Job ID = 8184565 SRX = SRX8047613 Genome = rn6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-08-10T04:39:04 prefetch.2.10.7: 1) Downloading 'SRR11471337'... 2020-08-10T04:39:04 prefetch.2.10.7: Downloading via HTTPS... 2020-08-10T04:40:05 prefetch.2.10.7: HTTPS download succeed 2020-08-10T04:40:05 prefetch.2.10.7: 1) 'SRR11471337' was downloaded successfully Read 19204691 spots for SRR11471337/SRR11471337.sra Written 19204691 spots for SRR11471337/SRR11471337.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: 00:00:00 Time loading mirror index: 00:00:01 Multiseed full-index search: 00:12:19 19204691 reads; of these: 19204691 (100.00%) were unpaired; of these: 2556967 (13.31%) aligned 0 times 14299489 (74.46%) aligned exactly 1 time 2348235 (12.23%) aligned >1 times 86.69% overall alignment rate Time searching: 00:12:21 Overall time: 00:12:21 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] 8176104 / 16647724 = 0.4911 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 13:57:08: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/SRX8047613/SRX8047613.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/SRX8047613/SRX8047613.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/SRX8047613/SRX8047613.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/SRX8047613/SRX8047613.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 13:57:08: #1 read tag files... INFO @ Mon, 10 Aug 2020 13:57:08: #1 read treatment tags... INFO @ Mon, 10 Aug 2020 13:57:14: 1000000 INFO @ Mon, 10 Aug 2020 13:57:20: 2000000 INFO @ Mon, 10 Aug 2020 13:57:26: 3000000 INFO @ Mon, 10 Aug 2020 13:57:32: 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 13:57:38: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/SRX8047613/SRX8047613.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/SRX8047613/SRX8047613.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/SRX8047613/SRX8047613.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/SRX8047613/SRX8047613.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 13:57:38: #1 read tag files... INFO @ Mon, 10 Aug 2020 13:57:38: #1 read treatment tags... INFO @ Mon, 10 Aug 2020 13:57:38: 5000000 INFO @ Mon, 10 Aug 2020 13:57:44: 1000000 INFO @ Mon, 10 Aug 2020 13:57:44: 6000000 INFO @ Mon, 10 Aug 2020 13:57:50: 2000000 INFO @ Mon, 10 Aug 2020 13:57:50: 7000000 INFO @ Mon, 10 Aug 2020 13:57:56: 3000000 INFO @ Mon, 10 Aug 2020 13:57:56: 8000000 INFO @ Mon, 10 Aug 2020 13:57:59: #1 tag size is determined as 50 bps INFO @ Mon, 10 Aug 2020 13:57:59: #1 tag size = 50 INFO @ Mon, 10 Aug 2020 13:57:59: #1 total tags in treatment: 8471620 INFO @ Mon, 10 Aug 2020 13:57:59: #1 user defined the maximum tags... INFO @ Mon, 10 Aug 2020 13:57:59: #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 13:58:00: #1 tags after filtering in treatment: 8471364 INFO @ Mon, 10 Aug 2020 13:58:00: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 10 Aug 2020 13:58:00: #1 finished! INFO @ Mon, 10 Aug 2020 13:58:00: #2 Build Peak Model... INFO @ Mon, 10 Aug 2020 13:58:00: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 10 Aug 2020 13:58:01: #2 number of paired peaks: 38505 INFO @ Mon, 10 Aug 2020 13:58:01: start model_add_line... INFO @ Mon, 10 Aug 2020 13:58:01: start X-correlation... INFO @ Mon, 10 Aug 2020 13:58:01: end of X-cor INFO @ Mon, 10 Aug 2020 13:58:01: #2 finished! INFO @ Mon, 10 Aug 2020 13:58:01: #2 predicted fragment length is 114 bps INFO @ Mon, 10 Aug 2020 13:58:01: #2 alternative fragment length(s) may be 114 bps INFO @ Mon, 10 Aug 2020 13:58:01: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/SRX8047613/SRX8047613.05_model.r INFO @ Mon, 10 Aug 2020 13:58:01: #3 Call peaks... INFO @ Mon, 10 Aug 2020 13:58:01: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 10 Aug 2020 13:58:02: 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 13:58:08: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/SRX8047613/SRX8047613.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/SRX8047613/SRX8047613.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/SRX8047613/SRX8047613.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/SRX8047613/SRX8047613.