Job ID = 6368992 SRX = SRX958297 Genome = ce11 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-16T00:33:40 prefetch.2.10.7: 1) Downloading 'SRR1917670'... 2020-06-16T00:33:40 prefetch.2.10.7: Downloading via HTTPS... 2020-06-16T00:36:03 prefetch.2.10.7: HTTPS download succeed 2020-06-16T00:36:03 prefetch.2.10.7: 1) 'SRR1917670' was downloaded successfully Read 19526266 spots for SRR1917670/SRR1917670.sra Written 19526266 spots for SRR1917670/SRR1917670.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: 00:05:16 19526266 reads; of these: 19526266 (100.00%) were unpaired; of these: 3388079 (17.35%) aligned 0 times 8553021 (43.80%) aligned exactly 1 time 7585166 (38.85%) aligned >1 times 82.65% overall alignment rate Time searching: 00:05:16 Overall time: 00:05:16 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] 11498888 / 16138187 = 0.7125 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 09:45:48: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX958297/SRX958297.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX958297/SRX958297.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX958297/SRX958297.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX958297/SRX958297.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 09:45:48: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:45:48: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:45:54: 1000000 INFO @ Tue, 16 Jun 2020 09:46:00: 2000000 INFO @ Tue, 16 Jun 2020 09:46:06: 3000000 INFO @ Tue, 16 Jun 2020 09:46:12: 4000000 INFO @ Tue, 16 Jun 2020 09:46:16: #1 tag size is determined as 51 bps INFO @ Tue, 16 Jun 2020 09:46:16: #1 tag size = 51 INFO @ Tue, 16 Jun 2020 09:46:16: #1 total tags in treatment: 4639299 INFO @ Tue, 16 Jun 2020 09:46:16: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:46:16: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) 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 09:46:16: #1 tags after filtering in treatment: 4639299 INFO @ Tue, 16 Jun 2020 09:46:16: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 09:46:16: #1 finished! INFO @ Tue, 16 Jun 2020 09:46:16: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:46:16: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:46:17: #2 number of paired peaks: 4759 INFO @ Tue, 16 Jun 2020 09:46:17: start model_add_line... INFO @ Tue, 16 Jun 2020 09:46:17: start X-correlation... INFO @ Tue, 16 Jun 2020 09:46:17: end of X-cor INFO @ Tue, 16 Jun 2020 09:46:17: #2 finished! INFO @ Tue, 16 Jun 2020 09:46:17: #2 predicted fragment length is 205 bps INFO @ Tue, 16 Jun 2020 09:46:17: #2 alternative fragment length(s) may be 205 bps INFO @ Tue, 16 Jun 2020 09:46:17: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX958297/SRX958297.05_model.r INFO @ Tue, 16 Jun 2020 09:46:17: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:46:17: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 09:46:18: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX958297/SRX958297.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX958297/SRX958297.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX958297/SRX958297.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX958297/SRX958297.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 09:46:18: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:46:18: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:46:23: 1000000 INFO @ Tue, 16 Jun 2020 09:46:29: 2000000 INFO @ Tue, 16 Jun 2020 09:46:33: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 09:46:34: 3000000 INFO @ Tue, 16 Jun 2020 09:46:40: 4000000 INFO @ Tue, 16 Jun 2020 09:46:40: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX958297/SRX958297.05_peaks.xls INFO @ Tue, 16 Jun 2020 09:46:40: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX958297/SRX958297.05_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:46:40: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX958297/SRX958297.05_summits.bed INFO @ Tue, 16 Jun 2020 09:46:40: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (5304 records, 4 fields): 6 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 09:46:43: #1 tag size is determined as 51 bps INFO @ Tue, 16 Jun 2020 09:46:43: #1 tag size = 51 INFO @ Tue, 16 Jun 2020 09:46:43: #1 total tags in treatment: 4639299 INFO @ Tue, 16 Jun 2020 09:46:43: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:46:43: #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 09:46:43: #1 tags after filtering in treatment: 4639299 INFO @ Tue, 16 Jun 2020 09:46:43: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 09:46:43: #1 finished! INFO @ Tue, 16 Jun 2020 09:46:43: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:46:43: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:46:44: #2 number of paired peaks: 4759 INFO @ Tue, 16 Jun 2020 09:46:44: start model_add_line... INFO @ Tue, 16 Jun 2020 09:46:44: start X-correlation... INFO @ Tue, 16 Jun 2020 09:46:44: end of X-cor INFO @ Tue, 16 Jun 2020 09:46:44: #2 finished! INFO @ Tue, 16 Jun 2020 09:46:44: #2 predicted fragment length is 205 bps INFO @ Tue, 16 Jun 2020 09:46:44: #2 alternative fragment length(s) may be 205 bps INFO @ Tue, 16 Jun 2020 09:46:44: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX958297/SRX958297.10_model.r INFO @ Tue, 16 Jun 2020 09:46:44: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:46:44: #3 Pre-compute pvalue-qvalue table... 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 09:46:48: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX958297/SRX958297.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX958297/SRX958297.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX958297/SRX958297.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX958297/SRX958297.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 09:46:48: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:46:48: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:46:53: 1000000 INFO @ Tue, 16 Jun 2020 09:46:59: 2000000 INFO @ Tue, 16 Jun 2020 09:47:01: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 09:47:04: 3000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 16 Jun 2020 09:47:08: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX958297/SRX958297.10_peaks.xls INFO @ Tue, 16 Jun 2020 09:47:08: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX958297/SRX958297.10_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:47:08: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX958297/SRX958297.10_summits.bed INFO @ Tue, 16 Jun 2020 09:47:08: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (3555 records, 4 fields): 5 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 09:47:10: 4000000 INFO @ Tue, 16 Jun 2020 09:47:13: #1 tag size is determined as 51 bps INFO @ Tue, 16 Jun 2020 09:47:13: #1 tag size = 51 INFO @ Tue, 16 Jun 2020 09:47:13: #1 total tags in treatment: 4639299 INFO @ Tue, 16 Jun 2020 09:47:13: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:47:13: #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 09:47:13: #1 tags after filtering in treatment: 4639299 INFO @ Tue, 16 Jun 2020 09:47:13: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 09:47:13: #1 finished! INFO @ Tue, 16 Jun 2020 09:47:13: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:47:13: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:47:14: #2 number of paired peaks: 4759 INFO @ Tue, 16 Jun 2020 09:47:14: start model_add_line... INFO @ Tue, 16 Jun 2020 09:47:14: start X-correlation... INFO @ Tue, 16 Jun 2020 09:47:14: end of X-cor INFO @ Tue, 16 Jun 2020 09:47:14: #2 finished! INFO @ Tue, 16 Jun 2020 09:47:14: #2 predicted fragment length is 205 bps INFO @ Tue, 16 Jun 2020 09:47:14: #2 alternative fragment length(s) may be 205 bps INFO @ Tue, 16 Jun 2020 09:47:14: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX958297/SRX958297.20_model.r INFO @ Tue, 16 Jun 2020 09:47:14: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:47:14: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Tue, 16 Jun 2020 09:47:31: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 09:47:37: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX958297/SRX958297.20_peaks.xls INFO @ Tue, 16 Jun 2020 09:47:37: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX958297/SRX958297.20_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:47:37: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX958297/SRX958297.20_summits.bed INFO @ Tue, 16 Jun 2020 09:47:37: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (2020 records, 4 fields): 3 millis CompletedMACS2peakCalling