Job ID = 5790680 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 17,043,287 reads read : 17,043,287 reads written : 17,043,287 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: 00:05:15 17043287 reads; of these: 17043287 (100.00%) were unpaired; of these: 2200523 (12.91%) aligned 0 times 8728309 (51.21%) aligned exactly 1 time 6114455 (35.88%) aligned >1 times 87.09% overall alignment rate Time searching: 00:05:16 Overall time: 00:05:16 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_rmdupse_core] 1258814 / 14842764 = 0.0848 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 06:10:30: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/SRX5761713/SRX5761713.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/SRX5761713/SRX5761713.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/SRX5761713/SRX5761713.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/SRX5761713/SRX5761713.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 06:10:30: #1 read tag files... INFO @ Wed, 22 Apr 2020 06:10:30: #1 read treatment tags... INFO @ Wed, 22 Apr 2020 06:10:35: 1000000 INFO @ Wed, 22 Apr 2020 06:10:40: 2000000 INFO @ Wed, 22 Apr 2020 06:10:45: 3000000 INFO @ Wed, 22 Apr 2020 06:10:49: 4000000 INFO @ Wed, 22 Apr 2020 06:10:54: 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 06:10:58: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/SRX5761713/SRX5761713.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/SRX5761713/SRX5761713.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/SRX5761713/SRX5761713.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/SRX5761713/SRX5761713.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 06:10:58: #1 read tag files... INFO @ Wed, 22 Apr 2020 06:10:58: #1 read treatment tags... INFO @ Wed, 22 Apr 2020 06:10:59: 6000000 INFO @ Wed, 22 Apr 2020 06:11:04: 1000000 INFO @ Wed, 22 Apr 2020 06:11:04: 7000000 INFO @ Wed, 22 Apr 2020 06:11:09: 8000000 INFO @ Wed, 22 Apr 2020 06:11:10: 2000000 INFO @ Wed, 22 Apr 2020 06:11:15: 9000000 INFO @ Wed, 22 Apr 2020 06:11:16: 3000000 INFO @ Wed, 22 Apr 2020 06:11:20: 10000000 INFO @ Wed, 22 Apr 2020 06:11:21: 4000000 INFO @ Wed, 22 Apr 2020 06:11:25: 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 06:11:27: 5000000 INFO @ Wed, 22 Apr 2020 06:11:28: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/SRX5761713/SRX5761713.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/SRX5761713/SRX5761713.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/SRX5761713/SRX5761713.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/SRX5761713/SRX5761713.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 06:11:28: #1 read tag files... INFO @ Wed, 22 Apr 2020 06:11:28: #1 read treatment tags... INFO @ Wed, 22 Apr 2020 06:11:31: 12000000 INFO @ Wed, 22 Apr 2020 06:11:33: 6000000 INFO @ Wed, 22 Apr 2020 06:11:34: 1000000 INFO @ Wed, 22 Apr 2020 06:11:36: 13000000 INFO @ Wed, 22 Apr 2020 06:11:39: 7000000 INFO @ Wed, 22 Apr 2020 06:11:39: #1 tag size is determined as 37 bps INFO @ Wed, 22 Apr 2020 06:11:39: #1 tag size = 37 INFO @ Wed, 22 Apr 2020 06:11:39: #1 total tags in treatment: 13583950 INFO @ Wed, 22 Apr 2020 06:11:39: #1 user defined the maximum tags... INFO @ Wed, 22 Apr 2020 06:11:39: #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 06:11:39: #1 tags after filtering in treatment: 13583791 INFO @ Wed, 22 Apr 2020 06:11:39: #1 Redundant rate of treatment: 0.00 INFO @ Wed, 22 Apr 2020 06:11:39: #1 finished! INFO @ Wed, 22 Apr 2020 06:11:39: #2 Build Peak Model... INFO @ Wed, 22 Apr 2020 06:11:39: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 22 Apr 2020 06:11:40: 2000000 INFO @ Wed, 22 Apr 2020 06:11:42: #2 number of paired peaks: 45469 INFO @ Wed, 22 Apr 2020 06:11:42: start model_add_line... INFO @ Wed, 22 Apr 2020 06:11:42: start X-correlation... INFO @ Wed, 22 Apr 2020 06:11:42: end of X-cor INFO @ Wed, 22 Apr 2020 06:11:42: #2 finished! INFO @ Wed, 22 Apr 2020 06:11:42: #2 predicted fragment length is 171 bps INFO @ Wed, 22 Apr 2020 06:11:42: #2 alternative fragment length(s) may be 171 bps INFO @ Wed, 22 Apr 2020 06:11:42: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/SRX5761713/SRX5761713.05_model.r INFO @ Wed, 22 Apr 2020 06:11:42: #3 Call peaks... INFO @ Wed, 22 Apr 2020 06:11:42: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 22 Apr 2020 06:11:44: 8000000 INFO @ Wed, 22 Apr 2020 06:11:46: 3000000 INFO @ Wed, 22 Apr 2020 06:11:50: 9000000 INFO @ Wed, 22 Apr 2020 06:11:52: 4000000 INFO @ Wed, 22 Apr 2020 06:11:56: 10000000 INFO @ Wed, 22 Apr 2020 06:11:58: 5000000 INFO @ Wed, 22 Apr 2020 06:12:02: 11000000 INFO @ Wed, 22 Apr 2020 06:12:04: 6000000 INFO @ Wed, 22 Apr 2020 06:12:07: 12000000 INFO @ Wed, 22 Apr 2020 06:12:10: 7000000 INFO @ Wed, 22 Apr 2020 06:12:13: 13000000 INFO @ Wed, 22 Apr 2020 06:12:13: #3 Call peaks for each chromosome... INFO @ Wed, 22 Apr 2020 06:12:16: 8000000 INFO @ Wed, 22 Apr 2020 06:12:17: #1 tag size is determined as 37 bps INFO @ Wed, 22 Apr 2020 06:12:17: #1 tag size = 37 INFO @ Wed, 22 Apr 2020 06:12:17: #1 total tags in treatment: 13583950 INFO @ Wed, 22 Apr 2020 06:12:17: #1 user defined the maximum tags... INFO @ Wed, 22 Apr 2020 06:12:17: #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 06:12:17: #1 tags after filtering in treatment: 13583791 INFO @ Wed, 22 Apr 2020 06:12:17: #1 Redundant rate of treatment: 0.00 INFO @ Wed, 22 Apr 2020 06:12:17: #1 finished! INFO @ Wed, 22 Apr 2020 06:12:17: #2 Build Peak Model... INFO @ Wed, 22 Apr 2020 06:12:17: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 22 Apr 2020 06:12:20: #2 number of paired peaks: 45469 INFO @ Wed, 22 Apr 2020 06:12:20: start model_add_line... INFO @ Wed, 22 Apr 2020 06:12:20: start X-correlation... INFO @ Wed, 22 Apr 2020 06:12:20: end of X-cor INFO @ Wed, 22 Apr 2020 06:12:20: #2 finished! INFO @ Wed, 22 Apr 2020 06:12:20: #2 predicted fragment length is 171 bps INFO @ Wed, 22 Apr 2020 06:12:20: #2 alternative fragment length(s) may be 171 bps INFO @ Wed, 22 Apr 2020 06:12:20: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/SRX5761713/SRX5761713.10_model.r INFO @ Wed, 22 Apr 2020 06:12:20: #3 Call peaks... INFO @ Wed, 22 Apr 2020 06:12:20: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 22 Apr 2020 06:12:22: 9000000 INFO @ Wed, 22 Apr 2020 06:12:27: 10000000 INFO @ Wed, 22 Apr 2020 06:12:29: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/SRX5761713/SRX5761713.05_peaks.xls