Job ID = 5720242 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 22,682,876 reads read : 22,682,876 reads written : 22,682,876 rm: cannot remove ‘[DSE]RR*’: No such file or directory rm: cannot remove ‘/home/okishinya/ncbi/public/sra/SRR9972853.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: 00:05:00 22682876 reads; of these: 22682876 (100.00%) were unpaired; of these: 1053560 (4.64%) aligned 0 times 18405056 (81.14%) aligned exactly 1 time 3224260 (14.21%) aligned >1 times 95.36% overall alignment rate Time searching: 00:05:00 Overall time: 00:05:00 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 12 files... [bam_rmdupse_core] 10156298 / 21629316 = 0.4696 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, 15 Apr 2020 22:45:45: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX6720177/SRX6720177.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX6720177/SRX6720177.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX6720177/SRX6720177.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX6720177/SRX6720177.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 @ Wed, 15 Apr 2020 22:45:45: #1 read tag files... INFO @ Wed, 15 Apr 2020 22:45:45: #1 read treatment tags... INFO @ Wed, 15 Apr 2020 22:45:50: 1000000 INFO @ Wed, 15 Apr 2020 22:45:54: 2000000 INFO @ Wed, 15 Apr 2020 22:45:59: 3000000 INFO @ Wed, 15 Apr 2020 22:46:03: 4000000 INFO @ Wed, 15 Apr 2020 22:46:08: 5000000 INFO @ Wed, 15 Apr 2020 22:46:12: 6000000 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, 15 Apr 2020 22:46:15: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX6720177/SRX6720177.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX6720177/SRX6720177.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX6720177/SRX6720177.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX6720177/SRX6720177.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 @ Wed, 15 Apr 2020 22:46:15: #1 read tag files... INFO @ Wed, 15 Apr 2020 22:46:15: #1 read treatment tags... INFO @ Wed, 15 Apr 2020 22:46:16: 7000000 INFO @ Wed, 15 Apr 2020 22:46:20: 1000000 INFO @ Wed, 15 Apr 2020 22:46:21: 8000000 INFO @ Wed, 15 Apr 2020 22:46:24: 2000000 INFO @ Wed, 15 Apr 2020 22:46:26: 9000000 INFO @ Wed, 15 Apr 2020 22:46:29: 3000000 INFO @ Wed, 15 Apr 2020 22:46:30: 10000000 INFO @ Wed, 15 Apr 2020 22:46:33: 4000000 INFO @ Wed, 15 Apr 2020 22:46:35: 11000000 INFO @ Wed, 15 Apr 2020 22:46:37: #1 tag size is determined as 50 bps INFO @ Wed, 15 Apr 2020 22:46:37: #1 tag size = 50 INFO @ Wed, 15 Apr 2020 22:46:37: #1 total tags in treatment: 11473018 INFO @ Wed, 15 Apr 2020 22:46:37: #1 user defined the maximum tags... INFO @ Wed, 15 Apr 2020 22:46:37: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Wed, 15 Apr 2020 22:46:37: #1 tags after filtering in treatment: 11473018 INFO @ Wed, 15 Apr 2020 22:46:37: #1 Redundant rate of treatment: 0.00 INFO @ Wed, 15 Apr 2020 22:46:37: #1 finished! INFO @ Wed, 15 Apr 2020 22:46:37: #2 Build Peak Model... INFO @ Wed, 15 Apr 2020 22:46:37: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 15 Apr 2020 22:46:38: 5000000 INFO @ Wed, 15 Apr 2020 22:46:38: #2 number of paired peaks: 1700 INFO @ Wed, 15 Apr 2020 22:46:38: start model_add_line... INFO @ Wed, 15 Apr 2020 22:46:38: start X-correlation... INFO @ Wed, 15 Apr 2020 22:46:38: end of X-cor INFO @ Wed, 15 Apr 2020 22:46:38: #2 finished! INFO @ Wed, 15 Apr 2020 22:46:38: #2 predicted fragment length is 166 bps INFO @ Wed, 15 Apr 2020 22:46:38: #2 alternative fragment length(s) may be 166 bps INFO @ Wed, 15 Apr 2020 22:46:38: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX6720177/SRX6720177.05_model.r INFO @ Wed, 15 Apr 2020 22:46:38: #3 Call peaks... INFO @ Wed, 15 Apr 2020 22:46:38: #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, 15 Apr 2020 22:46:43: 6000000 INFO @ Wed, 15 Apr 2020 22:46:46: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX6720177/SRX6720177.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX6720177/SRX6720177.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX6720177/SRX6720177.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX6720177/SRX6720177.