Job ID = 5790668 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 27,003,444 reads read : 27,003,444 reads written : 27,003,444 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: 00:00:00 Time loading forward index: 00:00:01 Time loading mirror index: 00:00:00 Multiseed full-index search: 00:10:11 27003444 reads; of these: 27003444 (100.00%) were unpaired; of these: 6603171 (24.45%) aligned 0 times 14172643 (52.48%) aligned exactly 1 time 6227630 (23.06%) aligned >1 times 75.55% overall alignment rate Time searching: 00:10:12 Overall time: 00:10:12 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] 1908629 / 20400273 = 0.0936 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 06:08:54: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/SRX5761703/SRX5761703.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/SRX5761703/SRX5761703.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/SRX5761703/SRX5761703.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/SRX5761703/SRX5761703.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 06:08:54: #1 read tag files... INFO @ Wed, 22 Apr 2020 06:08:54: #1 read treatment tags... INFO @ Wed, 22 Apr 2020 06:09:00: 1000000 INFO @ Wed, 22 Apr 2020 06:09:06: 2000000 INFO @ Wed, 22 Apr 2020 06:09:13: 3000000 INFO @ Wed, 22 Apr 2020 06:09:19: 4000000 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 06:09:23: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/SRX5761703/SRX5761703.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/SRX5761703/SRX5761703.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/SRX5761703/SRX5761703.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/SRX5761703/SRX5761703.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 06:09:23: #1 read tag files... INFO @ Wed, 22 Apr 2020 06:09:23: #1 read treatment tags... INFO @ Wed, 22 Apr 2020 06:09:26: 5000000 INFO @ Wed, 22 Apr 2020 06:09:30: 1000000 INFO @ Wed, 22 Apr 2020 06:09:32: 6000000 INFO @ Wed, 22 Apr 2020 06:09:37: 2000000 INFO @ Wed, 22 Apr 2020 06:09:39: 7000000 INFO @ Wed, 22 Apr 2020 06:09:44: 3000000 INFO @ Wed, 22 Apr 2020 06:09:46: 8000000 INFO @ Wed, 22 Apr 2020 06:09:51: 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 06:09:53: 9000000 INFO @ Wed, 22 Apr 2020 06:09:54: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/SRX5761703/SRX5761703.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/SRX5761703/SRX5761703.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/SRX5761703/SRX5761703.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/SRX5761703/SRX5761703.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 06:09:54: #1 read tag files... INFO @ Wed, 22 Apr 2020 06:09:54: #1 read treatment tags... INFO @ Wed, 22 Apr 2020 06:09:57: 5000000 INFO @ Wed, 22 Apr 2020 06:09:59: 10000000 INFO @ Wed, 22 Apr 2020 06:10:01: 1000000 INFO @ Wed, 22 Apr 2020 06:10:03: 6000000 INFO @ Wed, 22 Apr 2020 06:10:06: 11000000 INFO @ Wed, 22 Apr 2020 06:10:08: 2000000 INFO @ Wed, 22 Apr 2020 06:10:09: 7000000 INFO @ Wed, 22 Apr 2020 06:10:13: 12000000 INFO @ Wed, 22 Apr 2020 06:10:16: 3000000 INFO @ Wed, 22 Apr 2020 06:10:16: 8000000 INFO @ Wed, 22 Apr 2020 06:10:20: 13000000 INFO @ Wed, 22 Apr 2020 06:10:24: 9000000 INFO @ Wed, 22 Apr 2020 06:10:24: 4000000 INFO @ Wed, 22 Apr 2020 06:10:26: 14000000 INFO @ Wed, 22 Apr 2020 06:10:31: 10000000 INFO @ Wed, 22 Apr 2020 06:10:32: 5000000 INFO @ Wed, 22 Apr 2020 06:10:33: 15000000 INFO @ Wed, 22 Apr 2020 06:10:37: 