Job ID = 5790701 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 34,533,654 reads read : 34,533,654 reads written : 34,533,654 rm: cannot remove ‘[DSE]RR*’: No such file or directory rm: cannot remove ‘/home/okishinya/ncbi/public/sra/SRR8982434.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: 00:06:57 34533654 reads; of these: 34533654 (100.00%) were unpaired; of these: 7741002 (22.42%) aligned 0 times 22356571 (64.74%) aligned exactly 1 time 4436081 (12.85%) aligned >1 times 77.58% overall alignment rate Time searching: 00:06:57 Overall time: 00:06:57 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] 13736421 / 26792652 = 0.5127 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 06:28:16: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/SRX5761732/SRX5761732.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/SRX5761732/SRX5761732.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/SRX5761732/SRX5761732.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/SRX5761732/SRX5761732.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 06:28:16: #1 read tag files... INFO @ Wed, 22 Apr 2020 06:28:16: #1 read treatment tags... INFO @ Wed, 22 Apr 2020 06:28:21: 1000000 INFO @ Wed, 22 Apr 2020 06:28:25: 2000000 INFO @ Wed, 22 Apr 2020 06:28:30: 3000000 INFO @ Wed, 22 Apr 2020 06:28:35: 4000000 INFO @ Wed, 22 Apr 2020 06:28:40: 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 06:28:44: 6000000 INFO @ Wed, 22 Apr 2020 06:28:46: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/SRX5761732/SRX5761732.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/SRX5761732/SRX5761732.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/SRX5761732/SRX5761732.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/SRX5761732/SRX5761732.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 06:28:46: #1 read tag files... INFO @ Wed, 22 Apr 2020 06:28:46: #1 read treatment tags... INFO @ Wed, 22 Apr 2020 06:28:49: 7000000 INFO @ Wed, 22 Apr 2020 06:28:51: 1000000 INFO @ Wed, 22 Apr 2020 06:28:55: 8000000 INFO @ Wed, 22 Apr 2020 06:28:56: 2000000 INFO @ Wed, 22 Apr 2020 06:29:00: 9000000 INFO @ Wed, 22 Apr 2020 06:29:02: 3000000 INFO @ Wed, 22 Apr 2020 06:29:05: 10000000 INFO @ Wed, 22 Apr 2020 06:29:07: 4000000 INFO @ Wed, 22 Apr 2020 06:29:10: 11000000 INFO @ Wed, 22 Apr 2020 06:29:12: 5000000 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 06:29:15: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/SRX5761732/SRX5761732.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/SRX5761732/SRX5761732.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/SRX5761732/SRX5761732.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/SRX5761732/SRX5761732.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 06:29:15: #1 read tag files... INFO @ Wed, 22 Apr 2020 06:29:15: #1 read treatment tags... INFO @ Wed, 22 Apr 2020 06:29:15: 12000000 INFO @ Wed, 22 Apr 2020 06:29:17: 6000000 INFO @ Wed, 22 Apr 2020 06:29:20: 1000000 INFO @ Wed, 22 Apr 2020 06:29:21: 13000000 INFO @ Wed, 22 Apr 2020 06:29:21: #1 tag size is determined as 37 bps INFO @ Wed, 22 Apr 2020 06:29:21: #1 tag size = 37 INFO @ Wed, 22 Apr 2020 06:29:21: #1 total tags in treatment: 13056231 INFO @ Wed, 22 Apr 2020 06:29:21: #1 user defined