Job ID = 8184299 SRX = SRX8047581 Genome = rn6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-08-10T03:08:46 prefetch.2.10.7: 1) Downloading 'SRR11471306'... 2020-08-10T03:08:46 prefetch.2.10.7: Downloading via HTTPS... 2020-08-10T03:09:35 prefetch.2.10.7: HTTPS download succeed 2020-08-10T03:09:36 prefetch.2.10.7: 'SRR11471306' is valid 2020-08-10T03:09:36 prefetch.2.10.7: 1) 'SRR11471306' was downloaded successfully Read 12934059 spots for SRR11471306/SRR11471306.sra Written 12934059 spots for SRR11471306/SRR11471306.sra 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: 00:00:01 Time loading mirror index: 00:00:01 Multiseed full-index search: 00:09:15 12934059 reads; of these: 12934059 (100.00%) were unpaired; of these: 571811 (4.42%) aligned 0 times 9892617 (76.49%) aligned exactly 1 time 2469631 (19.09%) aligned >1 times 95.58% overall alignment rate Time searching: 00:09:18 Overall time: 00:09:18 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] 4383792 / 12362248 = 0.3546 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 @ Mon, 10 Aug 2020 12:22:50: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/SRX8047581/SRX8047581.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/SRX8047581/SRX8047581.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/SRX8047581/SRX8047581.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/SRX8047581/SRX8047581.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 @ Mon, 10 Aug 2020 12:22:50: #1 read tag files... INFO @ Mon, 10 Aug 2020 12:22:50: #1 read treatment tags... INFO @ Mon, 10 Aug 2020 12:22:56: 1000000 INFO @ Mon, 10 Aug 2020 12:23:02: 2000000 INFO @ Mon, 10 Aug 2020 12:23:08: 3000000 INFO @ Mon, 10 Aug 2020 12:23:14: 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 @ Mon, 10 Aug 2020 12:23:19: 5000000 INFO @ Mon, 10 Aug 2020 12:23:20: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/SRX8047581/SRX8047581.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/SRX8047581/SRX8047581.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/SRX8047581/SRX8047581.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/SRX8047581/SRX8047581.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 @ Mon, 10 Aug 2020 12:23:20: #1 read tag files... INFO @ Mon, 10 Aug 2020 12:23:20: #1 read treatment tags... INFO @ Mon, 10 Aug 2020 12:23:26: 6000000 INFO @ Mon, 10 Aug 2020 12:23:27: 1000000 INFO @ Mon, 10 Aug 2020 12:23:33: 7000000 INFO @ Mon, 10 Aug 2020 12:23:34: 2000000 INFO @ Mon, 10 Aug 2020 12:23:40: #1 tag size is determined as 50 bps INFO @ Mon, 10 Aug 2020 12:23:40: #1 tag size = 50 INFO @ Mon, 10 Aug 2020 12:23:40: #1 total tags in treatment: 7978456 INFO @ Mon, 10 Aug 2020 12:23:40: #1 user defined the maximum tags... INFO @ Mon, 10 Aug 2020 12:23:40: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Mon, 10 Aug 2020 12:23:40: #1 tags after filtering in treatment: 7978198 INFO @ Mon, 10 Aug 2020 12:23:40: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 10 Aug 2020 12:23:40: #1 finished! INFO @ Mon, 10 Aug 2020 12:23:40: #2 Build Peak Model... INFO @ Mon, 10 Aug 2020 12:23:40: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 10 Aug 2020 12:23:41: 3000000 INFO @ Mon, 10 Aug 2020 12:23:42: #2 number of paired peaks: 38897 INFO @ Mon, 10 Aug 2020 12:23:42: start model_add_line... INFO @ Mon, 10 Aug 2020 12:23:42: start X-correlation... INFO @ Mon, 10 Aug 2020 12:23:42: end of X-cor INFO @ Mon, 10 Aug 2020 12:23:42: #2 finished! INFO @ Mon, 10 Aug 2020 12:23:42: #2 predicted fragment length is 123 bps INFO @ Mon, 10 Aug 2020 12:23:42: #2 alternative fragment length(s) may be 123 bps INFO @ Mon, 10 Aug 2020 12:23:42: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/SRX8047581/SRX8047581.05_model.r INFO @ Mon, 10 Aug 2020 12:23:42: #3 Call peaks... INFO @ Mon, 10 Aug 2020 12:23:42: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 10 Aug 2020 12:23:47: 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 @ Mon, 10 Aug 2020 12:23:50: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/SRX8047581/SRX8047581.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/SRX8047581/SRX8047581.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/SRX8047581/SRX8047581.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/SRX8047581/SRX8047581.