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 @ Wed, 15 Apr 2020 22:46:46: #1 read tag files... INFO @ Wed, 15 Apr 2020 22:46:46: #1 read treatment tags... INFO @ Wed, 15 Apr 2020 22:46:47: 7000000 INFO @ Wed, 15 Apr 2020 22:46:50: 1000000 INFO @ Wed, 15 Apr 2020 22:46:52: 8000000 INFO @ Wed, 15 Apr 2020 22:46:55: 2000000 INFO @ Wed, 15 Apr 2020 22:46:56: 9000000 INFO @ Wed, 15 Apr 2020 22:46:59: 3000000 INFO @ Wed, 15 Apr 2020 22:47:01: 10000000 INFO @ Wed, 15 Apr 2020 22:47:04: 4000000 INFO @ Wed, 15 Apr 2020 22:47:04: #3 Call peaks for each chromosome... INFO @ Wed, 15 Apr 2020 22:47:06: 11000000 INFO @ Wed, 15 Apr 2020 22:47:08: #1 tag size is determined as 50 bps INFO @ Wed, 15 Apr 2020 22:47:08: #1 tag size = 50 INFO @ Wed, 15 Apr 2020 22:47:08: #1 total tags in treatment: 11473018 INFO @ Wed, 15 Apr 2020 22:47:08: #1 user defined the maximum tags... INFO @ Wed, 15 Apr 2020 22:47:08: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Wed, 15 Apr 2020 22:47:08: #1 tags after filtering in treatment: 11473018 INFO @ Wed, 15 Apr 2020 22:47:08: #1 Redundant rate of treatment: 0.00 INFO @ Wed, 15 Apr 2020 22:47:08: #1 finished! INFO @ Wed, 15 Apr 2020 22:47:08: #2 Build Peak Model... INFO @ Wed, 15 Apr 2020 22:47:08: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 15 Apr 2020 22:47:09: 5000000 INFO @ Wed, 15 Apr 2020 22:47:09: #2 number of paired peaks: 1700 INFO @ Wed, 15 Apr 2020 22:47:09: start model_add_line... INFO @ Wed, 15 Apr 2020 22:47:09: start X-correlation... INFO @ Wed, 15 Apr 2020 22:47:09: end of X-cor INFO @ Wed, 15 Apr 2020 22:47:09: #2 finished! INFO @ Wed, 15 Apr 2020 22:47:09: #2 predicted fragment length is 166 bps INFO @ Wed, 15 Apr 2020 22:47:09: #2 alternative fragment length(s) may be 166 bps INFO @ Wed, 15 Apr 2020 22:47:09: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX6720177/SRX6720177.10_model.r INFO @ Wed, 15 Apr 2020 22:47:09: #3 Call peaks... INFO @ Wed, 15 Apr 2020 22:47:09: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 15 Apr 2020 22:47:13: 6000000 INFO @ Wed, 15 Apr 2020 22:47:18: 7000000 INFO @ Wed, 15 Apr 2020 22:47:18: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX6720177/SRX6720177.05_peaks.xls INFO @ Wed, 15 Apr 2020 22:47:18: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX6720177/SRX6720177.05_peaks.narrowPeak INFO @ Wed, 15 Apr 2020 22:47:18: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX6720177/SRX6720177.05_summits.bed INFO @ Wed, 15 Apr 2020 22:47:18: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (5420 records, 4 fields): 6 millis CompletedMACS2peakCalling INFO @ Wed, 15 Apr 2020 22:47:22: 8000000 INFO @ Wed, 15 Apr 2020 22:47:27: 9000000 INFO @ Wed, 15 Apr 2020 22:47:31: 10000000 INFO @ Wed, 15 Apr 2020 22:47:36: #3 Call peaks for each chromosome... INFO @ Wed, 15 Apr 2020 22:47:36: 11000000 INFO @ Wed, 15 Apr 2020 22:47:38: #1 tag size is determined as 50 bps INFO @ Wed, 15 Apr 2020 22:47:38: #1 tag size = 50 INFO @ Wed, 15 Apr 2020 22:47:38: #1 total tags in treatment: 11473018 INFO @ Wed, 15 Apr 2020 22:47:38: #1 user defined the maximum tags... INFO @ Wed, 15 Apr 2020 22:47:38: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Wed, 15 Apr 2020 22:47:38: #1 tags after filtering in treatment: 11473018 INFO @ Wed, 15 Apr 2020 22:47:38: #1 Redundant rate of treatment: 0.00 INFO @ Wed, 15 Apr 2020 22:47:38: #1 finished! INFO @ Wed, 15 Apr 2020 22:47:38: #2 Build Peak Model... INFO @ Wed, 15 Apr 2020 22:47:38: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 15 Apr 2020 22:47:39: #2 number of paired peaks: 1700 INFO @ Wed, 15 Apr 2020 22:47:39: start model_add_line... INFO @ Wed, 15 Apr 2020 22:47:39: start X-correlation... INFO @ Wed, 15 Apr 2020 22:47:39: end of X-cor INFO @ Wed, 15 Apr 2020 22:47:39: #2 finished! INFO @ Wed, 15 Apr 2020 22:47:39: #2 predicted fragment length is 166 bps INFO @ Wed, 15 Apr 2020 22:47:39: #2 alternative fragment length(s) may be 166 bps INFO @ Wed, 15 Apr 2020 22:47:39: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX6720177/SRX6720177.20_model.r INFO @ Wed, 15 Apr 2020 22:47:39: #3 Call peaks... INFO @ Wed, 15 Apr 2020 22:47:39: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 15 Apr 2020 22:47:49: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX6720177/SRX6720177.10_peaks.xls INFO @ Wed, 15 Apr 2020 22:47:49: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX6720177/SRX6720177.10_peaks.narrowPeak INFO @ Wed, 15 Apr 2020 22:47:49: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX6720177/SRX6720177.10_summits.bed INFO @ Wed, 15 Apr 2020 22:47:49: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (3461 records, 4 fields): 4 millis CompletedMACS2peakCalling INFO @ Wed, 15 Apr 2020 22:48:06: #3 Call peaks for each chromosome... INFO @ Wed, 15 Apr 2020 22:48:18: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX6720177/SRX6720177.20_peaks.xls INFO @ Wed, 15 Apr 2020 22:48:18: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX6720177/SRX6720177.20_peaks.narrowPeak INFO @ Wed, 15 Apr 2020 22:48:18: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX6720177/SRX6720177.20_summits.bed INFO @ Wed, 15 Apr 2020 22:48:18: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (1804 records, 4 fields): 3 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。