Job ID = 8184303 SRX = SRX8047582 Genome = rn6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-08-10T03:10:12 prefetch.2.10.7: 1) Downloading 'SRR11471307'... 2020-08-10T03:10:12 prefetch.2.10.7: Downloading via HTTPS... 2020-08-10T03:11:02 prefetch.2.10.7: HTTPS download succeed 2020-08-10T03:11:03 prefetch.2.10.7: 'SRR11471307' is valid 2020-08-10T03:11:03 prefetch.2.10.7: 1) 'SRR11471307' was downloaded successfully Read 11428806 spots for SRR11471307/SRR11471307.sra Written 11428806 spots for SRR11471307/SRR11471307.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: 00:05:27 11428806 reads; of these: 11428806 (100.00%) were unpaired; of these: 961128 (8.41%) aligned 0 times 8674490 (75.90%) aligned exactly 1 time 1793188 (15.69%) aligned >1 times 91.59% overall alignment rate Time searching: 00:05:30 Overall time: 00:05:30 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] 4607678 / 10467678 = 0.4402 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 12:19:49: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/SRX8047582/SRX8047582.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/SRX8047582/SRX8047582.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/SRX8047582/SRX8047582.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/SRX8047582/SRX8047582.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 12:19:49: #1 read tag files... INFO @ Mon, 10 Aug 2020 12:19:49: #1 read treatment tags... INFO @ Mon, 10 Aug 2020 12:19:55: 1000000 INFO @ Mon, 10 Aug 2020 12:20:01: 2000000 INFO @ Mon, 10 Aug 2020 12:20:06: 3000000 INFO @ Mon, 10 Aug 2020 12:20:12: 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 12:20:18: 5000000 INFO @ Mon, 10 Aug 2020 12:20:19: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/SRX8047582/SRX8047582.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/SRX8047582/SRX8047582.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/SRX8047582/SRX8047582.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/SRX8047582/SRX8047582.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 12:20:19: #1 read tag files... INFO @ Mon, 10 Aug 2020 12:20:19: #1 read treatment tags... INFO @ Mon, 10 Aug 2020 12:20:23: #1 tag size is determined as 50 bps INFO @ Mon, 10 Aug 2020 12:20:23: #1 tag size = 50 INFO @ Mon, 10 Aug 2020 12:20:23: #1 total tags in treatment: 5860000 INFO @ Mon, 10 Aug 2020 12:20:23: #1 user defined the maximum tags... INFO @ Mon, 10 Aug 2020 12:20:23: #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 12:20:23: #1 tags after filtering in treatment: 5859723 INFO @ Mon, 10 Aug 2020 12:20:23: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 10 Aug 2020 12:20:23: #1 finished! INFO @ Mon, 10 Aug 2020 12:20:23: #2 Build Peak Model... INFO @ Mon, 10 Aug 2020 12:20:23: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 10 Aug 2020 12:20:25: #2 number of paired peaks: 40247 INFO @ Mon, 10 Aug 2020 12:20:25: start model_add_line... INFO @ Mon, 10 Aug 2020 12:20:25: start X-correlation... INFO @ Mon, 10 Aug 2020 12:20:25: end of X-cor INFO @ Mon, 10 Aug 2020 12:20:25: #2 finished! INFO @ Mon, 10 Aug 2020 12:20:25: #2 predicted fragment length is 123 bps INFO @ Mon, 10 Aug 2020 12:20:25: #2 alternative fragment length(s) may be 123 bps INFO @ Mon, 10 Aug 2020 12:20:25: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/SRX8047582/SRX8047582.05_model.r INFO @ Mon, 10 Aug 2020 12:20:25: #3 Call peaks... INFO @ Mon, 10 Aug 2020 12:20:25: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 10 Aug 2020 12:20:26: 1000000 INFO @ Mon, 10 Aug 2020 12:20:32: 2000000 INFO @ Mon, 10 Aug 2020 12:20:38: 3000000 INFO @ Mon, 10 Aug 2020 12:20:38: #3 Call peaks for each chromosome... INFO @ Mon, 10 Aug 2020 12:20:43: 4000000 INFO @ Mon, 10 Aug 2020 12:20:45: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/SRX8047582/SRX8047582.05_peaks.xls INFO @ Mon, 10 Aug 2020 12:20:45: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/SRX8047582/SRX8047582.05_peaks.narrowPeak INFO @ Mon, 10 Aug 2020 12:20:45: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/SRX8047582/SRX8047582.05_summits.bed INFO @ Mon, 10 Aug 2020 12:20:45: Done! pass1 - making usageList (115 chroms): 3 millis pass2 - checking and writing primary data (21850 records, 4 fields): 25 millis CompletedMACS2peakCalling 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 12:20:49: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/SRX8047582/SRX8047582.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/SRX8047582/SRX8047582.