Job ID = 6366005 SRX = SRX044016 Genome = ce11 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-15T22:37:10 prefetch.2.10.7: 1) Downloading 'SRR107598'... 2020-06-15T22:37:10 prefetch.2.10.7: Downloading via HTTPS... 2020-06-15T22:37:30 prefetch.2.10.7: HTTPS download succeed 2020-06-15T22:37:30 prefetch.2.10.7: 'SRR107598' is valid 2020-06-15T22:37:30 prefetch.2.10.7: 1) 'SRR107598' was downloaded successfully Read 1762709 spots for SRR107598/SRR107598.sra Written 1762709 spots for SRR107598/SRR107598.sra 2020-06-15T22:37:46 prefetch.2.10.7: 1) Downloading 'SRR107599'... 2020-06-15T22:37:46 prefetch.2.10.7: Downloading via HTTPS... 2020-06-15T22:38:12 prefetch.2.10.7: HTTPS download succeed 2020-06-15T22:38:12 prefetch.2.10.7: 'SRR107599' is valid 2020-06-15T22:38:12 prefetch.2.10.7: 1) 'SRR107599' was downloaded successfully Read 1417977 spots for SRR107599/SRR107599.sra Written 1417977 spots for SRR107599/SRR107599.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: 00:00:20 3180686 reads; of these: 3180686 (100.00%) were unpaired; of these: 1726602 (54.28%) aligned 0 times 1269218 (39.90%) aligned exactly 1 time 184866 (5.81%) aligned >1 times 45.72% overall alignment rate Time searching: 00:00:20 Overall time: 00:00:20 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] 392384 / 1454084 = 0.2698 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 07:39:28: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX044016/SRX044016.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX044016/SRX044016.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX044016/SRX044016.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX044016/SRX044016.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 07:39:28: #1 read tag files... INFO @ Tue, 16 Jun 2020 07:39:28: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 07:39:33: 1000000 INFO @ Tue, 16 Jun 2020 07:39:33: #1 tag size is determined as 32 bps INFO @ Tue, 16 Jun 2020 07:39:33: #1 tag size = 32 INFO @ Tue, 16 Jun 2020 07:39:33: #1 total tags in treatment: 1061700 INFO @ Tue, 16 Jun 2020 07:39:33: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 07:39:33: #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 07:39:33: #1 tags after filtering in treatment: 1061700 INFO @ Tue, 16 Jun 2020 07:39:33: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 07:39:33: #1 finished! INFO @ Tue, 16 Jun 2020 07:39:33: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 07:39:33: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 07:39:33: #2 number of paired peaks: 3390 INFO @ Tue, 16 Jun 2020 07:39:33: start model_add_line... INFO @ Tue, 16 Jun 2020 07:39:33: start X-correlation... INFO @ Tue, 16 Jun 2020 07:39:33: end of X-cor INFO @ Tue, 16 Jun 2020 07:39:33: #2 finished! INFO @ Tue, 16 Jun 2020 07:39:33: #2 predicted fragment length is 167 bps INFO @ Tue, 16 Jun 2020 07:39:33: #2 alternative fragment length(s) may be 167 bps INFO @ Tue, 16 Jun 2020 07:39:33: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX044016/SRX044016.05_model.r INFO @ Tue, 16 Jun 2020 07:39:33: #3 Call peaks... INFO @ Tue, 16 Jun 2020 07:39:33: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 07:39:36: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 07:39:38: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX044016/SRX044016.05_peaks.xls INFO @ Tue, 16 Jun 2020 07:39:38: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX044016/SRX044016.05_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 07:39:38: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX044016/SRX044016.05_summits.bed INFO @ Tue, 16 Jun 2020 07:39:38: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (4034 records, 4 fields): 6 millis CompletedMACS2peakCalling 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/SRX044016/SRX044016.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX044016/SRX044016.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX044016/SRX044016.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX044016/SRX044016.