Job ID = 5790704 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 30,731,367 reads read : 30,731,367 reads written : 30,731,367 rm: cannot remove ‘[DSE]RR*’: No such file or directory rm: cannot remove ‘/home/okishinya/ncbi/public/sra/SRR8982437.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: 00:00:00 Multiseed full-index search: 00:12:21 30731367 reads; of these: 30731367 (100.00%) were unpaired; of these: 7515532 (24.46%) aligned 0 times 14193996 (46.19%) aligned exactly 1 time 9021839 (29.36%) aligned >1 times 75.54% overall alignment rate Time searching: 00:12:23 Overall time: 00:12:23 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] 3116530 / 23215835 = 0.1342 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 06:35:50: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/SRX5761735/SRX5761735.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/SRX5761735/SRX5761735.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/SRX5761735/SRX5761735.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/SRX5761735/SRX5761735.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 06:35:50: #1 read tag files... INFO @ Wed, 22 Apr 2020 06:35:50: #1 read treatment tags... INFO @ Wed, 22 Apr 2020 06:35:57: 1000000 INFO @ Wed, 22 Apr 2020 06:36:05: 2000000 INFO @ Wed, 22 Apr 2020 06:36:12: 3000000 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 06:36:19: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/SRX5761735/SRX5761735.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/SRX5761735/SRX5761735.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/SRX5761735/SRX5761735.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/SRX5761735/SRX5761735.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 06:36:19: #1 read tag files... INFO @ Wed, 22 Apr 2020 06:36:19: #1 read treatment tags... INFO @ Wed, 22 Apr 2020 06:36:19: 4000000 INFO @ Wed, 22 Apr 2020 06:36:25: 1000000 INFO @ Wed, 22 Apr 2020 06:36:27: 5000000 INFO @ Wed, 22 Apr 2020 06:36:31: 2000000 INFO @ Wed, 22 Apr 2020 06:36:34: 6000000 INFO @ Wed, 22 Apr 2020 06:36:37: 3000000 INFO @ Wed, 22 Apr 2020 06:36:42: 7000000 INFO @ Wed, 22 Apr 2020 06:36:43: 4000000 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 06:36:49: 5000000 INFO @ Wed, 22 Apr 2020 06:36:49: 8000000 INFO @ Wed, 22 Apr 2020 06:36:50: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/SRX5761735/SRX5761735.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/SRX5761735/SRX5761735.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/SRX5761735/SRX5761735.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/SRX5761735/SRX5761735.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 06:36:50: #1 read tag files... INFO @ Wed, 22 Apr 2020 06:36:50: #1 read treatment tags... INFO @ Wed, 22 Apr 2020 06:36:55: 6000000 INFO @ Wed, 22 Apr 2020 06:36:55: 9000000 INFO @ Wed, 22 Apr 2020 06:36:56: 1000000 INFO @ Wed, 22 Apr 2020 06:37:01: 7000000 INFO @ Wed, 22 Apr 2020 06:37:01: 10000000 INFO @ Wed, 22 Apr 2020 06:37:02: 2000000 INFO @ Wed, 22 Apr 2020 06:37:07: 8000000 INFO @ Wed, 22 Apr 2020 06:37:07: 11000000 INFO @ Wed, 22 Apr 2020 06:37:08: 3000000 INFO @ Wed, 22 Apr 2020 06:37:12: 9000000 INFO @ Wed, 22 Apr 2020 06:37:13: 12000000 INFO @ Wed, 22 Apr 2020 06:37:14: 4000000 INFO @ Wed, 22 Apr 2020 06:37:18: 10000000 INFO @ Wed, 22 Apr 2020 06:37:19: 13000000 INFO @ Wed, 22 Apr 2020 06:37:20: 5000000 INFO @ Wed, 22 Apr 2020 06:37:24: 11000000 INFO @ Wed, 22 Apr 2020 06:37:25: 14000000 INFO @ Wed, 22 Apr 2020 06:37:25: 6000000 INFO @ Wed, 22 Apr 2020 06:37:30: 