Job ID = 5790681 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 24,482,945 reads read : 24,482,945 reads written : 24,482,945 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: 00:08:15 24482945 reads; of these: 24482945 (100.00%) were unpaired; of these: 5059285 (20.66%) aligned 0 times 10400742 (42.48%) aligned exactly 1 time 9022918 (36.85%) aligned >1 times 79.34% overall alignment rate Time searching: 00:08:17 Overall time: 00:08:17 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] 2415005 / 19423660 = 0.1243 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 06:18:39: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/SRX5761714/SRX5761714.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/SRX5761714/SRX5761714.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/SRX5761714/SRX5761714.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/SRX5761714/SRX5761714.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 06:18:39: #1 read tag files... INFO @ Wed, 22 Apr 2020 06:18:39: #1 read treatment tags... INFO @ Wed, 22 Apr 2020 06:18:45: 1000000 INFO @ Wed, 22 Apr 2020 06:18:50: 2000000 INFO @ Wed, 22 Apr 2020 06:18:56: 3000000 INFO @ Wed, 22 Apr 2020 06:19:01: 4000000 INFO @ Wed, 22 Apr 2020 06:19:06: 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 06:19:09: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/SRX5761714/SRX5761714.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/SRX5761714/SRX5761714.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/SRX5761714/SRX5761714.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/SRX5761714/SRX5761714.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 06:19:09: #1 read tag files... INFO @ Wed, 22 Apr 2020 06:19:09: #1 read treatment tags... INFO @ Wed, 22 Apr 2020 06:19:11: 6000000 INFO @ Wed, 22 Apr 2020 06:19:15: 1000000 INFO @ Wed, 22 Apr 2020 06:19:16: 7000000 INFO @ Wed, 22 Apr 2020 06:19:20: 2000000 INFO @ Wed, 22 Apr 2020 06:19:21: 8000000 INFO @ Wed, 22 Apr 2020 06:19:25: 3000000 INFO @ Wed, 22 Apr 2020 06:19:27: 9000000 INFO @ Wed, 22 Apr 2020 06:19:31: 4000000 INFO @ Wed, 22 Apr 2020 06:19:32: 10000000 INFO @ Wed, 22 Apr 2020 06:19:36: 5000000 INFO @ Wed, 22 Apr 2020 06:19:37: 11000000 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 06:19:39: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/SRX5761714/SRX5761714.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/SRX5761714/SRX5761714.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/SRX5761714/SRX5761714.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/SRX5761714/SRX5761714.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 06:19:39: #1 read tag files... INFO @ Wed, 22 Apr 2020 06:19:39: #1 read treatment tags... INFO @ Wed, 22 Apr 2020 06:19:42: 6000000 INFO @ Wed, 22 Apr 2020 06:19:43: 12000000 INFO @ Wed, 22 Apr 2020 06:19:45: 1000000 INFO @ Wed, 22 Apr 2020 06:19:47: 7000000 INFO @ Wed, 22 Apr 2020 06:19:49: 13000000 INFO @ Wed, 22 Apr 2020 06:19:52: 2000000 INFO @ Wed, 22 Apr 2020 06:19:53: 8000000 INFO @ Wed, 22 Apr 2020 06:19:54: 14000000 INFO @ Wed, 22 Apr 2020 06:19:58: 3000000 INFO @ Wed, 22 Apr 2020 06:19:58: 9000000 INFO @ Wed, 22 Apr 2020 06:20:00: 15000000 INFO @ Wed, 22 Apr 2020 06:20:04: 10000000 INFO @ Wed, 22 Apr 2020 06:20:04: 4000000 INFO @ Wed, 22 Apr 2020 06:20:06: 16000000 INFO @ Wed, 22 Apr 2020 06:20:10: 11000000 INFO @ Wed, 22 