Job ID = 6366082 SRX = SRX059254 Genome = ce11 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-15T22:32:36 prefetch.2.10.7: 1) Downloading 'SRR190694'... 2020-06-15T22:32:36 prefetch.2.10.7: Downloading via HTTPS... 2020-06-15T22:33:56 prefetch.2.10.7: HTTPS download succeed 2020-06-15T22:33:57 prefetch.2.10.7: 'SRR190694' is valid 2020-06-15T22:33:57 prefetch.2.10.7: 1) 'SRR190694' was downloaded successfully Read 11592789 spots for SRR190694/SRR190694.sra Written 11592789 spots for SRR190694/SRR190694.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: 00:02:04 11592789 reads; of these: 11592789 (100.00%) were unpaired; of these: 1265041 (10.91%) aligned 0 times 9037087 (77.95%) aligned exactly 1 time 1290661 (11.13%) aligned >1 times 89.09% overall alignment rate Time searching: 00:02:04 Overall time: 00:02:04 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_rmdupse_core] 2172626 / 10327748 = 0.2104 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 07:38:58: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX059254/SRX059254.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX059254/SRX059254.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX059254/SRX059254.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX059254/SRX059254.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 07:38:58: #1 read tag files... INFO @ Tue, 16 Jun 2020 07:38:58: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 07:39:04: 1000000 INFO @ Tue, 16 Jun 2020 07:39:09: 2000000 INFO @ Tue, 16 Jun 2020 07:39:14: 3000000 INFO @ Tue, 16 Jun 2020 07:39:19: 4000000 INFO @ Tue, 16 Jun 2020 07:39:24: 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 07:39:28: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX059254/SRX059254.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX059254/SRX059254.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX059254/SRX059254.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX059254/SRX059254.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 07:39:28: #1 read tag files... INFO @ Tue, 16 Jun 2020 07:39:28: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 07:39:30: 6000000 INFO @ Tue, 16 Jun 2020 07:39:34: 1000000 INFO @ Tue, 16 Jun 2020 07:39:35: 7000000 INFO @ Tue, 16 Jun 2020 07:39:40: 2000000 INFO @ Tue, 16 Jun 2020 07:39:42: 8000000 INFO @ Tue, 16 Jun 2020 07:39:43: #1 tag size is determined as 36 bps INFO @ Tue, 16 Jun 2020 07:39:43: #1 tag size = 36 INFO @ Tue, 16 Jun 2020 07:39:43: #1 total tags in treatment: 8155122 INFO @ Tue, 16 Jun 2020 07:39:43: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 07:39:43: #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 07:39:43: #1 tags after filtering in treatment: 8155122 INFO @ Tue, 16 Jun 2020 07:39:43: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 07:39:43: #1 finished! INFO @ Tue, 16 Jun 2020 07:39:43: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 07:39:43: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 07:39:43: #2 number of paired peaks: 3596 INFO @ Tue, 16 Jun 2020 07:39:43: start model_add_line... INFO @ Tue, 16 Jun 2020 07:39:44: start X-correlation... INFO @ Tue, 16 Jun 2020 07:39:44: end of X-cor INFO @ Tue, 16 Jun 2020 07:39:44: #2 finished! INFO @ Tue, 16 Jun 2020 07:39:44: #2 predicted fragment length is 137 bps INFO @ Tue, 16 Jun 2020 07:39:44: #2 alternative fragment length(s) may be 137 bps INFO @ Tue, 16 Jun 2020 07:39:44: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX059254/SRX059254.05_model.r INFO @ Tue, 16 Jun 2020 07:39:44: #3 Call peaks... INFO @ Tue, 16 Jun 2020 07:39:44: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 07:39:45: 3000000 INFO @ Tue, 16 Jun 2020 07:39:50: 4000000 INFO @ Tue, 16 Jun 2020 07:39:56: 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 07:39:58: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX059254/SRX059254.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX059254/SRX059254.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX059254/SRX059254.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX059254/SRX059254.