Job ID = 6366343 SRX = SRX113621 Genome = ce11 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-15T22:43:07 prefetch.2.10.7: 1) Downloading 'SRR393721'... 2020-06-15T22:43:07 prefetch.2.10.7: Downloading via HTTPS... 2020-06-15T22:43:33 prefetch.2.10.7: HTTPS download succeed 2020-06-15T22:43:33 prefetch.2.10.7: 'SRR393721' is valid 2020-06-15T22:43:33 prefetch.2.10.7: 1) 'SRR393721' was downloaded successfully Read 7751200 spots for SRR393721/SRR393721.sra Written 7751200 spots for SRR393721/SRR393721.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: 00:01:48 7751200 reads; of these: 7751200 (100.00%) were unpaired; of these: 331851 (4.28%) aligned 0 times 5161436 (66.59%) aligned exactly 1 time 2257913 (29.13%) aligned >1 times 95.72% overall alignment rate Time searching: 00:01:48 Overall time: 00:01:48 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] 3359838 / 7419349 = 0.4528 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 07:47:30: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX113621/SRX113621.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX113621/SRX113621.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX113621/SRX113621.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX113621/SRX113621.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 07:47:30: #1 read tag files... INFO @ Tue, 16 Jun 2020 07:47:30: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 07:47:36: 1000000 INFO @ Tue, 16 Jun 2020 07:47:42: 2000000 INFO @ Tue, 16 Jun 2020 07:47:49: 3000000 INFO @ Tue, 16 Jun 2020 07:47:55: 4000000 INFO @ Tue, 16 Jun 2020 07:47:55: #1 tag size is determined as 36 bps INFO @ Tue, 16 Jun 2020 07:47:55: #1 tag size = 36 INFO @ Tue, 16 Jun 2020 07:47:55: #1 total tags in treatment: 4059511 INFO @ Tue, 16 Jun 2020 07:47:55: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 07:47:55: #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 07:47:55: #1 tags after filtering in treatment: 4059511 INFO @ Tue, 16 Jun 2020 07:47:55: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 07:47:55: #1 finished! INFO @ Tue, 16 Jun 2020 07:47:55: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 07:47:55: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 07:47:56: #2 number of paired peaks: 3658 INFO @ Tue, 16 Jun 2020 07:47:56: start model_add_line... INFO @ Tue, 16 Jun 2020 07:47:56: start X-correlation... INFO @ Tue, 16 Jun 2020 07:47:56: end of X-cor INFO @ Tue, 16 Jun 2020 07:47:56: #2 finished! INFO @ Tue, 16 Jun 2020 07:47:56: #2 predicted fragment length is 181 bps INFO @ Tue, 16 Jun 2020 07:47:56: #2 alternative fragment length(s) may be 1,181 bps INFO @ Tue, 16 Jun 2020 07:47:56: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX113621/SRX113621.05_model.r INFO @ Tue, 16 Jun 2020 07:47:56: #3 Call peaks... INFO @ Tue, 16 Jun 2020 07:47:56: #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 07:48:00: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX113621/SRX113621.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX113621/SRX113621.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX113621/SRX113621.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX113621/SRX113621.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 07:48:00: #1 read tag files... INFO @ Tue, 16 Jun 2020 07:48:00: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 07:48:05: 1000000 INFO @ Tue, 16 Jun 2020 07:48:06: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 07:48:11: 2000000 INFO @ Tue, 16 Jun 2020 07:48:11: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX113621/SRX113621.05_peaks.xls INFO @ Tue, 16 Jun 2020 07:48:11: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX113621/SRX113621.05_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 07:48:11: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX113621/SRX113621.05_summits.bed INFO @ Tue, 16 Jun 2020 07:48:11: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (1449 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 07:48:16: 3000000 INFO @ Tue, 16 Jun 2020 07:48:21: 4000000 INFO @ Tue, 16 Jun 2020 07:48:21: #1 tag size is determined as 36 bps INFO @ Tue, 16 Jun 2020 07:48:21: #1 tag size = 36 INFO @ Tue, 16 Jun 2020 07:48:21: #1 total tags in treatment: 4059511 