Job ID = 6368090 SRX = SRX466553 Genome = ce11 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-16T00:07:54 prefetch.2.10.7: 1) Downloading 'SRR1163619'... 2020-06-16T00:07:54 prefetch.2.10.7: Downloading via HTTPS... 2020-06-16T00:09:19 prefetch.2.10.7: HTTPS download succeed 2020-06-16T00:09:19 prefetch.2.10.7: 'SRR1163619' is valid 2020-06-16T00:09:19 prefetch.2.10.7: 1) 'SRR1163619' was downloaded successfully Read 6508319 spots for SRR1163619/SRR1163619.sra Written 6508319 spots for SRR1163619/SRR1163619.sra 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: 00:00:00 Time loading mirror index: 00:00:00 Multiseed full-index search: 00:00:59 6508319 reads; of these: 6508319 (100.00%) were unpaired; of these: 1505301 (23.13%) aligned 0 times 4510161 (69.30%) aligned exactly 1 time 492857 (7.57%) aligned >1 times 76.87% overall alignment rate Time searching: 00:00:59 Overall time: 00:00:59 マッピングが完了しました。 samtools でBAM に変換中... [samopen] SAM header is present: 7 sequences. [bam_rmdupse_core] 1476723 / 5003018 = 0.2952 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 @ Tue, 16 Jun 2020 09:12:08: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX466553/SRX466553.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX466553/SRX466553.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX466553/SRX466553.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX466553/SRX466553.bam'] # control file = None # effective genome size = 9.00e+07 # 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 @ Tue, 16 Jun 2020 09:12:08: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:12:08: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:12:13: 1000000 INFO @ Tue, 16 Jun 2020 09:12:19: 2000000 INFO @ Tue, 16 Jun 2020 09:12:24: 3000000 INFO @ Tue, 16 Jun 2020 09:12:27: #1 tag size is determined as 42 bps INFO @ Tue, 16 Jun 2020 09:12:27: #1 tag size = 42 INFO @ Tue, 16 Jun 2020 09:12:27: #1 total tags in treatment: 3526295 INFO @ Tue, 16 Jun 2020 09:12:27: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:12:27: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 16 Jun 2020 09:12:27: #1 tags after filtering in treatment: 3526295 INFO @ Tue, 16 Jun 2020 09:12:27: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 09:12:27: #1 finished! INFO @ Tue, 16 Jun 2020 09:12:27: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:12:27: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:12:28: #2 number of paired peaks: 3807 INFO @ Tue, 16 Jun 2020 09:12:28: start model_add_line... INFO @ Tue, 16 Jun 2020 09:12:28: start X-correlation... INFO @ Tue, 16 Jun 2020 09:12:28: end of X-cor INFO @ Tue, 16 Jun 2020 09:12:28: #2 finished! INFO @ Tue, 16 Jun 2020 09:12:28: #2 predicted fragment length is 222 bps INFO @ Tue, 16 Jun 2020 09:12:28: #2 alternative fragment length(s) may be 4,222 bps INFO @ Tue, 16 Jun 2020 09:12:28: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX466553/SRX466553.05_model.r INFO @ Tue, 16 Jun 2020 09:12:28: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:12:28: #3 Pre-compute pvalue-qvalue table... 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 @ Tue, 16 Jun 2020 09:12:37: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 09:12:38: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX466553/SRX466553.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX466553/SRX466553.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX466553/SRX466553.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX466553/SRX466553.bam'] # control file = None # effective genome size = 9.00e+07 # 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 @ Tue, 16 Jun 2020 09:12:38: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:12:38: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:12:42: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX466553/SRX466553.05_peaks.xls INFO @ Tue, 16 Jun 2020 09:12:42: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX466553/SRX466553.05_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:12:42: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX466553/SRX466553.05_summits.bed INFO @ Tue, 16 Jun 2020 09:12:42: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (2389 records, 4 fields): 4 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 09:12:44: 1000000 INFO @ Tue, 16 Jun 2020 09:12:49: 2000000 INFO @ Tue, 16 Jun 2020 09:12:55: 3000000 INFO @ Tue, 16 Jun 2020 09:12:58: #1 tag size is determined as 42 bps INFO @ Tue, 16 Jun 2020 09:12:58: #1 tag size = 42 INFO @ Tue, 16 Jun 2020 09:12:58: #1 total tags in treatment: 3526295 INFO @ Tue, 16 Jun 2020 09:12:58: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:12:58: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 16 Jun 2020 09:12:58: #1 tags after filtering in treatment: 3526295 INFO @ Tue, 16 Jun 2020 09:12:58: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 09:12:58: #1 finished! INFO @ Tue, 16 Jun 2020 09:12:58: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:12:58: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:12:58: #2 number of paired peaks: 3807 INFO @ Tue, 16 Jun 2020 09:12:58: start model_add_line... INFO @ Tue, 16 Jun 2020 09:12:58: start X-correlation... INFO @ Tue, 16 Jun 2020 09:12:58: end of X-cor INFO @ Tue, 16 Jun 2020 09:12:58: #2 finished! INFO @ Tue, 16 Jun 2020 09:12:58: #2 predicted fragment length is 222 bps INFO @ Tue, 16 Jun 2020 09:12:58: #2 alternative fragment length(s) may be 4,222 bps INFO @ Tue, 16 Jun 2020 09:12:58: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX466553/SRX466553.10_model.r INFO @ Tue, 16 Jun 2020 09:12:58: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:12:58: #3 Pre-compute pvalue-qvalue table... 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 @ Tue, 16 Jun 2020 09:13:08: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX466553/SRX466553.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX466553/SRX466553.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX466553/SRX466553.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX466553/SRX466553.bam'] # control file = None # effective genome size = 9.00e+07 # 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 @ Tue, 16 Jun 2020 09:13:08: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:13:08: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:13:09: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 09:13:14: 1000000 INFO @ Tue, 16 Jun 2020 09:13:14: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX466553/SRX466553.10_peaks.xls INFO @ Tue, 16 Jun 2020 09:13:14: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX466553/SRX466553.10_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:13:14: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX466553/SRX466553.10_summits.bed INFO @ Tue, 16 Jun 2020 09:13:14: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (1124 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 09:13:19: 2000000 INFO @ Tue, 16 Jun 2020 09:13:25: 3000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 16 Jun 2020 09:13:28: #1 tag size is determined as 42 bps INFO @ Tue, 16 Jun 2020 09:13:28: #1 tag size = 42 INFO @ Tue, 16 Jun 2020 09:13:28: #1 total tags in treatment: 3526295 INFO @ Tue, 16 Jun 2020 09:13:28: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:13:28: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 16 Jun 2020 09:13:28: #1 tags after filtering in treatment: 3526295 INFO @ Tue, 16 Jun 2020 09:13:28: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 09:13:28: #1 finished! INFO @ Tue, 16 Jun 2020 09:13:28: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:13:28: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:13:28: #2 number of paired peaks: 3807 INFO @ Tue, 16 Jun 2020 09:13:28: start model_add_line... INFO @ Tue, 16 Jun 2020 09:13:28: start X-correlation... INFO @ Tue, 16 Jun 2020 09:13:28: end of X-cor INFO @ Tue, 16 Jun 2020 09:13:28: #2 finished! INFO @ Tue, 16 Jun 2020 09:13:28: #2 predicted fragment length is 222 bps INFO @ Tue, 16 Jun 2020 09:13:28: #2 alternative fragment length(s) may be 4,222 bps INFO @ Tue, 16 Jun 2020 09:13:28: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX466553/SRX466553.20_model.r INFO @ Tue, 16 Jun 2020 09:13:28: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:13:28: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Tue, 16 Jun 2020 09:13:38: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 09:13:43: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX466553/SRX466553.20_peaks.xls INFO @ Tue, 16 Jun 2020 09:13:43: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX466553/SRX466553.20_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:13:43: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX466553/SRX466553.20_summits.bed INFO @ Tue, 16 Jun 2020 09:13:43: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (306 records, 4 fields): 1 millis CompletedMACS2peakCalling