Job ID = 6366003 SRX = SRX044014 Genome = ce11 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-15T22:29:29 prefetch.2.10.7: 1) Downloading 'SRR107596'... 2020-06-15T22:29:29 prefetch.2.10.7: Downloading via HTTPS... 2020-06-15T22:29:52 prefetch.2.10.7: HTTPS download succeed 2020-06-15T22:29:53 prefetch.2.10.7: 'SRR107596' is valid 2020-06-15T22:29:53 prefetch.2.10.7: 1) 'SRR107596' was downloaded successfully Read 4416551 spots for SRR107596/SRR107596.sra Written 4416551 spots for SRR107596/SRR107596.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: 00:00:37 4416551 reads; of these: 4416551 (100.00%) were unpaired; of these: 1351429 (30.60%) aligned 0 times 2652869 (60.07%) aligned exactly 1 time 412253 (9.33%) aligned >1 times 69.40% overall alignment rate Time searching: 00:00:37 Overall time: 00:00:37 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] 816804 / 3065122 = 0.2665 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 07:31:56: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX044014/SRX044014.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX044014/SRX044014.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX044014/SRX044014.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX044014/SRX044014.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 07:31:56: #1 read tag files... INFO @ Tue, 16 Jun 2020 07:31:56: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 07:32:01: 1000000 INFO @ Tue, 16 Jun 2020 07:32:06: 2000000 INFO @ Tue, 16 Jun 2020 07:32:08: #1 tag size is determined as 32 bps INFO @ Tue, 16 Jun 2020 07:32:08: #1 tag size = 32 INFO @ Tue, 16 Jun 2020 07:32:08: #1 total tags in treatment: 2248318 INFO @ Tue, 16 Jun 2020 07:32:08: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 07:32:08: #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 07:32:08: #1 tags after filtering in treatment: 2248318 INFO @ Tue, 16 Jun 2020 07:32:08: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 07:32:08: #1 finished! INFO @ Tue, 16 Jun 2020 07:32:08: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 07:32:08: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 07:32:08: #2 number of paired peaks: 1423 INFO @ Tue, 16 Jun 2020 07:32:08: start model_add_line... INFO @ Tue, 16 Jun 2020 07:32:08: start X-correlation... INFO @ Tue, 16 Jun 2020 07:32:08: end of X-cor INFO @ Tue, 16 Jun 2020 07:32:08: #2 finished! INFO @ Tue, 16 Jun 2020 07:32:08: #2 predicted fragment length is 124 bps INFO @ Tue, 16 Jun 2020 07:32:08: #2 alternative fragment length(s) may be 124 bps INFO @ Tue, 16 Jun 2020 07:32:08: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX044014/SRX044014.05_model.r INFO @ Tue, 16 Jun 2020 07:32:08: #3 Call peaks... INFO @ Tue, 16 Jun 2020 07:32:08: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 07:32:14: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 07:32:17: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX044014/SRX044014.05_peaks.xls INFO @ Tue, 16 Jun 2020 07:32:17: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX044014/SRX044014.05_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 07:32:17: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX044014/SRX044014.05_summits.bed INFO @ Tue, 16 Jun 2020 07:32:17: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (3259 records, 4 fields): 5 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 07:32:26: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX044014/SRX044014.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX044014/SRX044014.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX044014/SRX044014.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX044014/SRX044014.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 07:32:26: #1 read tag files... INFO @ Tue, 16 Jun 2020 07:32:26: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 07:32:31: 1000000 INFO @ Tue, 16 Jun 2020 07:32:36: 2000000 INFO @ Tue, 16 Jun 2020 07:32:37: #1 tag size is determined as 32 bps INFO @ Tue, 16 Jun 2020 07:32:37: #1 tag size = 32 INFO @ Tue, 16 Jun 2020 07:32:37: #1 total tags in treatment: 2248318 INFO @ Tue, 16 Jun 2020 07:32:37: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 07:32:37: #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 07:32:37: #1 tags after filtering in treatment: 2248318 INFO @ Tue, 16 Jun 2020 07:32:37: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 07:32:37: #1 finished! INFO @ Tue, 16 Jun 2020 07:32:37: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 07:32:37: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 07:32:38: #2 number of paired peaks: 1423 INFO @ Tue, 16 Jun 2020 07:32:38: start model_add_line... INFO @ Tue, 16 Jun 2020 07:32:38: start X-correlation... INFO @ Tue, 16 Jun 2020 07:32:38: end of X-cor INFO @ Tue, 16 Jun 2020 07:32:38: #2 finished! INFO @ Tue, 16 Jun 2020 07:32:38: #2 predicted fragment length is 124 bps INFO @ Tue, 16 Jun 2020 07:32:38: #2 alternative fragment length(s) may be 124 bps INFO @ Tue, 16 Jun 2020 07:32:38: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX044014/SRX044014.10_model.r INFO @ Tue, 16 Jun 2020 07:32:38: #3 Call peaks... INFO @ Tue, 16 Jun 2020 07:32:38: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 07:32:44: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 07:32:46: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX044014/SRX044014.10_peaks.xls INFO @ Tue, 16 Jun 2020 07:32:46: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX044014/SRX044014.10_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 07:32:46: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX044014/SRX044014.10_summits.bed INFO @ Tue, 16 Jun 2020 07:32:46: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (1746 records, 4 fields): 3 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 07:32:56: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX044014/SRX044014.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX044014/SRX044014.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX044014/SRX044014.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX044014/SRX044014.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 07:32:56: #1 read tag files... INFO @ Tue, 16 Jun 2020 07:32:56: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 07:33:01: 1000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 16 Jun 2020 07:33:06: 2000000 INFO @ Tue, 16 Jun 2020 07:33:07: #1 tag size is determined as 32 bps INFO @ Tue, 16 Jun 2020 07:33:07: #1 tag size = 32 INFO @ Tue, 16 Jun 2020 07:33:07: #1 total tags in treatment: 2248318 INFO @ Tue, 16 Jun 2020 07:33:07: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 07:33:07: #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 07:33:07: #1 tags after filtering in treatment: 2248318 INFO @ Tue, 16 Jun 2020 07:33:07: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 07:33:07: #1 finished! INFO @ Tue, 16 Jun 2020 07:33:07: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 07:33:07: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 07:33:08: #2 number of paired peaks: 1423 INFO @ Tue, 16 Jun 2020 07:33:08: start model_add_line... INFO @ Tue, 16 Jun 2020 07:33:08: start X-correlation... INFO @ Tue, 16 Jun 2020 07:33:08: end of X-cor INFO @ Tue, 16 Jun 2020 07:33:08: #2 finished! INFO @ Tue, 16 Jun 2020 07:33:08: #2 predicted fragment length is 124 bps INFO @ Tue, 16 Jun 2020 07:33:08: #2 alternative fragment length(s) may be 124 bps INFO @ Tue, 16 Jun 2020 07:33:08: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX044014/SRX044014.20_model.r INFO @ Tue, 16 Jun 2020 07:33:08: #3 Call peaks... INFO @ Tue, 16 Jun 2020 07:33:08: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Tue, 16 Jun 2020 07:33:14: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 07:33:17: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX044014/SRX044014.20_peaks.xls INFO @ Tue, 16 Jun 2020 07:33:17: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX044014/SRX044014.20_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 07:33:17: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX044014/SRX044014.20_summits.bed INFO @ Tue, 16 Jun 2020 07:33:17: Done! pass1 - making usageList (7 chroms): 0 millis pass2 - checking and writing primary data (543 records, 4 fields): 2 millis CompletedMACS2peakCalling