INFO @ Tue, 16 Jun 2020 07:48:21: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 07:48:21: #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 07:48:21: #1 tags after filtering in treatment: 4059511 INFO @ Tue, 16 Jun 2020 07:48:21: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 07:48:21: #1 finished! INFO @ Tue, 16 Jun 2020 07:48:21: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 07:48:21: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 07:48:22: #2 number of paired peaks: 3658 INFO @ Tue, 16 Jun 2020 07:48:22: start model_add_line... INFO @ Tue, 16 Jun 2020 07:48:22: start X-correlation... INFO @ Tue, 16 Jun 2020 07:48:22: end of X-cor INFO @ Tue, 16 Jun 2020 07:48:22: #2 finished! INFO @ Tue, 16 Jun 2020 07:48:22: #2 predicted fragment length is 181 bps INFO @ Tue, 16 Jun 2020 07:48:22: #2 alternative fragment length(s) may be 1,181 bps INFO @ Tue, 16 Jun 2020 07:48:22: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX113621/SRX113621.10_model.r INFO @ Tue, 16 Jun 2020 07:48:22: #3 Call peaks... INFO @ Tue, 16 Jun 2020 07:48:22: #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 07:48:30: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX113621/SRX113621.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX113621/SRX113621.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX113621/SRX113621.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX113621/SRX113621.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 07:48:30: #1 read tag files... INFO @ Tue, 16 Jun 2020 07:48:30: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 07:48:32: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 07:48:35: 1000000 INFO @ Tue, 16 Jun 2020 07:48:36: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX113621/SRX113621.10_peaks.xls INFO @ Tue, 16 Jun 2020 07:48:36: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX113621/SRX113621.10_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 07:48:36: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX113621/SRX113621.10_summits.bed INFO @ Tue, 16 Jun 2020 07:48:36: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (476 records, 4 fields): 1 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 07:48:40: 2000000 INFO @ Tue, 16 Jun 2020 07:48:46: 3000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 16 Jun 2020 07:48:51: 4000000 INFO @ Tue, 16 Jun 2020 07:48:51: #1 tag size is determined as 36 bps INFO @ Tue, 16 Jun 2020 07:48:51: #1 tag size = 36 INFO @ Tue, 16 Jun 2020 07:48:51: #1 total tags in treatment: 4059511 INFO @ Tue, 16 Jun 2020 07:48:51: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 07:48:51: #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 07:48:51: #1 tags after filtering in treatment: 4059511 INFO @ Tue, 16 Jun 2020 07:48:51: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 07:48:51: #1 finished! INFO @ Tue, 16 Jun 2020 07:48:51: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 07:48:51: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 07:48:52: #2 number of paired peaks: 3658 INFO @ Tue, 16 Jun 2020 07:48:52: start model_add_line... INFO @ Tue, 16 Jun 2020 07:48:52: start X-correlation... INFO @ Tue, 16 Jun 2020 07:48:52: end of X-cor INFO @ Tue, 16 Jun 2020 07:48:52: #2 finished! INFO @ Tue, 16 Jun 2020 07:48:52: #2 predicted fragment length is 181 bps INFO @ Tue, 16 Jun 2020 07:48:52: #2 alternative fragment length(s) may be 1,181 bps INFO @ Tue, 16 Jun 2020 07:48:52: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX113621/SRX113621.20_model.r INFO @ Tue, 16 Jun 2020 07:48:52: #3 Call peaks... INFO @ Tue, 16 Jun 2020 07:48:52: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Tue, 16 Jun 2020 07:49:02: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 07:49:06: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX113621/SRX113621.20_peaks.xls INFO @ Tue, 16 Jun 2020 07:49:06: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX113621/SRX113621.20_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 07:49:06: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX113621/SRX113621.20_summits.bed INFO @ Tue, 16 Jun 2020 07:49:06: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (125 records, 4 fields): 1 millis CompletedMACS2peakCalling