12000000 INFO @ Wed, 22 Apr 2020 06:37:31: 15000000 INFO @ Wed, 22 Apr 2020 06:37:31: 7000000 INFO @ Wed, 22 Apr 2020 06:37:36: 13000000 INFO @ Wed, 22 Apr 2020 06:37:37: 16000000 INFO @ Wed, 22 Apr 2020 06:37:37: 8000000 INFO @ Wed, 22 Apr 2020 06:37:42: 14000000 INFO @ Wed, 22 Apr 2020 06:37:43: 9000000 INFO @ Wed, 22 Apr 2020 06:37:43: 17000000 INFO @ Wed, 22 Apr 2020 06:37:47: 15000000 INFO @ Wed, 22 Apr 2020 06:37:48: 10000000 INFO @ Wed, 22 Apr 2020 06:37:48: 18000000 INFO @ Wed, 22 Apr 2020 06:37:53: 16000000 INFO @ Wed, 22 Apr 2020 06:37:54: 11000000 INFO @ Wed, 22 Apr 2020 06:37:54: 19000000 INFO @ Wed, 22 Apr 2020 06:37:58: 17000000 INFO @ Wed, 22 Apr 2020 06:37:59: 12000000 INFO @ Wed, 22 Apr 2020 06:38:00: 20000000 INFO @ Wed, 22 Apr 2020 06:38:00: #1 tag size is determined as 37 bps INFO @ Wed, 22 Apr 2020 06:38:00: #1 tag size = 37 INFO @ Wed, 22 Apr 2020 06:38:00: #1 total tags in treatment: 20099305 INFO @ Wed, 22 Apr 2020 06:38:00: #1 user defined the maximum tags... INFO @ Wed, 22 Apr 2020 06:38:00: #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 06:38:01: #1 tags after filtering in treatment: 20099188 INFO @ Wed, 22 Apr 2020 06:38:01: #1 Redundant rate of treatment: 0.00 INFO @ Wed, 22 Apr 2020 06:38:01: #1 finished! INFO @ Wed, 22 Apr 2020 06:38:01: #2 Build Peak Model... INFO @ Wed, 22 Apr 2020 06:38:01: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 22 Apr 2020 06:38:03: #2 number of paired peaks: 21362 INFO @ Wed, 22 Apr 2020 06:38:03: start model_add_line... INFO @ Wed, 22 Apr 2020 06:38:03: start X-correlation... INFO @ Wed, 22 Apr 2020 06:38:03: end of X-cor INFO @ Wed, 22 Apr 2020 06:38:03: #2 finished! INFO @ Wed, 22 Apr 2020 06:38:03: #2 predicted fragment length is 142 bps INFO @ Wed, 22 Apr 2020 06:38:03: #2 alternative fragment length(s) may be 142 bps INFO @ Wed, 22 Apr 2020 06:38:03: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/SRX5761735/SRX5761735.05_model.r INFO @ Wed, 22 Apr 2020 06:38:03: #3 Call peaks... INFO @ Wed, 22 Apr 2020 06:38:03: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 22 Apr 2020 06:38:04: 18000000 INFO @ Wed, 22 Apr 2020 06:38:04: 13000000 INFO @ Wed, 22 Apr 2020 06:38:09: 19000000 INFO @ Wed, 22 Apr 2020 06:38:10: 14000000 INFO @ Wed, 22 Apr 2020 06:38:15: 20000000 INFO @ Wed, 22 Apr 2020 06:38:15: #1 tag size is determined as 37 bps INFO @ Wed, 22 Apr 2020 06:38:15: #1 tag size = 37 INFO @ Wed, 22 Apr 2020 06:38:15: #1 total tags in treatment: 20099305 INFO @ Wed, 22 Apr 2020 06:38:15: #1 user defined the maximum tags... INFO @ Wed, 22 Apr 2020 06:38:15: #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 06:38:15: 15000000 INFO @ Wed, 22 Apr 2020 06:38:16: #1 tags after filtering in treatment: 20099188 INFO @ Wed, 22 Apr 2020 06:38:16: #1 Redundant rate of treatment: 0.00 INFO @ Wed, 22 Apr 2020 06:38:16: #1 finished! INFO @ Wed, 22 Apr 2020 06:38:16: #2 Build Peak Model... INFO @ Wed, 22 Apr 2020 06:38:16: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 22 Apr 2020 06:38:18: #2 number of paired peaks: 21362 INFO @ Wed, 22 Apr 2020 06:38:18: start model_add_line... INFO @ Wed, 22 Apr 2020 06:38:18: start X-correlation... INFO @ Wed, 22 Apr 2020 06:38:18: end of X-cor INFO @ Wed, 22 Apr 2020 06:38:18: #2 finished! INFO @ Wed, 22 Apr 2020 06:38:18: #2 predicted fragment length is 142 bps INFO @ Wed, 22 Apr 2020 06:38:18: #2 alternative fragment length(s) may be 142 bps INFO @ Wed, 22 Apr 2020 06:38:18: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/SRX5761735/SRX5761735.10_model.r INFO @ Wed, 22 Apr 2020 06:38:18: #3 Call peaks... INFO @ Wed, 22 Apr 2020 06:38:18: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 22 Apr 2020 06:38:21: 16000000 INFO @ Wed, 22 Apr 2020 06:38:26: 17000000 INFO @ Wed, 22 Apr 2020 06:38:31: 18000000 INFO @ Wed, 22 Apr 2020 06:38:36: 19000000 INFO @ Wed, 22 Apr 2020 06:38:41: 20000000 INFO @ Wed, 22 Apr 2020 06:38:42: #1 tag size is determined as 37 bps INFO @ Wed, 22 Apr 2020 06:38:42: #1 tag size = 37 INFO @ Wed, 22 Apr 2020 06:38:42: #1 total tags in treatment: 20099305 INFO @ Wed, 22 Apr 2020 06:38:42: #1 user defined the maximum tags... INFO @ Wed, 22 Apr 2020 06:38:42: #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 06:38:42: #1 tags after filtering in treatment: 20099188 INFO @ Wed, 22 Apr 2020 06:38:42: #1 Redundant rate of treatment: 0.00 INFO @ Wed, 22 Apr 2020 06:38:42: #1 finished! INFO @ Wed, 22 Apr 2020 06:38:42: #2 Build Peak Model... INFO @ Wed, 22 Apr 2020 06:38:42: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 22 Apr 2020 06:38:44: #2 number of paired peaks: 21362 INFO @ Wed, 22 Apr 2020 06:38:44: start model_add_line... INFO @ Wed, 22 Apr 2020 06:38:45: start X-correlation... INFO @ Wed, 22 Apr 2020 06:38:45: end of X-cor INFO @ Wed, 22 Apr 2020 06:38:45: #2 finished! INFO @ Wed, 22 Apr 2020 06:38:45: #2 predicted fragment length is 142 bps INFO @ Wed, 22 Apr 2020 06:38:45: #2 alternative fragment length(s) may be 142 bps INFO @ Wed, 22 Apr 2020 06:38:45: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/SRX5761735/SRX5761735.20_model.r INFO @ Wed, 22 Apr 2020 06:38:45: #3 Call peaks... INFO @ Wed, 22 Apr 2020 06:38:45: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 22 Apr 2020 06:38:48: #3 Call peaks for each chromosome... INFO @ Wed, 22 Apr 2020 06:39:02: #3 Call peaks for each chromosome... INFO @ Wed, 22 Apr 2020 06:39:11: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/SRX5761735/SRX5761735.05_peaks.xls INFO @ Wed, 22 Apr 2020 06:39:12: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/SRX5761735/SRX5761735.05_peaks.narrowPeak INFO @ Wed, 22 Apr 2020 06:39:12: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/SRX5761735/SRX5761735.05_summits.bed INFO @ Wed, 22 Apr 2020 06:39:12: Done! pass1 - making usageList (103 chroms): 2 millis pass2 - checking and writing primary data (10567 records, 4 fields): 12 millis CompletedMACS2peakCalling INFO @ Wed, 22 Apr 2020 06:39:26: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/SRX5761735/SRX5761735.10_peaks.xls INFO @ Wed, 22 Apr 2020 06:39:26: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/SRX5761735/SRX5761735.10_peaks.narrowPeak INFO @ Wed, 22 Apr 2020 06:39:26: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/SRX5761735/SRX5761735.10_summits.bed INFO @ Wed, 22 Apr 2020 06:39:26: Done! INFO @ Wed, 22 Apr 2020 06:39:30: #3 Call peaks for each chromosome... pass1 - making usageList (66 chroms): 1 millis pass2 - checking and writing primary data (1920 records, 4 fields): 5 millis CompletedMACS2peakCalling INFO @ Wed, 22 Apr 2020 06:39:54: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/SRX5761735/SRX5761735.20_peaks.xls INFO @ Wed, 22 Apr 2020 06:39:54: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/SRX5761735/SRX5761735.20_peaks.narrowPeak INFO @ Wed, 22 Apr 2020 06:39:54: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/SRX5761735/SRX5761735.20_summits.bed INFO @ Wed, 22 Apr 2020 06:39:54: Done! pass1 - making usageList (42 chroms): 1 millis pass2 - checking and writing primary data (545 records, 4 fields): 2 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。