Job ID = 5790781 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 12,773,162 reads read : 25,546,324 reads written : 12,773,162 reads 0-length : 12,773,162 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: 00:00:00 Multiseed full-index search: 00:05:42 12773162 reads; of these: 12773162 (100.00%) were unpaired; of these: 8509753 (66.62%) aligned 0 times 3122379 (24.44%) aligned exactly 1 time 1141030 (8.93%) aligned >1 times 33.38% overall alignment rate Time searching: 00:05:43 Overall time: 00:05:43 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_rmdupse_core] 203391 / 4263409 = 0.0477 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 07:22:32: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/SRX7625154/SRX7625154.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/SRX7625154/SRX7625154.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/SRX7625154/SRX7625154.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/SRX7625154/SRX7625154.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 07:22:32: #1 read tag files... INFO @ Wed, 22 Apr 2020 07:22:32: #1 read treatment tags... INFO @ Wed, 22 Apr 2020 07:22:38: 1000000 INFO @ Wed, 22 Apr 2020 07:22:44: 2000000 INFO @ Wed, 22 Apr 2020 07:22:50: 3000000 INFO @ Wed, 22 Apr 2020 07:22:57: 4000000 INFO @ Wed, 22 Apr 2020 07:22:57: #1 tag size is determined as 74 bps INFO @ Wed, 22 Apr 2020 07:22:57: #1 tag size = 74 INFO @ Wed, 22 Apr 2020 07:22:57: #1 total tags in treatment: 4060018 INFO @ Wed, 22 Apr 2020 07:22:57: #1 user defined the maximum tags... INFO @ Wed, 22 Apr 2020 07:22:57: #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 07:22:57: #1 tags after filtering in treatment: 4059717 INFO @ Wed, 22 Apr 2020 07:22:57: #1 Redundant rate of treatment: 0.00 INFO @ Wed, 22 Apr 2020 07:22:57: #1 finished! INFO @ Wed, 22 Apr 2020 07:22:57: #2 Build Peak Model... INFO @ Wed, 22 Apr 2020 07:22:57: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 22 Apr 2020 07:22:59: #2 number of paired peaks: 10496 INFO @ Wed, 22 Apr 2020 07:22:59: start model_add_line... INFO @ Wed, 22 Apr 2020 07:22:59: start X-correlation... INFO @ Wed, 22 Apr 2020 07:22:59: end of X-cor INFO @ Wed, 22 Apr 2020 07:22:59: #2 finished! INFO @ Wed, 22 Apr 2020 07:22:59: #2 predicted fragment length is 79 bps INFO @ Wed, 22 Apr 2020 07:22:59: #2 alternative fragment length(s) may be 79,117,139,210,241 bps INFO @ Wed, 22 Apr 2020 07:22:59: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/SRX7625154/SRX7625154.05_model.r WARNING @ Wed, 22 Apr 2020 07:22:59: #2 Since the d (79) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Wed, 22 Apr 2020 07:22:59: #2 You may need to consider one of the other alternative d(s): 79,117,139,210,241 WARNING @ Wed, 22 Apr 2020 07:22:59: #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 07:22:59: #3 Call peaks... INFO @ Wed, 22 Apr 2020 07:22:59: #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 @ Wed, 22 Apr 2020 07:23:02: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/SRX7625154/SRX7625154.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/SRX7625154/SRX7625154.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/SRX7625154/SRX7625154.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/SRX7625154/SRX7625154.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 07:23:02: #1 read tag files... INFO @ Wed, 22 Apr 2020 07:23:02: #1 read treatment tags... INFO @ Wed, 22 Apr 2020 07:23:08: 1000000 INFO @ Wed, 22 Apr 2020 07:23:08: #3 Call peaks for each chromosome... INFO @ Wed, 22 Apr 2020 07:23:13: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/SRX7625154/SRX7625154.05_peaks.xls INFO @ Wed, 22 Apr 2020 07:23:13: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/SRX7625154/SRX7625154.05_peaks.narrowPeak INFO @ Wed, 22 Apr 2020 07:23:13: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/SRX7625154/SRX7625154.05_summits.bed INFO @ Wed, 22 Apr 2020 07:23:13: Done! pass1 - making usageList (50 chroms): 0 millis pass2 - checking and writing primary data (443 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Wed, 22 Apr 2020 07:23:14: 2000000 INFO @ Wed, 22 Apr 2020 07:23:20: 3000000 INFO @ Wed, 22 Apr 2020 07:23:26: 4000000 INFO @ Wed, 22 Apr 2020 07:23:27: #1 tag size is determined as 74 bps INFO @ Wed, 22 Apr 2020 07:23:27: #1 tag size = 74 INFO @ Wed, 22 Apr 2020 07:23:27: #1 total tags in treatment: 4060018 INFO @ Wed, 22 Apr 2020 07:23:27: #1 user defined the maximum tags... INFO @ Wed, 22 Apr 2020 07:23:27: #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 07:23:27: #1 tags after filtering in treatment: 4059717 INFO @ Wed, 22 Apr 2020 07:23:27: #1 Redundant rate of treatment: 0.00 INFO @ Wed, 