Job ID = 6507859 SRX = SRX494942 Genome = ce11 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-26T14:10:27 prefetch.2.10.7: 1) Downloading 'SRR1198474'... 2020-06-26T14:10:27 prefetch.2.10.7: Downloading via HTTPS... 2020-06-26T14:13:05 prefetch.2.10.7: HTTPS download succeed 2020-06-26T14:13:05 prefetch.2.10.7: 1) 'SRR1198474' was downloaded successfully Read 22264456 spots for SRR1198474/SRR1198474.sra Written 22264456 spots for SRR1198474/SRR1198474.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: 00:04:39 22264456 reads; of these: 22264456 (100.00%) were unpaired; of these: 2367254 (10.63%) aligned 0 times 17279345 (77.61%) aligned exactly 1 time 2617857 (11.76%) aligned >1 times 89.37% overall alignment rate Time searching: 00:04:39 Overall time: 00:04:39 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_sort_core] merging from 12 files... [bam_rmdupse_core] 6668603 / 19897202 = 0.3352 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 @ Fri, 26 Jun 2020 23:23:50: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX494942/SRX494942.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX494942/SRX494942.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX494942/SRX494942.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX494942/SRX494942.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 @ Fri, 26 Jun 2020 23:23:50: #1 read tag files... INFO @ Fri, 26 Jun 2020 23:23:50: #1 read treatment tags... INFO @ Fri, 26 Jun 2020 23:23:55: 1000000 INFO @ Fri, 26 Jun 2020 23:24:00: 2000000 INFO @ Fri, 26 Jun 2020 23:24:05: 3000000 INFO @ Fri, 26 Jun 2020 23:24:11: 4000000 INFO @ Fri, 26 Jun 2020 23:24:16: 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 @ Fri, 26 Jun 2020 23:24:20: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX494942/SRX494942.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX494942/SRX494942.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX494942/SRX494942.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX494942/SRX494942.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 @ Fri, 26 Jun 2020 23:24:20: #1 read tag files... INFO @ Fri, 26 Jun 2020 23:24:20: #1 read treatment tags... INFO @ Fri, 26 Jun 2020 23:24:21: 6000000 INFO @ Fri, 26 Jun 2020 23:24:26: 1000000 INFO @ Fri, 26 Jun 2020 23:24:26: 7000000 INFO @ Fri, 26 Jun 2020 23:24:31: 2000000 INFO @ Fri, 26 Jun 2020 23:24:31: 8000000 INFO @ Fri, 26 Jun 2020 23:24:36: 3000000 INFO @ Fri, 26 Jun 2020 23:24:36: 9000000 INFO @ Fri, 26 Jun 2020 23:24:41: 4000000 INFO @ Fri, 26 Jun 2020 23:24:42: 10000000 INFO @ Fri, 26 Jun 2020 23:24:47: 5000000 INFO @ Fri, 26 Jun 2020 23:24:47: 11000000 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 @ Fri, 26 Jun 2020 23:24:50: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX494942/SRX494942.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX494942/SRX494942.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX494942/SRX494942.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX494942/SRX494942.