11000000 INFO @ Wed, 22 Apr 2020 06:10:39: 6000000 INFO @ Wed, 22 Apr 2020 06:10:40: 16000000 INFO @ Wed, 22 Apr 2020 06:10:43: 12000000 INFO @ Wed, 22 Apr 2020 06:10:46: 7000000 INFO @ Wed, 22 Apr 2020 06:10:47: 17000000 INFO @ Wed, 22 Apr 2020 06:10:49: 13000000 INFO @ Wed, 22 Apr 2020 06:10:53: 8000000 INFO @ Wed, 22 Apr 2020 06:10:53: 18000000 INFO @ Wed, 22 Apr 2020 06:10:55: 14000000 INFO @ Wed, 22 Apr 2020 06:10:57: #1 tag size is determined as 37 bps INFO @ Wed, 22 Apr 2020 06:10:57: #1 tag size = 37 INFO @ Wed, 22 Apr 2020 06:10:57: #1 total tags in treatment: 18491644 INFO @ Wed, 22 Apr 2020 06:10:57: #1 user defined the maximum tags... INFO @ Wed, 22 Apr 2020 06:10:57: #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 06:10:57: #1 tags after filtering in treatment: 18491503 INFO @ Wed, 22 Apr 2020 06:10:57: #1 Redundant rate of treatment: 0.00 INFO @ Wed, 22 Apr 2020 06:10:57: #1 finished! INFO @ Wed, 22 Apr 2020 06:10:57: #2 Build Peak Model... INFO @ Wed, 22 Apr 2020 06:10:57: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 22 Apr 2020 06:10:59: #2 number of paired peaks: 14061 INFO @ Wed, 22 Apr 2020 06:10:59: start model_add_line... INFO @ Wed, 22 Apr 2020 06:10:59: start X-correlation... INFO @ Wed, 22 Apr 2020 06:10:59: end of X-cor INFO @ Wed, 22 Apr 2020 06:10:59: #2 finished! INFO @ Wed, 22 Apr 2020 06:10:59: #2 predicted fragment length is 174 bps INFO @ Wed, 22 Apr 2020 06:10:59: #2 alternative fragment length(s) may be 174 bps INFO @ Wed, 22 Apr 2020 06:10:59: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/SRX5761703/SRX5761703.05_model.r INFO @ Wed, 22 Apr 2020 06:10:59: #3 Call peaks... INFO @ Wed, 22 Apr 2020 06:10:59: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 22 Apr 2020 06:11:00: 9000000 INFO @ Wed, 22 Apr 2020 06:11:01: 15000000 INFO @ Wed, 22 Apr 2020 06:11:07: 10000000 INFO @ Wed, 22 Apr 2020 06:11:07: 16000000 INFO @ Wed, 22 Apr 2020 06:11:13: 17000000 INFO @ Wed, 22 Apr 2020 06:11:14: 11000000 INFO @ Wed, 22 Apr 2020 06:11:19: 18000000 INFO @ Wed, 22 Apr 2020 06:11:21: 12000000 INFO @ Wed, 22 Apr 2020 06:11:22: #1 tag size is determined as 37 bps INFO @ Wed, 22 Apr 2020 06:11:22: #1 tag size = 37 INFO @ Wed, 22 Apr 2020 06:11:22: #1 total tags in treatment: 18491644 INFO @ Wed, 22 Apr 2020 06:11:22: #1 user defined the maximum tags... INFO @ Wed, 22 Apr 2020 06:11:22: #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 06:11:23: #1 tags after filtering in treatment: 18491503 INFO @ Wed, 22 Apr 2020 06:11:23: #1 Redundant rate of treatment: 0.00 INFO @ Wed, 22 Apr 2020 06:11:23: #1 finished! INFO @ Wed, 22 Apr 2020 06:11:23: #2 Build Peak Model... INFO @ Wed, 22 Apr 2020 06:11:23: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 22 Apr 2020 06:11:25: #2 number of paired peaks: 14061 INFO @ Wed, 22 Apr 2020 06:11:25: start model_add_line... INFO @ Wed, 22 Apr 2020 06:11:25: start X-correlation... INFO @ Wed, 22 Apr 2020 06:11:25: end of X-cor INFO @ Wed, 22 Apr 2020 06:11:25: #2 finished! INFO @ Wed, 22 Apr 2020 06:11:25: #2 predicted fragment length is 174 bps INFO @ Wed, 22 Apr 2020 06:11:25: #2 alternative fragment length(s) may be 174 bps INFO @ Wed, 22 Apr 2020 06:11:25: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/SRX5761703/SRX5761703.10_model.r INFO @ Wed, 22 Apr 2020 06:11:25: #3 Call peaks... INFO @ Wed, 22 Apr 2020 06:11:25: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 22 Apr 2020 06:11:29: 13000000 INFO @ Wed, 22 Apr 2020 