Job ID = 6366244 SRX = SRX080098 Genome = ce11 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-15T22:42:38 prefetch.2.10.7: 1) Downloading 'SRR298918'... 2020-06-15T22:42:38 prefetch.2.10.7: Downloading via HTTPS... 2020-06-15T22:43:13 prefetch.2.10.7: HTTPS download succeed 2020-06-15T22:43:13 prefetch.2.10.7: 'SRR298918' is valid 2020-06-15T22:43:13 prefetch.2.10.7: 1) 'SRR298918' was downloaded successfully Read 7035155 spots for SRR298918/SRR298918.sra Written 7035155 spots for SRR298918/SRR298918.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: 00:00:01 Time loading mirror index: 00:00:00 Multiseed full-index search: 00:01:04 7035155 reads; of these: 7035155 (100.00%) were unpaired; of these: 747766 (10.63%) aligned 0 times 5500357 (78.18%) aligned exactly 1 time 787032 (11.19%) aligned >1 times 89.37% overall alignment rate Time searching: 00:01:05 Overall time: 00:01:05 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] 1147884 / 6287389 = 0.1826 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 07:46:24: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX080098/SRX080098.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX080098/SRX080098.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX080098/SRX080098.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX080098/SRX080098.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 07:46:24: #1 read tag files... INFO @ Tue, 16 Jun 2020 07:46:24: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 07:46:30: 1000000 INFO @ Tue, 16 Jun 2020 07:46:37: 2000000 INFO @ Tue, 16 Jun 2020 07:46:43: 3000000 INFO @ Tue, 16 Jun 2020 07:46:50: 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 07:46:54: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX080098/SRX080098.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX080098/SRX080098.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX080098/SRX080098.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX080098/SRX080098.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 07:46:54: #1 read tag files... INFO @ Tue, 16 Jun 2020 07:46:54: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 07:46:57: 5000000 INFO @ Tue, 16 Jun 2020 07:46:58: #1 tag size is determined as 32 bps INFO @ Tue, 16 Jun 2020 07:46:58: #1 tag size = 32 INFO @ Tue, 16 Jun 2020 07:46:58: #1 total tags in treatment: 5139505 INFO @ Tue, 16 Jun 2020 07:46:58: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 07:46:58: #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 07:46:58: #1 tags after filtering in treatment: 5139505 INFO @ Tue, 16 Jun 2020 07:46:58: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 07:46:58: #1 finished! INFO @ Tue, 16 Jun 2020 07:46:58: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 07:46:58: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 07:46:58: #2 number of paired peaks: 3302 INFO @ Tue, 16 Jun 2020 07:46:58: start model_add_line... INFO @ Tue, 16 Jun 2020 07:46:58: start X-correlation... INFO @ Tue, 16 Jun 2020 07:46:59: end of X-cor INFO @ Tue, 16 Jun 2020 07:46:59: #2 finished! INFO @ Tue, 16 Jun 2020 07:46:59: #2 predicted fragment length is 153 bps INFO @ Tue, 16 Jun 2020 07:46:59: #2 alternative fragment length(s) may be 153 bps INFO @ Tue, 16 Jun 2020 07:46:59: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX080098/SRX080098.05_model.r INFO @ Tue, 16 Jun 2020 07:46:59: #3 Call peaks... INFO @ Tue, 16 Jun 2020 07:46:59: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 07:47:00: 1000000 INFO @ Tue, 16 Jun 2020 07:47:06: 2000000 INFO @ Tue, 16 Jun 2020 07:47:11: 3000000 INFO @ Tue, 16 Jun 2020 07:47:15: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 07:47:17: 4000000 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 07:47:23: 5000000 INFO @ Tue, 16 Jun 2020 07:47:23: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX080098/SRX080098.05_peaks.xls INFO @ Tue, 16 Jun 2020 07:47:23: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX080098/SRX080098.05_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 07:47:23: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX080098/SRX080098.05_summits.bed INFO @ Tue, 16 Jun 2020 07:47:23: Done! INFO @ Tue, 16 Jun 2020 07:47:23: #1 tag size is determined as 32 bps INFO @ Tue, 16 Jun 2020 07:47:23: #1 tag size = 32 INFO @ Tue, 16 Jun 2020 07:47:23: #1 total tags in treatment: 5139505 INFO @ Tue, 16 Jun 2020 07:47:23: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 07:47:23: #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 07:47:23: #1 tags after filtering in treatment: 5139505 INFO @ Tue, 16 Jun 2020 07:47:23: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 07:47:23: #1 finished! INFO @ Tue, 16 Jun 2020 07:47:23: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 07:47:23: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 07:47:24: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX080098/SRX080098.