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 13:58:08: #1 read tag files... INFO @ Mon, 10 Aug 2020 13:58:08: #1 read treatment tags... INFO @ Mon, 10 Aug 2020 13:58:08: 5000000 INFO @ Mon, 10 Aug 2020 13:58:14: 6000000 INFO @ Mon, 10 Aug 2020 13:58:14: 1000000 INFO @ Mon, 10 Aug 2020 13:58:19: #3 Call peaks for each chromosome... INFO @ Mon, 10 Aug 2020 13:58:20: 7000000 INFO @ Mon, 10 Aug 2020 13:58:21: 2000000 INFO @ Mon, 10 Aug 2020 13:58:26: 8000000 INFO @ Mon, 10 Aug 2020 13:58:27: 3000000 INFO @ Mon, 10 Aug 2020 13:58:29: #1 tag size is determined as 50 bps INFO @ Mon, 10 Aug 2020 13:58:29: #1 tag size = 50 INFO @ Mon, 10 Aug 2020 13:58:29: #1 total tags in treatment: 8471620 INFO @ Mon, 10 Aug 2020 13:58:29: #1 user defined the maximum tags... INFO @ Mon, 10 Aug 2020 13:58:29: #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 13:58:30: #1 tags after filtering in treatment: 8471364 INFO @ Mon, 10 Aug 2020 13:58:30: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 10 Aug 2020 13:58:30: #1 finished! INFO @ Mon, 10 Aug 2020 13:58:30: #2 Build Peak Model... INFO @ Mon, 10 Aug 2020 13:58:30: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 10 Aug 2020 13:58:30: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/SRX8047613/SRX8047613.05_peaks.xls INFO @ Mon, 10 Aug 2020 13:58:30: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/SRX8047613/SRX8047613.05_peaks.narrowPeak INFO @ Mon, 10 Aug 2020 13:58:30: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/SRX8047613/SRX8047613.05_summits.bed INFO @ Mon, 10 Aug 2020 13:58:30: Done! pass1 - making usageList (138 chroms): 4 millis pass2 - checking and writing primary data (34204 records, 4 fields): 34 millis CompletedMACS2peakCalling INFO @ Mon, 10 Aug 2020 13:58:31: #2 number of paired peaks: 38505 INFO @ Mon, 10 Aug 2020 13:58:31: start model_add_line... INFO @ Mon, 10 Aug 2020 13:58:31: start X-correlation... INFO @ Mon, 10 Aug 2020 13:58:31: end of X-cor INFO @ Mon, 10 Aug 2020 13:58:31: #2 finished! INFO @ Mon, 10 Aug 2020 13:58:31: #2 predicted fragment length is 114 bps INFO @ Mon, 10 Aug 2020 13:58:31: #2 alternative fragment length(s) may be 114 bps INFO @ Mon, 10 Aug 2020 13:58:31: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/SRX8047613/SRX8047613.10_model.r INFO @ Mon, 10 Aug 2020 13:58:31: #3 Call peaks... INFO @ Mon, 10 Aug 2020 13:58:31: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 10 Aug 2020 13:58:33: 4000000 INFO @ Mon, 10 Aug 2020 13:58:39: 5000000 INFO @ Mon, 10 Aug 2020 13:58:45: 6000000 INFO @ Mon, 10 Aug 2020 13:58:49: #3 Call peaks for each chromosome... INFO @ Mon, 10 Aug 2020 13:58:51: 7000000 INFO @ Mon, 10 Aug 2020 13:58:56: 8000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Mon, 10 Aug 2020 13:58:59: #1 tag size is determined as 50 bps INFO @ Mon, 10 Aug 2020 13:58:59: #1 tag size = 50 INFO @ Mon, 10 Aug 2020 13:58:59: #1 total tags in treatment: 8471620 INFO @ Mon, 10 Aug 2020 13:58:59: #1 user defined the maximum tags... INFO @ Mon, 10 Aug 2020 13:58:59: #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 13:58:59: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/SRX8047613/SRX8047613.10_peaks.xls INFO @ Mon, 10 Aug 2020 13:58:59: #1 tags after filtering in treatment: 8471364 INFO @ Mon, 10 Aug 2020 13:58:59: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 10 Aug 2020 13:58:59: #1 finished! INFO @ Mon, 10 Aug 2020 13:58:59: #2 Build Peak Model... INFO @ Mon, 10 Aug 2020 13:58:59: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 10 Aug 2020 13:59:00: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/SRX8047613/SRX8047613.10_peaks.narrowPeak INFO @ Mon, 10 Aug 2020 13:59:00: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/SRX8047613/SRX8047613.10_summits.bed INFO @ Mon, 10 Aug 2020 13:59:00: Done! pass1 - making usageList (113 chroms): 4 millis pass2 - checking and writing primary data (24916 records, 4 fields): 25 millis CompletedMACS2peakCalling INFO @ Mon, 10 Aug 2020 13:59:01: #2 number of paired peaks: 38505 INFO @ Mon, 10 Aug 2020 13:59:01: start model_add_line... INFO @ Mon, 10 Aug 2020 13:59:01: start X-correlation... INFO @ Mon, 10 Aug 2020 13:59:01: end of X-cor INFO @ Mon, 10 Aug 2020 13:59:01: #2 finished! INFO @ Mon, 10 Aug 2020 13:59:01: #2 predicted fragment length is 114 bps INFO @ Mon, 10 Aug 2020 13:59:01: #2 alternative fragment length(s) may be 114 bps INFO @ Mon, 10 Aug 2020 13:59:01: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/SRX8047613/SRX8047613.20_model.r INFO @ Mon, 10 Aug 2020 13:59:01: #3 Call peaks... INFO @ Mon, 10 Aug 2020 13:59:01: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Mon, 10 Aug 2020 13:59:19: #3 Call peaks for each chromosome... INFO @ Mon, 10 Aug 2020 13:59:29: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/SRX8047613/SRX8047613.20_peaks.xls INFO @ Mon, 10 Aug 2020 13:59:29: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/SRX8047613/SRX8047613.20_peaks.narrowPeak INFO @ Mon, 10 Aug 2020 13:59:29: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/SRX8047613/SRX8047613.20_summits.bed INFO @ Mon, 10 Aug 2020 13:59:29: Done! pass1 - making usageList (88 chroms): 3 millis pass2 - checking and writing primary data (15464 records, 4 fields): 17 millis CompletedMACS2peakCalling