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 07:39:58: #1 read tag files... INFO @ Tue, 16 Jun 2020 07:39:58: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 07:40:03: 1000000 INFO @ Tue, 16 Jun 2020 07:40:04: #1 tag size is determined as 32 bps INFO @ Tue, 16 Jun 2020 07:40:04: #1 tag size = 32 INFO @ Tue, 16 Jun 2020 07:40:04: #1 total tags in treatment: 1061700 INFO @ Tue, 16 Jun 2020 07:40:04: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 07:40:04: #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 07:40:04: #1 tags after filtering in treatment: 1061700 INFO @ Tue, 16 Jun 2020 07:40:04: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 07:40:04: #1 finished! INFO @ Tue, 16 Jun 2020 07:40:04: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 07:40:04: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 07:40:04: #2 number of paired peaks: 3390 INFO @ Tue, 16 Jun 2020 07:40:04: start model_add_line... INFO @ Tue, 16 Jun 2020 07:40:04: start X-correlation... INFO @ Tue, 16 Jun 2020 07:40:04: end of X-cor INFO @ Tue, 16 Jun 2020 07:40:04: #2 finished! INFO @ Tue, 16 Jun 2020 07:40:04: #2 predicted fragment length is 167 bps INFO @ Tue, 16 Jun 2020 07:40:04: #2 alternative fragment length(s) may be 167 bps INFO @ Tue, 16 Jun 2020 07:40:04: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX044016/SRX044016.10_model.r INFO @ Tue, 16 Jun 2020 07:40:04: #3 Call peaks... INFO @ Tue, 16 Jun 2020 07:40:04: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 07:40:06: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 07:40:08: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX044016/SRX044016.10_peaks.xls INFO @ Tue, 16 Jun 2020 07:40:08: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX044016/SRX044016.10_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 07:40:08: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX044016/SRX044016.10_summits.bed INFO @ Tue, 16 Jun 2020 07:40:08: Done! pass1 - making usageList (7 chroms): 0 millis pass2 - checking and writing primary data (2029 records, 4 fields): 4 millis CompletedMACS2peakCalling 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 07:40:28: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX044016/SRX044016.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX044016/SRX044016.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX044016/SRX044016.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX044016/SRX044016.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 07:40:28: #1 read tag files... INFO @ Tue, 16 Jun 2020 07:40:28: #1 read treatment tags... BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。 INFO @ Tue, 16 Jun 2020 07:40:33: 1000000 INFO @ Tue, 16 Jun 2020 07:40:34: #1 tag size is determined as 32 bps INFO @ Tue, 16 Jun 2020 07:40:34: #1 tag size = 32 INFO @ Tue, 16 Jun 2020 07:40:34: #1 total tags in treatment: 1061700 INFO @ Tue, 16 Jun 2020 07:40:34: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 07:40:34: #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 07:40:34: #1 tags after filtering in treatment: 1061700 INFO @ Tue, 16 Jun 2020 07:40:34: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 07:40:34: #1 finished! INFO @ Tue, 16 Jun 2020 07:40:34: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 07:40:34: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 07:40:34: #2 number of paired peaks: 3390 INFO @ Tue, 16 Jun 2020 07:40:34: start model_add_line... INFO @ Tue, 16 Jun 2020 07:40:34: start X-correlation... INFO @ Tue, 16 Jun 2020 07:40:34: end of X-cor INFO @ Tue, 16 Jun 2020 07:40:34: #2 finished! INFO @ Tue, 16 Jun 2020 07:40:34: #2 predicted fragment length is 167 bps INFO @ Tue, 16 Jun 2020 07:40:34: #2 alternative fragment length(s) may be 167 bps INFO @ Tue, 16 Jun 2020 07:40:34: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX044016/SRX044016.20_model.r INFO @ Tue, 16 Jun 2020 07:40:34: #3 Call peaks... INFO @ Tue, 16 Jun 2020 07:40:34: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 07:40:37: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 07:40:38: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX044016/SRX044016.20_peaks.xls INFO @ Tue, 16 Jun 2020 07:40:38: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX044016/SRX044016.20_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 07:40:38: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX044016/SRX044016.20_summits.bed INFO @ Tue, 16 Jun 2020 07:40:38: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (584 records, 4 fields): 20 millis CompletedMACS2peakCalling