Job ID = 6367213 SRX = SRX3043399 Genome = ce11 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-15T23:19:46 prefetch.2.10.7: 1) Downloading 'SRR5875883'... 2020-06-15T23:19:46 prefetch.2.10.7: Downloading via HTTPS... 2020-06-15T23:21:14 prefetch.2.10.7: HTTPS download succeed 2020-06-15T23:21:14 prefetch.2.10.7: 'SRR5875883' is valid 2020-06-15T23:21:14 prefetch.2.10.7: 1) 'SRR5875883' was downloaded successfully Read 9470321 spots for SRR5875883/SRR5875883.sra Written 9470321 spots for SRR5875883/SRR5875883.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: 00:02:32 9470321 reads; of these: 9470321 (100.00%) were unpaired; of these: 182339 (1.93%) aligned 0 times 8223510 (86.83%) aligned exactly 1 time 1064472 (11.24%) aligned >1 times 98.07% overall alignment rate Time searching: 00:02:32 Overall time: 00:02:32 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] 1046345 / 9287982 = 0.1127 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 08:27:24: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX3043399/SRX3043399.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX3043399/SRX3043399.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX3043399/SRX3043399.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX3043399/SRX3043399.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 08:27:24: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:27:24: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:27:32: 1000000 INFO @ Tue, 16 Jun 2020 08:27:39: 2000000 INFO @ Tue, 16 Jun 2020 08:27:47: 3000000 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 08:27:54: 4000000 INFO @ Tue, 16 Jun 2020 08:27:55: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX3043399/SRX3043399.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX3043399/SRX3043399.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX3043399/SRX3043399.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX3043399/SRX3043399.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 08:27:55: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:27:55: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:28:02: 1000000 INFO @ Tue, 16 Jun 2020 08:28:03: 5000000 INFO @ Tue, 16 Jun 2020 08:28:10: 2000000 INFO @ Tue, 16 Jun 2020 08:28:11: 6000000 INFO @ Tue, 16 Jun 2020 08:28:18: 3000000 INFO @ Tue, 16 Jun 2020 08:28:19: 7000000 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 08:28:25: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX3043399/SRX3043399.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX3043399/SRX3043399.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX3043399/SRX3043399.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX3043399/SRX3043399.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 08:28:25: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:28:25: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:28:25: 4000000 INFO @ Tue, 16 Jun 2020 08:28:27: 8000000 INFO @ Tue, 16 Jun 2020 08:28:29: #1 tag size is determined as 51 bps INFO @ Tue, 16 Jun 2020 08:28:29: #1 tag size = 51 INFO @ Tue, 16 Jun 2020 08:28:29: #1 total tags in treatment: 8241637 INFO @ Tue, 16 Jun 2020 08:28:29: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:28:29: #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 08:28:29: #1 tags after filtering in treatment: 8241637 INFO @ Tue, 16 Jun 2020 08:28:29: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:28:29: #1 finished! INFO @ Tue, 16 Jun 2020 08:28:29: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:28:29: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:28:30: #2 number of paired peaks: 1038 INFO @ Tue, 16 Jun 2020 08:28:30: start model_add_line... INFO @ Tue, 16 Jun 2020 08:28:30: start X-correlation... INFO @ Tue, 16 Jun 2020 08:28:30: end of X-cor INFO @ Tue, 16 Jun 2020 08:28:30: #2 finished! INFO @ Tue, 16 Jun 2020 08:28:30: #2 predicted fragment length is 134 bps INFO @ Tue, 16 Jun 2020 08:28:30: #2 alternative fragment length(s) may be 134 bps INFO @ Tue, 16 Jun 2020 08:28:30: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX3043399/SRX3043399.05_model.r INFO @ Tue, 16 Jun 2020 08:28:30: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:28:30: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 08:28:32: 1000000 INFO @ Tue, 16 Jun 2020 08:28:33: 5000000 INFO @ Tue, 16 Jun 2020 08:28:40: 2000000 INFO @ Tue, 16 Jun 2020 08:28:40: 6000000 INFO @ Tue, 16 Jun 2020 08:28:47: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 08:28:47: 3000000 INFO @ Tue, 16 Jun 2020 08:28:48: 7000000 INFO @ Tue, 16 Jun 