Job ID = 5790787 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 11,585,346 reads read : 23,170,692 reads written : 11,585,346 reads 0-length : 11,585,346 rm: cannot remove ‘[DSE]RR*’: No such file or directory 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: 00:00:00 Time loading mirror index: 00:00:01 Multiseed full-index search: 00:07:22 11585346 reads; of these: 11585346 (100.00%) were unpaired; of these: 880913 (7.60%) aligned 0 times 7503670 (64.77%) aligned exactly 1 time 3200763 (27.63%) aligned >1 times 92.40% overall alignment rate Time searching: 00:07:24 Overall time: 00:07:24 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] 2998785 / 10704433 = 0.2801 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 @ Wed, 22 Apr 2020 07:29:25: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/SRX7625157/SRX7625157.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/SRX7625157/SRX7625157.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/SRX7625157/SRX7625157.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/SRX7625157/SRX7625157.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 @ Wed, 22 Apr 2020 07:29:25: #1 read tag files... INFO @ Wed, 22 Apr 2020 07:29:25: #1 read treatment tags... INFO @ Wed, 22 Apr 2020 07:29:31: 1000000 INFO @ Wed, 22 Apr 2020 07:29:38: 2000000 INFO @ Wed, 22 Apr 2020 07:29:44: 3000000 INFO @ Wed, 22 Apr 2020 07:29:50: 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 @ Wed, 22 Apr 2020 07:29:55: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/SRX7625157/SRX7625157.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/SRX7625157/SRX7625157.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/SRX7625157/SRX7625157.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/SRX7625157/SRX7625157.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 @ Wed, 22 Apr 2020 07:29:55: #1 read tag files... INFO @ Wed, 22 Apr 2020 07:29:55: #1 read treatment tags... INFO @ Wed, 22 Apr 2020 07:29:57: 5000000 INFO @ Wed, 22 Apr 2020 07:30:02: 1000000 INFO @ Wed, 22 Apr 2020 07:30:04: 6000000 INFO @ Wed, 22 Apr 2020 07:30:09: 2000000 INFO @ Wed, 22 Apr 2020 07:30:12: 7000000 INFO @ Wed, 22 Apr 2020 07:30:17: 3000000 INFO @ Wed, 22 Apr 2020 07:30:17: #1 tag size is determined as 74 bps INFO @ Wed, 22 Apr 2020 07:30:17: #1 tag size = 74 INFO @ Wed, 22 Apr 2020 07:30:17: #1 total tags in treatment: 7705648 INFO @ Wed, 22 Apr 2020 07:30:17: #1 user defined the maximum tags... INFO @ Wed, 22 Apr 2020 07:30:17: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Wed, 22 Apr 2020 07:30:17: #1 tags after filtering in treatment: 7705395 INFO @ Wed, 22 Apr 2020 07:30:17: #1 Redundant rate of treatment: 0.00 INFO @ Wed, 22 Apr 2020 07:30:17: #1 finished! INFO @ Wed, 22 Apr 2020 07:30:17: #2 Build Peak Model... INFO @ Wed, 22 Apr 2020 07:30:17: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 22 Apr 2020 07:30:18: #2 number of paired peaks: 6418 INFO @ Wed, 22 Apr 2020 07:30:18: start model_add_line... INFO @ Wed, 22 Apr 2020 07:30:19: start X-correlation... INFO @ Wed, 22 Apr 2020 07:30:19: end of X-cor INFO @ Wed, 22 Apr 2020 07:30:19: #2 finished! INFO @ Wed, 22 Apr 2020 07:30:19: #2 predicted fragment length is 74 bps INFO @ Wed, 22 Apr 2020 07:30:19: #2 alternative fragment length(s) may be 74 bps INFO @ Wed, 22 Apr 2020 07:30:19: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/SRX7625157/SRX7625157.05_model.r WARNING @ Wed, 22 Apr 2020 07:30:19: #2 Since the d (74) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Wed, 22 Apr 2020 07:30:19: #2 You may need to consider one of the other alternative d(s): 74 WARNING @ Wed, 22 Apr 2020 07:30:19: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Wed, 22 Apr 2020 07:30:19: #3 Call peaks... INFO @ Wed, 22 Apr 2020 07:30:19: #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 @ Wed, 22 Apr 2020 07:30:23: 4000000 INFO @ Wed, 22 Apr 2020 07:30:25: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/SRX7625157/SRX7625157.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/SRX7625157/SRX7625157.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/SRX7625157/SRX7625157.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/SRX7625157/SRX7625157.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 @ Wed, 22 Apr 2020 07:30:25: #1 read tag files... INFO @ Wed, 22 Apr 2020 07:30:25: #1 read treatment tags... INFO @ Wed, 22 Apr 2020 07:30:31: 5000000 INFO @ Wed, 22 Apr 2020 07:30:32: 1000000 INFO @ Wed, 22 Apr 2020 07:30:36: #3 Call peaks for each chromosome... INFO @ Wed, 22 Apr 2020 07:30:38: 6000000 INFO @ Wed, 22 Apr 2020 07:30:40: 2000000 INFO @ Wed, 22 Apr 2020 07:30:45: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/SRX7625157/SRX7625157.05_peaks.xls INFO @ Wed, 22 Apr 2020 07:30:45: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/SRX7625157/SRX7625157.05_peaks.narrowPeak INFO @ Wed, 22 Apr 2020 07:30:45: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/SRX7625157/SRX7625157.05_summits.bed