Apr 2020 06:20:10: 5000000 INFO @ Wed, 22 Apr 2020 06:20:11: 17000000 INFO @ Wed, 22 Apr 2020 06:20:12: #1 tag size is determined as 37 bps INFO @ Wed, 22 Apr 2020 06:20:12: #1 tag size = 37 INFO @ Wed, 22 Apr 2020 06:20:12: #1 total tags in treatment: 17008655 INFO @ Wed, 22 Apr 2020 06:20:12: #1 user defined the maximum tags... INFO @ Wed, 22 Apr 2020 06:20:12: #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 06:20:12: #1 tags after filtering in treatment: 17008536 INFO @ Wed, 22 Apr 2020 06:20:12: #1 Redundant rate of treatment: 0.00 INFO @ Wed, 22 Apr 2020 06:20:12: #1 finished! INFO @ Wed, 22 Apr 2020 06:20:12: #2 Build Peak Model... INFO @ Wed, 22 Apr 2020 06:20:12: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 22 Apr 2020 06:20:14: #2 number of paired peaks: 21424 INFO @ Wed, 22 Apr 2020 06:20:14: start model_add_line... INFO @ Wed, 22 Apr 2020 06:20:14: start X-correlation... INFO @ Wed, 22 Apr 2020 06:20:14: end of X-cor INFO @ Wed, 22 Apr 2020 06:20:14: #2 finished! INFO @ Wed, 22 Apr 2020 06:20:14: #2 predicted fragment length is 193 bps INFO @ Wed, 22 Apr 2020 06:20:14: #2 alternative fragment length(s) may be 193 bps INFO @ Wed, 22 Apr 2020 06:20:14: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/SRX5761714/SRX5761714.05_model.r INFO @ Wed, 22 Apr 2020 06:20:14: #3 Call peaks... INFO @ Wed, 22 Apr 2020 06:20:14: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 22 Apr 2020 06:20:15: 12000000 INFO @ Wed, 22 Apr 2020 06:20:16: 6000000 INFO @ Wed, 22 Apr 2020 06:20:21: 13000000 INFO @ Wed, 22 Apr 2020 06:20:23: 7000000 INFO @ Wed, 22 Apr 2020 06:20:27: 14000000 INFO @ Wed, 22 Apr 2020 06:20:29: 8000000 INFO @ Wed, 22 Apr 2020 06:20:32: 15000000 INFO @ Wed, 22 Apr 2020 06:20:35: 9000000 INFO @ Wed, 22 Apr 2020 06:20:38: 16000000 INFO @ Wed, 22 Apr 2020 06:20:42: 10000000 INFO @ Wed, 22 Apr 2020 06:20:44: 17000000 INFO @ Wed, 22 Apr 2020 06:20:44: #1 tag size is determined as 37 bps INFO @ Wed, 22 Apr 2020 06:20:44: #1 tag size = 37 INFO @ Wed, 22 Apr 2020 06:20:44: #1 total tags in treatment: 17008655 INFO @ Wed, 22 Apr 2020 06:20:44: #1 user defined the maximum tags... INFO @ Wed, 22 Apr 2020 06:20:44: #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 06:20:44: #1 tags after filtering in treatment: 17008536 INFO @ Wed, 22 Apr 2020 06:20:44: #1 Redundant rate of treatment: 0.00 INFO @ Wed, 22 Apr 2020 06:20:44: #1 finished! INFO @ Wed, 22 Apr 2020 06:20:44: #2 Build Peak Model... INFO @ Wed, 22 Apr 2020 06:20:44: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 22 Apr 2020 06:20:46: #2 number of paired peaks: 21424 INFO @ Wed, 22 Apr 2020 06:20:46: start model_add_line... INFO @ Wed, 22 Apr 2020 06:20:47: start X-correlation... INFO @ Wed, 22 Apr 2020 06:20:47: end of X-cor INFO @ Wed, 22 Apr 2020 06:20:47: #2 finished! INFO @ Wed, 22 Apr 2020 06:20:47: #2 predicted fragment length is 193 bps INFO @ Wed, 22 Apr 2020 06:20:47: #2 alternative fragment length(s) may be 193 bps INFO @ Wed, 22 Apr 2020 06:20:47: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/SRX5761714/SRX5761714.10_model.r INFO @ Wed, 22 Apr 2020 06:20:47: #3 Call peaks... INFO @ Wed, 22 Apr 2020 06:20:47: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 22 Apr 2020 06:20:48: 11000000 INFO @ Wed, 22 Apr 2020 06:20:53: #3 Call peaks for each chromosome... INFO @ Wed, 22 Apr 2020 06:20:54: 12000000 INFO @ Wed, 22 Apr 2020 