Job ID = 6366012 SRX = SRX044024 Genome = ce11 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-15T22:31:29 prefetch.2.10.7: 1) Downloading 'SRR107607'... 2020-06-15T22:31:29 prefetch.2.10.7: Downloading via HTTPS... 2020-06-15T22:32:24 prefetch.2.10.7: HTTPS download succeed 2020-06-15T22:32:24 prefetch.2.10.7: 'SRR107607' is valid 2020-06-15T22:32:24 prefetch.2.10.7: 1) 'SRR107607' was downloaded successfully Read 8501634 spots for SRR107607/SRR107607.sra Written 8501634 spots for SRR107607/SRR107607.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: 00:00:36 8501634 reads; of these: 8501634 (100.00%) were unpaired; of these: 7123298 (83.79%) aligned 0 times 1226247 (14.42%) aligned exactly 1 time 152089 (1.79%) aligned >1 times 16.21% overall alignment rate Time searching: 00:00:36 Overall time: 00:00:36 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] 333750 / 1378336 = 0.2421 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 07:34:16: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX044024/SRX044024.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX044024/SRX044024.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX044024/SRX044024.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX044024/SRX044024.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 07:34:16: #1 read tag files... INFO @ Tue, 16 Jun 2020 07:34:16: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 07:34:21: 1000000 INFO @ Tue, 16 Jun 2020 07:34:21: #1 tag size is determined as 34 bps INFO @ Tue, 16 Jun 2020 07:34:21: #1 tag size = 34 INFO @ Tue, 16 Jun 2020 07:34:21: #1 total tags in treatment: 1044586 INFO @ Tue, 16 Jun 2020 07:34:21: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 07:34:21: #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 07:34:22: #1 tags after filtering in treatment: 1044586 INFO @ Tue, 16 Jun 2020 07:34:22: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 07:34:22: #1 finished! INFO @ Tue, 16 Jun 2020 07:34:22: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 07:34:22: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 07:34:22: #2 number of paired peaks: 3402 INFO @ Tue, 16 Jun 2020 07:34:22: start model_add_line... INFO @ Tue, 16 Jun 2020 07:34:22: start X-correlation... INFO @ Tue, 16 Jun 2020 07:34:22: end of X-cor INFO @ Tue, 16 Jun 2020 07:34:22: #2 finished! INFO @ Tue, 16 Jun 2020 07:34:22: #2 predicted fragment length is 164 bps INFO @ Tue, 16 Jun 2020 07:34:22: #2 alternative fragment length(s) may be 164 bps INFO @ Tue, 16 Jun 2020 07:34:22: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX044024/SRX044024.05_model.r INFO @ Tue, 16 Jun 2020 07:34:22: #3 Call peaks... INFO @ Tue, 16 Jun 2020 07:34:22: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 07:34:25: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 07:34:26: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX044024/SRX044024.05_peaks.xls INFO @ Tue, 16 Jun 2020 07:34:26: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX044024/SRX044024.05_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 07:34:26: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX044024/SRX044024.05_summits.bed INFO @ Tue, 16 Jun 2020 07:34:26: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (3304 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 07:34:46: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX044024/SRX044024.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX044024/SRX044024.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX044024/SRX044024.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX044024/SRX044024.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 07:34:46: #1 read tag files... INFO @ Tue, 16 Jun 2020 07:34:46: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 07:34:51: 1000000 INFO @ Tue, 16 Jun 2020 07:34:52: #1 tag size is determined as 34 bps INFO @ Tue, 16 Jun 2020 07:34:52: #1 tag size = 34 INFO @ Tue, 16 Jun 2020 07:34:52: #1 total tags in treatment: 1044586 INFO @ Tue, 16 Jun 2020 07:34:52: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 07:34:52: #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 07:34:52: #1 tags after filtering in treatment: 1044586 INFO @ Tue, 16 Jun 2020 07:34:52: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 07:34:52: #1 finished! INFO @ Tue, 16 Jun 2020 07:34:52: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 07:34:52: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 07:34:52: #2 number of paired peaks: 3402 INFO @ Tue, 16 Jun 2020 07:34:52: start model_add_line... INFO @ Tue, 16 Jun 2020 07:34:52: start X-correlation... INFO @ Tue, 16 Jun 2020 07:34:52: end of X-cor INFO @ Tue, 16 Jun 2020 07:34:52: #2 finished! INFO @ Tue, 16 Jun 2020 07:34:52: #2 predicted fragment length is 164 bps INFO @ Tue, 16 Jun 2020 07:34:52: #2 alternative fragment length(s) may be 164 bps INFO @ Tue, 16 Jun 2020 07:34:52: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX044024/SRX044024.10_model.r INFO @ Tue, 16 Jun 2020 07:34:52: #3 Call peaks... INFO @ Tue, 16 Jun 2020 07:34:52: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 07:34:55: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 07:34:56: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX044024/SRX044024.10_peaks.xls INFO @ Tue, 16 Jun 2020 07:34:56: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX044024/SRX044024.10_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 07:34:56: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX044024/SRX044024.10_summits.bed INFO @ Tue, 16 Jun 2020 07:34:56: Done! pass1 - making usageList (7 chroms): 0 millis pass2 - checking and writing primary data (1449 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 07:35:16: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX044024/SRX044024.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX044024/SRX044024.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX044024/SRX044024.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX044024/SRX044024.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 07:35:16: #1 read tag files... INFO @ Tue, 16 Jun 2020 07:35:16: #1 read treatment tags... BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 16 Jun 2020 07:35:21: 1000000 INFO @ Tue, 16 Jun 2020 07:35:22: #1 tag size is determined as 34 bps INFO @ Tue, 16 Jun 2020 07:35:22: #1 tag size = 34 INFO @ Tue, 16 Jun 2020 07:35:22: #1 total tags in treatment: 1044586 INFO @ Tue, 16 Jun 2020 07:35:22: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 07:35:22: #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 07:35:22: #1 tags after filtering in treatment: 1044586 INFO @ Tue, 16 Jun 2020 07:35:22: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 07:35:22: #1 finished! INFO @ Tue, 16 Jun 2020 07:35:22: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 07:35:22: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 07:35:22: #2 number of paired peaks: 3402 INFO @ Tue, 16 Jun 2020 07:35:22: start model_add_line... INFO @ Tue, 16 Jun 2020 07:35:22: start X-correlation... INFO @ Tue, 16 Jun 2020 07:35:22: end of X-cor INFO @ Tue, 16 Jun 2020 07:35:22: #2 finished! INFO @ Tue, 16 Jun 2020 07:35:22: #2 predicted fragment length is 164 bps INFO @ Tue, 16 Jun 2020 07:35:22: #2 alternative fragment length(s) may be 164 bps INFO @ Tue, 16 Jun 2020 07:35:22: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX044024/SRX044024.20_model.r INFO @ Tue, 16 Jun 2020 07:35:22: #3 Call peaks... INFO @ Tue, 16 Jun 2020 07:35:22: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Tue, 16 Jun 2020 07:35:25: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 07:35:26: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX044024/SRX044024.20_peaks.xls INFO @ Tue, 16 Jun 2020 07:35:26: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX044024/SRX044024.20_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 07:35:26: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX044024/SRX044024.20_summits.bed INFO @ Tue, 16 Jun 2020 07:35:26: Done! pass1 - making usageList (7 chroms): 2 millis pass2 - checking and writing primary data (369 records, 4 fields): 3 millis CompletedMACS2peakCalling