Job ID = 5790714 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 31,603,940 reads read : 31,603,940 reads written : 31,603,940 rm: cannot remove ‘[DSE]RR*’: No such file or directory rm: cannot remove ‘/home/okishinya/ncbi/public/sra/SRR8982446.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: 00:00:01 Time loading mirror index: 00:00:01 Multiseed full-index search: 00:07:16 31603940 reads; of these: 31603940 (100.00%) were unpaired; of these: 10133770 (32.06%) aligned 0 times 17555846 (55.55%) aligned exactly 1 time 3914324 (12.39%) aligned >1 times 67.94% overall alignment rate Time searching: 00:07:18 Overall time: 00:07:18 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] 11056628 / 21470170 = 0.5150 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 06:36:50: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/SRX5761744/SRX5761744.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/SRX5761744/SRX5761744.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/SRX5761744/SRX5761744.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/SRX5761744/SRX5761744.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 06:36:50: #1 read tag files... INFO @ Wed, 22 Apr 2020 06:36:50: #1 read treatment tags... INFO @ Wed, 22 Apr 2020 06:36:54: 1000000 INFO @ Wed, 22 Apr 2020 06:36:59: 2000000 INFO @ Wed, 22 Apr 2020 06:37:03: 3000000 INFO @ Wed, 22 Apr 2020 06:37:08: 4000000 INFO @ Wed, 22 Apr 2020 06:37:12: 5000000 INFO @ Wed, 22 Apr 2020 06:37:17: 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, 22 Apr 2020 06:37:20: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/SRX5761744/SRX5761744.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/SRX5761744/SRX5761744.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/SRX5761744/SRX5761744.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/SRX5761744/SRX5761744.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 06:37:20: #1 read tag files... INFO @ Wed, 22 Apr 2020 06:37:20: #1 read treatment tags... INFO @ Wed, 22 Apr 2020 06:37:21: 7000000 INFO @ Wed, 22 Apr 2020 06:37:24: 1000000 INFO @ Wed, 22 Apr 2020 06:37:26: 8000000 INFO @ Wed, 22 Apr 2020 06:37:29: 2000000 INFO @ Wed, 22 Apr 2020 06:37:31: 9000000 INFO @ Wed, 22 Apr 2020 06:37:34: 3000000 INFO @ Wed, 22 Apr 2020 06:37:36: 10000000 INFO @ Wed, 22 Apr 2020 06:37:38: #1 tag size is determined as 37 bps INFO @ Wed, 22 Apr 2020 06:37:38: #1 tag size = 37 INFO @ Wed, 22 Apr 2020 06:37:38: #1 total tags in treatment: 10413542 INFO @ Wed, 22 Apr 2020 06:37:38: #1 user defined the maximum tags... INFO @ Wed, 22 Apr 2020 06:37:38: #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 06:37:38: #1 tags after filtering in treatment: 10413300 INFO @ Wed, 22 Apr 2020 06:37:38: #1 Redundant rate of treatment: 0.00 INFO @ Wed, 22 Apr 2020 06:37:38: #1 finished! INFO @ Wed, 22 Apr 2020 06:37:38: #2 Build Peak Model... INFO @ Wed, 22 Apr 2020 06:37:38: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 22 Apr 2020 06:37:38: 4000000 INFO @ Wed, 22 Apr 2020 06:37:39: #2 number of paired peaks: 21266 INFO @ Wed, 22 Apr 2020 06:37:39: start model_add_line... INFO @ Wed, 22 Apr 2020 06:37:39: start X-correlation... INFO @ Wed, 22 Apr 2020 06:37:39: end of X-cor INFO @ Wed, 22 Apr 2020 06:37:39: #2 finished! INFO @ Wed, 22 Apr 2020 06:37:39: #2 predicted fragment length is 216 bps INFO @ Wed, 22 Apr 2020 06:37:39: #2 alternative fragment length(s) may be 216 bps INFO @ Wed, 22 Apr 2020 06:37:39: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/SRX5761744/SRX5761744.05_model.r INFO @ Wed, 22 Apr 2020 06:37:39: #3 Call peaks... INFO @ Wed, 22 Apr 2020 06:37:39: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 22 Apr 2020 06:37:43: 5000000 INFO @ Wed, 22 Apr 2020 06:37:47: 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 06:37:50: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/SRX5761744/SRX5761744.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/SRX5761744/SRX5761744.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/SRX5761744/SRX5761744.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/SRX5761744/SRX5761744.