2020 08:28:54: 4000000 INFO @ Tue, 16 Jun 2020 08:28:55: 8000000 INFO @ Tue, 16 Jun 2020 08:28:56: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX3043399/SRX3043399.05_peaks.xls INFO @ Tue, 16 Jun 2020 08:28:56: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX3043399/SRX3043399.05_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:28:56: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX3043399/SRX3043399.05_summits.bed INFO @ Tue, 16 Jun 2020 08:28:56: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (4544 records, 4 fields): 6 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 08:28:57: #1 tag size is determined as 51 bps INFO @ Tue, 16 Jun 2020 08:28:57: #1 tag size = 51 INFO @ Tue, 16 Jun 2020 08:28:57: #1 total tags in treatment: 8241637 INFO @ Tue, 16 Jun 2020 08:28:57: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:28:57: #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 08:28:57: #1 tags after filtering in treatment: 8241637 INFO @ Tue, 16 Jun 2020 08:28:57: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:28:57: #1 finished! INFO @ Tue, 16 Jun 2020 08:28:57: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:28:57: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:28:58: #2 number of paired peaks: 1038 INFO @ Tue, 16 Jun 2020 08:28:58: start model_add_line... INFO @ Tue, 16 Jun 2020 08:28:58: start X-correlation... INFO @ Tue, 16 Jun 2020 08:28:58: end of X-cor INFO @ Tue, 16 Jun 2020 08:28:58: #2 finished! INFO @ Tue, 16 Jun 2020 08:28:58: #2 predicted fragment length is 134 bps INFO @ Tue, 16 Jun 2020 08:28:58: #2 alternative fragment length(s) may be 134 bps INFO @ Tue, 16 Jun 2020 08:28:58: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX3043399/SRX3043399.10_model.r INFO @ Tue, 16 Jun 2020 08:28:58: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:28:58: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 08:29:01: 5000000 INFO @ Tue, 16 Jun 2020 08:29:08: 6000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 16 Jun 2020 08:29:15: 7000000 INFO @ Tue, 16 Jun 2020 08:29:16: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 08:29:22: 8000000 INFO @ Tue, 16 Jun 2020 08:29:23: #1 tag size is determined as 51 bps INFO @ Tue, 16 Jun 2020 08:29:23: #1 tag size = 51 INFO @ Tue, 16 Jun 2020 08:29:23: #1 total tags in treatment: 8241637 INFO @ Tue, 16 Jun 2020 08:29:23: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:29:23: #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 08:29:24: #1 tags after filtering in treatment: 8241637 INFO @ Tue, 16 Jun 2020 08:29:24: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:29:24: #1 finished! INFO @ Tue, 16 Jun 2020 08:29:24: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:29:24: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:29:24: #2 number of paired peaks: 1038 INFO @ Tue, 16 Jun 2020 08:29:24: start model_add_line... INFO @ Tue, 16 Jun 2020 08:29:24: start X-correlation... INFO @ Tue, 16 Jun 2020 08:29:24: end of X-cor INFO @ Tue, 16 Jun 2020 08:29:24: #2 finished! INFO @ Tue, 16 Jun 2020 08:29:24: #2 predicted fragment length is 134 bps INFO @ Tue, 16 Jun 2020 08:29:24: #2 alternative fragment length(s) may be 134 bps INFO @ Tue, 16 Jun 2020 08:29:24: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX3043399/SRX3043399.20_model.r INFO @ Tue, 16 Jun 2020 08:29:24: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:29:24: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 08:29:25: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX3043399/SRX3043399.10_peaks.xls INFO @ Tue, 16 Jun 2020 08:29:25: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX3043399/SRX3043399.10_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:29:25: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX3043399/SRX3043399.10_summits.bed INFO @ Tue, 16 Jun 2020 08:29:25: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (3195 records, 4 fields): 4 millis CompletedMACS2peakCalling BigWig に変換しました。 INFO @ Tue, 16 Jun 2020 08:29:43: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 08:29:52: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX3043399/SRX3043399.20_peaks.xls INFO @ Tue, 16 Jun 2020 08:29:52: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX3043399/SRX3043399.20_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:29:52: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX3043399/SRX3043399.20_summits.bed INFO @ Tue, 16 Jun 2020 08:29:52: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (1893 records, 4 fields): 3 millis CompletedMACS2peakCalling