Job ID = 6368906 SRX = SRX6720169 Genome = ce11 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-16T00:39:04 prefetch.2.10.7: 1) Downloading 'SRR9972861'... 2020-06-16T00:39:04 prefetch.2.10.7: Downloading via HTTPS... 2020-06-16T00:42:53 prefetch.2.10.7: HTTPS download succeed 2020-06-16T00:42:53 prefetch.2.10.7: 1) 'SRR9972861' was downloaded successfully Read 19128664 spots for SRR9972861/SRR9972861.sra Written 19128664 spots for SRR9972861/SRR9972861.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: 00:04:14 19128664 reads; of these: 19128664 (100.00%) were unpaired; of these: 369797 (1.93%) aligned 0 times 16018825 (83.74%) aligned exactly 1 time 2740042 (14.32%) aligned >1 times 98.07% overall alignment rate Time searching: 00:04:14 Overall time: 00:04:14 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] 6320216 / 18758867 = 0.3369 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 09:52:29: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX6720169/SRX6720169.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX6720169/SRX6720169.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX6720169/SRX6720169.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX6720169/SRX6720169.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 09:52:29: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:52:29: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:52:34: 1000000 INFO @ Tue, 16 Jun 2020 09:52:40: 2000000 INFO @ Tue, 16 Jun 2020 09:52:46: 3000000 INFO @ Tue, 16 Jun 2020 09:52:52: 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 09:52:57: 5000000 INFO @ Tue, 16 Jun 2020 09:52:59: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX6720169/SRX6720169.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX6720169/SRX6720169.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX6720169/SRX6720169.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX6720169/SRX6720169.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 09:52:59: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:52:59: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:53:03: 6000000 INFO @ Tue, 16 Jun 2020 09:53:04: 1000000 INFO @ Tue, 16 Jun 2020 09:53:09: 2000000 INFO @ Tue, 16 Jun 2020 09:53:09: 7000000 INFO @ Tue, 16 Jun 2020 09:53:15: 3000000 INFO @ Tue, 16 Jun 2020 09:53:15: 8000000 INFO @ Tue, 16 Jun 2020 09:53:20: 4000000 INFO @ Tue, 16 Jun 2020 09:53:21: 9000000 INFO @ Tue, 16 Jun 2020 09:53:25: 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 09:53:27: 10000000 INFO @ Tue, 16 Jun 2020 09:53:29: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX6720169/SRX6720169.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX6720169/SRX6720169.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX6720169/SRX6720169.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX6720169/SRX6720169.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 09:53:29: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:53:29: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:53:30: 6000000 INFO @ Tue, 16 Jun 2020 09:53:33: 11000000 INFO @ Tue, 16 Jun 2020 09:53:34: 1000000 INFO @ Tue, 16 Jun 2020 09:53:36: 7000000 INFO @ Tue, 16 Jun 2020 09:53:39: 12000000 INFO @ Tue, 16 Jun 2020 09:53:40: 2000000 INFO @ Tue, 16 Jun 2020 09:53:41: 8000000 INFO @ Tue, 16 Jun 2020 09:53:42: #1 tag size is determined as 50 bps INFO @ Tue, 16 Jun 2020 09:53:42: #1 tag size = 50 INFO @ Tue, 16 Jun 2020 09:53:42: #1 total tags in treatment: 12438651 INFO @ Tue, 16 Jun 2020 09:53:42: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:53:42: #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 09:53:42: #1 tags after filtering in treatment: 12438651 INFO @ Tue, 16 Jun 2020 09:53:42: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 09:53:42: #1 finished! INFO @ Tue, 16 Jun 2020 09:53:42: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:53:42: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:53:43: #2 number of paired peaks: 1498 INFO @ Tue, 16 Jun 2020 09:53:43: start model_add_line... INFO @ Tue, 16 Jun 2020 09:53:43: start X-correlation... INFO @ Tue, 16 Jun 2020 09:53:43: end of X-cor INFO @ Tue, 16 Jun 2020 09:53:43: #2 finished! INFO @ Tue, 16 Jun 2020 09:53:43: #2 predicted fragment length is 163 bps INFO @ Tue, 16 Jun 2020 09:53:43: #2 alternative fragment length(s) may be 163 bps INFO @ Tue, 16 Jun 2020 09:53:43: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX6720169/SRX6720169.05_model.r INFO @ Tue, 16 Jun 2020 09:53:43: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:53:43: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 09:53:45: 3000000 INFO @ Tue, 16 Jun 2020 09:53:46: 9000000 INFO @ Tue, 16 Jun 2020 09:53:51: 4000000 INFO @ Tue, 16 Jun 2020 09:53:52: 10000000 INFO @ Tue, 16 Jun 2020 09:53:56: 5000000 INFO @ Tue, 16 Jun 2020 09:53:57: 