Job ID = 6367217 SRX = SRX3043403 Genome = ce11 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-15T23:23:01 prefetch.2.10.7: 1) Downloading 'SRR5875887'... 2020-06-15T23:23:01 prefetch.2.10.7: Downloading via HTTPS... 2020-06-15T23:23:42 prefetch.2.10.7: HTTPS download succeed 2020-06-15T23:23:42 prefetch.2.10.7: 'SRR5875887' is valid 2020-06-15T23:23:42 prefetch.2.10.7: 1) 'SRR5875887' was downloaded successfully Read 9419509 spots for SRR5875887/SRR5875887.sra Written 9419509 spots for SRR5875887/SRR5875887.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: 00:02:44 9419509 reads; of these: 9419509 (100.00%) were unpaired; of these: 151520 (1.61%) aligned 0 times 8163859 (86.67%) aligned exactly 1 time 1104130 (11.72%) aligned >1 times 98.39% overall alignment rate Time searching: 00:02:44 Overall time: 00:02:44 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] 1089646 / 9267989 = 0.1176 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 08:30:02: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX3043403/SRX3043403.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX3043403/SRX3043403.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX3043403/SRX3043403.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX3043403/SRX3043403.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 08:30:02: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:30:02: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:30:08: 1000000 INFO @ Tue, 16 Jun 2020 08:30:15: 2000000 INFO @ Tue, 16 Jun 2020 08:30:22: 3000000 INFO @ Tue, 16 Jun 2020 08:30:28: 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 @ Tue, 16 Jun 2020 08:30:32: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX3043403/SRX3043403.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX3043403/SRX3043403.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX3043403/SRX3043403.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX3043403/SRX3043403.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 08:30:32: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:30:32: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:30:35: 5000000 INFO @ Tue, 16 Jun 2020 08:30:41: 1000000 INFO @ Tue, 16 Jun 2020 08:30:43: 6000000 INFO @ Tue, 16 Jun 2020 08:30:49: 2000000 INFO @ Tue, 16 Jun 2020 08:30:51: 7000000 INFO @ Tue, 16 Jun 2020 08:30:57: 3000000 INFO @ Tue, 16 Jun 2020 08:30:59: 8000000 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 08:31:00: #1 tag size is determined as 50 bps INFO @ Tue, 16 Jun 2020 08:31:00: #1 tag size = 50 INFO @ Tue, 16 Jun 2020 08:31:00: #1 total tags in treatment: 8178343 INFO @ Tue, 16 Jun 2020 08:31:00: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:31:00: #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 08:31:00: #1 tags after filtering in treatment: 8178343 INFO @ Tue, 16 Jun 2020 08:31:00: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:31:00: #1 finished! INFO @ Tue, 16 Jun 2020 08:31:00: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:31:00: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:31:01: #2 number of paired peaks: 1253 INFO @ Tue, 16 Jun 2020 08:31:01: start model_add_line... INFO @ Tue, 16 Jun 2020 08:31:01: start X-correlation... INFO @ Tue, 16 Jun 2020 08:31:01: end of X-cor INFO @ Tue, 16 Jun 2020 08:31:01: #2 finished! INFO @ Tue, 16 Jun 2020 08:31:01: #2 predicted fragment length is 171 bps INFO @ Tue, 16 Jun 2020 08:31:01: #2 alternative fragment length(s) may be 171 bps INFO @ Tue, 16 Jun 2020 08:31:01: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX3043403/SRX3043403.05_model.r INFO @ Tue, 16 Jun 2020 08:31:01: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:31:01: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 08:31:02: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX3043403/SRX3043403.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX3043403/SRX3043403.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX3043403/SRX3043403.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX3043403/SRX3043403.