Job ID = 6366610 SRX = SRX208774 Genome = ce11 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-15T22:53:15 prefetch.2.10.7: 1) Downloading 'SRR628908'... 2020-06-15T22:53:15 prefetch.2.10.7: Downloading via HTTPS... 2020-06-15T22:54:46 prefetch.2.10.7: HTTPS download succeed 2020-06-15T22:54:46 prefetch.2.10.7: 1) 'SRR628908' was downloaded successfully Read 19098144 spots for SRR628908/SRR628908.sra Written 19098144 spots for SRR628908/SRR628908.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: 00:05:57 19098144 reads; of these: 19098144 (100.00%) were unpaired; of these: 2232554 (11.69%) aligned 0 times 13291970 (69.60%) aligned exactly 1 time 3573620 (18.71%) aligned >1 times 88.31% overall alignment rate Time searching: 00:05:57 Overall time: 00:05:57 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] 12983709 / 16865590 = 0.7698 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 08:05:31: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX208774/SRX208774.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX208774/SRX208774.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX208774/SRX208774.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX208774/SRX208774.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 08:05:31: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:05:31: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:05:38: 1000000 INFO @ Tue, 16 Jun 2020 08:05:46: 2000000 INFO @ Tue, 16 Jun 2020 08:05:53: 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 08:05:59: #1 tag size is determined as 50 bps INFO @ Tue, 16 Jun 2020 08:05:59: #1 tag size = 50 INFO @ Tue, 16 Jun 2020 08:05:59: #1 total tags in treatment: 3881881 INFO @ Tue, 16 Jun 2020 08:05:59: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:05:59: #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 08:06:00: #1 tags after filtering in treatment: 3881881 INFO @ Tue, 16 Jun 2020 08:06:00: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:06:00: #1 finished! INFO @ Tue, 16 Jun 2020 08:06:00: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:06:00: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:06:00: #2 number of paired peaks: 2135 INFO @ Tue, 16 Jun 2020 08:06:00: start model_add_line... INFO @ Tue, 16 Jun 2020 08:06:00: start X-correlation... INFO @ Tue, 16 Jun 2020 08:06:00: end of X-cor INFO @ Tue, 16 Jun 2020 08:06:00: #2 finished! INFO @ Tue, 16 Jun 2020 08:06:00: #2 predicted fragment length is 263 bps INFO @ Tue, 16 Jun 2020 08:06:00: #2 alternative fragment length(s) may be 263 bps INFO @ Tue, 16 Jun 2020 08:06:00: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX208774/SRX208774.05_model.r INFO @ Tue, 16 Jun 2020 08:06:00: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:06:00: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 08:06:01: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX208774/SRX208774.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX208774/SRX208774.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX208774/SRX208774.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX208774/SRX208774.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 08:06:01: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:06:01: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:06:07: 1000000 INFO @ Tue, 16 Jun 2020 08:06:11: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 08:06:13: 2000000 INFO @ Tue, 16 Jun 2020 08:06:16: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX208774/SRX208774.05_peaks.xls INFO @ Tue, 16 Jun 2020 08:06:16: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX208774/SRX208774.05_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:06:16: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX208774/SRX208774.05_summits.bed INFO @ Tue, 16 Jun 2020 08:06:16: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (2363 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 08:06:19: 3000000 INFO @ Tue, 16 Jun 2020 08:06:24: #1 tag size is determined as 50 bps INFO @ Tue, 16 Jun 2020 08:06:24: #1 tag size = 50 INFO @ Tue, 16 Jun 2020 08:06:24: #1 total tags in treatment: 3881881 INFO @ Tue, 16 Jun 2020 08:06:24: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:06:24: #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 08:06:24: #1 tags after filtering in treatment: 3881881 INFO @ Tue, 16 Jun 2020 08:06:24: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:06:24: #1 finished! INFO @ Tue, 16 Jun 2020 08:06:24: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:06:24: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:06:25: #2 number of paired peaks: 2135 INFO @ Tue, 16 Jun 2020 08:06:25: start model_add_line... INFO @ Tue, 16 Jun 2020 08:06:25: start X-correlation... INFO @ Tue, 16 Jun 2020 08:06:25: end of X-cor INFO @ Tue, 16 Jun 2020 08:06:25: #2 finished! INFO @ Tue, 16 Jun 2020 08:06:25: #2 predicted fragment length is 263 bps INFO @ Tue, 16 Jun 2020 08:06:25: #2 alternative fragment length(s) may be 263 bps INFO @ Tue, 16 Jun 2020 08:06:25: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX208774/SRX208774.10_model.r INFO @ Tue, 16 Jun 2020 08:06:25: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:06:25: #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 08:06:31: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX208774/SRX208774.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX208774/SRX208774.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX208774/SRX208774.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX208774/SRX208774.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 08:06:31: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:06:31: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:06:35: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 08:06:37: 1000000 INFO @ Tue, 16 Jun 2020 08:06:40: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX208774/SRX208774.10_peaks.xls INFO @ Tue, 16 Jun 2020 08:06:40: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX208774/SRX208774.10_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:06:40: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX208774/SRX208774.10_summits.bed INFO @ Tue, 16 Jun 2020 08:06:40: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (1876 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 08:06:43: 2000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 16 Jun 2020 08:06:49: 3000000 INFO @ Tue, 16 Jun 2020 08:06:55: #1 tag size is determined as 50 bps INFO @ Tue, 16 Jun 2020 08:06:55: #1 tag size = 50 INFO @ Tue, 16 Jun 2020 08:06:55: #1 total tags in treatment: 3881881 INFO @ Tue, 16 Jun 2020 08:06:55: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:06:55: #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 08:06:55: #1 tags after filtering in treatment: 3881881 INFO @ Tue, 16 Jun 2020 08:06:55: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:06:55: #1 finished! INFO @ Tue, 16 Jun 2020 08:06:55: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:06:55: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:06:55: #2 number of paired peaks: 2135 INFO @ Tue, 16 Jun 2020 08:06:55: start model_add_line... INFO @ Tue, 16 Jun 2020 08:06:55: start X-correlation... INFO @ Tue, 16 Jun 2020 08:06:55: end of X-cor INFO @ Tue, 16 Jun 2020 08:06:55: #2 finished! INFO @ Tue, 16 Jun 2020 08:06:55: #2 predicted fragment length is 263 bps INFO @ Tue, 16 Jun 2020 08:06:55: #2 alternative fragment length(s) may be 263 bps INFO @ Tue, 16 Jun 2020 08:06:55: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX208774/SRX208774.20_model.r INFO @ Tue, 16 Jun 2020 08:06:55: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:06:55: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Tue, 16 Jun 2020 08:07:06: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 08:07:10: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX208774/SRX208774.20_peaks.xls INFO @ Tue, 16 Jun 2020 08:07:10: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX208774/SRX208774.20_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:07:10: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX208774/SRX208774.20_summits.bed INFO @ Tue, 16 Jun 2020 08:07:10: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (1454 records, 4 fields): 3 millis CompletedMACS2peakCalling