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 07:39:58: #1 read tag files... INFO @ Tue, 16 Jun 2020 07:39:58: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 07:40:01: 6000000 INFO @ Tue, 16 Jun 2020 07:40:04: 1000000 INFO @ Tue, 16 Jun 2020 07:40:05: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 07:40:06: 7000000 INFO @ Tue, 16 Jun 2020 07:40:09: 2000000 INFO @ Tue, 16 Jun 2020 07:40:12: 8000000 INFO @ Tue, 16 Jun 2020 07:40:13: #1 tag size is determined as 36 bps INFO @ Tue, 16 Jun 2020 07:40:13: #1 tag size = 36 INFO @ Tue, 16 Jun 2020 07:40:13: #1 total tags in treatment: 8155122 INFO @ Tue, 16 Jun 2020 07:40:13: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 07:40:13: #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 07:40:13: #1 tags after filtering in treatment: 8155122 INFO @ Tue, 16 Jun 2020 07:40:13: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 07:40:13: #1 finished! INFO @ Tue, 16 Jun 2020 07:40:13: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 07:40:13: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 07:40:14: #2 number of paired peaks: 3596 INFO @ Tue, 16 Jun 2020 07:40:14: start model_add_line... INFO @ Tue, 16 Jun 2020 07:40:14: start X-correlation... INFO @ Tue, 16 Jun 2020 07:40:14: end of X-cor INFO @ Tue, 16 Jun 2020 07:40:14: #2 finished! INFO @ Tue, 16 Jun 2020 07:40:14: #2 predicted fragment length is 137 bps INFO @ Tue, 16 Jun 2020 07:40:14: #2 alternative fragment length(s) may be 137 bps INFO @ Tue, 16 Jun 2020 07:40:14: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX059254/SRX059254.10_model.r INFO @ Tue, 16 Jun 2020 07:40:14: #3 Call peaks... INFO @ Tue, 16 Jun 2020 07:40:14: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 07:40:15: 3000000 INFO @ Tue, 16 Jun 2020 07:40:15: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX059254/SRX059254.05_peaks.xls INFO @ Tue, 16 Jun 2020 07:40:15: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX059254/SRX059254.05_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 07:40:15: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX059254/SRX059254.05_summits.bed INFO @ Tue, 16 Jun 2020 07:40:15: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (6130 records, 4 fields): 7 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 07:40:20: 4000000 INFO @ Tue, 16 Jun 2020 07:40:25: 5000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 16 Jun 2020 07:40:30: 6000000 INFO @ Tue, 16 Jun 2020 07:40:34: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 07:40:35: 7000000 INFO @ Tue, 16 Jun 2020 07:40:40: 8000000 INFO @ Tue, 16 Jun 2020 07:40:41: #1 tag size is determined as 36 bps INFO @ Tue, 16 Jun 2020 07:40:41: #1 tag size = 36 INFO @ Tue, 16 Jun 2020 07:40:41: #1 total tags in treatment: 8155122 INFO @ Tue, 16 Jun 2020 07:40:41: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 07:40:41: #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 07:40:41: #1 tags after filtering in treatment: 8155122 INFO @ Tue, 16 Jun 2020 07:40:41: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 07:40:41: #1 finished! INFO @ Tue, 16 Jun 2020 07:40:41: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 07:40:41: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 07:40:42: #2 number of paired peaks: 3596 INFO @ Tue, 16 Jun 2020 07:40:42: start model_add_line... INFO @ Tue, 16 Jun 2020 07:40:42: start X-correlation... INFO @ Tue, 16 Jun 2020 07:40:42: end of X-cor INFO @ Tue, 16 Jun 2020 07:40:42: #2 finished! INFO @ Tue, 16 Jun 2020 07:40:42: #2 predicted fragment length is 137 bps INFO @ Tue, 16 Jun 2020 07:40:42: #2 alternative fragment length(s) may be 137 bps INFO @ Tue, 16 Jun 2020 07:40:42: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX059254/SRX059254.20_model.r INFO @ Tue, 16 Jun 2020 07:40:42: #3 Call peaks... INFO @ Tue, 16 Jun 2020 07:40:42: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 07:40:44: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX059254/SRX059254.10_peaks.xls INFO @ Tue, 16 Jun 2020 07:40:44: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX059254/SRX059254.10_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 07:40:44: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX059254/SRX059254.10_summits.bed INFO @ Tue, 16 Jun 2020 07:40:44: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (4725 records, 4 fields): 6 millis CompletedMACS2peakCalling BigWig に変換しました。 INFO @ Tue, 16 Jun 2020 07:41:03: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 07:41:13: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX059254/SRX059254.20_peaks.xls INFO @ Tue, 16 Jun 2020 07:41:14: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX059254/SRX059254.20_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 07:41:14: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX059254/SRX059254.20_summits.bed INFO @ Tue, 16 Jun 2020 07:41:14: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (3518 records, 4 fields): 7 millis CompletedMACS2peakCalling