INFO @ Wed, 22 Apr 2020 07:30:45: Done! pass1 - making usageList (36 chroms): 0 millis pass2 - checking and writing primary data (608 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Wed, 22 Apr 2020 07:30:46: 7000000 INFO @ Wed, 22 Apr 2020 07:30:47: 3000000 INFO @ Wed, 22 Apr 2020 07:30:51: #1 tag size is determined as 74 bps INFO @ Wed, 22 Apr 2020 07:30:51: #1 tag size = 74 INFO @ Wed, 22 Apr 2020 07:30:51: #1 total tags in treatment: 7705648 INFO @ Wed, 22 Apr 2020 07:30:51: #1 user defined the maximum tags... INFO @ Wed, 22 Apr 2020 07:30:51: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Wed, 22 Apr 2020 07:30:51: #1 tags after filtering in treatment: 7705395 INFO @ Wed, 22 Apr 2020 07:30:51: #1 Redundant rate of treatment: 0.00 INFO @ Wed, 22 Apr 2020 07:30:51: #1 finished! INFO @ Wed, 22 Apr 2020 07:30:51: #2 Build Peak Model... INFO @ Wed, 22 Apr 2020 07:30:51: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 22 Apr 2020 07:30:53: #2 number of paired peaks: 6418 INFO @ Wed, 22 Apr 2020 07:30:53: start model_add_line... INFO @ Wed, 22 Apr 2020 07:30:53: start X-correlation... INFO @ Wed, 22 Apr 2020 07:30:53: end of X-cor INFO @ Wed, 22 Apr 2020 07:30:53: #2 finished! INFO @ Wed, 22 Apr 2020 07:30:53: #2 predicted fragment length is 74 bps INFO @ Wed, 22 Apr 2020 07:30:53: #2 alternative fragment length(s) may be 74 bps INFO @ Wed, 22 Apr 2020 07:30:53: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/SRX7625157/SRX7625157.10_model.r WARNING @ Wed, 22 Apr 2020 07:30:53: #2 Since the d (74) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Wed, 22 Apr 2020 07:30:53: #2 You may need to consider one of the other alternative d(s): 74 WARNING @ Wed, 22 Apr 2020 07:30:53: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Wed, 22 Apr 2020 07:30:53: #3 Call peaks... INFO @ Wed, 22 Apr 2020 07:30:53: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 22 Apr 2020 07:30:55: 4000000 INFO @ Wed, 22 Apr 2020 07:31:01: 5000000 INFO @ Wed, 22 Apr 2020 07:31:08: 6000000 INFO @ Wed, 22 Apr 2020 07:31:10: #3 Call peaks for each chromosome... INFO @ Wed, 22 Apr 2020 07:31:14: 7000000 INFO @ Wed, 22 Apr 2020 07:31:19: #1 tag size is determined as 74 bps INFO @ Wed, 22 Apr 2020 07:31:19: #1 tag size = 74 INFO @ Wed, 22 Apr 2020 07:31:19: #1 total tags in treatment: 7705648 INFO @ Wed, 22 Apr 2020 07:31:19: #1 user defined the maximum tags... INFO @ Wed, 22 Apr 2020 07:31:19: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Wed, 22 Apr 2020 07:31:19: #1 tags after filtering in treatment: 7705395 INFO @ Wed, 22 Apr 2020 07:31:19: #1 Redundant rate of treatment: 0.00 INFO @ Wed, 22 Apr 2020 07:31:19: #1 finished! INFO @ Wed, 22 Apr 2020 07:31:19: #2 Build Peak Model... INFO @ Wed, 22 Apr 2020 07:31:19: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 22 Apr 2020 07:31:19: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/SRX7625157/SRX7625157.10_peaks.xls INFO @ Wed, 22 Apr 2020 07:31:19: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/SRX7625157/SRX7625157.10_peaks.narrowPeak INFO @ Wed, 22 Apr 2020 07:31:19: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/SRX7625157/SRX7625157.10_summits.bed INFO @ Wed, 22 Apr 2020 07:31:19: Done! pass1 - making usageList (29 chroms): 0 millis pass2 - checking and writing primary data (380 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Wed, 22 Apr 2020 07:31:20: #2 number of paired peaks: 6418 INFO @ Wed, 22 Apr 2020 07:31:20: start model_add_line... INFO @ Wed, 22 Apr 2020 07:31:20: start X-correlation... INFO @ Wed, 22 Apr 2020 07:31:20: end of X-cor INFO @ Wed, 22 Apr 2020 07:31:20: #2 finished! INFO @ Wed, 22 Apr 2020 07:31:20: #2 predicted fragment length is 74 bps INFO @ Wed, 22 Apr 2020 07:31:20: #2 alternative fragment length(s) may be 74 bps INFO @ Wed, 22 Apr 2020 07:31:20: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/SRX7625157/SRX7625157.20_model.r WARNING @ Wed, 22 Apr 2020 07:31:20: #2 Since the d (74) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Wed, 22 Apr 2020 07:31:20: #2 You may need to consider one of the other alternative d(s): 74 WARNING @ Wed, 22 Apr 2020 07:31:20: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Wed, 22 Apr 2020 07:31:20: #3 Call peaks... INFO @ Wed, 22 Apr 2020 07:31:20: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 22 Apr 2020 07:31:38: #3 Call peaks for each chromosome... INFO @ Wed, 22 Apr 2020 07:31:46: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/SRX7625157/SRX7625157.20_peaks.xls INFO @ Wed, 22 Apr 2020 07:31:46: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/SRX7625157/SRX7625157.20_peaks.narrowPeak INFO @ Wed, 22 Apr 2020 07:31:46: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/SRX7625157/SRX7625157.20_summits.bed INFO @ Wed, 22 Apr 2020 07:31:46: Done! pass1 - making usageList (25 chroms): 0 millis pass2 - checking and writing primary data (201 records, 4 fields): 5 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。