Job ID = 6497541 SRX = SRX514729 Genome = ce10 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-25T21:40:42 prefetch.2.10.7: 1) Downloading 'SRR1231450'... 2020-06-25T21:40:42 prefetch.2.10.7: Downloading via HTTPS... 2020-06-25T21:41:35 prefetch.2.10.7: HTTPS download succeed 2020-06-25T21:41:36 prefetch.2.10.7: 'SRR1231450' is valid 2020-06-25T21:41:36 prefetch.2.10.7: 1) 'SRR1231450' was downloaded successfully Read 4104181 spots for SRR1231450/SRR1231450.sra Written 4104181 spots for SRR1231450/SRR1231450.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: 00:01:09 4104181 reads; of these: 4104181 (100.00%) were unpaired; of these: 67269 (1.64%) aligned 0 times 3570119 (86.99%) aligned exactly 1 time 466793 (11.37%) aligned >1 times 98.36% overall alignment rate Time searching: 00:01:09 Overall time: 00:01:09 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] 302524 / 4036912 = 0.0749 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 06:44:53: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX514729/SRX514729.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX514729/SRX514729.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX514729/SRX514729.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX514729/SRX514729.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 06:44:53: #1 read tag files... INFO @ Fri, 26 Jun 2020 06:44:53: #1 read treatment tags... INFO @ Fri, 26 Jun 2020 06:44:59: 1000000 INFO @ Fri, 26 Jun 2020 06:45:05: 2000000 INFO @ Fri, 26 Jun 2020 06:45:12: 3000000 INFO @ Fri, 26 Jun 2020 06:45:16: #1 tag size is determined as 42 bps INFO @ Fri, 26 Jun 2020 06:45:16: #1 tag size = 42 INFO @ Fri, 26 Jun 2020 06:45:16: #1 total tags in treatment: 3734388 INFO @ Fri, 26 Jun 2020 06:45:16: #1 user defined the maximum tags... INFO @ Fri, 26 Jun 2020 06:45:16: #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 06:45:16: #1 tags after filtering in treatment: 3734388 INFO @ Fri, 26 Jun 2020 06:45:16: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 26 Jun 2020 06:45:16: #1 finished! INFO @ Fri, 26 Jun 2020 06:45:16: #2 Build Peak Model... INFO @ Fri, 26 Jun 2020 06:45:16: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 26 Jun 2020 06:45:17: #2 number of paired peaks: 2450 INFO @ Fri, 26 Jun 2020 06:45:17: start model_add_line... INFO @ Fri, 26 Jun 2020 06:45:17: start X-correlation... INFO @ Fri, 26 Jun 2020 06:45:17: end of X-cor INFO @ Fri, 26 Jun 2020 06:45:17: #2 finished! INFO @ Fri, 26 Jun 2020 06:45:17: #2 predicted fragment length is 235 bps INFO @ Fri, 26 Jun 2020 06:45:17: #2 alternative fragment length(s) may be 235 bps INFO @ Fri, 26 Jun 2020 06:45:17: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX514729/SRX514729.05_model.r INFO @ Fri, 26 Jun 2020 06:45:18: #3 Call peaks... INFO @ Fri, 26 Jun 2020 06:45:18: #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 @ Fri, 26 Jun 2020 06:45:23: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX514729/SRX514729.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX514729/SRX514729.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX514729/SRX514729.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX514729/SRX514729.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 06:45:23: #1 read tag files... INFO @ Fri, 26 Jun 2020 06:45:23: #1 read treatment tags... INFO @ Fri, 26 Jun 2020 06:45:28: #3 Call peaks for each chromosome... INFO @ Fri, 26 Jun 2020 06:45:29: 1000000 INFO @ Fri, 26 Jun 2020 06:45:34: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX514729/SRX514729.05_peaks.xls INFO @ Fri, 26 Jun 2020 06:45:34: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX514729/SRX514729.05_peaks.narrowPeak INFO @ Fri, 26 Jun 2020 06:45:34: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX514729/SRX514729.05_summits.bed INFO @ Fri, 26 Jun 2020 06:45:34: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (5369 records, 4 fields): 7 millis CompletedMACS2peakCalling INFO @ Fri, 26 Jun 2020 06:45:36: 2000000 INFO @ Fri, 26 Jun 2020 06:45:43: 3000000 INFO @ Fri, 26 Jun 2020 06:45:47: #1 tag size is determined as 42 bps INFO @ Fri, 26 Jun 2020 06:45:47: #1 tag size = 42 INFO @ Fri, 26 Jun 2020 06:45:47: #1 total tags in treatment: 3734388 INFO @ Fri, 26 Jun 2020 