr 2021 08:12:34: #3 Pre-compute pvalue-qvalue table... BedGraph に変換中... WARNING: Skipping mount /opt/pkg/singularity/3.7.1/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Sat, 17 Apr 2021 08:12:38: 4000000 INFO @ Sat, 17 Apr 2021 08:12:38: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/SRX8142331/SRX8142331.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/SRX8142331/SRX8142331.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/SRX8142331/SRX8142331.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/SRX8142331/SRX8142331.bam'] # control file = None # effective genome size = 2.15e+09 # 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 @ Sat, 17 Apr 2021 08:12:38: #1 read tag files... INFO @ Sat, 17 Apr 2021 08:12:38: #1 read treatment tags... INFO @ Sat, 17 Apr 2021 08:12:45: 5000000 INFO @ Sat, 17 Apr 2021 08:12:45: 1000000 INFO @ Sat, 17 Apr 2021 08:12:49: #3 Call peaks for each chromosome... INFO @ Sat, 17 Apr 2021 08:12:52: 6000000 INFO @ Sat, 17 Apr 2021 08:12:53: 2000000 INFO @ Sat, 17 Apr 2021 08:12:57: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/SRX8142331/SRX8142331.05_peaks.xls INFO @ Sat, 17 Apr 2021 08:12:57: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/SRX8142331/SRX8142331.05_peaks.narrowPeak INFO @ Sat, 17 Apr 2021 08:12:57: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/SRX8142331/SRX8142331.05_summits.bed INFO @ Sat, 17 Apr 2021 08:12:57: Done! pass1 - making usageList (34 chroms): 1 millis pass2 - checking and writing primary data (479 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Sat, 17 Apr 2021 08:13:00: 7000000 INFO @ Sat, 17 Apr 2021 08:13:01: 3000000 INFO @ Sat, 17 Apr 2021 08:13:03: #1 tag size is determined as 84 bps INFO @ Sat, 17 Apr 2021 08:13:03: #1 tag size = 84 INFO @ Sat, 17 Apr 2021 08:13:03: #1 total tags in treatment: 7360152 INFO @ Sat, 17 Apr 2021 08:13:03: #1 user defined the maximum tags... INFO @ Sat, 17 Apr 2021 08:13:03: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 17 Apr 2021 08:13:03: #1 tags after filtering in treatment: 7359943 INFO @ Sat, 17 Apr 2021 08:13:03: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 17 Apr 2021 08:13:03: #1 finished! INFO @ Sat, 17 Apr 2021 08:13:03: #2 Build Peak Model... INFO @ Sat, 17 Apr 2021 08:13:03: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 17 Apr 2021 08:13:04: #2 number of paired peaks: 7932 INFO @ Sat, 17 Apr 2021 08:13:04: start model_add_line... INFO @ Sat, 17 Apr 2021 08:13:05: start X-correlation... INFO @ Sat, 17 Apr 2021 08:13:05: end of X-cor INFO @ Sat, 17 Apr 2021 08:13:05: #2 finished! INFO @ Sat, 17 Apr 2021 08:13:05: #2 predicted fragment length is 86 bps INFO @ Sat, 17 Apr 2021 08:13:05: #2 alternative fragment length(s) may be 86 bps INFO @ Sat, 17 Apr 2021 08:13:05: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/SRX8142331/SRX8142331.10_model.r WARNING @ Sat, 17 Apr 2021 08:13:05: #2 Since the d (86) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 17 Apr 2021 08:13:05: #2 You may need to consider one of the other alternative d(s): 86 WARNING @ Sat, 17 Apr 2021 08:13:05: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sat, 17 Apr 2021 08:13:05: #3 Call peaks... INFO @ Sat, 17 Apr 2021 08:13:05: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 17 Apr 2021 08:13:08: 4000000 INFO @ Sat, 17 Apr 2021 08:13:14: 5000000 INFO @ Sat, 17 Apr 2021 08:13:19: #3 Call peaks for each chromosome... INFO @ Sat, 17 Apr 2021 08:13:21: 6000000 INFO @ Sat, 17 Apr 2021 08:13:27: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/SRX8142331/SRX8142331.10_peaks.xls INFO @ Sat, 17 Apr 2021 08:13:27: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/SRX8142331/SRX8142331.10_peaks.narrowPeak INFO @ Sat, 17 Apr 2021 08:13:27: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/SRX8142331/SRX8142331.10_summits.bed INFO @ Sat, 17 Apr 2021 08:13:27: Done! pass1 - making usageList (26 chroms): 1 millis pass2 - checking and writing primary data (256 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Sat, 17 Apr 2021 08:13:29: 7000000 INFO @ Sat, 17 Apr 2021 08:13:31: #1 tag size is determined as 84 bps INFO @ Sat, 17 Apr 2021 08:13:31: #1 tag size = 84 INFO @ Sat, 17 Apr 2021 08:13:31: #1 total tags in treatment: 7360152 INFO @ Sat, 17 Apr 2021 08:13:31: #1 user defined the maximum tags... INFO @ Sat, 17 Apr 2021 08:13:31: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 17 Apr 2021 08:13:31: #1 tags after filtering in treatment: 7359943 INFO @ Sat, 17 Apr 2021 08:13:31: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 17 Apr 2021 08:13:31: #1 finished! INFO @ Sat, 17 Apr 2021 08:13:31: #2 Build Peak Model... INFO @ Sat, 17 Apr 2021 08:13:31: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 17 Apr 2021 08:13:33: #2 number of paired peaks: 7932 INFO @ Sat, 17 Apr 2021 08:13:33: start model_add_line... INFO @ Sat, 17 Apr 2021 08:13:33: start X-correlation... INFO @ Sat, 17 Apr 2021 08:13:33: end of X-cor INFO @ Sat, 17 Apr 2021 08:13:33: #2 finished! INFO @ Sat, 17 Apr 2021 08:13:33: #2 predicted fragment length is 86 bps INFO @ Sat, 17 Apr 2021 08:13:33: #2 alternative fragment length(s) may be 86 bps INFO @ Sat, 17 Apr 2021 08:13:33: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/SRX8142331/SRX8142331.20_model.r WARNING @ Sat, 17 Apr 2021 08:13:33: #2 Since the d (86) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 17 Apr 2021 08:13:33: #2 You may need to consider one of the other alternative d(s): 86 WARNING @ Sat, 17 Apr 2021 08:13:33: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sat, 17 Apr 2021 08:13:33: #3 Call peaks... INFO @ Sat, 17 Apr 2021 08:13:33: #3 Pre-compute pvalue-qvalue table... BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 17 Apr 2021 08:13:48: #3 Call peaks for each chromosome... INFO @ Sat, 17 Apr 2021 08:13:55: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/SRX8142331/SRX8142331.20_peaks.xls INFO @ Sat, 17 Apr 2021 08:13:55: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/SRX8142331/SRX8142331.20_peaks.narrowPeak INFO @ Sat, 17 Apr 2021 08:13:55: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/SRX8142331/SRX8142331.20_summits.bed INFO @ Sat, 17 Apr 2021 08:13:55: Done! pass1 - making usageList (22 chroms): 1 millis pass2 - checking and writing primary data (104 records, 4 fields): 2 millis CompletedMACS2peakCalling BigWig に変換しました。