Job ID = 6367438 SRX = SRX331196 Genome = ce11 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-15T23:20:31 prefetch.2.10.7: 1) Downloading 'SRR947428'... 2020-06-15T23:20:31 prefetch.2.10.7: Downloading via HTTPS... 2020-06-15T23:21:17 prefetch.2.10.7: HTTPS download succeed 2020-06-15T23:21:17 prefetch.2.10.7: 'SRR947428' is valid 2020-06-15T23:21:17 prefetch.2.10.7: 1) 'SRR947428' was downloaded successfully Read 7354875 spots for SRR947428/SRR947428.sra Written 7354875 spots for SRR947428/SRR947428.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: 00:00:55 7354875 reads; of these: 7354875 (100.00%) were unpaired; of these: 1596478 (21.71%) aligned 0 times 4970215 (67.58%) aligned exactly 1 time 788182 (10.72%) aligned >1 times 78.29% overall alignment rate Time searching: 00:00:55 Overall time: 00:00:55 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] 1213178 / 5758397 = 0.2107 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 08:23:57: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX331196/SRX331196.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX331196/SRX331196.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX331196/SRX331196.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX331196/SRX331196.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 08:23:57: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:23:57: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:24:01: 1000000 INFO @ Tue, 16 Jun 2020 08:24:06: 2000000 INFO @ Tue, 16 Jun 2020 08:24:11: 3000000 INFO @ Tue, 16 Jun 2020 08:24:15: 4000000 INFO @ Tue, 16 Jun 2020 08:24:17: #1 tag size is determined as 32 bps INFO @ Tue, 16 Jun 2020 08:24:17: #1 tag size = 32 INFO @ Tue, 16 Jun 2020 08:24:17: #1 total tags in treatment: 4545219 INFO @ Tue, 16 Jun 2020 08:24:17: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:24:17: #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 08:24:18: #1 tags after filtering in treatment: 4545219 INFO @ Tue, 16 Jun 2020 08:24:18: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:24:18: #1 finished! INFO @ Tue, 16 Jun 2020 08:24:18: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:24:18: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:24:18: #2 number of paired peaks: 1680 INFO @ Tue, 16 Jun 2020 08:24:18: start model_add_line... INFO @ Tue, 16 Jun 2020 08:24:18: start X-correlation... INFO @ Tue, 16 Jun 2020 08:24:18: end of X-cor INFO @ Tue, 16 Jun 2020 08:24:18: #2 finished! INFO @ Tue, 16 Jun 2020 08:24:18: #2 predicted fragment length is 173 bps INFO @ Tue, 16 Jun 2020 08:24:18: #2 alternative fragment length(s) may be 173 bps INFO @ Tue, 16 Jun 2020 08:24:18: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX331196/SRX331196.05_model.r INFO @ Tue, 16 Jun 2020 08:24:18: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:24:18: #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 @ Tue, 16 Jun 2020 08:24:27: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX331196/SRX331196.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX331196/SRX331196.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX331196/SRX331196.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX331196/SRX331196.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 08:24:27: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:24:27: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:24:28: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 08:24:32: 1000000 INFO @ Tue, 16 Jun 2020 08:24:33: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX331196/SRX331196.05_peaks.xls INFO @ Tue, 16 Jun 2020 08:24:33: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX331196/SRX331196.05_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:24:33: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX331196/SRX331196.05_summits.bed INFO @ Tue, 16 Jun 2020 08:24:33: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (5507 records, 4 fields): 6 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 08:24:36: 2000000 INFO @ Tue, 16 Jun 2020 08:24:41: 3000000 INFO @ Tue, 16 Jun 2020 08:24:46: 4000000 INFO @ Tue, 16 Jun 2020 08:24:48: #1 tag size is determined as 32 bps INFO @ Tue, 16 Jun 2020 08:24:48: #1 tag size = 32 INFO @ Tue, 16 Jun 2020 08:24:48: #1 total tags in treatment: 4545219 INFO @ Tue, 16 Jun 2020 08:24:48: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:24:48: #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 08:24:48: #1 tags after filtering in treatment: 4545219 INFO @ Tue, 16 Jun 2020 08:24:48: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:24:48: #1 finished! INFO @ Tue, 16 Jun 2020 08:24:48: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:24:48: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:24:49: #2 number of paired peaks: 1680 INFO @ Tue, 16 Jun 2020 08:24:49: start model_add_line... INFO @ Tue, 16 Jun 2020 08:24:49: start X-correlation... INFO @ Tue, 16 Jun 2020 08:24:49: end of X-cor INFO @ Tue, 16 Jun 2020 08:24:49: #2 finished! INFO @ Tue, 16 Jun 2020 08:24:49: #2 predicted fragment length is 173 bps INFO @ Tue, 16 Jun 2020 08:24:49: #2 alternative fragment length(s) may be 173 bps INFO @ Tue, 16 Jun 2020 08:24:49: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX331196/SRX331196.10_model.r INFO @ Tue, 16 Jun 2020 08:24:49: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:24:49: #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 08:24:57: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX331196/SRX331196.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX331196/SRX331196.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX331196/SRX331196.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX331196/SRX331196.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 08:24:57: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:24:57: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:24:59: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 08:25:01: 1000000 INFO @ Tue, 16 Jun 2020 08:25:04: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX331196/SRX331196.10_peaks.xls INFO @ Tue, 16 Jun 2020 08:25:04: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX331196/SRX331196.10_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:25:04: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX331196/SRX331196.10_summits.bed INFO @ Tue, 16 Jun 2020 08:25:04: Done! pass1 - making usageList (7 chroms): 0 millis pass2 - checking and writing primary data (3615 records, 4 fields): 5 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 08:25:06: 2000000 INFO @ Tue, 16 Jun 2020 08:25:10: 3000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 16 Jun 2020 08:25:15: 4000000 INFO @ Tue, 16 Jun 2020 08:25:18: #1 tag size is determined as 32 bps INFO @ Tue, 16 Jun 2020 08:25:18: #1 tag size = 32 INFO @ Tue, 16 Jun 2020 08:25:18: #1 total tags in treatment: 4545219 INFO @ Tue, 16 Jun 2020 08:25:18: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:25:18: #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 08:25:18: #1 tags after filtering in treatment: 4545219 INFO @ Tue, 16 Jun 2020 08:25:18: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:25:18: #1 finished! INFO @ Tue, 16 Jun 2020 08:25:18: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:25:18: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:25:18: #2 number of paired peaks: 1680 INFO @ Tue, 16 Jun 2020 08:25:18: start model_add_line... INFO @ Tue, 16 Jun 2020 08:25:18: start X-correlation... INFO @ Tue, 16 Jun 2020 08:25:18: end of X-cor INFO @ Tue, 16 Jun 2020 08:25:18: #2 finished! INFO @ Tue, 16 Jun 2020 08:25:18: #2 predicted fragment length is 173 bps INFO @ Tue, 16 Jun 2020 08:25:18: #2 alternative fragment length(s) may be 173 bps INFO @ Tue, 16 Jun 2020 08:25:18: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX331196/SRX331196.20_model.r INFO @ Tue, 16 Jun 2020 08:25:18: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:25:18: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Tue, 16 Jun 2020 08:25:28: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 08:25:33: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX331196/SRX331196.20_peaks.xls INFO @ Tue, 16 Jun 2020 08:25:33: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX331196/SRX331196.20_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:25:33: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX331196/SRX331196.20_summits.bed INFO @ Tue, 16 Jun 2020 08:25:33: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (1828 records, 4 fields): 2 millis CompletedMACS2peakCalling