06:21:00: 13000000 INFO @ Wed, 22 Apr 2020 06:21:06: 14000000 INFO @ Wed, 22 Apr 2020 06:21:12: 15000000 INFO @ Wed, 22 Apr 2020 06:21:13: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/SRX5761714/SRX5761714.05_peaks.xls INFO @ Wed, 22 Apr 2020 06:21:13: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/SRX5761714/SRX5761714.05_peaks.narrowPeak INFO @ Wed, 22 Apr 2020 06:21:13: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/SRX5761714/SRX5761714.05_summits.bed INFO @ Wed, 22 Apr 2020 06:21:13: Done! pass1 - making usageList (113 chroms): 2 millis pass2 - checking and writing primary data (13329 records, 4 fields): 14 millis CompletedMACS2peakCalling INFO @ Wed, 22 Apr 2020 06:21:18: 16000000 INFO @ Wed, 22 Apr 2020 06:21:24: 17000000 INFO @ Wed, 22 Apr 2020 06:21:24: #1 tag size is determined as 37 bps INFO @ Wed, 22 Apr 2020 06:21:24: #1 tag size = 37 INFO @ Wed, 22 Apr 2020 06:21:24: #1 total tags in treatment: 17008655 INFO @ Wed, 22 Apr 2020 06:21:24: #1 user defined the maximum tags... INFO @ Wed, 22 Apr 2020 06:21:24: #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 06:21:24: #1 tags after filtering in treatment: 17008536 INFO @ Wed, 22 Apr 2020 06:21:24: #1 Redundant rate of treatment: 0.00 INFO @ Wed, 22 Apr 2020 06:21:24: #1 finished! INFO @ Wed, 22 Apr 2020 06:21:24: #2 Build Peak Model... INFO @ Wed, 22 Apr 2020 06:21:24: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 22 Apr 2020 06:21:26: #3 Call peaks for each chromosome... INFO @ Wed, 22 Apr 2020 06:21:26: #2 number of paired peaks: 21424 INFO @ Wed, 22 Apr 2020 06:21:26: start model_add_line... INFO @ Wed, 22 Apr 2020 06:21:27: start X-correlation... INFO @ Wed, 22 Apr 2020 06:21:27: end of X-cor INFO @ Wed, 22 Apr 2020 06:21:27: #2 finished! INFO @ Wed, 22 Apr 2020 06:21:27: #2 predicted fragment length is 193 bps INFO @ Wed, 22 Apr 2020 06:21:27: #2 alternative fragment length(s) may be 193 bps INFO @ Wed, 22 Apr 2020 06:21:27: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/SRX5761714/SRX5761714.20_model.r INFO @ Wed, 22 Apr 2020 06:21:27: #3 Call peaks... INFO @ Wed, 22 Apr 2020 06:21:27: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 22 Apr 2020 06:21:48: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/SRX5761714/SRX5761714.10_peaks.xls INFO @ Wed, 22 Apr 2020 06:21:48: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/SRX5761714/SRX5761714.10_peaks.narrowPeak INFO @ Wed, 22 Apr 2020 06:21:48: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/SRX5761714/SRX5761714.10_summits.bed INFO @ Wed, 22 Apr 2020 06:21:48: Done! pass1 - making usageList (69 chroms): 1 millis pass2 - checking and writing primary data (7930 records, 4 fields): 9 millis CompletedMACS2peakCalling INFO @ Wed, 22 Apr 2020 06:22:07: #3 Call peaks for each chromosome... INFO @ Wed, 22 Apr 2020 06:22:27: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/SRX5761714/SRX5761714.20_peaks.xls INFO @ Wed, 22 Apr 2020 06:22:27: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/SRX5761714/SRX5761714.20_peaks.narrowPeak INFO @ Wed, 22 Apr 2020 06:22:27: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/SRX5761714/SRX5761714.20_summits.bed INFO @ Wed, 22 Apr 2020 06:22:27: Done! pass1 - making usageList (44 chroms): 1 millis pass2 - checking and writing primary data (3945 records, 4 fields): 6 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。