Job ID = 6367375 SRX = SRX331134 Genome = ce11 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-15T23:23:46 prefetch.2.10.7: 1) Downloading 'SRR947365'... 2020-06-15T23:23:46 prefetch.2.10.7: Downloading via HTTPS... 2020-06-15T23:24:07 prefetch.2.10.7: HTTPS download succeed 2020-06-15T23:24:07 prefetch.2.10.7: 'SRR947365' is valid 2020-06-15T23:24:07 prefetch.2.10.7: 1) 'SRR947365' was downloaded successfully Read 4294213 spots for SRR947365/SRR947365.sra Written 4294213 spots for SRR947365/SRR947365.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: 00:00:25 4294213 reads; of these: 4294213 (100.00%) were unpaired; of these: 2575655 (59.98%) aligned 0 times 1530674 (35.65%) aligned exactly 1 time 187884 (4.38%) aligned >1 times 40.02% overall alignment rate Time searching: 00:00:25 Overall time: 00:00:25 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] 475708 / 1718558 = 0.2768 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 08:25:34: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX331134/SRX331134.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX331134/SRX331134.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX331134/SRX331134.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX331134/SRX331134.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 08:25:34: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:25:34: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:25:39: 1000000 INFO @ Tue, 16 Jun 2020 08:25:41: #1 tag size is determined as 32 bps INFO @ Tue, 16 Jun 2020 08:25:41: #1 tag size = 32 INFO @ Tue, 16 Jun 2020 08:25:41: #1 total tags in treatment: 1242850 INFO @ Tue, 16 Jun 2020 08:25:41: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:25:41: #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 08:25:41: #1 tags after filtering in treatment: 1242850 INFO @ Tue, 16 Jun 2020 08:25:41: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:25:41: #1 finished! INFO @ Tue, 16 Jun 2020 08:25:41: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:25:41: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:25:41: #2 number of paired peaks: 3641 INFO @ Tue, 16 Jun 2020 08:25:41: start model_add_line... INFO @ Tue, 16 Jun 2020 08:25:41: start X-correlation... INFO @ Tue, 16 Jun 2020 08:25:41: end of X-cor INFO @ Tue, 16 Jun 2020 08:25:41: #2 finished! INFO @ Tue, 16 Jun 2020 08:25:41: #2 predicted fragment length is 140 bps INFO @ Tue, 16 Jun 2020 08:25:41: #2 alternative fragment length(s) may be 140 bps INFO @ Tue, 16 Jun 2020 08:25:41: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX331134/SRX331134.05_model.r INFO @ Tue, 16 Jun 2020 08:25:41: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:25:41: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 08:25:44: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 08:25:46: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX331134/SRX331134.05_peaks.xls INFO @ Tue, 16 Jun 2020 08:25:46: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX331134/SRX331134.05_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:25:46: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX331134/SRX331134.05_summits.bed INFO @ Tue, 16 Jun 2020 08:25:46: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (4032 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 08:26:03: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX331134/SRX331134.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX331134/SRX331134.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX331134/SRX331134.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX331134/SRX331134.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 08:26:03: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:26:03: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:26:08: 1000000 INFO @ Tue, 16 Jun 2020 08:26:10: #1 tag size is determined as 32 bps INFO @ Tue, 16 Jun 2020 08:26:10: #1 tag size = 32 INFO @ Tue, 16 Jun 2020 08:26:10: #1 total tags in treatment: 1242850 INFO @ Tue, 16 Jun 2020 08:26:10: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:26:10: #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 08:26:10: #1 tags after filtering in treatment: 1242850 INFO @ Tue, 16 Jun 2020 08:26:10: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:26:10: #1 finished! INFO @ Tue, 16 Jun 2020 08:26:10: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:26:10: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:26:10: #2 number of paired peaks: 3641 INFO @ Tue, 16 Jun 2020 08:26:10: start model_add_line... INFO @ Tue, 16 Jun 2020 08:26:10: start X-correlation... INFO @ Tue, 16 Jun 2020 08:26:10: end of X-cor INFO @ Tue, 16 Jun 2020 08:26:10: #2 finished! INFO @ Tue, 16 Jun 2020 08:26:10: #2 predicted fragment length is 140 bps INFO @ Tue, 16 Jun 2020 08:26:10: #2 alternative fragment length(s) may be 140 bps INFO @ Tue, 16 Jun 2020 08:26:10: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX331134/SRX331134.10_model.r INFO @ Tue, 16 Jun 2020 08:26:10: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:26:10: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 08:26:13: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 08:26:15: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX331134/SRX331134.10_peaks.xls INFO @ Tue, 16 Jun 2020 08:26:15: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX331134/SRX331134.10_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:26:15: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX331134/SRX331134.10_summits.bed INFO @ Tue, 16 Jun 2020 08:26:15: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (2086 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 08:26:33: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX331134/SRX331134.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX331134/SRX331134.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX331134/SRX331134.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX331134/SRX331134.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 08:26:33: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:26:33: #1 read treatment tags... BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 16 Jun 2020 08:26:38: 1000000 INFO @ Tue, 16 Jun 2020 08:26:40: #1 tag size is determined as 32 bps INFO @ Tue, 16 Jun 2020 08:26:40: #1 tag size = 32 INFO @ Tue, 16 Jun 2020 08:26:40: #1 total tags in treatment: 1242850 INFO @ Tue, 16 Jun 2020 08:26:40: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:26:40: #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 08:26:40: #1 tags after filtering in treatment: 1242850 INFO @ Tue, 16 Jun 2020 08:26:40: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:26:40: #1 finished! INFO @ Tue, 16 Jun 2020 08:26:40: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:26:40: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:26:40: #2 number of paired peaks: 3641 INFO @ Tue, 16 Jun 2020 08:26:40: start model_add_line... INFO @ Tue, 16 Jun 2020 08:26:40: start X-correlation... INFO @ Tue, 16 Jun 2020 08:26:40: end of X-cor INFO @ Tue, 16 Jun 2020 08:26:40: #2 finished! INFO @ Tue, 16 Jun 2020 08:26:40: #2 predicted fragment length is 140 bps INFO @ Tue, 16 Jun 2020 08:26:40: #2 alternative fragment length(s) may be 140 bps INFO @ Tue, 16 Jun 2020 08:26:40: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX331134/SRX331134.20_model.r INFO @ Tue, 16 Jun 2020 08:26:40: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:26:40: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Tue, 16 Jun 2020 08:26:43: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 08:26:45: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX331134/SRX331134.20_peaks.xls INFO @ Tue, 16 Jun 2020 08:26:45: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX331134/SRX331134.20_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:26:45: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX331134/SRX331134.20_summits.bed INFO @ Tue, 16 Jun 2020 08:26:45: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (703 records, 4 fields): 1 millis CompletedMACS2peakCalling