06:45:47: #1 user defined the maximum tags... INFO @ Fri, 26 Jun 2020 06:45:47: #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 06:45:48: #1 tags after filtering in treatment: 3734388 INFO @ Fri, 26 Jun 2020 06:45:48: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 26 Jun 2020 06:45:48: #1 finished! INFO @ Fri, 26 Jun 2020 06:45:48: #2 Build Peak Model... INFO @ Fri, 26 Jun 2020 06:45:48: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 26 Jun 2020 06:45:48: #2 number of paired peaks: 2450 INFO @ Fri, 26 Jun 2020 06:45:48: start model_add_line... INFO @ Fri, 26 Jun 2020 06:45:48: start X-correlation... INFO @ Fri, 26 Jun 2020 06:45:48: end of X-cor INFO @ Fri, 26 Jun 2020 06:45:48: #2 finished! INFO @ Fri, 26 Jun 2020 06:45:48: #2 predicted fragment length is 235 bps INFO @ Fri, 26 Jun 2020 06:45:48: #2 alternative fragment length(s) may be 235 bps INFO @ Fri, 26 Jun 2020 06:45:48: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX514729/SRX514729.10_model.r INFO @ Fri, 26 Jun 2020 06:45:48: #3 Call peaks... INFO @ Fri, 26 Jun 2020 06:45:48: #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 @ Fri, 26 Jun 2020 06:45:53: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX514729/SRX514729.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX514729/SRX514729.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX514729/SRX514729.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX514729/SRX514729.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 06:45:53: #1 read tag files... INFO @ Fri, 26 Jun 2020 06:45:53: #1 read treatment tags... INFO @ Fri, 26 Jun 2020 06:45:58: #3 Call peaks for each chromosome... INFO @ Fri, 26 Jun 2020 06:45:59: 1000000 INFO @ Fri, 26 Jun 2020 06:46:03: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX514729/SRX514729.10_peaks.xls INFO @ Fri, 26 Jun 2020 06:46:05: 2000000 BedGraph に変換しました。 INFO @ Fri, 26 Jun 2020 06:46:12: 3000000 INFO @ Fri, 26 Jun 2020 06:46:16: #1 tag size is determined as 42 bps INFO @ Fri, 26 Jun 2020 06:46:16: #1 tag size = 42 INFO @ Fri, 26 Jun 2020 06:46:16: #1 total tags in treatment: 3734388 INFO @ Fri, 26 Jun 2020 06:46:16: #1 user defined the maximum tags... INFO @ Fri, 26 Jun 2020 06:46:16: #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 06:46:16: #1 tags after filtering in treatment: 3734388 INFO @ Fri, 26 Jun 2020 06:46:16: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 26 Jun 2020 06:46:16: #1 finished! INFO @ Fri, 26 Jun 2020 06:46:16: #2 Build Peak Model... INFO @ Fri, 26 Jun 2020 06:46:16: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 26 Jun 2020 06:46:17: #2 number of paired peaks: 2450 INFO @ Fri, 26 Jun 2020 06:46:17: start model_add_line... INFO @ Fri, 26 Jun 2020 06:46:17: start X-correlation... INFO @ Fri, 26 Jun 2020 06:46:17: end of X-cor INFO @ Fri, 26 Jun 2020 06:46:17: #2 finished! INFO @ Fri, 26 Jun 2020 06:46:17: #2 predicted fragment length is 235 bps INFO @ Fri, 26 Jun 2020 06:46:17: #2 alternative fragment length(s) may be 235 bps INFO @ Fri, 26 Jun 2020 06:46:17: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX514729/SRX514729.20_model.r BigWig に変換中... INFO @ Fri, 26 Jun 2020 06:46:28: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX514729/SRX514729.10_peaks.narrowPeak INFO @ Fri, 26 Jun 2020 06:46:28: #3 Call peaks... INFO @ Fri, 26 Jun 2020 06:46:28: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 26 Jun 2020 06:46:28: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX514729/SRX514729.10_summits.bed INFO @ Fri, 26 Jun 2020 06:46:28: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (3109 records, 4 fields): 48 millis CompletedMACS2peakCalling BigWig に変換しました。 INFO @ Fri, 26 Jun 2020 06:46:38: #3 Call peaks for each chromosome... INFO @ Fri, 26 Jun 2020 06:46:44: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX514729/SRX514729.20_peaks.xls INFO @ Fri, 26 Jun 2020 06:46:44: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX514729/SRX514729.20_peaks.narrowPeak INFO @ Fri, 26 Jun 2020 06:46:44: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX514729/SRX514729.20_summits.bed INFO @ Fri, 26 Jun 2020 06:46:44: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (1020 records, 4 fields): 5 millis CompletedMACS2peakCalling