Job ID = 6368991 SRX = SRX958296 Genome = ce11 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-16T00:29:16 prefetch.2.10.7: 1) Downloading 'SRR1917669'... 2020-06-16T00:29:16 prefetch.2.10.7: Downloading via HTTPS... 2020-06-16T00:36:23 prefetch.2.10.7: HTTPS download succeed 2020-06-16T00:36:23 prefetch.2.10.7: 1) 'SRR1917669' was downloaded successfully Read 62865092 spots for SRR1917669/SRR1917669.sra Written 62865092 spots for SRR1917669/SRR1917669.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: 00:13:11 62865092 reads; of these: 62865092 (100.00%) were unpaired; of these: 23299547 (37.06%) aligned 0 times 23484599 (37.36%) aligned exactly 1 time 16080946 (25.58%) aligned >1 times 62.94% overall alignment rate Time searching: 00:13:11 Overall time: 00:13:11 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 20 files... [bam_rmdupse_core] 26003176 / 39565545 = 0.6572 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 10:02:27: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX958296/SRX958296.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX958296/SRX958296.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX958296/SRX958296.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX958296/SRX958296.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 10:02:27: #1 read tag files... INFO @ Tue, 16 Jun 2020 10:02:27: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 10:02:33: 1000000 INFO @ Tue, 16 Jun 2020 10:02:38: 2000000 INFO @ Tue, 16 Jun 2020 10:02:43: 3000000 INFO @ Tue, 16 Jun 2020 10:02:49: 4000000 INFO @ Tue, 16 Jun 2020 10:02:54: 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 @ Tue, 16 Jun 2020 10:02:57: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX958296/SRX958296.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX958296/SRX958296.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX958296/SRX958296.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX958296/SRX958296.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 10:02:57: #1 read tag files... INFO @ Tue, 16 Jun 2020 10:02:57: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 10:02:59: 6000000 INFO @ Tue, 16 Jun 2020 10:03:03: 1000000 INFO @ Tue, 16 Jun 2020 10:03:05: 7000000 INFO @ Tue, 16 Jun 2020 10:03:09: 2000000 INFO @ Tue, 16 Jun 2020 10:03:11: 8000000 INFO @ Tue, 16 Jun 2020 10:03:15: 3000000 INFO @ Tue, 16 Jun 2020 10:03:17: 9000000 INFO @ Tue, 16 Jun 2020 10:03:21: 4000000 INFO @ Tue, 16 Jun 2020 10:03:23: 10000000 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 10:03:27: 5000000 INFO @ Tue, 16 Jun 2020 10:03:27: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX958296/SRX958296.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX958296/SRX958296.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX958296/SRX958296.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX958296/SRX958296.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 10:03:27: #1 read tag files... INFO @ Tue, 16 Jun 2020 10:03:27: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 10:03:28: 11000000 INFO @ Tue, 16 Jun 2020 10:03:33: 6000000 INFO @ Tue, 16 Jun 2020 10:03:33: 1000000 INFO @ Tue, 16 Jun 2020 10:03:34: 12000000 INFO @ Tue, 16 Jun 2020 10:03:38: 7000000 INFO @ Tue, 16 Jun 2020 10:03:39: 2000000 INFO @ Tue, 16 Jun 2020 10:03:40: 13000000 INFO @ Tue, 16 Jun 2020 10:03:43: #1 tag size is determined as 51 bps INFO @ Tue, 16 Jun 2020 10:03:43: #1 tag size = 51 INFO @ Tue, 16 Jun 2020 10:03:43: #1 total tags in treatment: 13562369 INFO @ Tue, 16 Jun 2020 10:03:43: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 10:03:43: #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 10:03:44: #1 tags after filtering in treatment: 13562369 INFO @ Tue, 16 Jun 2020 10:03:44: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 10:03:44: #1 finished! INFO @ Tue, 16 Jun 2020 10:03:44: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 10:03:44: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 10:03:44: 3000000 INFO @ Tue, 16 Jun 2020 10:03:44: 8000000 INFO @ Tue, 16 Jun 2020 10:03:45: #2 number of paired peaks: 2185 INFO @ Tue, 16 Jun 2020 10:03:45: start model_add_line... INFO @ Tue, 16 Jun 2020 10:03:45: start X-correlation... INFO @ Tue, 16 Jun 2020 10:03:45: end of X-cor INFO @ Tue, 16 Jun 2020 10:03:45: #2 finished! INFO @ Tue, 16 Jun 2020 10:03:45: #2 predicted fragment length is 135 bps INFO @ Tue, 16 Jun 2020 10:03:45: #2 alternative fragment length(s) may be 4,135 bps INFO @ Tue, 16 Jun 2020 10:03:45: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX958296/SRX958296.05_model.r INFO @ Tue, 16 Jun 2020 10:03:45: #3 Call peaks... INFO @ Tue, 16 Jun 2020 10:03:45: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 10:03:49: 9000000 INFO @ Tue, 16 Jun 2020 10:03:50: 4000000 INFO @ Tue, 16 Jun 2020 10:03:55: 10000000 INFO @ Tue, 16 Jun 2020 10:03:55: 5000000 INFO @ Tue, 16 Jun 2020 