the maximum tags... INFO @ Wed, 22 Apr 2020 06:29:21: #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 06:29:21: #1 tags after filtering in treatment: 13056030 INFO @ Wed, 22 Apr 2020 06:29:21: #1 Redundant rate of treatment: 0.00 INFO @ Wed, 22 Apr 2020 06:29:21: #1 finished! INFO @ Wed, 22 Apr 2020 06:29:21: #2 Build Peak Model... INFO @ Wed, 22 Apr 2020 06:29:21: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 22 Apr 2020 06:29:22: 7000000 INFO @ Wed, 22 Apr 2020 06:29:23: #2 number of paired peaks: 22212 INFO @ Wed, 22 Apr 2020 06:29:23: start model_add_line... INFO @ Wed, 22 Apr 2020 06:29:23: start X-correlation... INFO @ Wed, 22 Apr 2020 06:29:23: end of X-cor INFO @ Wed, 22 Apr 2020 06:29:23: #2 finished! INFO @ Wed, 22 Apr 2020 06:29:23: #2 predicted fragment length is 231 bps INFO @ Wed, 22 Apr 2020 06:29:23: #2 alternative fragment length(s) may be 231 bps INFO @ Wed, 22 Apr 2020 06:29:23: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/SRX5761732/SRX5761732.05_model.r INFO @ Wed, 22 Apr 2020 06:29:23: #3 Call peaks... INFO @ Wed, 22 Apr 2020 06:29:23: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 22 Apr 2020 06:29:25: 2000000 INFO @ Wed, 22 Apr 2020 06:29:27: 8000000 INFO @ Wed, 22 Apr 2020 06:29:31: 3000000 INFO @ Wed, 22 Apr 2020 06:29:32: 9000000 INFO @ Wed, 22 Apr 2020 06:29:36: 4000000 INFO @ Wed, 22 Apr 2020 06:29:38: 10000000 INFO @ Wed, 22 Apr 2020 06:29:41: 5000000 INFO @ Wed, 22 Apr 2020 06:29:43: 11000000 INFO @ Wed, 22 Apr 2020 06:29:46: 6000000 INFO @ Wed, 22 Apr 2020 06:29:48: 12000000 INFO @ Wed, 22 Apr 2020 06:29:51: 7000000 INFO @ Wed, 22 Apr 2020 06:29:53: 13000000 INFO @ Wed, 22 Apr 2020 06:29:54: #1 tag size is determined as 37 bps INFO @ Wed, 22 Apr 2020 06:29:54: #1 tag size = 37 INFO @ Wed, 22 Apr 2020 06:29:54: #1 total tags in treatment: 13056231 INFO @ Wed, 22 Apr 2020 06:29:54: #1 user defined the maximum tags... INFO @ Wed, 22 Apr 2020 06:29:54: #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 06:29:54: #1 tags after filtering in treatment: 13056030 INFO @ Wed, 22 Apr 2020 06:29:54: #1 Redundant rate of treatment: 0.00 INFO @ Wed, 22 Apr 2020 06:29:54: #1 finished! INFO @ Wed, 22 Apr 2020 06:29:54: #2 Build Peak Model... INFO @ Wed, 22 Apr 2020 06:29:54: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 22 Apr 2020 06:29:54: #3 Call peaks for each chromosome... INFO @ Wed, 22 Apr 2020 06:29:56: #2 number of paired peaks: 22212 INFO @ Wed, 22 Apr 2020 06:29:56: start model_add_line... INFO @ Wed, 22 Apr 2020 06:29:56: start X-correlation... INFO @ Wed, 22 Apr 2020 06:29:56: end of X-cor INFO @ Wed, 22 Apr 2020 06:29:56: #2 finished! INFO @ Wed, 22 Apr 2020 06:29:56: #2 predicted fragment length is 231 bps INFO @ Wed, 22 Apr 2020 06:29:56: #2 alternative fragment length(s) may be 231 bps INFO @ Wed, 22 Apr 2020 06:29:56: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/SRX5761732/SRX5761732.10_model.r INFO @ Wed, 22 Apr 2020 06:29:56: #3 Call peaks... INFO @ Wed, 22 Apr 2020 06:29:56: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 22 Apr 2020 06:29:56: 8000000 INFO @ Wed, 22 Apr 2020 06:30:01: 9000000 INFO @ Wed, 22 Apr 2020 06:30:06: 10000000 INFO @ Wed, 22 Apr 2020 06:30:09: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/SRX5761732/SRX5761732.05_peaks.xls