Job ID = 6366517 SRX = SRX1674097 Genome = ce11 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-15T22:54:29 prefetch.2.10.7: 1) Downloading 'SRR3320143'... 2020-06-15T22:54:29 prefetch.2.10.7: Downloading via HTTPS... 2020-06-15T22:58:53 prefetch.2.10.7: HTTPS download succeed 2020-06-15T22:58:53 prefetch.2.10.7: 1) 'SRR3320143' was downloaded successfully Read 72777330 spots for SRR3320143/SRR3320143.sra Written 72777330 spots for SRR3320143/SRR3320143.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: 00:10:33 72777330 reads; of these: 72777330 (100.00%) were unpaired; of these: 43839270 (60.24%) aligned 0 times 23191179 (31.87%) aligned exactly 1 time 5746881 (7.90%) aligned >1 times 39.76% overall alignment rate Time searching: 00:10:33 Overall time: 00:10:33 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 12 files... [bam_rmdupse_core] 14569782 / 28938060 = 0.5035 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 08:19:34: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX1674097/SRX1674097.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX1674097/SRX1674097.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX1674097/SRX1674097.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX1674097/SRX1674097.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 08:19:34: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:19:34: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:19:39: 1000000 INFO @ Tue, 16 Jun 2020 08:19:44: 2000000 INFO @ Tue, 16 Jun 2020 08:19:49: 3000000 INFO @ Tue, 16 Jun 2020 08:19:55: 4000000 INFO @ Tue, 16 Jun 2020 08:20:00: 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 08:20:04: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX1674097/SRX1674097.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX1674097/SRX1674097.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX1674097/SRX1674097.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX1674097/SRX1674097.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 08:20:04: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:20:04: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:20:05: 6000000 INFO @ Tue, 16 Jun 2020 08:20:09: 1000000 INFO @ Tue, 16 Jun 2020 08:20:10: 7000000 INFO @ Tue, 16 Jun 2020 08:20:15: 2000000 INFO @ Tue, 16 Jun 2020 08:20:16: 8000000 INFO @ Tue, 16 Jun 2020 08:20:20: 3000000 INFO @ Tue, 16 Jun 2020 08:20:22: 9000000 INFO @ Tue, 16 Jun 2020 08:20:26: 4000000 INFO @ Tue, 16 Jun 2020 08:20:27: 10000000 INFO @ Tue, 16 Jun 2020 08:20:32: 5000000 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 08:20:33: 11000000 INFO @ Tue, 16 Jun 2020 08:20:34: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX1674097/SRX1674097.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX1674097/SRX1674097.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX1674097/SRX1674097.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX1674097/SRX1674097.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 08:20:34: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:20:34: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:20:37: 6000000 INFO @ Tue, 16 Jun 2020 08:20:38: 12000000 INFO @ Tue, 16 Jun 2020 08:20:39: 1000000 INFO @ Tue, 16 Jun 2020 08:20:43: 7000000 INFO @ Tue, 16 Jun 2020 08:20:44: 13000000 INFO @ Tue, 16 Jun 2020 08:20:45: 2000000 INFO @ Tue, 16 Jun 2020 08:20:48: 8000000 INFO @ Tue, 16 Jun 2020 08:20:49: 14000000 INFO @ Tue, 16 Jun 2020 08:20:50: 3000000 INFO @ Tue, 16 Jun 2020 08:20:51: #1 tag size is determined as 51 bps INFO @ Tue, 16 Jun 2020 08:20:51: #1 tag size = 51 INFO @ Tue, 16 Jun 2020 08:20:51: #1 total tags in treatment: 14368278 INFO @ Tue, 16 Jun 2020 08:20:51: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:20:51: #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 08:20:52: #1 tags after filtering in treatment: 14368278 INFO @ Tue, 16 Jun 2020 08:20:52: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:20:52: #1 finished! INFO @ Tue, 16 Jun 2020 08:20:52: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:20:52: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:20:53: #2 number of paired peaks: 2378 INFO @ Tue, 16 Jun 2020 08:20:53: start model_add_line... INFO @ Tue, 16 Jun 2020 08:20:53: start X-correlation... INFO @ Tue, 16 Jun 2020 08:20:53: end of X-cor INFO @ Tue, 16 Jun 2020 08:20:53: #2 finished! INFO @ Tue, 16 Jun 2020 08:20:53: #2 predicted fragment length is 262 bps INFO @ Tue, 16 Jun 2020 08:20:53: #2 alternative fragment length(s) may be 262 bps INFO @ Tue, 16 Jun 2020 08:20:53: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX1674097/SRX1674097.05_model.r INFO @ Tue, 16 Jun 2020 08:20:53: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:20:53: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 08:20:54: 9000000 INFO @ Tue, 16 Jun 2020 08:20:56: 4000000 INFO @ Tue, 16 Jun 2020 08:20:59: 10000000 INFO @ Tue, 16 Jun 2020 08:21:02: 5000000 INFO @ Tue, 16 Jun 2020 08:21:04: 11000000 INFO @ Tue, 16 