Job ID = 5790705 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 35,255,796 reads read : 35,255,796 reads written : 35,255,796 rm: cannot remove ‘[DSE]RR*’: No such file or directory rm: cannot remove ‘/home/okishinya/ncbi/public/sra/SRR8982438.sra.cache’: No such file or directory fastq に変換しました。 bowtie でマッピング中... Time loading reference: 00:00:00 Time loading forward index: 00:00:00 Time loading mirror index: 00:00:00 Multiseed full-index search: 00:07:46 35255796 reads; of these: 35255796 (100.00%) were unpaired; of these: 9722828 (27.58%) aligned 0 times 20108529 (57.04%) aligned exactly 1 time 5424439 (15.39%) aligned >1 times 72.42% overall alignment rate Time searching: 00:07:46 Overall time: 00:07:46 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] 12415197 / 25532968 = 0.4862 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 06:31:45: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/SRX5761736/SRX5761736.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/SRX5761736/SRX5761736.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/SRX5761736/SRX5761736.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/SRX5761736/SRX5761736.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 06:31:45: #1 read tag files... INFO @ Wed, 22 Apr 2020 06:31:45: #1 read treatment tags... INFO @ Wed, 22 Apr 2020 06:31:50: 1000000 INFO @ Wed, 22 Apr 2020 06:31:55: 2000000 INFO @ Wed, 22 Apr 2020 06:32:00: 3000000 INFO @ Wed, 22 Apr 2020 06:32:05: 4000000 INFO @ Wed, 22 Apr 2020 06:32:10: 5000000 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 06:32:15: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/SRX5761736/SRX5761736.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/SRX5761736/SRX5761736.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/SRX5761736/SRX5761736.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/SRX5761736/SRX5761736.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 06:32:15: #1 read tag files... INFO @ Wed, 22 Apr 2020 06:32:15: #1 read treatment tags... INFO @ Wed, 22 Apr 2020 06:32:16: 6000000 INFO @ Wed, 22 Apr 2020 06:32:19: 1000000 INFO @ Wed, 22 Apr 2020 06:32:21: 7000000 INFO @ Wed, 22 Apr 2020 06:32:24: 2000000 INFO @ Wed, 22 Apr 2020 06:32:26: 8000000 INFO @ Wed, 22 Apr 2020 06:32:29: 3000000 INFO @ Wed, 22 Apr 2020 06:32:31: 9000000 INFO @ Wed, 22 Apr 2020 06:32:33: 4000000 INFO @ Wed, 22 Apr 2020 06:32:36: 10000000 INFO @ Wed, 22 Apr 2020 06:32:38: 5000000 INFO @ Wed, 22 Apr 2020 06:32:41: 11000000 INFO @ Wed, 22 Apr 2020 06:32:42: 6000000 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 06:32:45: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/SRX5761736/SRX5761736.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/SRX5761736/SRX5761736.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/SRX5761736/SRX5761736.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/SRX5761736/SRX5761736.