Job ID = 6366076 SRX = SRX059248 Genome = ce11 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-15T22:25:44 prefetch.2.10.7: 1) Downloading 'SRR190688'... 2020-06-15T22:25:44 prefetch.2.10.7: Downloading via HTTPS... 2020-06-15T22:26:11 prefetch.2.10.7: HTTPS download succeed 2020-06-15T22:26:11 prefetch.2.10.7: 'SRR190688' is valid 2020-06-15T22:26:11 prefetch.2.10.7: 1) 'SRR190688' was downloaded successfully Read 8114172 spots for SRR190688/SRR190688.sra Written 8114172 spots for SRR190688/SRR190688.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: 00:01:12 8114172 reads; of these: 8114172 (100.00%) were unpaired; of these: 116499 (1.44%) aligned 0 times 6555503 (80.79%) aligned exactly 1 time 1442170 (17.77%) aligned >1 times 98.56% overall alignment rate Time searching: 00:01:12 Overall time: 00:01:12 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] 2055197 / 7997673 = 0.2570 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 07:29:31: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX059248/SRX059248.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX059248/SRX059248.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX059248/SRX059248.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX059248/SRX059248.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 07:29:31: #1 read tag files... INFO @ Tue, 16 Jun 2020 07:29:31: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 07:29:36: 1000000 INFO @ Tue, 16 Jun 2020 07:29:41: 2000000 INFO @ Tue, 16 Jun 2020 07:29:47: 3000000 INFO @ Tue, 16 Jun 2020 07:29:52: 4000000 INFO @ Tue, 16 Jun 2020 07:29:58: 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 @ Tue, 16 Jun 2020 07:30:00: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX059248/SRX059248.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX059248/SRX059248.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX059248/SRX059248.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX059248/SRX059248.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 07:30:00: #1 read tag files... INFO @ Tue, 16 Jun 2020 07:30:00: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 07:30:03: #1 tag size is determined as 28 bps INFO @ Tue, 16 Jun 2020 07:30:03: #1 tag size = 28 INFO @ Tue, 16 Jun 2020 07:30:03: #1 total tags in treatment: 5942476 INFO @ Tue, 16 Jun 2020 07:30:03: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 07:30:03: #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 07:30:03: #1 tags after filtering in treatment: 5942476 INFO @ Tue, 16 Jun 2020 07:30:03: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 07:30:03: #1 finished! INFO @ Tue, 16 Jun 2020 07:30:03: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 07:30:03: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 07:30:04: #2 number of paired peaks: 1145 INFO @ Tue, 16 Jun 2020 07:30:04: start model_add_line... INFO @ Tue, 16 Jun 2020 07:30:04: start X-correlation... INFO @ Tue, 16 Jun 2020 07:30:04: end of X-cor INFO @ Tue, 16 Jun 2020 07:30:04: #2 finished! INFO @ Tue, 16 Jun 2020 07:30:04: #2 predicted fragment length is 241 bps INFO @ Tue, 16 Jun 2020 07:30:04: #2 alternative fragment length(s) may be 241 bps INFO @ Tue, 16 Jun 2020 07:30:04: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX059248/SRX059248.05_model.r INFO @ Tue, 16 Jun 2020 07:30:04: #3 Call peaks... INFO @ Tue, 16 Jun 2020 07:30:04: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 07:30:06: 1000000 INFO @ Tue, 16 Jun 2020 07:30:12: 2000000 INFO @ Tue, 16 Jun 2020 07:30:17: 3000000 INFO @ Tue, 16 Jun 2020 07:30:19: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 07:30:23: 4000000 INFO @ Tue, 16 Jun 2020 07:30:25: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX059248/SRX059248.05_peaks.xls INFO @ Tue, 16 Jun 2020 07:30:25: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX059248/SRX059248.05_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 07:30:25: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX059248/SRX059248.05_summits.bed INFO @ Tue, 16 Jun 2020 07:30:25: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (3034 records, 4 fields): 5 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 07:30:28: 5000000 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 07:30:30: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX059248/SRX059248.