Job ID = 6367580 SRX = SRX331336 Genome = ce11 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-15T23:34:35 prefetch.2.10.7: 1) Downloading 'SRR947573'... 2020-06-15T23:34:35 prefetch.2.10.7: Downloading via HTTPS... 2020-06-15T23:37:53 prefetch.2.10.7: HTTPS download succeed 2020-06-15T23:37:53 prefetch.2.10.7: 'SRR947573' is valid 2020-06-15T23:37:53 prefetch.2.10.7: 1) 'SRR947573' was downloaded successfully Read 9464299 spots for SRR947573/SRR947573.sra Written 9464299 spots for SRR947573/SRR947573.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: 00:01:32 9464299 reads; of these: 9464299 (100.00%) were unpaired; of these: 1408476 (14.88%) aligned 0 times 5348733 (56.51%) aligned exactly 1 time 2707090 (28.60%) aligned >1 times 85.12% overall alignment rate Time searching: 00:01:32 Overall time: 00:01:32 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] 5065473 / 8055823 = 0.6288 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 08:41:42: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX331336/SRX331336.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX331336/SRX331336.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX331336/SRX331336.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX331336/SRX331336.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 08:41:42: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:41:42: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:41:46: 1000000 INFO @ Tue, 16 Jun 2020 08:41:51: 2000000 INFO @ Tue, 16 Jun 2020 08:41:56: #1 tag size is determined as 42 bps INFO @ Tue, 16 Jun 2020 08:41:56: #1 tag size = 42 INFO @ Tue, 16 Jun 2020 08:41:56: #1 total tags in treatment: 2990350 INFO @ Tue, 16 Jun 2020 08:41:56: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:41:56: #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 08:41:56: #1 tags after filtering in treatment: 2990350 INFO @ Tue, 16 Jun 2020 08:41:56: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:41:56: #1 finished! INFO @ Tue, 16 Jun 2020 08:41:56: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:41:56: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:41:56: #2 number of paired peaks: 5312 INFO @ Tue, 16 Jun 2020 08:41:56: start model_add_line... INFO @ Tue, 16 Jun 2020 08:41:56: start X-correlation... INFO @ Tue, 16 Jun 2020 08:41:56: end of X-cor INFO @ Tue, 16 Jun 2020 08:41:56: #2 finished! INFO @ Tue, 16 Jun 2020 08:41:56: #2 predicted fragment length is 197 bps INFO @ Tue, 16 Jun 2020 08:41:56: #2 alternative fragment length(s) may be 2,197 bps INFO @ Tue, 16 Jun 2020 08:41:56: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX331336/SRX331336.05_model.r INFO @ Tue, 16 Jun 2020 08:41:56: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:41:56: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 08:42:05: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 08:42:08: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX331336/SRX331336.05_peaks.xls INFO @ Tue, 16 Jun 2020 08:42:08: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX331336/SRX331336.05_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:42:08: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX331336/SRX331336.05_summits.bed INFO @ Tue, 16 Jun 2020 08:42:08: Done! pass1 - making usageList (7 chroms): 0 millis pass2 - checking and writing primary data (1189 records, 4 fields): 2 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 08:42:12: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX331336/SRX331336.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX331336/SRX331336.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX331336/SRX331336.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX331336/SRX331336.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 08:42:12: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:42:12: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:42:16: 1000000 INFO @ Tue, 16 Jun 2020 08:42:21: 2000000 INFO @ Tue, 16 Jun 2020 08:42:26: #1 tag size is determined as 42 bps INFO @ Tue, 16 Jun 2020 08:42:26: #1 tag size = 42 INFO @ Tue, 16 Jun 2020 08:42:26: #1 total tags in treatment: 2990350 INFO @ Tue, 16 Jun 2020 08:42:26: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:42:26: #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 08:42:26: #1 tags after filtering in treatment: 2990350 INFO @ Tue, 16 Jun 2020 08:42:26: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:42:26: #1 finished! INFO @ Tue, 16 Jun 2020 08:42:26: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:42:26: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:42:26: #2 number of paired peaks: 5312 INFO @ Tue, 16 Jun 2020 08:42:26: start model_add_line... INFO @ Tue, 16 Jun 2020 08:42:26: start X-correlation... INFO @ Tue, 16 Jun 2020 08:42:26: end of X-cor INFO @ Tue, 16 Jun 2020 08:42:26: #2 finished! INFO @ Tue, 16 Jun 2020 08:42:26: #2 predicted fragment length is 197 bps INFO @ Tue, 16 Jun 2020 08:42:26: #2 alternative fragment length(s) may be 2,197 bps INFO @ Tue, 16 Jun 2020 08:42:26: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX331336/SRX331336.10_model.r INFO @ Tue, 16 Jun 2020 08:42:26: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:42:26: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 08:42:35: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 08:42:38: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX331336/SRX331336.10_peaks.xls INFO @ Tue, 16 Jun 2020 08:42:38: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX331336/SRX331336.10_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:42:38: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX331336/SRX331336.10_summits.bed INFO @ Tue, 16 Jun 2020 08:42:39: Done! pass1 - making usageList (7 chroms): 0 millis pass2 - checking and writing primary data (561 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 08:42:42: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX331336/SRX331336.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX331336/SRX331336.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX331336/SRX331336.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX331336/SRX331336.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 08:42:42: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:42:42: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:42:46: 1000000 INFO @ Tue, 16 Jun 2020 08:42:51: 2000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 16 Jun 2020 08:42:56: #1 tag size is determined as 42 bps INFO @ Tue, 16 Jun 2020 08:42:56: #1 tag size = 42 INFO @ Tue, 16 Jun 2020 08:42:56: #1 total tags in treatment: 2990350 INFO @ Tue, 16 Jun 2020 08:42:56: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:42:56: #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 08:42:56: #1 tags after filtering in treatment: 2990350 INFO @ Tue, 16 Jun 2020 08:42:56: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:42:56: #1 finished! INFO @ Tue, 16 Jun 2020 08:42:56: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:42:56: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:42:56: #2 number of paired peaks: 5312 INFO @ Tue, 16 Jun 2020 08:42:56: start model_add_line... INFO @ Tue, 16 Jun 2020 08:42:56: start X-correlation... INFO @ Tue, 16 Jun 2020 08:42:56: end of X-cor INFO @ Tue, 16 Jun 2020 08:42:56: #2 finished! INFO @ Tue, 16 Jun 2020 08:42:56: #2 predicted fragment length is 197 bps INFO @ Tue, 16 Jun 2020 08:42:56: #2 alternative fragment length(s) may be 2,197 bps INFO @ Tue, 16 Jun 2020 08:42:56: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX331336/SRX331336.20_model.r INFO @ Tue, 16 Jun 2020 08:42:56: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:42:56: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Tue, 16 Jun 2020 08:43:05: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 08:43:09: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX331336/SRX331336.20_peaks.xls INFO @ Tue, 16 Jun 2020 08:43:09: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX331336/SRX331336.20_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:43:09: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX331336/SRX331336.20_summits.bed INFO @ Tue, 16 Jun 2020 08:43:09: Done! pass1 - making usageList (6 chroms): 2 millis pass2 - checking and writing primary data (213 records, 4 fields): 1 millis CompletedMACS2peakCalling