Job ID = 6368774 SRX = SRX554735 Genome = ce11 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-16T00:33:26 prefetch.2.10.7: 1) Downloading 'SRR1301085'... 2020-06-16T00:33:26 prefetch.2.10.7: Downloading via HTTPS... 2020-06-16T00:35:53 prefetch.2.10.7: HTTPS download succeed 2020-06-16T00:35:54 prefetch.2.10.7: 'SRR1301085' is valid 2020-06-16T00:35:54 prefetch.2.10.7: 1) 'SRR1301085' was downloaded successfully Read 11146393 spots for SRR1301085/SRR1301085.sra Written 11146393 spots for SRR1301085/SRR1301085.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: 00:02:59 11146393 reads; of these: 11146393 (100.00%) were unpaired; of these: 240542 (2.16%) aligned 0 times 9596342 (86.09%) aligned exactly 1 time 1309509 (11.75%) aligned >1 times 97.84% overall alignment rate Time searching: 00:03:00 Overall time: 00:03:00 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 8 files... [bam_rmdupse_core] 8244766 / 10905851 = 0.7560 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 09:41:56: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX554735/SRX554735.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX554735/SRX554735.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX554735/SRX554735.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX554735/SRX554735.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 09:41:56: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:41:56: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:42:03: 1000000 INFO @ Tue, 16 Jun 2020 09:42:10: 2000000 INFO @ Tue, 16 Jun 2020 09:42:14: #1 tag size is determined as 50 bps INFO @ Tue, 16 Jun 2020 09:42:14: #1 tag size = 50 INFO @ Tue, 16 Jun 2020 09:42:14: #1 total tags in treatment: 2661085 INFO @ Tue, 16 Jun 2020 09:42:14: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:42:14: #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 09:42:14: #1 tags after filtering in treatment: 2661085 INFO @ Tue, 16 Jun 2020 09:42:14: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 09:42:14: #1 finished! INFO @ Tue, 16 Jun 2020 09:42:14: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:42:14: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:42:14: #2 number of paired peaks: 2318 INFO @ Tue, 16 Jun 2020 09:42:14: start model_add_line... INFO @ Tue, 16 Jun 2020 09:42:14: start X-correlation... INFO @ Tue, 16 Jun 2020 09:42:14: end of X-cor INFO @ Tue, 16 Jun 2020 09:42:14: #2 finished! INFO @ Tue, 16 Jun 2020 09:42:14: #2 predicted fragment length is 151 bps INFO @ Tue, 16 Jun 2020 09:42:14: #2 alternative fragment length(s) may be 151 bps INFO @ Tue, 16 Jun 2020 09:42:14: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX554735/SRX554735.05_model.r INFO @ Tue, 16 Jun 2020 09:42:14: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:42:14: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 09:42:21: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 09:42:24: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX554735/SRX554735.05_peaks.xls INFO @ Tue, 16 Jun 2020 09:42:24: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX554735/SRX554735.05_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:42:24: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX554735/SRX554735.05_summits.bed INFO @ Tue, 16 Jun 2020 09:42:24: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (2065 records, 4 fields): 3 millis CompletedMACS2peakCalling 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 09:42:26: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX554735/SRX554735.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX554735/SRX554735.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX554735/SRX554735.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX554735/SRX554735.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 09:42:26: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:42:26: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:42:33: 1000000 INFO @ Tue, 16 Jun 2020 09:42:40: 2000000 INFO @ Tue, 16 Jun 2020 09:42:44: #1 tag size is determined as 50 bps INFO @ Tue, 16 Jun 2020 09:42:44: #1 tag size = 50 INFO @ Tue, 16 Jun 2020 09:42:44: #1 total tags in treatment: 2661085 INFO @ Tue, 16 Jun 2020 09:42:44: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:42:44: #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 09:42:44: #1 tags after filtering in treatment: 2661085 INFO @ Tue, 16 Jun 2020 09:42:44: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 09:42:44: #1 finished! INFO @ Tue, 16 Jun 2020 09:42:44: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:42:44: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:42:44: #2 number of paired peaks: 2318 INFO @ Tue, 16 Jun 2020 09:42:44: start model_add_line... INFO @ Tue, 16 Jun 2020 09:42:44: start X-correlation... INFO @ Tue, 16 Jun 2020 09:42:45: end of X-cor INFO @ Tue, 16 Jun 2020 09:42:45: #2 finished! INFO @ Tue, 16 Jun 2020 09:42:45: #2 predicted fragment length is 151 bps INFO @ Tue, 16 Jun 2020 09:42:45: #2 alternative fragment length(s) may be 151 bps INFO @ Tue, 16 Jun 2020 09:42:45: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX554735/SRX554735.10_model.r INFO @ Tue, 16 Jun 2020 09:42:45: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:42:45: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 09:42:51: #3 Call peaks for each chromosome... 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 09:42:55: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX554735/SRX554735.10_peaks.xls INFO @ Tue, 16 Jun 2020 09:42:55: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX554735/SRX554735.10_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:42:55: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX554735/SRX554735.10_summits.bed INFO @ Tue, 16 Jun 2020 09:42:55: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (824 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 09:42:56: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX554735/SRX554735.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX554735/SRX554735.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX554735/SRX554735.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX554735/SRX554735.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 09:42:56: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:42:56: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:43:03: 1000000 INFO @ Tue, 16 Jun 2020 09:43:10: 2000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 16 Jun 2020 09:43:14: #1 tag size is determined as 50 bps INFO @ Tue, 16 Jun 2020 09:43:14: #1 tag size = 50 INFO @ Tue, 16 Jun 2020 09:43:14: #1 total tags in treatment: 2661085 INFO @ Tue, 16 Jun 2020 09:43:14: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:43:14: #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 09:43:14: #1 tags after filtering in treatment: 2661085 INFO @ Tue, 16 Jun 2020 09:43:14: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 09:43:14: #1 finished! INFO @ Tue, 16 Jun 2020 09:43:14: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:43:14: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:43:14: #2 number of paired peaks: 2318 INFO @ Tue, 16 Jun 2020 09:43:14: start model_add_line... INFO @ Tue, 16 Jun 2020 09:43:14: start X-correlation... INFO @ Tue, 16 Jun 2020 09:43:14: end of X-cor INFO @ Tue, 16 Jun 2020 09:43:14: #2 finished! INFO @ Tue, 16 Jun 2020 09:43:14: #2 predicted fragment length is 151 bps INFO @ Tue, 16 Jun 2020 09:43:14: #2 alternative fragment length(s) may be 151 bps INFO @ Tue, 16 Jun 2020 09:43:14: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX554735/SRX554735.20_model.r INFO @ Tue, 16 Jun 2020 09:43:14: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:43:14: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Tue, 16 Jun 2020 09:43:21: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 09:43:25: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX554735/SRX554735.20_peaks.xls INFO @ Tue, 16 Jun 2020 09:43:25: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX554735/SRX554735.20_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:43:25: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX554735/SRX554735.20_summits.bed INFO @ Tue, 16 Jun 2020 09:43:25: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (292 records, 4 fields): 1 millis CompletedMACS2peakCalling