Job ID = 6367485 SRX = SRX331242 Genome = ce11 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-15T23:31:50 prefetch.2.10.7: 1) Downloading 'SRR947474'... 2020-06-15T23:31:50 prefetch.2.10.7: Downloading via HTTPS... 2020-06-15T23:32:35 prefetch.2.10.7: HTTPS download succeed 2020-06-15T23:32:35 prefetch.2.10.7: 'SRR947474' is valid 2020-06-15T23:32:35 prefetch.2.10.7: 1) 'SRR947474' was downloaded successfully Read 3815829 spots for SRR947474/SRR947474.sra Written 3815829 spots for SRR947474/SRR947474.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: 00:00:33 3815829 reads; of these: 3815829 (100.00%) were unpaired; of these: 496902 (13.02%) aligned 0 times 2788986 (73.09%) aligned exactly 1 time 529941 (13.89%) aligned >1 times 86.98% overall alignment rate Time searching: 00:00:33 Overall time: 00:00:33 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] 700889 / 3318927 = 0.2112 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 08:34:26: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX331242/SRX331242.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX331242/SRX331242.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX331242/SRX331242.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX331242/SRX331242.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 08:34:26: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:34:26: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:34:31: 1000000 INFO @ Tue, 16 Jun 2020 08:34:36: 2000000 INFO @ Tue, 16 Jun 2020 08:34:39: #1 tag size is determined as 32 bps INFO @ Tue, 16 Jun 2020 08:34:39: #1 tag size = 32 INFO @ Tue, 16 Jun 2020 08:34:39: #1 total tags in treatment: 2618038 INFO @ Tue, 16 Jun 2020 08:34:39: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:34:39: #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 08:34:39: #1 tags after filtering in treatment: 2618038 INFO @ Tue, 16 Jun 2020 08:34:39: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:34:39: #1 finished! INFO @ Tue, 16 Jun 2020 08:34:39: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:34:39: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:34:39: #2 number of paired peaks: 1015 INFO @ Tue, 16 Jun 2020 08:34:39: start model_add_line... INFO @ Tue, 16 Jun 2020 08:34:39: start X-correlation... INFO @ Tue, 16 Jun 2020 08:34:39: end of X-cor INFO @ Tue, 16 Jun 2020 08:34:39: #2 finished! INFO @ Tue, 16 Jun 2020 08:34:39: #2 predicted fragment length is 151 bps INFO @ Tue, 16 Jun 2020 08:34:39: #2 alternative fragment length(s) may be 151 bps INFO @ Tue, 16 Jun 2020 08:34:39: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX331242/SRX331242.05_model.r INFO @ Tue, 16 Jun 2020 08:34:39: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:34:39: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 08:34:46: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 08:34:49: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX331242/SRX331242.05_peaks.xls INFO @ Tue, 16 Jun 2020 08:34:49: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX331242/SRX331242.05_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:34:49: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX331242/SRX331242.05_summits.bed INFO @ Tue, 16 Jun 2020 08:34:49: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (1949 records, 4 fields): 3 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 08:34:57: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX331242/SRX331242.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX331242/SRX331242.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX331242/SRX331242.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX331242/SRX331242.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 08:34:57: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:34:57: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:35:02: 1000000 INFO @ Tue, 16 Jun 2020 08:35:06: 2000000 INFO @ Tue, 16 Jun 2020 08:35:09: #1 tag size is determined as 32 bps INFO @ Tue, 16 Jun 2020 08:35:09: #1 tag size = 32 INFO @ Tue, 16 Jun 2020 08:35:09: #1 total tags in treatment: 2618038 INFO @ Tue, 16 Jun 2020 08:35:09: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:35:09: #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 08:35:09: #1 tags after filtering in treatment: 2618038 INFO @ Tue, 16 Jun 2020 08:35:09: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:35:09: #1 finished! INFO @ Tue, 16 Jun 2020 08:35:09: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:35:09: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:35:09: #2 number of paired peaks: 1015 INFO @ Tue, 16 Jun 2020 08:35:09: start model_add_line... INFO @ Tue, 16 Jun 2020 08:35:09: start X-correlation... INFO @ Tue, 16 Jun 2020 08:35:10: end of X-cor INFO @ Tue, 16 Jun 2020 08:35:10: #2 finished! INFO @ Tue, 16 Jun 2020 08:35:10: #2 predicted fragment length is 151 bps INFO @ Tue, 16 Jun 2020 08:35:10: #2 alternative fragment length(s) may be 151 bps INFO @ Tue, 16 Jun 2020 08:35:10: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX331242/SRX331242.10_model.r INFO @ Tue, 16 Jun 2020 08:35:10: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:35:10: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 08:35:16: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 08:35:19: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX331242/SRX331242.10_peaks.xls INFO @ Tue, 16 Jun 2020 08:35:19: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX331242/SRX331242.10_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:35:19: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX331242/SRX331242.10_summits.bed INFO @ Tue, 16 Jun 2020 08:35:19: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (1047 records, 4 fields): 2 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 08:35:26: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX331242/SRX331242.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX331242/SRX331242.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX331242/SRX331242.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX331242/SRX331242.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 08:35:26: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:35:26: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:35:30: 1000000 INFO @ Tue, 16 Jun 2020 08:35:35: 2000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 16 Jun 2020 08:35:38: #1 tag size is determined as 32 bps INFO @ Tue, 16 Jun 2020 08:35:38: #1 tag size = 32 INFO @ Tue, 16 Jun 2020 08:35:38: #1 total tags in treatment: 2618038 INFO @ Tue, 16 Jun 2020 08:35:38: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:35:38: #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 08:35:38: #1 tags after filtering in treatment: 2618038 INFO @ Tue, 16 Jun 2020 08:35:38: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:35:38: #1 finished! INFO @ Tue, 16 Jun 2020 08:35:38: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:35:38: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:35:38: #2 number of paired peaks: 1015 INFO @ Tue, 16 Jun 2020 08:35:38: start model_add_line... INFO @ Tue, 16 Jun 2020 08:35:38: start X-correlation... INFO @ Tue, 16 Jun 2020 08:35:38: end of X-cor INFO @ Tue, 16 Jun 2020 08:35:38: #2 finished! INFO @ Tue, 16 Jun 2020 08:35:38: #2 predicted fragment length is 151 bps INFO @ Tue, 16 Jun 2020 08:35:38: #2 alternative fragment length(s) may be 151 bps INFO @ Tue, 16 Jun 2020 08:35:38: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX331242/SRX331242.20_model.r INFO @ Tue, 16 Jun 2020 08:35:38: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:35:38: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Tue, 16 Jun 2020 08:35:44: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 08:35:47: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX331242/SRX331242.20_peaks.xls INFO @ Tue, 16 Jun 2020 08:35:47: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX331242/SRX331242.20_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:35:47: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX331242/SRX331242.20_summits.bed INFO @ Tue, 16 Jun 2020 08:35:47: Done! pass1 - making usageList (7 chroms): 0 millis pass2 - checking and writing primary data (427 records, 4 fields): 2 millis CompletedMACS2peakCalling