Job ID = 6367542 SRX = SRX331298 Genome = ce11 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-15T23:34:20 prefetch.2.10.7: 1) Downloading 'SRR947535'... 2020-06-15T23:34:20 prefetch.2.10.7: Downloading via HTTPS... 2020-06-15T23:34:42 prefetch.2.10.7: HTTPS download succeed 2020-06-15T23:34:42 prefetch.2.10.7: 'SRR947535' is valid 2020-06-15T23:34:42 prefetch.2.10.7: 1) 'SRR947535' was downloaded successfully Read 2309911 spots for SRR947535/SRR947535.sra Written 2309911 spots for SRR947535/SRR947535.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: 00:00:21 2309911 reads; of these: 2309911 (100.00%) were unpaired; of these: 375276 (16.25%) aligned 0 times 1721399 (74.52%) aligned exactly 1 time 213236 (9.23%) aligned >1 times 83.75% overall alignment rate Time searching: 00:00:21 Overall time: 00:00:21 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] 313277 / 1934635 = 0.1619 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 08:36:00: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX331298/SRX331298.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX331298/SRX331298.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX331298/SRX331298.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX331298/SRX331298.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 08:36:00: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:36:00: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:36:06: 1000000 INFO @ Tue, 16 Jun 2020 08:36:09: #1 tag size is determined as 32 bps INFO @ Tue, 16 Jun 2020 08:36:09: #1 tag size = 32 INFO @ Tue, 16 Jun 2020 08:36:09: #1 total tags in treatment: 1621358 INFO @ Tue, 16 Jun 2020 08:36:09: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:36:09: #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 08:36:09: #1 tags after filtering in treatment: 1621358 INFO @ Tue, 16 Jun 2020 08:36:09: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:36:09: #1 finished! INFO @ Tue, 16 Jun 2020 08:36:09: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:36:09: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:36:09: #2 number of paired peaks: 3349 INFO @ Tue, 16 Jun 2020 08:36:09: start model_add_line... INFO @ Tue, 16 Jun 2020 08:36:09: start X-correlation... INFO @ Tue, 16 Jun 2020 08:36:09: end of X-cor INFO @ Tue, 16 Jun 2020 08:36:09: #2 finished! INFO @ Tue, 16 Jun 2020 08:36:09: #2 predicted fragment length is 178 bps INFO @ Tue, 16 Jun 2020 08:36:09: #2 alternative fragment length(s) may be 178 bps INFO @ Tue, 16 Jun 2020 08:36:09: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX331298/SRX331298.05_model.r INFO @ Tue, 16 Jun 2020 08:36:09: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:36:09: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 08:36:13: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 08:36:15: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX331298/SRX331298.05_peaks.xls INFO @ Tue, 16 Jun 2020 08:36:15: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX331298/SRX331298.05_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:36:15: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX331298/SRX331298.05_summits.bed INFO @ Tue, 16 Jun 2020 08:36:15: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (4431 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 08:36:31: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX331298/SRX331298.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX331298/SRX331298.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX331298/SRX331298.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX331298/SRX331298.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 08:36:31: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:36:31: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:36:36: 1000000 INFO @ Tue, 16 Jun 2020 08:36:39: #1 tag size is determined as 32 bps INFO @ Tue, 16 Jun 2020 08:36:39: #1 tag size = 32 INFO @ Tue, 16 Jun 2020 08:36:39: #1 total tags in treatment: 1621358 INFO @ Tue, 16 Jun 2020 08:36:39: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:36:39: #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 08:36:39: #1 tags after filtering in treatment: 1621358 INFO @ Tue, 16 Jun 2020 08:36:39: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:36:39: #1 finished! INFO @ Tue, 16 Jun 2020 08:36:39: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:36:39: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:36:40: #2 number of paired peaks: 3349 INFO @ Tue, 16 Jun 2020 08:36:40: start model_add_line... INFO @ Tue, 16 Jun 2020 08:36:40: start X-correlation... INFO @ Tue, 16 Jun 2020 08:36:40: end of X-cor INFO @ Tue, 16 Jun 2020 08:36:40: #2 finished! INFO @ Tue, 16 Jun 2020 08:36:40: #2 predicted fragment length is 178 bps INFO @ Tue, 16 Jun 2020 08:36:40: #2 alternative fragment length(s) may be 178 bps INFO @ Tue, 16 Jun 2020 08:36:40: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX331298/SRX331298.10_model.r INFO @ Tue, 16 Jun 2020 08:36:40: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:36:40: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 08:36:44: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 08:36:46: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX331298/SRX331298.10_peaks.xls INFO @ Tue, 16 Jun 2020 08:36:46: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX331298/SRX331298.10_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:36:46: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX331298/SRX331298.10_summits.bed INFO @ Tue, 16 Jun 2020 08:36:46: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (2076 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 08:37:01: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX331298/SRX331298.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX331298/SRX331298.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX331298/SRX331298.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX331298/SRX331298.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 08:37:01: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:37:01: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:37:06: 1000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 16 Jun 2020 08:37:09: #1 tag size is determined as 32 bps INFO @ Tue, 16 Jun 2020 08:37:09: #1 tag size = 32 INFO @ Tue, 16 Jun 2020 08:37:09: #1 total tags in treatment: 1621358 INFO @ Tue, 16 Jun 2020 08:37:09: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:37:09: #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 08:37:09: #1 tags after filtering in treatment: 1621358 INFO @ Tue, 16 Jun 2020 08:37:09: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:37:09: #1 finished! INFO @ Tue, 16 Jun 2020 08:37:09: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:37:09: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:37:10: #2 number of paired peaks: 3349 INFO @ Tue, 16 Jun 2020 08:37:10: start model_add_line... INFO @ Tue, 16 Jun 2020 08:37:10: start X-correlation... INFO @ Tue, 16 Jun 2020 08:37:10: end of X-cor INFO @ Tue, 16 Jun 2020 08:37:10: #2 finished! INFO @ Tue, 16 Jun 2020 08:37:10: #2 predicted fragment length is 178 bps INFO @ Tue, 16 Jun 2020 08:37:10: #2 alternative fragment length(s) may be 178 bps INFO @ Tue, 16 Jun 2020 08:37:10: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX331298/SRX331298.20_model.r INFO @ Tue, 16 Jun 2020 08:37:10: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:37:10: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Tue, 16 Jun 2020 08:37:14: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 08:37:16: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX331298/SRX331298.20_peaks.xls INFO @ Tue, 16 Jun 2020 08:37:16: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX331298/SRX331298.20_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:37:16: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX331298/SRX331298.20_summits.bed INFO @ Tue, 16 Jun 2020 08:37:16: Done! pass1 - making usageList (7 chroms): 0 millis pass2 - checking and writing primary data (621 records, 4 fields): 2 millis CompletedMACS2peakCalling