Job ID = 6368696 SRX = SRX5402722 Genome = ce11 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-16T00:27:49 prefetch.2.10.7: 1) Downloading 'SRR8602956'... 2020-06-16T00:27:49 prefetch.2.10.7: Downloading via HTTPS... 2020-06-16T00:28:47 prefetch.2.10.7: HTTPS download succeed 2020-06-16T00:28:47 prefetch.2.10.7: 'SRR8602956' is valid 2020-06-16T00:28:47 prefetch.2.10.7: 1) 'SRR8602956' was downloaded successfully 2020-06-16T00:28:47 prefetch.2.10.7: 'SRR8602956' has 0 unresolved dependencies Read 11328065 spots for SRR8602956/SRR8602956.sra Written 11328065 spots for SRR8602956/SRR8602956.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: 00:02:11 11328065 reads; of these: 11328065 (100.00%) were unpaired; of these: 313649 (2.77%) aligned 0 times 10003067 (88.30%) aligned exactly 1 time 1011349 (8.93%) aligned >1 times 97.23% overall alignment rate Time searching: 00:02:11 Overall time: 00:02:11 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 8 files... [bam_rmdupse_core] 2406542 / 11014416 = 0.2185 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 09:33:58: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX5402722/SRX5402722.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX5402722/SRX5402722.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX5402722/SRX5402722.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX5402722/SRX5402722.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 09:33:58: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:33:58: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:34:02: 1000000 INFO @ Tue, 16 Jun 2020 09:34:07: 2000000 INFO @ Tue, 16 Jun 2020 09:34:12: 3000000 INFO @ Tue, 16 Jun 2020 09:34:16: 4000000 INFO @ Tue, 16 Jun 2020 09:34:21: 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 09:34:26: 6000000 INFO @ Tue, 16 Jun 2020 09:34:28: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX5402722/SRX5402722.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX5402722/SRX5402722.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX5402722/SRX5402722.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX5402722/SRX5402722.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 09:34:28: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:34:28: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:34:31: 7000000 INFO @ Tue, 16 Jun 2020 09:34:33: 1000000 INFO @ Tue, 16 Jun 2020 09:34:36: 8000000 INFO @ Tue, 16 Jun 2020 09:34:39: #1 tag size is determined as 51 bps INFO @ Tue, 16 Jun 2020 09:34:39: #1 tag size = 51 INFO @ Tue, 16 Jun 2020 09:34:39: #1 total tags in treatment: 8607874 INFO @ Tue, 16 Jun 2020 09:34:39: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:34:39: #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 09:34:39: #1 tags after filtering in treatment: 8607874 INFO @ Tue, 16 Jun 2020 09:34:39: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 09:34:39: #1 finished! INFO @ Tue, 16 Jun 2020 09:34:39: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:34:39: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:34:39: 2000000 INFO @ Tue, 16 Jun 2020 09:34:40: #2 number of paired peaks: 2582 INFO @ Tue, 16 Jun 2020 09:34:40: start model_add_line... INFO @ Tue, 16 Jun 2020 09:34:40: start X-correlation... INFO @ Tue, 16 Jun 2020 09:34:40: end of X-cor INFO @ Tue, 16 Jun 2020 09:34:40: #2 finished! INFO @ Tue, 16 Jun 2020 09:34:40: #2 predicted fragment length is 152 bps INFO @ Tue, 16 Jun 2020 09:34:40: #2 alternative fragment length(s) may be 3,152 bps INFO @ Tue, 16 Jun 2020 09:34:40: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX5402722/SRX5402722.05_model.r INFO @ Tue, 16 Jun 2020 09:34:40: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:34:40: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 09:34:45: 3000000 INFO @ Tue, 16 Jun 2020 09:34:51: 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 09:34:57: 5000000 INFO @ Tue, 16 Jun 2020 09:34:57: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX5402722/SRX5402722.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX5402722/SRX5402722.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX5402722/SRX5402722.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX5402722/SRX5402722.