10:04:00: 11000000 INFO @ Tue, 16 Jun 2020 10:04:00: 6000000 INFO @ Tue, 16 Jun 2020 10:04:05: 12000000 INFO @ Tue, 16 Jun 2020 10:04:06: 7000000 INFO @ Tue, 16 Jun 2020 10:04:11: 13000000 INFO @ Tue, 16 Jun 2020 10:04:11: 8000000 INFO @ Tue, 16 Jun 2020 10:04:14: #1 tag size is determined as 51 bps INFO @ Tue, 16 Jun 2020 10:04:14: #1 tag size = 51 INFO @ Tue, 16 Jun 2020 10:04:14: #1 total tags in treatment: 13562369 INFO @ Tue, 16 Jun 2020 10:04:14: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 10:04:14: #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 10:04:14: #1 tags after filtering in treatment: 13562369 INFO @ Tue, 16 Jun 2020 10:04:14: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 10:04:14: #1 finished! INFO @ Tue, 16 Jun 2020 10:04:14: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 10:04:14: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 10:04:15: #2 number of paired peaks: 2185 INFO @ Tue, 16 Jun 2020 10:04:15: start model_add_line... INFO @ Tue, 16 Jun 2020 10:04:15: start X-correlation... INFO @ Tue, 16 Jun 2020 10:04:15: end of X-cor INFO @ Tue, 16 Jun 2020 10:04:15: #2 finished! INFO @ Tue, 16 Jun 2020 10:04:15: #2 predicted fragment length is 135 bps INFO @ Tue, 16 Jun 2020 10:04:15: #2 alternative fragment length(s) may be 4,135 bps INFO @ Tue, 16 Jun 2020 10:04:15: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX958296/SRX958296.10_model.r INFO @ Tue, 16 Jun 2020 10:04:15: #3 Call peaks... INFO @ Tue, 16 Jun 2020 10:04:15: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 10:04:17: 9000000 INFO @ Tue, 16 Jun 2020 10:04:21: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 10:04:22: 10000000 INFO @ Tue, 16 Jun 2020 10:04:28: 11000000 INFO @ Tue, 16 Jun 2020 10:04:33: 12000000 INFO @ Tue, 16 Jun 2020 10:04:34: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX958296/SRX958296.05_peaks.xls INFO @ Tue, 16 Jun 2020 10:04:34: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX958296/SRX958296.05_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 10:04:34: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX958296/SRX958296.05_summits.bed INFO @ Tue, 16 Jun 2020 10:04:34: Done! pass1 - making usageList (7 chroms): 2 millis pass2 - checking and writing primary data (7993 records, 4 fields): 10 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 16 Jun 2020 10:04:39: 13000000 INFO @ Tue, 16 Jun 2020 10:04:42: #1 tag size is determined as 51 bps INFO @ Tue, 16 Jun 2020 10:04:42: #1 tag size = 51 INFO @ Tue, 16 Jun 2020 10:04:42: #1 total tags in treatment: 13562369 INFO @ Tue, 16 Jun 2020 10:04:42: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 10:04:42: #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 10:04:42: #1 tags after filtering in treatment: 13562369 INFO @ Tue, 16 Jun 2020 10:04:42: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 10:04:42: #1 finished! INFO @ Tue, 16 Jun 2020 10:04:42: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 10:04:42: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 10:04:43: #2 number of paired peaks: 2185 INFO @ Tue, 16 Jun 2020 10:04:43: start model_add_line... INFO @ Tue, 16 Jun 2020 10:04:43: start X-correlation... INFO @ Tue, 16 Jun 2020 10:04:43: end of X-cor INFO @ Tue, 16 Jun 2020 10:04:43: #2 finished! INFO @ Tue, 16 Jun 2020 10:04:43: #2 predicted fragment length is 135 bps INFO @ Tue, 16 Jun 2020 10:04:43: #2 alternative fragment length(s) may be 4,135 bps INFO @ Tue, 16 Jun 2020 10:04:43: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX958296/SRX958296.20_model.r INFO @ Tue, 16 Jun 2020 10:04:43: #3 Call peaks... INFO @ Tue, 16 Jun 2020 10:04:43: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 10:04:51: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 10:05:04: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX958296/SRX958296.10_peaks.xls INFO @ Tue, 16 Jun 2020 10:05:04: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX958296/SRX958296.10_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 10:05:04: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX958296/SRX958296.10_summits.bed INFO @ Tue, 16 Jun 2020 10:05:04: Done! pass1 - making usageList (7 chroms): 2 millis pass2 - checking and writing primary data (5308 records, 4 fields): 7 millis CompletedMACS2peakCalling BigWig に変換しました。 INFO @ Tue, 16 Jun 2020 10:05:19: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 10:05:32: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX958296/SRX958296.20_peaks.xls INFO @ Tue, 16 Jun 2020 10:05:32: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX958296/SRX958296.20_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 10:05:32: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX958296/SRX958296.20_summits.bed INFO @ Tue, 16 Jun 2020 10:05:32: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (2732 records, 4 fields): 5 millis CompletedMACS2peakCalling