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX059248/SRX059248.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX059248/SRX059248.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX059248/SRX059248.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 07:30:30: #1 read tag files... INFO @ Tue, 16 Jun 2020 07:30:30: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 07:30:34: #1 tag size is determined as 28 bps INFO @ Tue, 16 Jun 2020 07:30:34: #1 tag size = 28 INFO @ Tue, 16 Jun 2020 07:30:34: #1 total tags in treatment: 5942476 INFO @ Tue, 16 Jun 2020 07:30:34: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 07:30:34: #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 07:30:34: #1 tags after filtering in treatment: 5942476 INFO @ Tue, 16 Jun 2020 07:30:34: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 07:30:34: #1 finished! INFO @ Tue, 16 Jun 2020 07:30:34: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 07:30:34: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 07:30:34: #2 number of paired peaks: 1145 INFO @ Tue, 16 Jun 2020 07:30:34: start model_add_line... INFO @ Tue, 16 Jun 2020 07:30:34: start X-correlation... INFO @ Tue, 16 Jun 2020 07:30:34: end of X-cor INFO @ Tue, 16 Jun 2020 07:30:34: #2 finished! INFO @ Tue, 16 Jun 2020 07:30:34: #2 predicted fragment length is 241 bps INFO @ Tue, 16 Jun 2020 07:30:34: #2 alternative fragment length(s) may be 241 bps INFO @ Tue, 16 Jun 2020 07:30:34: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX059248/SRX059248.10_model.r INFO @ Tue, 16 Jun 2020 07:30:34: #3 Call peaks... INFO @ Tue, 16 Jun 2020 07:30:34: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 07:30:36: 1000000 INFO @ Tue, 16 Jun 2020 07:30:42: 2000000 INFO @ Tue, 16 Jun 2020 07:30:47: 3000000 INFO @ Tue, 16 Jun 2020 07:30:50: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 07:30:52: 4000000 INFO @ Tue, 16 Jun 2020 07:30:57: 5000000 INFO @ Tue, 16 Jun 2020 07:30:57: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX059248/SRX059248.10_peaks.xls INFO @ Tue, 16 Jun 2020 07:30:57: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX059248/SRX059248.10_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 07:30:57: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX059248/SRX059248.10_summits.bed INFO @ Tue, 16 Jun 2020 07:30:57: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (2029 records, 4 fields): 3 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 16 Jun 2020 07:31:02: #1 tag size is determined as 28 bps INFO @ Tue, 16 Jun 2020 07:31:02: #1 tag size = 28 INFO @ Tue, 16 Jun 2020 07:31:02: #1 total tags in treatment: 5942476 INFO @ Tue, 16 Jun 2020 07:31:02: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 07:31:02: #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 07:31:02: #1 tags after filtering in treatment: 5942476 INFO @ Tue, 16 Jun 2020 07:31:02: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 07:31:02: #1 finished! INFO @ Tue, 16 Jun 2020 07:31:02: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 07:31:02: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 07:31:02: #2 number of paired peaks: 1145 INFO @ Tue, 16 Jun 2020 07:31:02: start model_add_line... INFO @ Tue, 16 Jun 2020 07:31:02: start X-correlation... INFO @ Tue, 16 Jun 2020 07:31:02: end of X-cor INFO @ Tue, 16 Jun 2020 07:31:02: #2 finished! INFO @ Tue, 16 Jun 2020 07:31:02: #2 predicted fragment length is 241 bps INFO @ Tue, 16 Jun 2020 07:31:02: #2 alternative fragment length(s) may be 241 bps INFO @ Tue, 16 Jun 2020 07:31:02: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX059248/SRX059248.20_model.r INFO @ Tue, 16 Jun 2020 07:31:02: #3 Call peaks... INFO @ Tue, 16 Jun 2020 07:31:02: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Tue, 16 Jun 2020 07:31:17: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 07:31:24: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX059248/SRX059248.20_peaks.xls INFO @ Tue, 16 Jun 2020 07:31:24: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX059248/SRX059248.20_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 07:31:24: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX059248/SRX059248.20_summits.bed INFO @ Tue, 16 Jun 2020 07:31:24: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (1212 records, 4 fields): 5 millis CompletedMACS2peakCalling