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 @ Mon, 10 Aug 2020 12:23:50: #1 read tag files... INFO @ Mon, 10 Aug 2020 12:23:50: #1 read treatment tags... INFO @ Mon, 10 Aug 2020 12:23:53: 5000000 INFO @ Mon, 10 Aug 2020 12:23:57: 1000000 INFO @ Mon, 10 Aug 2020 12:23:59: #3 Call peaks for each chromosome... INFO @ Mon, 10 Aug 2020 12:24:00: 6000000 INFO @ Mon, 10 Aug 2020 12:24:04: 2000000 INFO @ Mon, 10 Aug 2020 12:24:07: 7000000 INFO @ Mon, 10 Aug 2020 12:24:09: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/SRX8047581/SRX8047581.05_peaks.xls INFO @ Mon, 10 Aug 2020 12:24:09: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/SRX8047581/SRX8047581.05_peaks.narrowPeak INFO @ Mon, 10 Aug 2020 12:24:09: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/SRX8047581/SRX8047581.05_summits.bed INFO @ Mon, 10 Aug 2020 12:24:09: Done! pass1 - making usageList (104 chroms): 4 millis pass2 - checking and writing primary data (21357 records, 4 fields): 22 millis CompletedMACS2peakCalling INFO @ Mon, 10 Aug 2020 12:24:11: 3000000 INFO @ Mon, 10 Aug 2020 12:24:14: #1 tag size is determined as 50 bps INFO @ Mon, 10 Aug 2020 12:24:14: #1 tag size = 50 INFO @ Mon, 10 Aug 2020 12:24:14: #1 total tags in treatment: 7978456 INFO @ Mon, 10 Aug 2020 12:24:14: #1 user defined the maximum tags... INFO @ Mon, 10 Aug 2020 12:24:14: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Mon, 10 Aug 2020 12:24:14: #1 tags after filtering in treatment: 7978198 INFO @ Mon, 10 Aug 2020 12:24:14: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 10 Aug 2020 12:24:14: #1 finished! INFO @ Mon, 10 Aug 2020 12:24:14: #2 Build Peak Model... INFO @ Mon, 10 Aug 2020 12:24:14: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 10 Aug 2020 12:24:16: #2 number of paired peaks: 38897 INFO @ Mon, 10 Aug 2020 12:24:16: start model_add_line... INFO @ Mon, 10 Aug 2020 12:24:16: start X-correlation... INFO @ Mon, 10 Aug 2020 12:24:16: end of X-cor INFO @ Mon, 10 Aug 2020 12:24:16: #2 finished! INFO @ Mon, 10 Aug 2020 12:24:16: #2 predicted fragment length is 123 bps INFO @ Mon, 10 Aug 2020 12:24:16: #2 alternative fragment length(s) may be 123 bps INFO @ Mon, 10 Aug 2020 12:24:16: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/SRX8047581/SRX8047581.10_model.r INFO @ Mon, 10 Aug 2020 12:24:16: #3 Call peaks... INFO @ Mon, 10 Aug 2020 12:24:16: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 10 Aug 2020 12:24:17: 4000000 INFO @ Mon, 10 Aug 2020 12:24:23: 5000000 INFO @ Mon, 10 Aug 2020 12:24:29: 6000000 INFO @ Mon, 10 Aug 2020 12:24:33: #3 Call peaks for each chromosome... INFO @ Mon, 10 Aug 2020 12:24:35: 7000000 INFO @ Mon, 10 Aug 2020 12:24:41: #1 tag size is determined as 50 bps INFO @ Mon, 10 Aug 2020 12:24:41: #1 tag size = 50 INFO @ Mon, 10 Aug 2020 12:24:41: #1 total tags in treatment: 7978456 INFO @ Mon, 10 Aug 2020 12:24:41: #1 user defined the maximum tags... INFO @ Mon, 10 Aug 2020 12:24:41: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Mon, 10 Aug 2020 12:24:41: #1 tags after filtering in treatment: 7978198 INFO @ Mon, 10 Aug 2020 12:24:41: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 10 Aug 2020 12:24:41: #1 finished! INFO @ Mon, 10 Aug 2020 12:24:41: #2 Build Peak Model... INFO @ Mon, 10 Aug 2020 12:24:41: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 10 Aug 2020 12:24:42: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/SRX8047581/SRX8047581.10_peaks.xls INFO @ Mon, 10 Aug 2020 12:24:42: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/SRX8047581/SRX8047581.10_peaks.narrowPeak INFO @ Mon, 10 Aug 2020 12:24:42: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/SRX8047581/SRX8047581.10_summits.bed INFO @ Mon, 10 Aug 2020 12:24:42: Done! pass1 - making usageList (82 chroms): 2 millis pass2 - checking and writing primary data (13285 records, 4 fields): 14 millis BedGraph に変換しました。 BigWig に変換中... CompletedMACS2peakCalling INFO @ Mon, 10 Aug 2020 12:24:43: #2 number of paired peaks: 38897 INFO @ Mon, 10 Aug 2020 12:24:43: start model_add_line... INFO @ Mon, 10 Aug 2020 12:24:43: start X-correlation... INFO @ Mon, 10 Aug 2020 12:24:43: end of X-cor INFO @ Mon, 10 Aug 2020 12:24:43: #2 finished! INFO @ Mon, 10 Aug 2020 12:24:43: #2 predicted fragment length is 123 bps INFO @ Mon, 10 Aug 2020 12:24:43: #2 alternative fragment length(s) may be 123 bps INFO @ Mon, 10 Aug 2020 12:24:43: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/SRX8047581/SRX8047581.20_model.r INFO @ Mon, 10 Aug 2020 12:24:43: #3 Call peaks... INFO @ Mon, 10 Aug 2020 12:24:43: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Mon, 10 Aug 2020 12:25:01: #3 Call peaks for each chromosome... INFO @ Mon, 10 Aug 2020 12:25:10: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/SRX8047581/SRX8047581.20_peaks.xls INFO @ Mon, 10 Aug 2020 12:25:10: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/SRX8047581/SRX8047581.20_peaks.narrowPeak INFO @ Mon, 10 Aug 2020 12:25:10: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/SRX8047581/SRX8047581.20_summits.bed INFO @ Mon, 10 Aug 2020 12:25:10: Done! pass1 - making usageList (40 chroms): 1 millis pass2 - checking and writing primary data (4721 records, 4 fields): 7 millis CompletedMACS2peakCalling