Job ID = 6366112 SRX = SRX065628 Genome = ce11 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-15T23:01:53 prefetch.2.10.7: 1) Downloading 'SRR217334'... 2020-06-15T23:01:53 prefetch.2.10.7: Downloading via HTTPS... 2020-06-15T23:02:19 prefetch.2.10.7: HTTPS download succeed 2020-06-15T23:02:19 prefetch.2.10.7: 'SRR217334' is valid 2020-06-15T23:02:19 prefetch.2.10.7: 1) 'SRR217334' was downloaded successfully Read 5037643 spots for SRR217334/SRR217334.sra Written 5037643 spots for SRR217334/SRR217334.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: 00:00:28 5037643 reads; of these: 5037643 (100.00%) were unpaired; of these: 2809986 (55.78%) aligned 0 times 1973834 (39.18%) aligned exactly 1 time 253823 (5.04%) aligned >1 times 44.22% overall alignment rate Time searching: 00:00:28 Overall time: 00:00:28 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] 174730 / 2227657 = 0.0784 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 08:03:58: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX065628/SRX065628.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX065628/SRX065628.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX065628/SRX065628.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX065628/SRX065628.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 08:03:58: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:03:58: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:04:03: 1000000 INFO @ Tue, 16 Jun 2020 08:04:08: 2000000 INFO @ Tue, 16 Jun 2020 08:04:09: #1 tag size is determined as 32 bps INFO @ Tue, 16 Jun 2020 08:04:09: #1 tag size = 32 INFO @ Tue, 16 Jun 2020 08:04:09: #1 total tags in treatment: 2052927 INFO @ Tue, 16 Jun 2020 08:04:09: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:04:09: #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 08:04:09: #1 tags after filtering in treatment: 2052927 INFO @ Tue, 16 Jun 2020 08:04:09: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:04:09: #1 finished! INFO @ Tue, 16 Jun 2020 08:04:09: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:04:09: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:04:09: #2 number of paired peaks: 3048 INFO @ Tue, 16 Jun 2020 08:04:09: start model_add_line... INFO @ Tue, 16 Jun 2020 08:04:09: start X-correlation... INFO @ Tue, 16 Jun 2020 08:04:09: end of X-cor INFO @ Tue, 16 Jun 2020 08:04:09: #2 finished! INFO @ Tue, 16 Jun 2020 08:04:09: #2 predicted fragment length is 137 bps INFO @ Tue, 16 Jun 2020 08:04:09: #2 alternative fragment length(s) may be 137 bps INFO @ Tue, 16 Jun 2020 08:04:09: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX065628/SRX065628.05_model.r INFO @ Tue, 16 Jun 2020 08:04:09: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:04:09: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 08:04:14: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 08:04:17: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX065628/SRX065628.05_peaks.xls INFO @ Tue, 16 Jun 2020 08:04:17: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX065628/SRX065628.05_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:04:17: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX065628/SRX065628.05_summits.bed INFO @ Tue, 16 Jun 2020 08:04:17: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (5959 records, 4 fields): 7 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 08:04:28: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX065628/SRX065628.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX065628/SRX065628.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX065628/SRX065628.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX065628/SRX065628.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 08:04:28: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:04:28: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:04:34: 1000000 INFO @ Tue, 16 Jun 2020 08:04:39: 2000000 INFO @ Tue, 16 Jun 2020 08:04:39: #1 tag size is determined as 32 bps INFO @ Tue, 16 Jun 2020 08:04:39: #1 tag size = 32 INFO @ Tue, 16 Jun 2020 08:04:39: #1 total tags in treatment: 2052927 INFO @ Tue, 16 Jun 2020 08:04:39: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:04:39: #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 08:04:39: #1 tags after filtering in treatment: 2052927 INFO @ Tue, 16 Jun 2020 08:04:39: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:04:39: #1 finished! INFO @ Tue, 16 Jun 2020 08:04:39: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:04:39: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:04:39: #2 number of paired peaks: 3048 INFO @ Tue, 16 Jun 2020 08:04:39: start model_add_line... INFO @ Tue, 16 Jun 2020 08:04:39: start X-correlation... INFO @ Tue, 16 Jun 2020 08:04:39: end of X-cor INFO @ Tue, 16 Jun 2020 08:04:39: #2 finished! INFO @ Tue, 16 Jun 2020 08:04:39: #2 predicted fragment length is 137 bps INFO @ Tue, 16 Jun 2020 08:04:39: #2 alternative fragment length(s) may be 137 bps INFO @ Tue, 16 Jun 2020 08:04:39: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX065628/SRX065628.10_model.r INFO @ Tue, 16 Jun 2020 08:04:39: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:04:39: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 08:04:44: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 08:04:47: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX065628/SRX065628.10_peaks.xls INFO @ Tue, 16 Jun 2020 08:04:47: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX065628/SRX065628.10_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:04:47: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX065628/SRX065628.10_summits.bed INFO @ Tue, 16 Jun 2020 08:04:47: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (3431 records, 4 fields): 5 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 08:04:58: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX065628/SRX065628.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX065628/SRX065628.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX065628/SRX065628.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX065628/SRX065628.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 08:04:58: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:04:58: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:05:04: 1000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 16 Jun 2020 08:05:09: 2000000 INFO @ Tue, 16 Jun 2020 08:05:09: #1 tag size is determined as 32 bps INFO @ Tue, 16 Jun 2020 08:05:09: #1 tag size = 32 INFO @ Tue, 16 Jun 2020 08:05:09: #1 total tags in treatment: 2052927 INFO @ Tue, 16 Jun 2020 08:05:09: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:05:09: #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 08:05:09: #1 tags after filtering in treatment: 2052927 INFO @ Tue, 16 Jun 2020 08:05:09: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:05:09: #1 finished! INFO @ Tue, 16 Jun 2020 08:05:09: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:05:09: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:05:09: #2 number of paired peaks: 3048 INFO @ Tue, 16 Jun 2020 08:05:09: start model_add_line... INFO @ Tue, 16 Jun 2020 08:05:09: start X-correlation... INFO @ Tue, 16 Jun 2020 08:05:09: end of X-cor INFO @ Tue, 16 Jun 2020 08:05:09: #2 finished! INFO @ Tue, 16 Jun 2020 08:05:09: #2 predicted fragment length is 137 bps INFO @ Tue, 16 Jun 2020 08:05:09: #2 alternative fragment length(s) may be 137 bps INFO @ Tue, 16 Jun 2020 08:05:09: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX065628/SRX065628.20_model.r INFO @ Tue, 16 Jun 2020 08:05:10: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:05:10: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Tue, 16 Jun 2020 08:05:15: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 08:05:17: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX065628/SRX065628.20_peaks.xls INFO @ Tue, 16 Jun 2020 08:05:17: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX065628/SRX065628.20_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:05:17: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX065628/SRX065628.20_summits.bed INFO @ Tue, 16 Jun 2020 08:05:17: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (1332 records, 4 fields): 2 millis CompletedMACS2peakCalling