Job ID = 6365946 SRX = SRX043878 Genome = ce11 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-15T22:45:07 prefetch.2.10.7: 1) Downloading 'SRR107350'... 2020-06-15T22:45:07 prefetch.2.10.7: Downloading via HTTPS... 2020-06-15T22:45:32 prefetch.2.10.7: HTTPS download succeed 2020-06-15T22:45:32 prefetch.2.10.7: 'SRR107350' is valid 2020-06-15T22:45:32 prefetch.2.10.7: 1) 'SRR107350' was downloaded successfully Read 3432445 spots for SRR107350/SRR107350.sra Written 3432445 spots for SRR107350/SRR107350.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: 00:00:23 3432445 reads; of these: 3432445 (100.00%) were unpaired; of these: 1750124 (50.99%) aligned 0 times 1495811 (43.58%) aligned exactly 1 time 186510 (5.43%) aligned >1 times 49.01% overall alignment rate Time searching: 00:00:23 Overall time: 00:00:23 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] 211963 / 1682321 = 0.1260 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 07:47:11: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX043878/SRX043878.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX043878/SRX043878.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX043878/SRX043878.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX043878/SRX043878.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 07:47:11: #1 read tag files... INFO @ Tue, 16 Jun 2020 07:47:11: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 07:47:15: 1000000 INFO @ Tue, 16 Jun 2020 07:47:18: #1 tag size is determined as 34 bps INFO @ Tue, 16 Jun 2020 07:47:18: #1 tag size = 34 INFO @ Tue, 16 Jun 2020 07:47:18: #1 total tags in treatment: 1470358 INFO @ Tue, 16 Jun 2020 07:47:18: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 07:47:18: #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 07:47:18: #1 tags after filtering in treatment: 1470358 INFO @ Tue, 16 Jun 2020 07:47:18: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 07:47:18: #1 finished! INFO @ Tue, 16 Jun 2020 07:47:18: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 07:47:18: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 07:47:18: #2 number of paired peaks: 2489 INFO @ Tue, 16 Jun 2020 07:47:18: start model_add_line... INFO @ Tue, 16 Jun 2020 07:47:18: start X-correlation... INFO @ Tue, 16 Jun 2020 07:47:18: end of X-cor INFO @ Tue, 16 Jun 2020 07:47:18: #2 finished! INFO @ Tue, 16 Jun 2020 07:47:18: #2 predicted fragment length is 125 bps INFO @ Tue, 16 Jun 2020 07:47:18: #2 alternative fragment length(s) may be 125,582 bps INFO @ Tue, 16 Jun 2020 07:47:18: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX043878/SRX043878.05_model.r INFO @ Tue, 16 Jun 2020 07:47:18: #3 Call peaks... INFO @ Tue, 16 Jun 2020 07:47:18: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 07:47:21: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 07:47:23: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX043878/SRX043878.05_peaks.xls INFO @ Tue, 16 Jun 2020 07:47:23: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX043878/SRX043878.05_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 07:47:23: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX043878/SRX043878.05_summits.bed INFO @ Tue, 16 Jun 2020 07:47:23: Done! pass1 - making usageList (7 chroms): 0 millis pass2 - checking and writing primary data (839 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 07:47:40: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX043878/SRX043878.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX043878/SRX043878.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX043878/SRX043878.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX043878/SRX043878.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 07:47:40: #1 read tag files... INFO @ Tue, 16 Jun 2020 07:47:40: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 07:47:45: 1000000 INFO @ Tue, 16 Jun 2020 07:47:47: #1 tag size is determined as 34 bps INFO @ Tue, 16 Jun 2020 07:47:47: #1 tag size = 34 INFO @ Tue, 16 Jun 2020 07:47:47: #1 total tags in treatment: 1470358 INFO @ Tue, 16 Jun 2020 07:47:47: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 07:47:47: #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 07:47:47: #1 tags after filtering in treatment: 1470358 INFO @ Tue, 16 Jun 2020 07:47:47: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 07:47:47: #1 finished! INFO @ Tue, 16 Jun 2020 07:47:47: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 07:47:47: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 07:47:48: #2 number of paired peaks: 2489 INFO @ Tue, 16 Jun 2020 07:47:48: start model_add_line... INFO @ Tue, 16 Jun 2020 07:47:48: start X-correlation... INFO @ Tue, 16 Jun 2020 07:47:48: end of X-cor INFO @ Tue, 16 Jun 2020 07:47:48: #2 finished! INFO @ Tue, 16 Jun 2020 07:47:48: #2 predicted fragment length is 125 bps INFO @ Tue, 16 Jun 2020 07:47:48: #2 alternative fragment length(s) may be 125,582 bps INFO @ Tue, 16 Jun 2020 07:47:48: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX043878/SRX043878.10_model.r INFO @ Tue, 16 Jun 2020 07:47:48: #3 Call peaks... INFO @ Tue, 16 Jun 2020 07:47:48: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 07:47:51: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 07:47:53: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX043878/SRX043878.10_peaks.xls INFO @ Tue, 16 Jun 2020 07:47:53: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX043878/SRX043878.10_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 07:47:53: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX043878/SRX043878.10_summits.bed INFO @ Tue, 16 Jun 2020 07:47:53: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (306 records, 4 fields): 1 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 07:48:10: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX043878/SRX043878.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX043878/SRX043878.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX043878/SRX043878.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX043878/SRX043878.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 07:48:10: #1 read tag files... INFO @ Tue, 16 Jun 2020 07:48:10: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 07:48:15: 1000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 16 Jun 2020 07:48:18: #1 tag size is determined as 34 bps INFO @ Tue, 16 Jun 2020 07:48:18: #1 tag size = 34 INFO @ Tue, 16 Jun 2020 07:48:18: #1 total tags in treatment: 1470358 INFO @ Tue, 16 Jun 2020 07:48:18: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 07:48:18: #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 07:48:18: #1 tags after filtering in treatment: 1470358 INFO @ Tue, 16 Jun 2020 07:48:18: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 07:48:18: #1 finished! INFO @ Tue, 16 Jun 2020 07:48:18: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 07:48:18: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 07:48:18: #2 number of paired peaks: 2489 INFO @ Tue, 16 Jun 2020 07:48:18: start model_add_line... INFO @ Tue, 16 Jun 2020 07:48:18: start X-correlation... INFO @ Tue, 16 Jun 2020 07:48:18: end of X-cor INFO @ Tue, 16 Jun 2020 07:48:18: #2 finished! INFO @ Tue, 16 Jun 2020 07:48:18: #2 predicted fragment length is 125 bps INFO @ Tue, 16 Jun 2020 07:48:18: #2 alternative fragment length(s) may be 125,582 bps INFO @ Tue, 16 Jun 2020 07:48:18: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX043878/SRX043878.20_model.r INFO @ Tue, 16 Jun 2020 07:48:18: #3 Call peaks... INFO @ Tue, 16 Jun 2020 07:48:18: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Tue, 16 Jun 2020 07:48:21: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 07:48:23: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX043878/SRX043878.20_peaks.xls INFO @ Tue, 16 Jun 2020 07:48:23: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX043878/SRX043878.20_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 07:48:23: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX043878/SRX043878.20_summits.bed INFO @ Tue, 16 Jun 2020 07:48:23: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (100 records, 4 fields): 2 millis CompletedMACS2peakCalling