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/SRX8047582/SRX8047582.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/SRX8047582/SRX8047582.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 12:20:49: #1 read tag files... INFO @ Mon, 10 Aug 2020 12:20:49: #1 read treatment tags... INFO @ Mon, 10 Aug 2020 12:20:49: 5000000 INFO @ Mon, 10 Aug 2020 12:20:55: #1 tag size is determined as 50 bps INFO @ Mon, 10 Aug 2020 12:20:55: #1 tag size = 50 INFO @ Mon, 10 Aug 2020 12:20:55: #1 total tags in treatment: 5860000 INFO @ Mon, 10 Aug 2020 12:20:55: #1 user defined the maximum tags... INFO @ Mon, 10 Aug 2020 12:20:55: #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 12:20:55: #1 tags after filtering in treatment: 5859723 INFO @ Mon, 10 Aug 2020 12:20:55: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 10 Aug 2020 12:20:55: #1 finished! INFO @ Mon, 10 Aug 2020 12:20:55: #2 Build Peak Model... INFO @ Mon, 10 Aug 2020 12:20:55: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 10 Aug 2020 12:20:56: 1000000 INFO @ Mon, 10 Aug 2020 12:20:57: #2 number of paired peaks: 40247 INFO @ Mon, 10 Aug 2020 12:20:57: start model_add_line... INFO @ Mon, 10 Aug 2020 12:20:57: start X-correlation... INFO @ Mon, 10 Aug 2020 12:20:57: end of X-cor INFO @ Mon, 10 Aug 2020 12:20:57: #2 finished! INFO @ Mon, 10 Aug 2020 12:20:57: #2 predicted fragment length is 123 bps INFO @ Mon, 10 Aug 2020 12:20:57: #2 alternative fragment length(s) may be 123 bps INFO @ Mon, 10 Aug 2020 12:20:57: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/SRX8047582/SRX8047582.10_model.r INFO @ Mon, 10 Aug 2020 12:20:57: #3 Call peaks... INFO @ Mon, 10 Aug 2020 12:20:57: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 10 Aug 2020 12:21:02: 2000000 INFO @ Mon, 10 Aug 2020 12:21:07: 3000000 INFO @ Mon, 10 Aug 2020 12:21:10: #3 Call peaks for each chromosome... INFO @ Mon, 10 Aug 2020 12:21:13: 4000000 INFO @ Mon, 10 Aug 2020 12:21:16: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/SRX8047582/SRX8047582.10_peaks.xls INFO @ Mon, 10 Aug 2020 12:21:16: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/SRX8047582/SRX8047582.10_peaks.narrowPeak INFO @ Mon, 10 Aug 2020 12:21:16: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/SRX8047582/SRX8047582.10_summits.bed INFO @ Mon, 10 Aug 2020 12:21:16: Done! pass1 - making usageList (92 chroms): 2 millis pass2 - checking and writing primary data (13439 records, 4 fields): 14 millis CompletedMACS2peakCalling INFO @ Mon, 10 Aug 2020 12:21:19: 5000000 INFO @ Mon, 10 Aug 2020 12:21:24: #1 tag size is determined as 50 bps INFO @ Mon, 10 Aug 2020 12:21:24: #1 tag size = 50 INFO @ Mon, 10 Aug 2020 12:21:24: #1 total tags in treatment: 5860000 INFO @ Mon, 10 Aug 2020 12:21:24: #1 user defined the maximum tags... INFO @ Mon, 10 Aug 2020 12:21:24: #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 12:21:24: #1 tags after filtering in treatment: 5859723 INFO @ Mon, 10 Aug 2020 12:21:24: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 10 Aug 2020 12:21:24: #1 finished! INFO @ Mon, 10 Aug 2020 12:21:24: #2 Build Peak Model... INFO @ Mon, 10 Aug 2020 12:21:24: #2 looking for paired plus/minus strand peaks... BedGraph に変換しました。 BigWig に変換中... INFO @ Mon, 10 Aug 2020 12:21:26: #2 number of paired peaks: 40247 INFO @ Mon, 10 Aug 2020 12:21:26: start model_add_line... INFO @ Mon, 10 Aug 2020 12:21:26: start X-correlation... INFO @ Mon, 10 Aug 2020 12:21:26: end of X-cor INFO @ Mon, 10 Aug 2020 12:21:26: #2 finished! INFO @ Mon, 10 Aug 2020 12:21:26: #2 predicted fragment length is 123 bps INFO @ Mon, 10 Aug 2020 12:21:26: #2 alternative fragment length(s) may be 123 bps INFO @ Mon, 10 Aug 2020 12:21:26: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/SRX8047582/SRX8047582.20_model.r INFO @ Mon, 10 Aug 2020 12:21:26: #3 Call peaks... INFO @ Mon, 10 Aug 2020 12:21:26: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Mon, 10 Aug 2020 12:21:39: #3 Call peaks for each chromosome... INFO @ Mon, 10 Aug 2020 12:21:45: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/SRX8047582/SRX8047582.20_peaks.xls INFO @ Mon, 10 Aug 2020 12:21:45: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/SRX8047582/SRX8047582.20_peaks.narrowPeak INFO @ Mon, 10 Aug 2020 12:21:45: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/SRX8047582/SRX8047582.20_summits.bed INFO @ Mon, 10 Aug 2020 12:21:45: Done! pass1 - making usageList (43 chroms): 1 millis pass2 - checking and writing primary data (4239 records, 4 fields): 7 millis CompletedMACS2peakCalling