22 Apr 2020 07:23:27: #1 finished! INFO @ Wed, 22 Apr 2020 07:23:27: #2 Build Peak Model... INFO @ Wed, 22 Apr 2020 07:23:27: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 22 Apr 2020 07:23:29: #2 number of paired peaks: 10496 INFO @ Wed, 22 Apr 2020 07:23:29: start model_add_line... INFO @ Wed, 22 Apr 2020 07:23:29: start X-correlation... INFO @ Wed, 22 Apr 2020 07:23:29: end of X-cor INFO @ Wed, 22 Apr 2020 07:23:29: #2 finished! INFO @ Wed, 22 Apr 2020 07:23:29: #2 predicted fragment length is 79 bps INFO @ Wed, 22 Apr 2020 07:23:29: #2 alternative fragment length(s) may be 79,117,139,210,241 bps INFO @ Wed, 22 Apr 2020 07:23:29: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/SRX7625154/SRX7625154.10_model.r WARNING @ Wed, 22 Apr 2020 07:23:29: #2 Since the d (79) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Wed, 22 Apr 2020 07:23:29: #2 You may need to consider one of the other alternative d(s): 79,117,139,210,241 WARNING @ Wed, 22 Apr 2020 07:23:29: #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 07:23:29: #3 Call peaks... INFO @ Wed, 22 Apr 2020 07:23:29: #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 07:23:32: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/SRX7625154/SRX7625154.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/SRX7625154/SRX7625154.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/SRX7625154/SRX7625154.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/SRX7625154/SRX7625154.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 07:23:32: #1 read tag files... INFO @ Wed, 22 Apr 2020 07:23:32: #1 read treatment tags... INFO @ Wed, 22 Apr 2020 07:23:38: #3 Call peaks for each chromosome... INFO @ Wed, 22 Apr 2020 07:23:38: 1000000 INFO @ Wed, 22 Apr 2020 07:23:42: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/SRX7625154/SRX7625154.10_peaks.xls INFO @ Wed, 22 Apr 2020 07:23:42: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/SRX7625154/SRX7625154.10_peaks.narrowPeak INFO @ Wed, 22 Apr 2020 07:23:42: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/SRX7625154/SRX7625154.10_summits.bed INFO @ Wed, 22 Apr 2020 07:23:42: Done! pass1 - making usageList (37 chroms): 1 millis pass2 - checking and writing primary data (264 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Wed, 22 Apr 2020 07:23:45: 2000000 INFO @ Wed, 22 Apr 2020 07:23:51: 3000000 INFO @ Wed, 22 Apr 2020 07:23:57: 4000000 INFO @ Wed, 22 Apr 2020 07:23:57: #1 tag size is determined as 74 bps INFO @ Wed, 22 Apr 2020 07:23:57: #1 tag size = 74 INFO @ Wed, 22 Apr 2020 07:23:57: #1 total tags in treatment: 4060018 INFO @ Wed, 22 Apr 2020 07:23:57: #1 user defined the maximum tags... INFO @ Wed, 22 Apr 2020 07:23:57: #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 07:23:57: #1 tags after filtering in treatment: 4059717 INFO @ Wed, 22 Apr 2020 07:23:57: #1 Redundant rate of treatment: 0.00 INFO @ Wed, 22 Apr 2020 07:23:57: #1 finished! INFO @ Wed, 22 Apr 2020 07:23:57: #2 Build Peak Model... INFO @ Wed, 22 Apr 2020 07:23:57: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 22 Apr 2020 07:23:59: #2 number of paired peaks: 10496 INFO @ Wed, 22 Apr 2020 07:23:59: start model_add_line... INFO @ Wed, 22 Apr 2020 07:23:59: start X-correlation... INFO @ Wed, 22 Apr 2020 07:23:59: end of X-cor INFO @ Wed, 22 Apr 2020 07:23:59: #2 finished! INFO @ Wed, 22 Apr 2020 07:23:59: #2 predicted fragment length is 79 bps INFO @ Wed, 22 Apr 2020 07:23:59: #2 alternative fragment length(s) may be 79,117,139,210,241 bps INFO @ Wed, 22 Apr 2020 07:23:59: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/SRX7625154/SRX7625154.20_model.r WARNING @ Wed, 22 Apr 2020 07:23:59: #2 Since the d (79) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Wed, 22 Apr 2020 07:23:59: #2 You may need to consider one of the other alternative d(s): 79,117,139,210,241 WARNING @ Wed, 22 Apr 2020 07:23:59: #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 07:23:59: #3 Call peaks... INFO @ Wed, 22 Apr 2020 07:23:59: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 22 Apr 2020 07:24:08: #3 Call peaks for each chromosome... INFO @ Wed, 22 Apr 2020 07:24:13: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/SRX7625154/SRX7625154.20_peaks.xls INFO @ Wed, 22 Apr 2020 07:24:13: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/SRX7625154/SRX7625154.20_peaks.narrowPeak INFO @ Wed, 22 Apr 2020 07:24:13: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/SRX7625154/SRX7625154.20_summits.bed INFO @ Wed, 22 Apr 2020 07:24:13: Done! pass1 - making usageList (24 chroms): 1 millis pass2 - checking and writing primary data (132 records, 4 fields): 1 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。