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX080098/SRX080098.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX080098/SRX080098.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX080098/SRX080098.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 07:47:24: #1 read tag files... INFO @ Tue, 16 Jun 2020 07:47:24: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 07:47:24: #2 number of paired peaks: 3302 INFO @ Tue, 16 Jun 2020 07:47:24: start model_add_line... INFO @ Tue, 16 Jun 2020 07:47:24: start X-correlation... INFO @ Tue, 16 Jun 2020 07:47:24: end of X-cor INFO @ Tue, 16 Jun 2020 07:47:24: #2 finished! INFO @ Tue, 16 Jun 2020 07:47:24: #2 predicted fragment length is 153 bps INFO @ Tue, 16 Jun 2020 07:47:24: #2 alternative fragment length(s) may be 153 bps INFO @ Tue, 16 Jun 2020 07:47:24: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX080098/SRX080098.10_model.r INFO @ Tue, 16 Jun 2020 07:47:24: #3 Call peaks... INFO @ Tue, 16 Jun 2020 07:47:24: #3 Pre-compute pvalue-qvalue table... pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (8042 records, 4 fields): 11 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 07:47:29: 1000000 INFO @ Tue, 16 Jun 2020 07:47:35: 2000000 INFO @ Tue, 16 Jun 2020 07:47:40: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 07:47:40: 3000000 INFO @ Tue, 16 Jun 2020 07:47:46: 4000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 16 Jun 2020 07:47:48: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX080098/SRX080098.10_peaks.xls INFO @ Tue, 16 Jun 2020 07:47:48: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX080098/SRX080098.10_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 07:47:48: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX080098/SRX080098.10_summits.bed INFO @ Tue, 16 Jun 2020 07:47:48: Done! pass1 - making usageList (7 chroms): 2 millis pass2 - checking and writing primary data (5774 records, 4 fields): 8 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 07:47:51: 5000000 INFO @ Tue, 16 Jun 2020 07:47:52: #1 tag size is determined as 32 bps INFO @ Tue, 16 Jun 2020 07:47:52: #1 tag size = 32 INFO @ Tue, 16 Jun 2020 07:47:52: #1 total tags in treatment: 5139505 INFO @ Tue, 16 Jun 2020 07:47:52: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 07:47:52: #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 07:47:52: #1 tags after filtering in treatment: 5139505 INFO @ Tue, 16 Jun 2020 07:47:52: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 07:47:52: #1 finished! INFO @ Tue, 16 Jun 2020 07:47:52: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 07:47:52: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 07:47:53: #2 number of paired peaks: 3302 INFO @ Tue, 16 Jun 2020 07:47:53: start model_add_line... INFO @ Tue, 16 Jun 2020 07:47:53: start X-correlation... INFO @ Tue, 16 Jun 2020 07:47:53: end of X-cor INFO @ Tue, 16 Jun 2020 07:47:53: #2 finished! INFO @ Tue, 16 Jun 2020 07:47:53: #2 predicted fragment length is 153 bps INFO @ Tue, 16 Jun 2020 07:47:53: #2 alternative fragment length(s) may be 153 bps INFO @ Tue, 16 Jun 2020 07:47:53: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX080098/SRX080098.20_model.r INFO @ Tue, 16 Jun 2020 07:47:53: #3 Call peaks... INFO @ Tue, 16 Jun 2020 07:47:53: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Tue, 16 Jun 2020 07:48:09: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 07:48:17: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX080098/SRX080098.20_peaks.xls INFO @ Tue, 16 Jun 2020 07:48:17: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX080098/SRX080098.20_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 07:48:17: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX080098/SRX080098.20_summits.bed INFO @ Tue, 16 Jun 2020 07:48:17: Done! pass1 - making usageList (7 chroms): 2 millis pass2 - checking and writing primary data (3736 records, 4 fields): 7 millis CompletedMACS2peakCalling