INFO @ Wed, 22 Apr 2020 06:12:29: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/SRX5761713/SRX5761713.05_peaks.narrowPeak INFO @ Wed, 22 Apr 2020 06:12:29: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/SRX5761713/SRX5761713.05_summits.bed INFO @ Wed, 22 Apr 2020 06:12:29: Done! pass1 - making usageList (96 chroms): 2 millis pass2 - checking and writing primary data (10643 records, 4 fields): 12 millis CompletedMACS2peakCalling INFO @ Wed, 22 Apr 2020 06:12:33: 11000000 INFO @ Wed, 22 Apr 2020 06:12:39: 12000000 INFO @ Wed, 22 Apr 2020 06:12:45: 13000000 INFO @ Wed, 22 Apr 2020 06:12:48: #1 tag size is determined as 37 bps INFO @ Wed, 22 Apr 2020 06:12:48: #1 tag size = 37 INFO @ Wed, 22 Apr 2020 06:12:48: #1 total tags in treatment: 13583950 INFO @ Wed, 22 Apr 2020 06:12:48: #1 user defined the maximum tags... INFO @ Wed, 22 Apr 2020 06:12:48: #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 06:12:48: #1 tags after filtering in treatment: 13583791 INFO @ Wed, 22 Apr 2020 06:12:48: #1 Redundant rate of treatment: 0.00 INFO @ Wed, 22 Apr 2020 06:12:48: #1 finished! INFO @ Wed, 22 Apr 2020 06:12:48: #2 Build Peak Model... INFO @ Wed, 22 Apr 2020 06:12:48: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 22 Apr 2020 06:12:51: #2 number of paired peaks: 45469 INFO @ Wed, 22 Apr 2020 06:12:51: start model_add_line... INFO @ Wed, 22 Apr 2020 06:12:51: start X-correlation... INFO @ Wed, 22 Apr 2020 06:12:51: end of X-cor INFO @ Wed, 22 Apr 2020 06:12:51: #2 finished! INFO @ Wed, 22 Apr 2020 06:12:51: #2 predicted fragment length is 171 bps INFO @ Wed, 22 Apr 2020 06:12:51: #2 alternative fragment length(s) may be 171 bps INFO @ Wed, 22 Apr 2020 06:12:51: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/SRX5761713/SRX5761713.20_model.r INFO @ Wed, 22 Apr 2020 06:12:51: #3 Call peaks... INFO @ Wed, 22 Apr 2020 06:12:51: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 22 Apr 2020 06:12:51: #3 Call peaks for each chromosome... INFO @ Wed, 22 Apr 2020 06:13:06: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/SRX5761713/SRX5761713.10_peaks.xls INFO @ Wed, 22 Apr 2020 06:13:06: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/SRX5761713/SRX5761713.10_peaks.narrowPeak INFO @ Wed, 22 Apr 2020 06:13:06: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/SRX5761713/SRX5761713.10_summits.bed INFO @ Wed, 22 Apr 2020 06:13:06: Done! pass1 - making usageList (54 chroms): 1 millis pass2 - checking and writing primary data (2828 records, 4 fields): 5 millis CompletedMACS2peakCalling INFO @ Wed, 22 Apr 2020 06:13:22: #3 Call peaks for each chromosome... INFO @ Wed, 22 Apr 2020 06:13:38: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/SRX5761713/SRX5761713.20_peaks.xls INFO @ Wed, 22 Apr 2020 06:13:38: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/SRX5761713/SRX5761713.20_peaks.narrowPeak INFO @ Wed, 22 Apr 2020 06:13:38: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/SRX5761713/SRX5761713.20_summits.bed INFO @ Wed, 22 Apr 2020 06:13:38: Done! pass1 - making usageList (36 chroms): 1 millis pass2 - checking and writing primary data (505 records, 4 fields): 4 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。