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 06:32:45: #1 read tag files... INFO @ Wed, 22 Apr 2020 06:32:45: #1 read treatment tags... INFO @ Wed, 22 Apr 2020 06:32:46: 12000000 INFO @ Wed, 22 Apr 2020 06:32:47: 7000000 INFO @ Wed, 22 Apr 2020 06:32:49: 1000000 INFO @ Wed, 22 Apr 2020 06:32:52: 13000000 INFO @ Wed, 22 Apr 2020 06:32:52: 8000000 INFO @ Wed, 22 Apr 2020 06:32:52: #1 tag size is determined as 37 bps INFO @ Wed, 22 Apr 2020 06:32:52: #1 tag size = 37 INFO @ Wed, 22 Apr 2020 06:32:52: #1 total tags in treatment: 13117771 INFO @ Wed, 22 Apr 2020 06:32:52: #1 user defined the maximum tags... INFO @ Wed, 22 Apr 2020 06:32:52: #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 06:32:53: #1 tags after filtering in treatment: 13117557 INFO @ Wed, 22 Apr 2020 06:32:53: #1 Redundant rate of treatment: 0.00 INFO @ Wed, 22 Apr 2020 06:32:53: #1 finished! INFO @ Wed, 22 Apr 2020 06:32:53: #2 Build Peak Model... INFO @ Wed, 22 Apr 2020 06:32:53: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 22 Apr 2020 06:32:54: 2000000 INFO @ Wed, 22 Apr 2020 06:32:54: #2 number of paired peaks: 21968 INFO @ Wed, 22 Apr 2020 06:32:54: start model_add_line... INFO @ Wed, 22 Apr 2020 06:32:54: start X-correlation... INFO @ Wed, 22 Apr 2020 06:32:54: end of X-cor INFO @ Wed, 22 Apr 2020 06:32:54: #2 finished! INFO @ Wed, 22 Apr 2020 06:32:54: #2 predicted fragment length is 187 bps INFO @ Wed, 22 Apr 2020 06:32:54: #2 alternative fragment length(s) may be 187 bps INFO @ Wed, 22 Apr 2020 06:32:54: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/SRX5761736/SRX5761736.05_model.r INFO @ Wed, 22 Apr 2020 06:32:54: #3 Call peaks... INFO @ Wed, 22 Apr 2020 06:32:54: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 22 Apr 2020 06:32:56: 9000000 INFO @ Wed, 22 Apr 2020 06:32:58: 3000000 INFO @ Wed, 22 Apr 2020 06:33:01: 10000000 INFO @ Wed, 22 Apr 2020 06:33:03: 4000000 INFO @ Wed, 22 Apr 2020 06:33:05: 11000000 INFO @ Wed, 22 Apr 2020 06:33:08: 5000000 INFO @ Wed, 22 Apr 2020 06:33:10: 12000000 INFO @ Wed, 22 Apr 2020 06:33:12: 6000000 INFO @ Wed, 22 Apr 2020 06:33:15: 13000000 INFO @ Wed, 22 Apr 2020 06:33:15: #1 tag size is determined as 37 bps INFO @ Wed, 22 Apr 2020 06:33:15: #1 tag size = 37 INFO @ Wed, 22 Apr 2020 06:33:15: #1 total tags in treatment: 13117771 INFO @ Wed, 22 Apr 2020 06:33:15: #1 user defined the maximum tags... INFO @ Wed, 22 Apr 2020 06:33:15: #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 06:33:16: #1 tags after filtering in treatment: 13117557 INFO @ Wed, 22 Apr 2020 06:33:16: #1 Redundant rate of treatment: 0.00 INFO @ Wed, 22 Apr 2020 06:33:16: #1 finished! INFO @ Wed, 22 Apr 2020 06:33:16: #2 Build Peak Model... INFO @ Wed, 22 Apr 2020 06:33:16: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 22 Apr 2020 06:33:17: 7000000 INFO @ Wed, 22 Apr 2020 06:33:17: #2 number of paired peaks: 21968 INFO @ Wed, 22 Apr 2020 06:33:17: start model_add_line... INFO @ Wed, 22 Apr 2020 06:33:17: start X-correlation... INFO @ Wed, 22 Apr 2020 06:33:17: end of X-cor INFO @ Wed, 22 Apr 2020 06:33:17: #2 finished! INFO @ Wed, 22 Apr 2020 06:33:17: #2 predicted fragment length is 187 bps INFO @ Wed, 22 Apr 2020 06:33:17: #2 alternative fragment length(s) may be 187 bps INFO @ Wed, 22 Apr 2020 06:33:17: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/SRX5761736/SRX5761736.10_model.r INFO @ Wed, 22 Apr 2020 06:33:17: #3 Call peaks... INFO @ Wed, 22 Apr 2020 06:33:17: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 22 Apr 2020 06:33:21: 8000000 INFO @ Wed, 22 Apr 2020 06:33:25: #3 Call peaks for each chromosome... INFO @ Wed, 22 Apr 2020 06:33:26: 9000000 INFO @ Wed, 22 Apr 2020 06:33:30: 10000000 INFO @ Wed, 22 Apr 