11000000 INFO @ Tue, 16 Jun 2020 09:54:02: 6000000 INFO @ Tue, 16 Jun 2020 09:54:02: 12000000 INFO @ Tue, 16 Jun 2020 09:54:04: #1 tag size is determined as 50 bps INFO @ Tue, 16 Jun 2020 09:54:04: #1 tag size = 50 INFO @ Tue, 16 Jun 2020 09:54:04: #1 total tags in treatment: 12438651 INFO @ Tue, 16 Jun 2020 09:54:04: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:54:04: #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 09:54:05: #1 tags after filtering in treatment: 12438651 INFO @ Tue, 16 Jun 2020 09:54:05: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 09:54:05: #1 finished! INFO @ Tue, 16 Jun 2020 09:54:05: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:54:05: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:54:06: #2 number of paired peaks: 1498 INFO @ Tue, 16 Jun 2020 09:54:06: start model_add_line... INFO @ Tue, 16 Jun 2020 09:54:06: start X-correlation... INFO @ Tue, 16 Jun 2020 09:54:06: end of X-cor INFO @ Tue, 16 Jun 2020 09:54:06: #2 finished! INFO @ Tue, 16 Jun 2020 09:54:06: #2 predicted fragment length is 163 bps INFO @ Tue, 16 Jun 2020 09:54:06: #2 alternative fragment length(s) may be 163 bps INFO @ Tue, 16 Jun 2020 09:54:06: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX6720169/SRX6720169.10_model.r INFO @ Tue, 16 Jun 2020 09:54:06: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:54:06: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 09:54:07: 7000000 INFO @ Tue, 16 Jun 2020 09:54:12: 8000000 INFO @ Tue, 16 Jun 2020 09:54:13: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 09:54:17: 9000000 INFO @ Tue, 16 Jun 2020 09:54:22: 10000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 16 Jun 2020 09:54:27: 11000000 INFO @ Tue, 16 Jun 2020 09:54:29: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX6720169/SRX6720169.05_peaks.xls INFO @ Tue, 16 Jun 2020 09:54:29: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX6720169/SRX6720169.05_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:54:29: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX6720169/SRX6720169.05_summits.bed INFO @ Tue, 16 Jun 2020 09:54:29: Done! pass1 - making usageList (7 chroms): 2 millis pass2 - checking and writing primary data (5350 records, 4 fields): 6 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 09:54:32: 12000000 INFO @ Tue, 16 Jun 2020 09:54:34: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 09:54:35: #1 tag size is determined as 50 bps INFO @ Tue, 16 Jun 2020 09:54:35: #1 tag size = 50 INFO @ Tue, 16 Jun 2020 09:54:35: #1 total tags in treatment: 12438651 INFO @ Tue, 16 Jun 2020 09:54:35: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:54:35: #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 09:54:35: #1 tags after filtering in treatment: 12438651 INFO @ Tue, 16 Jun 2020 09:54:35: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 09:54:35: #1 finished! INFO @ Tue, 16 Jun 2020 09:54:35: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:54:35: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:54:36: #2 number of paired peaks: 1498 INFO @ Tue, 16 Jun 2020 09:54:36: start model_add_line... INFO @ Tue, 16 Jun 2020 09:54:36: start X-correlation... INFO @ Tue, 16 Jun 2020 09:54:36: end of X-cor INFO @ Tue, 16 Jun 2020 09:54:36: #2 finished! INFO @ Tue, 16 Jun 2020 09:54:36: #2 predicted fragment length is 163 bps INFO @ Tue, 16 Jun 2020 09:54:36: #2 alternative fragment length(s) may be 163 bps INFO @ Tue, 16 Jun 2020 09:54:36: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX6720169/SRX6720169.20_model.r INFO @ Tue, 16 Jun 2020 09:54:36: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:54:36: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Tue, 16 Jun 2020 09:54:49: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX6720169/SRX6720169.10_peaks.xls INFO @ Tue, 16 Jun 2020 09:54:49: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX6720169/SRX6720169.10_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:54:49: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX6720169/SRX6720169.10_summits.bed INFO @ Tue, 16 Jun 2020 09:54:49: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (3521 records, 4 fields): 5 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 09:55:05: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 09:55:20: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX6720169/SRX6720169.20_peaks.xls INFO @ Tue, 16 Jun 2020 09:55:20: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX6720169/SRX6720169.20_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:55:20: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX6720169/SRX6720169.20_summits.bed INFO @ Tue, 16 Jun 2020 09:55:20: Done! pass1 - making usageList (7 chroms): 0 millis pass2 - checking and writing primary data (1847 records, 4 fields): 4 millis CompletedMACS2peakCalling