Job ID = 6366248 SRX = SRX080102 Genome = ce11 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-15T22:38:51 prefetch.2.10.7: 1) Downloading 'SRR298922'... 2020-06-15T22:38:51 prefetch.2.10.7: Downloading via HTTPS... 2020-06-15T22:39:29 prefetch.2.10.7: HTTPS download succeed 2020-06-15T22:39:30 prefetch.2.10.7: 'SRR298922' is valid 2020-06-15T22:39:30 prefetch.2.10.7: 1) 'SRR298922' was downloaded successfully Read 6275526 spots for SRR298922/SRR298922.sra Written 6275526 spots for SRR298922/SRR298922.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: 00:01:00 6275526 reads; of these: 6275526 (100.00%) were unpaired; of these: 473571 (7.55%) aligned 0 times 4930058 (78.56%) aligned exactly 1 time 871897 (13.89%) aligned >1 times 92.45% overall alignment rate Time searching: 00:01:00 Overall time: 00:01:00 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] 796430 / 5801955 = 0.1373 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 07:42:26: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX080102/SRX080102.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX080102/SRX080102.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX080102/SRX080102.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX080102/SRX080102.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 07:42:26: #1 read tag files... INFO @ Tue, 16 Jun 2020 07:42:26: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 07:42:31: 1000000 INFO @ Tue, 16 Jun 2020 07:42:36: 2000000 INFO @ Tue, 16 Jun 2020 07:42:41: 3000000 INFO @ Tue, 16 Jun 2020 07:42:46: 4000000 INFO @ Tue, 16 Jun 2020 07:42:51: 5000000 INFO @ Tue, 16 Jun 2020 07:42:51: #1 tag size is determined as 32 bps INFO @ Tue, 16 Jun 2020 07:42:51: #1 tag size = 32 INFO @ Tue, 16 Jun 2020 07:42:51: #1 total tags in treatment: 5005525 INFO @ Tue, 16 Jun 2020 07:42:51: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 07:42:51: #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 07:42:51: #1 tags after filtering in treatment: 5005525 INFO @ Tue, 16 Jun 2020 07:42:51: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 07:42:51: #1 finished! INFO @ Tue, 16 Jun 2020 07:42:51: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 07:42:51: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 07:42:51: #2 number of paired peaks: 1190 INFO @ Tue, 16 Jun 2020 07:42:51: start model_add_line... INFO @ Tue, 16 Jun 2020 07:42:51: start X-correlation... INFO @ Tue, 16 Jun 2020 07:42:51: end of X-cor INFO @ Tue, 16 Jun 2020 07:42:51: #2 finished! INFO @ Tue, 16 Jun 2020 07:42:51: #2 predicted fragment length is 141 bps INFO @ Tue, 16 Jun 2020 07:42:51: #2 alternative fragment length(s) may be 141 bps INFO @ Tue, 16 Jun 2020 07:42:51: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX080102/SRX080102.05_model.r INFO @ Tue, 16 Jun 2020 07:42:51: #3 Call peaks... INFO @ Tue, 16 Jun 2020 07:42:51: #3 Pre-compute pvalue-qvalue table... 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 07:42:56: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX080102/SRX080102.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX080102/SRX080102.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX080102/SRX080102.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX080102/SRX080102.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 07:42:56: #1 read tag files... INFO @ Tue, 16 Jun 2020 07:42:56: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 07:43:01: 1000000 INFO @ Tue, 16 Jun 2020 07:43:03: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 07:43:06: 2000000 INFO @ Tue, 16 Jun 2020 07:43:09: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX080102/SRX080102.05_peaks.xls INFO @ Tue, 16 Jun 2020 07:43:09: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX080102/SRX080102.05_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 07:43:09: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX080102/SRX080102.05_summits.bed INFO @ Tue, 16 Jun 2020 07:43:09: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (4603 records, 4 fields): 5 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 07:43:11: 3000000 INFO @ Tue, 16 Jun 2020 07:43:15: 4000000 INFO @ Tue, 16 Jun 2020 07:43:20: 5000000 INFO @ Tue, 16 Jun 2020 07:43:20: #1 tag size is determined as 32 bps INFO @ Tue, 16 Jun 2020 07:43:20: #1 tag size = 32 INFO @ Tue, 16 Jun 2020 07:43:20: #1 total