Job ID = 6366332 SRX = SRX113606 Genome = ce11 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-15T22:46:37 prefetch.2.10.7: 1) Downloading 'SRR393706'... 2020-06-15T22:46:37 prefetch.2.10.7: Downloading via HTTPS... 2020-06-15T22:47:33 prefetch.2.10.7: HTTPS download succeed 2020-06-15T22:47:33 prefetch.2.10.7: 'SRR393706' is valid 2020-06-15T22:47:33 prefetch.2.10.7: 1) 'SRR393706' was downloaded successfully Read 9740995 spots for SRR393706/SRR393706.sra Written 9740995 spots for SRR393706/SRR393706.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: 00:02:18 9740995 reads; of these: 9740995 (100.00%) were unpaired; of these: 537959 (5.52%) aligned 0 times 6072605 (62.34%) aligned exactly 1 time 3130431 (32.14%) aligned >1 times 94.48% overall alignment rate Time searching: 00:02:18 Overall time: 00:02:18 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] 3674430 / 9203036 = 0.3993 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 07:52:39: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX113606/SRX113606.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX113606/SRX113606.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX113606/SRX113606.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX113606/SRX113606.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 07:52:39: #1 read tag files... INFO @ Tue, 16 Jun 2020 07:52:39: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 07:52:45: 1000000 INFO @ Tue, 16 Jun 2020 07:52:51: 2000000 INFO @ Tue, 16 Jun 2020 07:52:57: 3000000 INFO @ Tue, 16 Jun 2020 07:53:03: 4000000 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 07:53:09: 5000000 INFO @ Tue, 16 Jun 2020 07:53:09: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX113606/SRX113606.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX113606/SRX113606.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX113606/SRX113606.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX113606/SRX113606.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 07:53:09: #1 read tag files... INFO @ Tue, 16 Jun 2020 07:53:09: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 07:53:12: #1 tag size is determined as 36 bps INFO @ Tue, 16 Jun 2020 07:53:12: #1 tag size = 36 INFO @ Tue, 16 Jun 2020 07:53:12: #1 total tags in treatment: 5528606 INFO @ Tue, 16 Jun 2020 07:53:12: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 07:53:12: #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 07:53:12: #1 tags after filtering in treatment: 5528606 INFO @ Tue, 16 Jun 2020 07:53:12: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 07:53:12: #1 finished! INFO @ Tue, 16 Jun 2020 07:53:12: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 07:53:12: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 07:53:13: #2 number of paired peaks: 5070 INFO @ Tue, 16 Jun 2020 07:53:13: start model_add_line... INFO @ Tue, 16 Jun 2020 07:53:13: start X-correlation... INFO @ Tue, 16 Jun 2020 07:53:13: end of X-cor INFO @ Tue, 16 Jun 2020 07:53:13: #2 finished! INFO @ Tue, 16 Jun 2020 07:53:13: #2 predicted fragment length is 125 bps INFO @ Tue, 16 Jun 2020 07:53:13: #2 alternative fragment length(s) may be 1,125 bps INFO @ Tue, 16 Jun 2020 07:53:13: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX113606/SRX113606.05_model.r INFO @ Tue, 16 Jun 2020 07:53:13: #3 Call peaks... INFO @ Tue, 16 Jun 2020 07:53:13: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 07:53:16: 1000000 INFO @ Tue, 16 Jun 2020 07:53:21: 2000000 INFO @ Tue, 16 Jun 2020 07:53:26: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 07:53:27: 3000000 INFO @ Tue, 16 Jun 2020 07:53:33: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX113606/SRX113606.05_peaks.xls INFO @ Tue, 16 Jun 2020 07:53:33: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX113606/SRX113606.05_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 07:53:33: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX113606/SRX113606.05_summits.bed INFO @ Tue, 16 Jun 2020 07:53:33: Done! pass1 - making usageList (6 chroms): 1 millis INFO @ Tue, 16 Jun 2020 07:53:33: 4000000 pass2 - checking and writing primary data (3178 records, 4 fields): 25 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 07:53:39: 5000000 INFO @ Tue, 16 Jun 2020 07:53:39: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX113606/SRX113606.