INFO @ Wed, 22 Apr 2020 06:30:09: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/SRX5761732/SRX5761732.05_peaks.narrowPeak INFO @ Wed, 22 Apr 2020 06:30:09: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/SRX5761732/SRX5761732.05_summits.bed INFO @ Wed, 22 Apr 2020 06:30:10: Done! INFO @ Wed, 22 Apr 2020 06:30:11: 11000000 pass1 - making usageList (130 chroms): 3 millis pass2 - checking and writing primary data (18524 records, 4 fields): 20 millis CompletedMACS2peakCalling INFO @ Wed, 22 Apr 2020 06:30:16: 12000000 INFO @ Wed, 22 Apr 2020 06:30:21: 13000000 INFO @ Wed, 22 Apr 2020 06:30:21: #1 tag size is determined as 37 bps INFO @ Wed, 22 Apr 2020 06:30:21: #1 tag size = 37 INFO @ Wed, 22 Apr 2020 06:30:21: #1 total tags in treatment: 13056231 INFO @ Wed, 22 Apr 2020 06:30:21: #1 user defined the maximum tags... INFO @ Wed, 22 Apr 2020 06:30:21: #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 06:30:21: #1 tags after filtering in treatment: 13056030 INFO @ Wed, 22 Apr 2020 06:30:21: #1 Redundant rate of treatment: 0.00 INFO @ Wed, 22 Apr 2020 06:30:21: #1 finished! INFO @ Wed, 22 Apr 2020 06:30:21: #2 Build Peak Model... INFO @ Wed, 22 Apr 2020 06:30:21: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 22 Apr 2020 06:30:23: #2 number of paired peaks: 22212 INFO @ Wed, 22 Apr 2020 06:30:23: start model_add_line... INFO @ Wed, 22 Apr 2020 06:30:23: start X-correlation... INFO @ Wed, 22 Apr 2020 06:30:23: end of X-cor INFO @ Wed, 22 Apr 2020 06:30:23: #2 finished! INFO @ Wed, 22 Apr 2020 06:30:23: #2 predicted fragment length is 231 bps INFO @ Wed, 22 Apr 2020 06:30:23: #2 alternative fragment length(s) may be 231 bps INFO @ Wed, 22 Apr 2020 06:30:23: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/SRX5761732/SRX5761732.20_model.r INFO @ Wed, 22 Apr 2020 06:30:23: #3 Call peaks... INFO @ Wed, 22 Apr 2020 06:30:23: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 22 Apr 2020 06:30:25: #3 Call peaks for each chromosome... INFO @ Wed, 22 Apr 2020 06:30:41: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/SRX5761732/SRX5761732.10_peaks.xls INFO @ Wed, 22 Apr 2020 06:30:41: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/SRX5761732/SRX5761732.10_peaks.narrowPeak INFO @ Wed, 22 Apr 2020 06:30:41: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/SRX5761732/SRX5761732.10_summits.bed INFO @ Wed, 22 Apr 2020 06:30:41: Done! pass1 - making usageList (116 chroms): 2 millis pass2 - checking and writing primary data (16095 records, 4 fields): 18 millis CompletedMACS2peakCalling INFO @ Wed, 22 Apr 2020 06:30:54: #3 Call peaks for each chromosome... BedGraph に変換しました。 BigWig に変換中... INFO @ Wed, 22 Apr 2020 06:31:09: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/SRX5761732/SRX5761732.20_peaks.xls INFO @ Wed, 22 Apr 2020 06:31:09: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/SRX5761732/SRX5761732.20_peaks.narrowPeak INFO @ Wed, 22 Apr 2020 06:31:09: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/SRX5761732/SRX5761732.20_summits.bed INFO @ Wed, 22 Apr 2020 06:31:09: Done! pass1 - making usageList (95 chroms): 3 millis pass2 - checking and writing primary data (13700 records, 4 fields): 14 millis CompletedMACS2peakCalling BigWig に変換しました。