06:11:35: 14000000 INFO @ Wed, 22 Apr 2020 06:11:42: #3 Call peaks for each chromosome... INFO @ Wed, 22 Apr 2020 06:11:42: 15000000 INFO @ Wed, 22 Apr 2020 06:11:48: 16000000 INFO @ Wed, 22 Apr 2020 06:11:55: 17000000 INFO @ Wed, 22 Apr 2020 06:12:02: 18000000 INFO @ Wed, 22 Apr 2020 06:12:03: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/SRX5761703/SRX5761703.05_peaks.xls INFO @ Wed, 22 Apr 2020 06:12:03: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/SRX5761703/SRX5761703.05_peaks.narrowPeak INFO @ Wed, 22 Apr 2020 06:12:03: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/SRX5761703/SRX5761703.05_summits.bed INFO @ Wed, 22 Apr 2020 06:12:03: Done! pass1 - making usageList (52 chroms): 2 millis pass2 - checking and writing primary data (6360 records, 4 fields): 9 millis CompletedMACS2peakCalling INFO @ Wed, 22 Apr 2020 06:12:05: #1 tag size is determined as 37 bps INFO @ Wed, 22 Apr 2020 06:12:05: #1 tag size = 37 INFO @ Wed, 22 Apr 2020 06:12:05: #1 total tags in treatment: 18491644 INFO @ Wed, 22 Apr 2020 06:12:05: #1 user defined the maximum tags... INFO @ Wed, 22 Apr 2020 06:12:05: #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 06:12:05: #3 Call peaks for each chromosome... INFO @ Wed, 22 Apr 2020 06:12:05: #1 tags after filtering in treatment: 18491503 INFO @ Wed, 22 Apr 2020 06:12:05: #1 Redundant rate of treatment: 0.00 INFO @ Wed, 22 Apr 2020 06:12:05: #1 finished! INFO @ Wed, 22 Apr 2020 06:12:05: #2 Build Peak Model... INFO @ Wed, 22 Apr 2020 06:12:05: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 22 Apr 2020 06:12:07: #2 number of paired peaks: 14061 INFO @ Wed, 22 Apr 2020 06:12:07: start model_add_line... INFO @ Wed, 22 Apr 2020 06:12:08: start X-correlation... INFO @ Wed, 22 Apr 2020 06:12:08: end of X-cor INFO @ Wed, 22 Apr 2020 06:12:08: #2 finished! INFO @ Wed, 22 Apr 2020 06:12:08: #2 predicted fragment length is 174 bps INFO @ Wed, 22 Apr 2020 06:12:08: #2 alternative fragment length(s) may be 174 bps INFO @ Wed, 22 Apr 2020 06:12:08: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/SRX5761703/SRX5761703.20_model.r INFO @ Wed, 22 Apr 2020 06:12:08: #3 Call peaks... INFO @ Wed, 22 Apr 2020 06:12:08: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 22 Apr 2020 06:12:28: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/SRX5761703/SRX5761703.10_peaks.xls INFO @ Wed, 22 Apr 2020 06:12:28: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/SRX5761703/SRX5761703.10_peaks.narrowPeak INFO @ Wed, 22 Apr 2020 06:12:28: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/SRX5761703/SRX5761703.10_summits.bed INFO @ Wed, 22 Apr 2020 06:12:28: Done! pass1 - making usageList (31 chroms): 1 millis pass2 - checking and writing primary data (1640 records, 4 fields): 4 millis CompletedMACS2peakCalling INFO @ Wed, 22 Apr 2020 06:12:50: #3 Call peaks for each chromosome... BedGraph に変換しました。 BigWig に変換中... INFO @ Wed, 22 Apr 2020 06:13:12: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/SRX5761703/SRX5761703.20_peaks.xls INFO @ Wed, 22 Apr 2020 06:13:12: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/SRX5761703/SRX5761703.20_peaks.narrowPeak INFO @ Wed, 22 Apr 2020 06:13:12: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/SRX5761703/SRX5761703.20_summits.bed INFO @ Wed, 22 Apr 2020 06:13:12: Done! pass1 - making usageList (27 chroms): 0 millis pass2 - checking and writing primary data (317 records, 4 fields): 2 millis CompletedMACS2peakCalling BigWig に変換しました。