Jun 2020 08:21:07: 6000000 INFO @ Tue, 16 Jun 2020 08:21:10: 12000000 INFO @ Tue, 16 Jun 2020 08:21:13: 7000000 INFO @ Tue, 16 Jun 2020 08:21:15: 13000000 INFO @ Tue, 16 Jun 2020 08:21:19: 8000000 INFO @ Tue, 16 Jun 2020 08:21:21: 14000000 INFO @ Tue, 16 Jun 2020 08:21:23: #1 tag size is determined as 51 bps INFO @ Tue, 16 Jun 2020 08:21:23: #1 tag size = 51 INFO @ Tue, 16 Jun 2020 08:21:23: #1 total tags in treatment: 14368278 INFO @ Tue, 16 Jun 2020 08:21:23: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:21:23: #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 08:21:23: #1 tags after filtering in treatment: 14368278 INFO @ Tue, 16 Jun 2020 08:21:23: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:21:23: #1 finished! INFO @ Tue, 16 Jun 2020 08:21:23: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:21:23: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:21:24: #2 number of paired peaks: 2378 INFO @ Tue, 16 Jun 2020 08:21:24: start model_add_line... INFO @ Tue, 16 Jun 2020 08:21:24: 9000000 INFO @ Tue, 16 Jun 2020 08:21:24: start X-correlation... INFO @ Tue, 16 Jun 2020 08:21:24: end of X-cor INFO @ Tue, 16 Jun 2020 08:21:24: #2 finished! INFO @ Tue, 16 Jun 2020 08:21:24: #2 predicted fragment length is 262 bps INFO @ Tue, 16 Jun 2020 08:21:24: #2 alternative fragment length(s) may be 262 bps INFO @ Tue, 16 Jun 2020 08:21:24: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX1674097/SRX1674097.10_model.r INFO @ Tue, 16 Jun 2020 08:21:24: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:21:24: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 08:21:30: 10000000 INFO @ Tue, 16 Jun 2020 08:21:35: 11000000 INFO @ Tue, 16 Jun 2020 08:21:38: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 08:21:40: 12000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 16 Jun 2020 08:21:45: 13000000 INFO @ Tue, 16 Jun 2020 08:21:51: 14000000 INFO @ Tue, 16 Jun 2020 08:21:53: #1 tag size is determined as 51 bps INFO @ Tue, 16 Jun 2020 08:21:53: #1 tag size = 51 INFO @ Tue, 16 Jun 2020 08:21:53: #1 total tags in treatment: 14368278 INFO @ Tue, 16 Jun 2020 08:21:53: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:21:53: #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 08:21:53: #1 tags after filtering in treatment: 14368278 INFO @ Tue, 16 Jun 2020 08:21:53: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:21:53: #1 finished! INFO @ Tue, 16 Jun 2020 08:21:53: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:21:53: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:21:54: #2 number of paired peaks: 2378 INFO @ Tue, 16 Jun 2020 08:21:54: start model_add_line... INFO @ Tue, 16 Jun 2020 08:21:54: start X-correlation... INFO @ Tue, 16 Jun 2020 08:21:54: end of X-cor INFO @ Tue, 16 Jun 2020 08:21:54: #2 finished! INFO @ Tue, 16 Jun 2020 08:21:54: #2 predicted fragment length is 262 bps INFO @ Tue, 16 Jun 2020 08:21:54: #2 alternative fragment length(s) may be 262 bps INFO @ Tue, 16 Jun 2020 08:21:54: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX1674097/SRX1674097.20_model.r INFO @ Tue, 16 Jun 2020 08:21:54: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:21:54: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 08:21:56: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX1674097/SRX1674097.05_peaks.xls INFO @ Tue, 16 Jun 2020 08:21:56: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX1674097/SRX1674097.05_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:21:56: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX1674097/SRX1674097.05_summits.bed INFO @ Tue, 16 Jun 2020 08:21:56: Done! pass1 - making usageList (7 chroms): 3 millis pass2 - checking and writing primary data (18091 records, 4 fields): 28 millis CompletedMACS2peakCalling BigWig に変換しました。 INFO @ Tue, 16 Jun 2020 08:22:08: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 08:22:26: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX1674097/SRX1674097.10_peaks.xls INFO @ Tue, 16 Jun 2020 08:22:26: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX1674097/SRX1674097.10_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:22:26: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX1674097/SRX1674097.10_summits.bed INFO @ Tue, 16 Jun 2020 08:22:26: Done! pass1 - making usageList (7 chroms): 2 millis pass2 - checking and writing primary data (12917 records, 4 fields): 13 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 08:22:38: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 08:22:55: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX1674097/SRX1674097.20_peaks.xls INFO @ Tue, 16 Jun 2020 08:22:55: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX1674097/SRX1674097.20_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:22:55: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX1674097/SRX1674097.20_summits.bed INFO @ Tue, 16 Jun 2020 08:22:55: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (7465 records, 4 fields): 8 millis CompletedMACS2peakCalling