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX113606/SRX113606.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX113606/SRX113606.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX113606/SRX113606.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 07:53:39: #1 read tag files... INFO @ Tue, 16 Jun 2020 07:53:39: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 07:53:43: #1 tag size is determined as 36 bps INFO @ Tue, 16 Jun 2020 07:53:43: #1 tag size = 36 INFO @ Tue, 16 Jun 2020 07:53:43: #1 total tags in treatment: 5528606 INFO @ Tue, 16 Jun 2020 07:53:43: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 07:53:43: #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 07:53:43: #1 tags after filtering in treatment: 5528606 INFO @ Tue, 16 Jun 2020 07:53:43: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 07:53:43: #1 finished! INFO @ Tue, 16 Jun 2020 07:53:43: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 07:53:43: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 07:53:43: #2 number of paired peaks: 5070 INFO @ Tue, 16 Jun 2020 07:53:43: start model_add_line... INFO @ Tue, 16 Jun 2020 07:53:43: start X-correlation... INFO @ Tue, 16 Jun 2020 07:53:43: end of X-cor INFO @ Tue, 16 Jun 2020 07:53:43: #2 finished! INFO @ Tue, 16 Jun 2020 07:53:43: #2 predicted fragment length is 125 bps INFO @ Tue, 16 Jun 2020 07:53:43: #2 alternative fragment length(s) may be 1,125 bps INFO @ Tue, 16 Jun 2020 07:53:43: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX113606/SRX113606.10_model.r INFO @ Tue, 16 Jun 2020 07:53:43: #3 Call peaks... INFO @ Tue, 16 Jun 2020 07:53:43: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 07:53:46: 1000000 INFO @ Tue, 16 Jun 2020 07:53:52: 2000000 INFO @ Tue, 16 Jun 2020 07:53:57: 3000000 INFO @ Tue, 16 Jun 2020 07:53:58: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 07:54:03: 4000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 16 Jun 2020 07:54:05: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX113606/SRX113606.10_peaks.xls INFO @ Tue, 16 Jun 2020 07:54:05: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX113606/SRX113606.10_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 07:54:05: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX113606/SRX113606.10_summits.bed INFO @ Tue, 16 Jun 2020 07:54:05: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (810 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 07:54:09: 5000000 INFO @ Tue, 16 Jun 2020 07:54:12: #1 tag size is determined as 36 bps INFO @ Tue, 16 Jun 2020 07:54:12: #1 tag size = 36 INFO @ Tue, 16 Jun 2020 07:54:12: #1 total tags in treatment: 5528606 INFO @ Tue, 16 Jun 2020 07:54:12: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 07:54:12: #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 07:54:12: #1 tags after filtering in treatment: 5528606 INFO @ Tue, 16 Jun 2020 07:54:12: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 07:54:12: #1 finished! INFO @ Tue, 16 Jun 2020 07:54:12: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 07:54:12: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 07:54:13: #2 number of paired peaks: 5070 INFO @ Tue, 16 Jun 2020 07:54:13: start model_add_line... INFO @ Tue, 16 Jun 2020 07:54:13: start X-correlation... INFO @ Tue, 16 Jun 2020 07:54:13: end of X-cor INFO @ Tue, 16 Jun 2020 07:54:13: #2 finished! INFO @ Tue, 16 Jun 2020 07:54:13: #2 predicted fragment length is 125 bps INFO @ Tue, 16 Jun 2020 07:54:13: #2 alternative fragment length(s) may be 1,125 bps INFO @ Tue, 16 Jun 2020 07:54:13: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX113606/SRX113606.20_model.r INFO @ Tue, 16 Jun 2020 07:54:13: #3 Call peaks... INFO @ Tue, 16 Jun 2020 07:54:13: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Tue, 16 Jun 2020 07:54:26: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 07:54:33: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX113606/SRX113606.20_peaks.xls INFO @ Tue, 16 Jun 2020 07:54:33: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX113606/SRX113606.20_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 07:54:33: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX113606/SRX113606.20_summits.bed INFO @ Tue, 16 Jun 2020 07:54:33: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (163 records, 4 fields): 1 millis CompletedMACS2peakCalling