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 @ Fri, 26 Jun 2020 23:24:50: #1 read tag files... INFO @ Fri, 26 Jun 2020 23:24:50: #1 read treatment tags... INFO @ Fri, 26 Jun 2020 23:24:52: 6000000 INFO @ Fri, 26 Jun 2020 23:24:52: 12000000 INFO @ Fri, 26 Jun 2020 23:24:56: 1000000 INFO @ Fri, 26 Jun 2020 23:24:57: 7000000 INFO @ Fri, 26 Jun 2020 23:24:58: 13000000 INFO @ Fri, 26 Jun 2020 23:24:59: #1 tag size is determined as 50 bps INFO @ Fri, 26 Jun 2020 23:24:59: #1 tag size = 50 INFO @ Fri, 26 Jun 2020 23:24:59: #1 total tags in treatment: 13228599 INFO @ Fri, 26 Jun 2020 23:24:59: #1 user defined the maximum tags... INFO @ Fri, 26 Jun 2020 23:24:59: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 26 Jun 2020 23:24:59: #1 tags after filtering in treatment: 13228599 INFO @ Fri, 26 Jun 2020 23:24:59: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 26 Jun 2020 23:24:59: #1 finished! INFO @ Fri, 26 Jun 2020 23:24:59: #2 Build Peak Model... INFO @ Fri, 26 Jun 2020 23:24:59: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 26 Jun 2020 23:25:01: #2 number of paired peaks: 3003 INFO @ Fri, 26 Jun 2020 23:25:01: start model_add_line... INFO @ Fri, 26 Jun 2020 23:25:01: start X-correlation... INFO @ Fri, 26 Jun 2020 23:25:01: end of X-cor INFO @ Fri, 26 Jun 2020 23:25:01: #2 finished! INFO @ Fri, 26 Jun 2020 23:25:01: #2 predicted fragment length is 168 bps INFO @ Fri, 26 Jun 2020 23:25:01: #2 alternative fragment length(s) may be 168 bps INFO @ Fri, 26 Jun 2020 23:25:01: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX494942/SRX494942.05_model.r INFO @ Fri, 26 Jun 2020 23:25:01: #3 Call peaks... INFO @ Fri, 26 Jun 2020 23:25:01: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 26 Jun 2020 23:25:02: 2000000 INFO @ Fri, 26 Jun 2020 23:25:03: 8000000 INFO @ Fri, 26 Jun 2020 23:25:08: 3000000 INFO @ Fri, 26 Jun 2020 23:25:08: 9000000 INFO @ Fri, 26 Jun 2020 23:25:14: 10000000 INFO @ Fri, 26 Jun 2020 23:25:14: 4000000 INFO @ Fri, 26 Jun 2020 23:25:19: 11000000 INFO @ Fri, 26 Jun 2020 23:25:20: 5000000 INFO @ Fri, 26 Jun 2020 23:25:25: 12000000 INFO @ Fri, 26 Jun 2020 23:25:26: 6000000 INFO @ Fri, 26 Jun 2020 23:25:31: 13000000 INFO @ Fri, 26 Jun 2020 23:25:33: #1 tag size is determined as 50 bps INFO @ Fri, 26 Jun 2020 23:25:33: #1 tag size = 50 INFO @ Fri, 26 Jun 2020 23:25:33: #1 total tags in treatment: 13228599 INFO @ Fri, 26 Jun 2020 23:25:33: #1 user defined the maximum tags... INFO @ Fri, 26 Jun 2020 23:25:33: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 26 Jun 2020 23:25:33: #1 tags after filtering in treatment: 13228599 INFO @ Fri, 26 Jun 2020 23:25:33: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 26 Jun 2020 23:25:33: #1 finished! INFO @ Fri, 26 Jun 2020 23:25:33: #2 Build Peak Model... INFO @ Fri, 26 Jun 2020 23:25:33: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 26 Jun 2020 23:25:33: 7000000 INFO @ Fri, 26 Jun 2020 23:25:34: #2 number of paired peaks: 3003 INFO @ Fri, 26 Jun 2020 23:25:34: start model_add_line... INFO @ Fri, 26 Jun 2020 23:25:34: start X-correlation... INFO @ Fri, 26 Jun 2020 23:25:34: end of X-cor INFO @ Fri, 26 Jun 2020 23:25:34: #2 finished! INFO @ Fri, 26 Jun 2020 23:25:34: #2 predicted fragment length is 168 bps INFO @ Fri, 26 Jun 2020 23:25:34: #2 alternative fragment length(s) may be 168 bps INFO @ Fri, 26 Jun 2020 23:25:34: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX494942/SRX494942.10_model.r INFO @ Fri, 26 Jun 2020 23:25:34: #3 Call peaks... INFO @ Fri, 26 Jun 2020 23:25:34: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 26 Jun 2020 23:25:39: 8000000 INFO @ Fri, 26 Jun 2020 23:25:40: #3 Call peaks for each chromosome... INFO @ Fri, 26 Jun 2020 23:25:46: 9000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Fri, 26 Jun 2020 23:25:52: 10000000 INFO @ Fri, 26 Jun 2020 23:25:58: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX494942/SRX494942.05_peaks.xls INFO @ Fri, 26 Jun 2020 23:25:58: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX494942/SRX494942.05_peaks.narrowPeak INFO @ Fri, 26 Jun 2020 23:25:58: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX494942/SRX494942.05_summits.bed INFO @ Fri, 26 Jun 2020 23:25:58: Done! pass1 - making usageList (6 chroms): 2 millis pass2 - checking and writing primary data (12053 records, 4 fields): 16 millis CompletedMACS2peakCalling INFO @ Fri, 26 Jun 2020 23:25:59: 11000000 INFO @ Fri, 26 Jun 2020 23:26:06: 12000000 INFO @ Fri, 26 Jun 2020 23:26:12: 13000000 INFO @ Fri, 26 Jun 2020 23:26:14: #1 tag size is determined as 50 bps INFO @ Fri, 26 Jun 2020 23:26:14: #1 tag size = 50 INFO @ Fri, 26 Jun 2020 23:26:14: #1 total tags in treatment: 13228599 INFO @ Fri, 26 Jun 2020 23:26:14: #1 user defined the maximum tags... INFO @ Fri, 26 Jun 2020 23:26:14: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 26 Jun 2020 23:26:14: #1 tags after filtering in treatment: 13228599 INFO @ Fri, 26 Jun 2020 23:26:14: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 26 Jun 2020 23:26:14: #1 finished! INFO @ Fri, 26 Jun 2020 23:26:14: #2 Build Peak Model... INFO @ Fri, 26 Jun 2020 23:26:14: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 26 Jun 2020 23:26:14: #3 Call peaks for each chromosome... INFO @ Fri, 26 Jun 2020 23:26:15: #2 number of paired peaks: 3003 INFO @ Fri, 26 Jun 2020 23:26:15: start model_add_line... INFO @ Fri, 26 Jun 2020 23:26:16: start X-correlation... INFO @ Fri, 26 Jun 2020 23:26:16: end of X-cor INFO @ Fri, 26 Jun 2020 23:26:16: #2 finished! INFO @ Fri, 26 Jun 2020 23:26:16: #2 predicted fragment length is 168 bps INFO @ Fri, 26 Jun 2020 23:26:16: #2 alternative fragment length(s) may be 168 bps INFO @ Fri, 26 Jun 2020 23:26:16: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX494942/SRX494942.20_model.r INFO @ Fri, 26 Jun 2020 23:26:16: #3 Call peaks... INFO @ Fri, 26 Jun 2020 23:26:16: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Fri, 26 Jun 2020 23:26:33: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX494942/SRX494942.10_peaks.xls INFO @ Fri, 26 Jun 2020 23:26:33: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX494942/SRX494942.10_peaks.narrowPeak INFO @ Fri, 26 Jun 2020 23:26:33: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX494942/SRX494942.10_summits.bed INFO @ Fri, 26 Jun 2020 23:26:33: Done! pass1 - making usageList (6 chroms): 3 millis pass2 - checking and writing primary data (8408 records, 4 fields): 17 millis CompletedMACS2peakCalling INFO @ Fri, 26 Jun 2020 23:26:54: #3 Call peaks for each chromosome... INFO @ Fri, 26 Jun 2020 23:27:11: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX494942/SRX494942.20_peaks.xls INFO @ Fri, 26 Jun 2020 23:27:11: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX494942/SRX494942.20_peaks.narrowPeak INFO @ Fri, 26 Jun 2020 23:27:11: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX494942/SRX494942.20_summits.bed INFO @ Fri, 26 Jun 2020 23:27:12: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (5057 records, 4 fields): 10 millis CompletedMACS2peakCalling