Job ID = 6368059 SRX = SRX466522 Genome = ce11 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-15T23:41:59 prefetch.2.10.7: 1) Downloading 'SRR1163588'... 2020-06-15T23:41:59 prefetch.2.10.7: Downloading via HTTPS... 2020-06-15T23:47:41 prefetch.2.10.7: HTTPS download succeed 2020-06-15T23:47:42 prefetch.2.10.7: 'SRR1163588' is valid 2020-06-15T23:47:42 prefetch.2.10.7: 1) 'SRR1163588' was downloaded successfully Read 10244663 spots for SRR1163588/SRR1163588.sra Written 10244663 spots for SRR1163588/SRR1163588.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: 00:02:00 10244663 reads; of these: 10244663 (100.00%) were unpaired; of these: 604016 (5.90%) aligned 0 times 8348973 (81.50%) aligned exactly 1 time 1291674 (12.61%) aligned >1 times 94.10% overall alignment rate Time searching: 00:02:00 Overall time: 00:02:00 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] 7030236 / 9640647 = 0.7292 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 08:52:41: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX466522/SRX466522.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX466522/SRX466522.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX466522/SRX466522.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX466522/SRX466522.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 08:52:41: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:52:41: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:52:48: 1000000 INFO @ Tue, 16 Jun 2020 08:52:55: 2000000 INFO @ Tue, 16 Jun 2020 08:52:59: #1 tag size is determined as 42 bps INFO @ Tue, 16 Jun 2020 08:52:59: #1 tag size = 42 INFO @ Tue, 16 Jun 2020 08:52:59: #1 total tags in treatment: 2610411 INFO @ Tue, 16 Jun 2020 08:52:59: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:52:59: #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 08:52:59: #1 tags after filtering in treatment: 2610411 INFO @ Tue, 16 Jun 2020 08:52:59: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:52:59: #1 finished! INFO @ Tue, 16 Jun 2020 08:52:59: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:52:59: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:53:00: #2 number of paired peaks: 3277 INFO @ Tue, 16 Jun 2020 08:53:00: start model_add_line... INFO @ Tue, 16 Jun 2020 08:53:00: start X-correlation... INFO @ Tue, 16 Jun 2020 08:53:00: end of X-cor INFO @ Tue, 16 Jun 2020 08:53:00: #2 finished! INFO @ Tue, 16 Jun 2020 08:53:00: #2 predicted fragment length is 265 bps INFO @ Tue, 16 Jun 2020 08:53:00: #2 alternative fragment length(s) may be 265 bps INFO @ Tue, 16 Jun 2020 08:53:00: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX466522/SRX466522.05_model.r INFO @ Tue, 16 Jun 2020 08:53:00: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:53:00: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 08:53:08: #3 Call peaks for each chromosome... 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 08:53:11: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX466522/SRX466522.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX466522/SRX466522.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX466522/SRX466522.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX466522/SRX466522.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 08:53:11: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:53:11: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:53:12: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX466522/SRX466522.05_peaks.xls INFO @ Tue, 16 Jun 2020 08:53:12: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX466522/SRX466522.05_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:53:12: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX466522/SRX466522.05_summits.bed INFO @ Tue, 16 Jun 2020 08:53:12: Done! pass1 - making usageList (6 chroms): 2 millis pass2 - checking and writing primary data (3837 records, 4 fields): 5 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 08:53:19: 1000000 INFO @ Tue, 16 Jun 2020 08:53:27: 2000000 INFO @ Tue, 16 Jun 2020 08:53:32: #1 tag size is determined as 42 bps INFO @ Tue, 16 Jun 2020 08:53:32: #1 tag size = 42 INFO @ Tue, 16 Jun 2020 08:53:32: #1 total tags in treatment: 2610411 INFO @ Tue, 16 Jun 2020 08:53:32: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:53:32: #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 08:53:32: #1 tags after filtering in treatment: 2610411 INFO @ Tue, 16 Jun 2020 08:53:32: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:53:32: #1 finished! INFO @ Tue, 16 Jun 2020 08:53:32: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:53:32: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:53:32: #2 number of paired peaks: 3277 INFO @ Tue, 16 Jun 2020 08:53:32: start model_add_line... INFO @ Tue, 16 Jun 2020 08:53:32: start X-correlation... INFO @ Tue, 16 Jun 2020 08:53:32: end of X-cor INFO @ Tue, 16 Jun 2020 08:53:32: #2 finished! INFO @ Tue, 16 Jun 2020 08:53:32: #2 predicted fragment length is 265 bps INFO @ Tue, 16 Jun 2020 08:53:32: #2 alternative fragment length(s) may be 265 bps INFO @ Tue, 16 Jun 2020 08:53:32: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX466522/SRX466522.10_model.r INFO @ Tue, 16 Jun 2020 08:53:32: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:53:32: #3 Pre-compute pvalue-qvalue table... 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 08:53:41: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 08:53:42: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX466522/SRX466522.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX466522/SRX466522.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX466522/SRX466522.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX466522/SRX466522.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 08:53:42: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:53:42: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:53:44: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX466522/SRX466522.10_peaks.xls INFO @ Tue, 16 Jun 2020 08:53:44: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX466522/SRX466522.10_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:53:44: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX466522/SRX466522.10_summits.bed INFO @ Tue, 16 Jun 2020 08:53:44: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (2228 records, 4 fields): 4 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 08:53:48: 1000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 16 Jun 2020 08:53:54: 2000000 INFO @ Tue, 16 Jun 2020 08:53:58: #1 tag size is determined as 42 bps INFO @ Tue, 16 Jun 2020 08:53:58: #1 tag size = 42 INFO @ Tue, 16 Jun 2020 08:53:58: #1 total tags in treatment: 2610411 INFO @ Tue, 16 Jun 2020 08:53:58: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:53:58: #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 08:53:58: #1 tags after filtering in treatment: 2610411 INFO @ Tue, 16 Jun 2020 08:53:58: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:53:58: #1 finished! INFO @ Tue, 16 Jun 2020 08:53:58: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:53:58: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:53:59: #2 number of paired peaks: 3277 INFO @ Tue, 16 Jun 2020 08:53:59: start model_add_line... INFO @ Tue, 16 Jun 2020 08:53:59: start X-correlation... INFO @ Tue, 16 Jun 2020 08:53:59: end of X-cor INFO @ Tue, 16 Jun 2020 08:53:59: #2 finished! INFO @ Tue, 16 Jun 2020 08:53:59: #2 predicted fragment length is 265 bps INFO @ Tue, 16 Jun 2020 08:53:59: #2 alternative fragment length(s) may be 265 bps INFO @ Tue, 16 Jun 2020 08:53:59: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX466522/SRX466522.20_model.r INFO @ Tue, 16 Jun 2020 08:53:59: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:53:59: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Tue, 16 Jun 2020 08:54:06: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 08:54:10: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX466522/SRX466522.20_peaks.xls INFO @ Tue, 16 Jun 2020 08:54:10: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX466522/SRX466522.20_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:54:10: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX466522/SRX466522.20_summits.bed INFO @ Tue, 16 Jun 2020 08:54:10: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (785 records, 4 fields): 2 millis CompletedMACS2peakCalling