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 06:37:50: #1 read tag files... INFO @ Wed, 22 Apr 2020 06:37:50: #1 read treatment tags... INFO @ Wed, 22 Apr 2020 06:37:52: 7000000 INFO @ Wed, 22 Apr 2020 06:37:55: 1000000 INFO @ Wed, 22 Apr 2020 06:37:57: 8000000 INFO @ Wed, 22 Apr 2020 06:38:00: 2000000 INFO @ Wed, 22 Apr 2020 06:38:01: 9000000 INFO @ Wed, 22 Apr 2020 06:38:04: #3 Call peaks for each chromosome... INFO @ Wed, 22 Apr 2020 06:38:06: 3000000 INFO @ Wed, 22 Apr 2020 06:38:06: 10000000 INFO @ Wed, 22 Apr 2020 06:38:08: #1 tag size is determined as 37 bps INFO @ Wed, 22 Apr 2020 06:38:08: #1 tag size = 37 INFO @ Wed, 22 Apr 2020 06:38:08: #1 total tags in treatment: 10413542 INFO @ Wed, 22 Apr 2020 06:38:08: #1 user defined the maximum tags... INFO @ Wed, 22 Apr 2020 06:38:08: #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 06:38:08: #1 tags after filtering in treatment: 10413300 INFO @ Wed, 22 Apr 2020 06:38:08: #1 Redundant rate of treatment: 0.00 INFO @ Wed, 22 Apr 2020 06:38:08: #1 finished! INFO @ Wed, 22 Apr 2020 06:38:08: #2 Build Peak Model... INFO @ Wed, 22 Apr 2020 06:38:08: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 22 Apr 2020 06:38:10: #2 number of paired peaks: 21266 INFO @ Wed, 22 Apr 2020 06:38:10: start model_add_line... INFO @ Wed, 22 Apr 2020 06:38:10: start X-correlation... INFO @ Wed, 22 Apr 2020 06:38:10: end of X-cor INFO @ Wed, 22 Apr 2020 06:38:10: #2 finished! INFO @ Wed, 22 Apr 2020 06:38:10: #2 predicted fragment length is 216 bps INFO @ Wed, 22 Apr 2020 06:38:10: #2 alternative fragment length(s) may be 216 bps INFO @ Wed, 22 Apr 2020 06:38:10: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/SRX5761744/SRX5761744.10_model.r INFO @ Wed, 22 Apr 2020 06:38:10: #3 Call peaks... INFO @ Wed, 22 Apr 2020 06:38:10: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 22 Apr 2020 06:38:11: 4000000 INFO @ Wed, 22 Apr 2020 06:38:16: 5000000 INFO @ Wed, 22 Apr 2020 06:38:17: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/SRX5761744/SRX5761744.05_peaks.xls INFO @ Wed, 22 Apr 2020 06:38:17: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/SRX5761744/SRX5761744.05_peaks.narrowPeak INFO @ Wed, 22 Apr 2020 06:38:17: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/SRX5761744/SRX5761744.05_summits.bed INFO @ Wed, 22 Apr 2020 06:38:17: Done! pass1 - making usageList (131 chroms): 2 millis pass2 - checking and writing primary data (17145 records, 4 fields): 20 millis CompletedMACS2peakCalling INFO @ Wed, 22 Apr 2020 06:38:22: 6000000 INFO @ Wed, 22 Apr 2020 06:38:27: 7000000 INFO @ Wed, 22 Apr 2020 06:38:33: 8000000 INFO @ Wed, 22 Apr 2020 06:38:34: #3 Call peaks for each chromosome... INFO @ Wed, 22 Apr 2020 06:38:38: 9000000 INFO @ Wed, 22 Apr 2020 06:38:43: 10000000 INFO @ Wed, 22 Apr 2020 06:38:46: #1 tag size is determined as 37 bps INFO @ Wed, 22 Apr 2020 06:38:46: #1 tag size = 37 INFO @ Wed, 22 Apr 2020 06:38:46: #1 total tags in treatment: 10413542 INFO @ Wed, 22 Apr 2020 06:38:46: #1 user defined the maximum tags... INFO @ Wed, 22 Apr 2020 06:38:46: #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 06:38:46: #1 tags after filtering in treatment: 10413300 INFO @ Wed, 22 Apr 2020 06:38:46: #1 Redundant rate of treatment: 0.00 INFO @ Wed, 22 Apr 2020 06:38:46: #1 finished! INFO @ Wed, 22 Apr 2020 06:38:46: #2 Build Peak Model... INFO @ Wed, 22 Apr 2020 06:38:46: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 22 Apr 2020 06:38:46: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/SRX5761744/SRX5761744.10_peaks.xls INFO @ Wed, 22 Apr 2020 06:38:46: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/SRX5761744/SRX5761744.10_peaks.narrowPeak INFO @ Wed, 22 Apr 2020 06:38:46: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/SRX5761744/SRX5761744.10_summits.bed INFO @ Wed, 22 Apr 2020 06:38:46: Done! INFO @ Wed, 22 Apr 2020 06:38:47: #2 number of paired peaks: 21266 INFO @ Wed, 22 Apr 2020 06:38:47: start model_add_line... INFO @ Wed, 22 Apr 2020 06:38:47: start X-correlation... INFO @ Wed, 22 Apr 2020 06:38:48: end of X-cor INFO @ Wed, 22 Apr 2020 06:38:48: #2 finished! INFO @ Wed, 22 Apr 2020 06:38:48: #2 predicted fragment length is 216 bps INFO @ Wed, 22 Apr 2020 06:38:48: #2 alternative fragment length(s) may be 216 bps INFO @ Wed, 22 Apr 2020 06:38:48: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/SRX5761744/SRX5761744.20_model.r INFO @ Wed, 22 Apr 2020 06:38:48: #3 Call peaks... INFO @ Wed, 22 Apr 2020 06:38:48: #3 Pre-compute pvalue-qvalue table... pass1 - making usageList (108 chroms): 3 millis pass2 - checking and writing primary data (14731 records, 4 fields): 17 millis CompletedMACS2peakCalling INFO @ Wed, 22 Apr 2020 06:39:12: #3 Call peaks for each chromosome... INFO @ Wed, 22 Apr 2020 06:39:24: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/SRX5761744/SRX5761744.20_peaks.xls INFO @ Wed, 22 Apr 2020 06:39:24: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/SRX5761744/SRX5761744.20_peaks.narrowPeak INFO @ Wed, 22 Apr 2020 06:39:24: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/SRX5761744/SRX5761744.20_summits.bed INFO @ Wed, 22 Apr 2020 06:39:24: Done! pass1 - making usageList (84 chroms): 3 millis pass2 - checking and writing primary data (12293 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。