tags in treatment: 5005525 INFO @ Tue, 16 Jun 2020 07:43:20: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 07:43:20: #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 07:43:20: #1 tags after filtering in treatment: 5005525 INFO @ Tue, 16 Jun 2020 07:43:20: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 07:43:20: #1 finished! INFO @ Tue, 16 Jun 2020 07:43:20: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 07:43:20: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 07:43:21: #2 number of paired peaks: 1190 INFO @ Tue, 16 Jun 2020 07:43:21: start model_add_line... INFO @ Tue, 16 Jun 2020 07:43:21: start X-correlation... INFO @ Tue, 16 Jun 2020 07:43:21: end of X-cor INFO @ Tue, 16 Jun 2020 07:43:21: #2 finished! INFO @ Tue, 16 Jun 2020 07:43:21: #2 predicted fragment length is 141 bps INFO @ Tue, 16 Jun 2020 07:43:21: #2 alternative fragment length(s) may be 141 bps INFO @ Tue, 16 Jun 2020 07:43:21: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX080102/SRX080102.10_model.r INFO @ Tue, 16 Jun 2020 07:43:21: #3 Call peaks... INFO @ Tue, 16 Jun 2020 07:43:21: #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 07:43:26: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX080102/SRX080102.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX080102/SRX080102.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX080102/SRX080102.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX080102/SRX080102.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 07:43:26: #1 read tag files... INFO @ Tue, 16 Jun 2020 07:43:26: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 07:43:31: 1000000 INFO @ Tue, 16 Jun 2020 07:43:33: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 07:43:36: 2000000 INFO @ Tue, 16 Jun 2020 07:43:38: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX080102/SRX080102.10_peaks.xls INFO @ Tue, 16 Jun 2020 07:43:38: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX080102/SRX080102.10_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 07:43:38: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX080102/SRX080102.10_summits.bed INFO @ Tue, 16 Jun 2020 07:43:38: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (2786 records, 4 fields): 9 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 07:43:41: 3000000 INFO @ Tue, 16 Jun 2020 07:43:46: 4000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 16 Jun 2020 07:43:51: 5000000 INFO @ Tue, 16 Jun 2020 07:43:51: #1 tag size is determined as 32 bps INFO @ Tue, 16 Jun 2020 07:43:51: #1 tag size = 32 INFO @ Tue, 16 Jun 2020 07:43:51: #1 total tags in treatment: 5005525 INFO @ Tue, 16 Jun 2020 07:43:51: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 07:43:51: #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 07:43:51: #1 tags after filtering in treatment: 5005525 INFO @ Tue, 16 Jun 2020 07:43:51: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 07:43:51: #1 finished! INFO @ Tue, 16 Jun 2020 07:43:51: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 07:43:51: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 07:43:51: #2 number of paired peaks: 1190 INFO @ Tue, 16 Jun 2020 07:43:51: start model_add_line... INFO @ Tue, 16 Jun 2020 07:43:51: start X-correlation... INFO @ Tue, 16 Jun 2020 07:43:51: end of X-cor INFO @ Tue, 16 Jun 2020 07:43:51: #2 finished! INFO @ Tue, 16 Jun 2020 07:43:51: #2 predicted fragment length is 141 bps INFO @ Tue, 16 Jun 2020 07:43:51: #2 alternative fragment length(s) may be 141 bps INFO @ Tue, 16 Jun 2020 07:43:51: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX080102/SRX080102.20_model.r INFO @ Tue, 16 Jun 2020 07:43:51: #3 Call peaks... INFO @ Tue, 16 Jun 2020 07:43:51: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Tue, 16 Jun 2020 07:44:03: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 07:44:09: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX080102/SRX080102.20_peaks.xls INFO @ Tue, 16 Jun 2020 07:44:09: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX080102/SRX080102.20_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 07:44:09: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX080102/SRX080102.20_summits.bed INFO @ Tue, 16 Jun 2020 07:44:09: Done! pass1 - making usageList (7 chroms): 3 millis pass2 - checking and writing primary data (1248 records, 4 fields): 3 millis CompletedMACS2peakCalling