2020 06:33:35: 11000000 INFO @ Wed, 22 Apr 2020 06:33:39: 12000000 INFO @ Wed, 22 Apr 2020 06:33:40: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/SRX5761736/SRX5761736.05_peaks.xls INFO @ Wed, 22 Apr 2020 06:33:40: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/SRX5761736/SRX5761736.05_peaks.narrowPeak INFO @ Wed, 22 Apr 2020 06:33:40: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/SRX5761736/SRX5761736.05_summits.bed INFO @ Wed, 22 Apr 2020 06:33:40: Done! pass1 - making usageList (140 chroms): 3 millis pass2 - checking and writing primary data (17177 records, 4 fields): 19 millis CompletedMACS2peakCalling INFO @ Wed, 22 Apr 2020 06:33:44: 13000000 INFO @ Wed, 22 Apr 2020 06:33:44: #1 tag size is determined as 37 bps INFO @ Wed, 22 Apr 2020 06:33:44: #1 tag size = 37 INFO @ Wed, 22 Apr 2020 06:33:44: #1 total tags in treatment: 13117771 INFO @ Wed, 22 Apr 2020 06:33:44: #1 user defined the maximum tags... INFO @ Wed, 22 Apr 2020 06:33:44: #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 06:33:45: #1 tags after filtering in treatment: 13117557 INFO @ Wed, 22 Apr 2020 06:33:45: #1 Redundant rate of treatment: 0.00 INFO @ Wed, 22 Apr 2020 06:33:45: #1 finished! INFO @ Wed, 22 Apr 2020 06:33:45: #2 Build Peak Model... INFO @ Wed, 22 Apr 2020 06:33:45: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 22 Apr 2020 06:33:46: #2 number of paired peaks: 21968 INFO @ Wed, 22 Apr 2020 06:33:46: start model_add_line... INFO @ Wed, 22 Apr 2020 06:33:46: start X-correlation... INFO @ Wed, 22 Apr 2020 06:33:46: end of X-cor INFO @ Wed, 22 Apr 2020 06:33:46: #2 finished! INFO @ Wed, 22 Apr 2020 06:33:46: #2 predicted fragment length is 187 bps INFO @ Wed, 22 Apr 2020 06:33:46: #2 alternative fragment length(s) may be 187 bps INFO @ Wed, 22 Apr 2020 06:33:46: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/SRX5761736/SRX5761736.20_model.r INFO @ Wed, 22 Apr 2020 06:33:46: #3 Call peaks... INFO @ Wed, 22 Apr 2020 06:33:46: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 22 Apr 2020 06:33:48: #3 Call peaks for each chromosome... INFO @ Wed, 22 Apr 2020 06:34:02: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/SRX5761736/SRX5761736.10_peaks.xls INFO @ Wed, 22 Apr 2020 06:34:02: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/SRX5761736/SRX5761736.10_peaks.narrowPeak INFO @ Wed, 22 Apr 2020 06:34:03: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/SRX5761736/SRX5761736.10_summits.bed INFO @ Wed, 22 Apr 2020 06:34:03: Done! pass1 - making usageList (122 chroms): 2 millis pass2 - checking and writing primary data (14592 records, 4 fields): 17 millis CompletedMACS2peakCalling INFO @ Wed, 22 Apr 2020 06:34:17: #3 Call peaks for each chromosome... INFO @ Wed, 22 Apr 2020 06:34:31: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/SRX5761736/SRX5761736.20_peaks.xls INFO @ Wed, 22 Apr 2020 06:34:31: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/SRX5761736/SRX5761736.20_peaks.narrowPeak INFO @ Wed, 22 Apr 2020 06:34:31: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/SRX5761736/SRX5761736.20_summits.bed INFO @ Wed, 22 Apr 2020 06:34:31: Done! pass1 - making usageList (100 chroms): 2 millis pass2 - checking and writing primary data (11893 records, 4 fields): 14 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。