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 09:34:57: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:34:57: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:34:58: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 09:35:02: 6000000 INFO @ Tue, 16 Jun 2020 09:35:03: 1000000 INFO @ Tue, 16 Jun 2020 09:35:07: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX5402722/SRX5402722.05_peaks.xls INFO @ Tue, 16 Jun 2020 09:35:07: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX5402722/SRX5402722.05_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:35:07: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX5402722/SRX5402722.05_summits.bed INFO @ Tue, 16 Jun 2020 09:35:07: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (7888 records, 4 fields): 8 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 09:35:08: 2000000 INFO @ Tue, 16 Jun 2020 09:35:08: 7000000 INFO @ Tue, 16 Jun 2020 09:35:13: 3000000 INFO @ Tue, 16 Jun 2020 09:35:14: 8000000 INFO @ Tue, 16 Jun 2020 09:35:18: 4000000 INFO @ Tue, 16 Jun 2020 09:35:18: #1 tag size is determined as 51 bps INFO @ Tue, 16 Jun 2020 09:35:18: #1 tag size = 51 INFO @ Tue, 16 Jun 2020 09:35:18: #1 total tags in treatment: 8607874 INFO @ Tue, 16 Jun 2020 09:35:18: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:35:18: #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 09:35:18: #1 tags after filtering in treatment: 8607874 INFO @ Tue, 16 Jun 2020 09:35:18: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 09:35:18: #1 finished! INFO @ Tue, 16 Jun 2020 09:35:18: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:35:18: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:35:19: #2 number of paired peaks: 2582 INFO @ Tue, 16 Jun 2020 09:35:19: start model_add_line... INFO @ Tue, 16 Jun 2020 09:35:19: start X-correlation... INFO @ Tue, 16 Jun 2020 09:35:19: end of X-cor INFO @ Tue, 16 Jun 2020 09:35:19: #2 finished! INFO @ Tue, 16 Jun 2020 09:35:19: #2 predicted fragment length is 152 bps INFO @ Tue, 16 Jun 2020 09:35:19: #2 alternative fragment length(s) may be 3,152 bps INFO @ Tue, 16 Jun 2020 09:35:19: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX5402722/SRX5402722.10_model.r INFO @ Tue, 16 Jun 2020 09:35:19: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:35:19: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 09:35:23: 5000000 INFO @ Tue, 16 Jun 2020 09:35:27: 6000000 INFO @ Tue, 16 Jun 2020 09:35:32: 7000000 INFO @ Tue, 16 Jun 2020 09:35:37: 8000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 16 Jun 2020 09:35:38: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 09:35:40: #1 tag size is determined as 51 bps INFO @ Tue, 16 Jun 2020 09:35:40: #1 tag size = 51 INFO @ Tue, 16 Jun 2020 09:35:40: #1 total tags in treatment: 8607874 INFO @ Tue, 16 Jun 2020 09:35:40: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:35:40: #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 09:35:40: #1 tags after filtering in treatment: 8607874 INFO @ Tue, 16 Jun 2020 09:35:40: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 09:35:40: #1 finished! INFO @ Tue, 16 Jun 2020 09:35:40: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:35:40: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:35:41: #2 number of paired peaks: 2582 INFO @ Tue, 16 Jun 2020 09:35:41: start model_add_line... INFO @ Tue, 16 Jun 2020 09:35:41: start X-correlation... INFO @ Tue, 16 Jun 2020 09:35:41: end of X-cor INFO @ Tue, 16 Jun 2020 09:35:41: #2 finished! INFO @ Tue, 16 Jun 2020 09:35:41: #2 predicted fragment length is 152 bps INFO @ Tue, 16 Jun 2020 09:35:41: #2 alternative fragment length(s) may be 3,152 bps INFO @ Tue, 16 Jun 2020 09:35:41: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX5402722/SRX5402722.20_model.r INFO @ Tue, 16 Jun 2020 09:35:41: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:35:41: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 09:35:48: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX5402722/SRX5402722.10_peaks.xls INFO @ Tue, 16 Jun 2020 09:35:48: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX5402722/SRX5402722.10_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:35:48: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX5402722/SRX5402722.10_summits.bed INFO @ Tue, 16 Jun 2020 09:35:48: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (3368 records, 4 fields): 4 millis CompletedMACS2peakCalling BigWig に変換しました。 INFO @ Tue, 16 Jun 2020 09:35:59: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 09:36:08: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX5402722/SRX5402722.20_peaks.xls INFO @ Tue, 16 Jun 2020 09:36:08: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX5402722/SRX5402722.20_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:36:08: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX5402722/SRX5402722.20_summits.bed INFO @ Tue, 16 Jun 2020 09:36:08: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (592 records, 4 fields): 1 millis CompletedMACS2peakCalling