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 08:31:02: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:31:02: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:31:06: 4000000 INFO @ Tue, 16 Jun 2020 08:31:10: 1000000 INFO @ Tue, 16 Jun 2020 08:31:14: 5000000 INFO @ Tue, 16 Jun 2020 08:31:18: 2000000 INFO @ Tue, 16 Jun 2020 08:31:22: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 08:31:23: 6000000 INFO @ Tue, 16 Jun 2020 08:31:26: 3000000 INFO @ Tue, 16 Jun 2020 08:31:31: 7000000 INFO @ Tue, 16 Jun 2020 08:31:33: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX3043403/SRX3043403.05_peaks.xls INFO @ Tue, 16 Jun 2020 08:31:33: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX3043403/SRX3043403.05_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:31:33: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX3043403/SRX3043403.05_summits.bed INFO @ Tue, 16 Jun 2020 08:31:33: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (5118 records, 4 fields): 7 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 08:31:33: 4000000 INFO @ Tue, 16 Jun 2020 08:31:40: 8000000 INFO @ Tue, 16 Jun 2020 08:31:41: #1 tag size is determined as 50 bps INFO @ Tue, 16 Jun 2020 08:31:41: #1 tag size = 50 INFO @ Tue, 16 Jun 2020 08:31:41: #1 total tags in treatment: 8178343 INFO @ Tue, 16 Jun 2020 08:31:41: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:31:41: #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 08:31:41: #1 tags after filtering in treatment: 8178343 INFO @ Tue, 16 Jun 2020 08:31:41: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:31:41: #1 finished! INFO @ Tue, 16 Jun 2020 08:31:41: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:31:41: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:31:41: 5000000 INFO @ Tue, 16 Jun 2020 08:31:42: #2 number of paired peaks: 1253 INFO @ Tue, 16 Jun 2020 08:31:42: start model_add_line... INFO @ Tue, 16 Jun 2020 08:31:42: start X-correlation... INFO @ Tue, 16 Jun 2020 08:31:42: end of X-cor INFO @ Tue, 16 Jun 2020 08:31:42: #2 finished! INFO @ Tue, 16 Jun 2020 08:31:42: #2 predicted fragment length is 171 bps INFO @ Tue, 16 Jun 2020 08:31:42: #2 alternative fragment length(s) may be 171 bps INFO @ Tue, 16 Jun 2020 08:31:42: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX3043403/SRX3043403.10_model.r INFO @ Tue, 16 Jun 2020 08:31:42: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:31:42: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 08:31:48: 6000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 16 Jun 2020 08:31:55: 7000000 INFO @ Tue, 16 Jun 2020 08:32:02: 8000000 INFO @ Tue, 16 Jun 2020 08:32:02: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 08:32:03: #1 tag size is determined as 50 bps INFO @ Tue, 16 Jun 2020 08:32:03: #1 tag size = 50 INFO @ Tue, 16 Jun 2020 08:32:03: #1 total tags in treatment: 8178343 INFO @ Tue, 16 Jun 2020 08:32:03: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:32:03: #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 08:32:03: #1 tags after filtering in treatment: 8178343 INFO @ Tue, 16 Jun 2020 08:32:03: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:32:03: #1 finished! INFO @ Tue, 16 Jun 2020 08:32:03: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:32:03: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:32:04: #2 number of paired peaks: 1253 INFO @ Tue, 16 Jun 2020 08:32:04: start model_add_line... INFO @ Tue, 16 Jun 2020 08:32:04: start X-correlation... INFO @ Tue, 16 Jun 2020 08:32:04: end of X-cor INFO @ Tue, 16 Jun 2020 08:32:04: #2 finished! INFO @ Tue, 16 Jun 2020 08:32:04: #2 predicted fragment length is 171 bps INFO @ Tue, 16 Jun 2020 08:32:04: #2 alternative fragment length(s) may be 171 bps INFO @ Tue, 16 Jun 2020 08:32:04: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX3043403/SRX3043403.20_model.r INFO @ Tue, 16 Jun 2020 08:32:04: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:32:04: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Tue, 16 Jun 2020 08:32:13: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX3043403/SRX3043403.10_peaks.xls INFO @ Tue, 16 Jun 2020 08:32:13: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX3043403/SRX3043403.10_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:32:13: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX3043403/SRX3043403.10_summits.bed INFO @ Tue, 16 Jun 2020 08:32:13: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (3677 records, 4 fields): 5 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 08:32:24: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 08:32:34: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX3043403/SRX3043403.20_peaks.xls INFO @ Tue, 16 Jun 2020 08:32:34: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX3043403/SRX3043403.20_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:32:34: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX3043403/SRX3043403.20_summits.bed INFO @ Tue, 16 Jun 2020 08:32:34: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (2297 records, 4 fields): 4 millis CompletedMACS2peakCalling