Job ID = 6367312 SRX = SRX331074 Genome = ce11 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-15T23:28:50 prefetch.2.10.7: 1) Downloading 'SRR947298'... 2020-06-15T23:28:50 prefetch.2.10.7: Downloading via HTTPS... 2020-06-15T23:29:43 prefetch.2.10.7: HTTPS download succeed 2020-06-15T23:29:43 prefetch.2.10.7: 'SRR947298' is valid 2020-06-15T23:29:43 prefetch.2.10.7: 1) 'SRR947298' was downloaded successfully Read 8389667 spots for SRR947298/SRR947298.sra Written 8389667 spots for SRR947298/SRR947298.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: 00:01:14 8389667 reads; of these: 8389667 (100.00%) were unpaired; of these: 1274036 (15.19%) aligned 0 times 6162418 (73.45%) aligned exactly 1 time 953213 (11.36%) aligned >1 times 84.81% overall alignment rate Time searching: 00:01:14 Overall time: 00:01:14 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] 1525787 / 7115631 = 0.2144 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 08:33:06: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX331074/SRX331074.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX331074/SRX331074.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX331074/SRX331074.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX331074/SRX331074.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 08:33:06: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:33:06: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:33:11: 1000000 INFO @ Tue, 16 Jun 2020 08:33:16: 2000000 INFO @ Tue, 16 Jun 2020 08:33:21: 3000000 INFO @ Tue, 16 Jun 2020 08:33:26: 4000000 INFO @ Tue, 16 Jun 2020 08:33:31: 5000000 INFO @ Tue, 16 Jun 2020 08:33:34: #1 tag size is determined as 32 bps INFO @ Tue, 16 Jun 2020 08:33:34: #1 tag size = 32 INFO @ Tue, 16 Jun 2020 08:33:34: #1 total tags in treatment: 5589844 INFO @ Tue, 16 Jun 2020 08:33:34: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:33:34: #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 08:33:34: #1 tags after filtering in treatment: 5589844 INFO @ Tue, 16 Jun 2020 08:33:34: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:33:34: #1 finished! INFO @ Tue, 16 Jun 2020 08:33:34: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:33:34: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:33:34: #2 number of paired peaks: 1312 INFO @ Tue, 16 Jun 2020 08:33:34: start model_add_line... INFO @ Tue, 16 Jun 2020 08:33:34: start X-correlation... INFO @ Tue, 16 Jun 2020 08:33:34: end of X-cor INFO @ Tue, 16 Jun 2020 08:33:34: #2 finished! INFO @ Tue, 16 Jun 2020 08:33:34: #2 predicted fragment length is 161 bps INFO @ Tue, 16 Jun 2020 08:33:34: #2 alternative fragment length(s) may be 161 bps INFO @ Tue, 16 Jun 2020 08:33:34: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX331074/SRX331074.05_model.r INFO @ Tue, 16 Jun 2020 08:33:35: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:33:35: #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 08:33:36: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX331074/SRX331074.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX331074/SRX331074.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX331074/SRX331074.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX331074/SRX331074.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 08:33:36: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:33:36: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:33:41: 1000000 INFO @ Tue, 16 Jun 2020 08:33:46: 2000000 INFO @ Tue, 16 Jun 2020 08:33:48: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 08:33:51: 3000000 INFO @ Tue, 16 Jun 2020 08:33:55: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX331074/SRX331074.05_peaks.xls INFO @ Tue, 16 Jun 2020 08:33:55: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX331074/SRX331074.05_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:33:55: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX331074/SRX331074.05_summits.bed INFO @ Tue, 16 Jun 2020 08:33:55: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (5314 records, 4 fields): 6 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 08:33:56: 4000000 INFO @ Tue, 16 Jun 2020 08:34:01: 5000000 INFO @ Tue, 16 Jun 2020 08:34:04: #1 tag size is determined as 32 bps INFO @ Tue, 16 Jun 2020 08:34:04: #1 tag size = 32 INFO @ Tue, 16 Jun 2020 08:34:04: #1 total tags in treatment: 5589844 INFO @ Tue, 16 Jun 2020 08:34:04: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:34:04: #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 08:34:04: #1 tags after filtering in treatment: 5589844 INFO @ Tue, 16 Jun 2020 08:34:04: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:34:04: #1 finished! INFO @ Tue, 16 Jun 2020 08:34:04: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:34:04: #2 looking for paired plus/minus strand peaks... 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 08:34:05: #2 number of paired peaks: 1312 INFO @ Tue, 16 Jun 2020 08:34:05: start model_add_line... INFO @ Tue, 16 Jun 2020 08:34:05: start X-correlation... INFO @ Tue, 16 Jun 2020 08:34:05: end of X-cor INFO @ Tue, 16 Jun 2020 08:34:05: #2 finished! INFO @ Tue, 16 Jun 2020 08:34:05: #2 predicted fragment length is 161 bps INFO @ Tue, 16 Jun 2020 08:34:05: #2 alternative fragment length(s) may be 161 bps INFO @ Tue, 16 Jun 2020 08:34:05: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX331074/SRX331074.10_model.r INFO @ Tue, 16 Jun 2020 08:34:05: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:34:05: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 08:34:06: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX331074/SRX331074.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX331074/SRX331074.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX331074/SRX331074.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX331074/SRX331074.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 08:34:06: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:34:06: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:34:11: 1000000 INFO @ Tue, 16 Jun 2020 08:34:16: 2000000 INFO @ Tue, 16 Jun 2020 08:34:18: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 08:34:21: 3000000 INFO @ Tue, 16 Jun 2020 08:34:25: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX331074/SRX331074.10_peaks.xls INFO @ Tue, 16 Jun 2020 08:34:25: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX331074/SRX331074.10_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:34:25: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX331074/SRX331074.10_summits.bed INFO @ Tue, 16 Jun 2020 08:34:25: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (3586 records, 4 fields): 5 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 08:34:27: 4000000 INFO @ Tue, 16 Jun 2020 08:34:32: 5000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 16 Jun 2020 08:34:34: #1 tag size is determined as 32 bps INFO @ Tue, 16 Jun 2020 08:34:34: #1 tag size = 32 INFO @ Tue, 16 Jun 2020 08:34:34: #1 total tags in treatment: 5589844 INFO @ Tue, 16 Jun 2020 08:34:34: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:34:34: #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 08:34:35: #1 tags after filtering in treatment: 5589844 INFO @ Tue, 16 Jun 2020 08:34:35: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:34:35: #1 finished! INFO @ Tue, 16 Jun 2020 08:34:35: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:34:35: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:34:35: #2 number of paired peaks: 1312 INFO @ Tue, 16 Jun 2020 08:34:35: start model_add_line... INFO @ Tue, 16 Jun 2020 08:34:35: start X-correlation... INFO @ Tue, 16 Jun 2020 08:34:35: end of X-cor INFO @ Tue, 16 Jun 2020 08:34:35: #2 finished! INFO @ Tue, 16 Jun 2020 08:34:35: #2 predicted fragment length is 161 bps INFO @ Tue, 16 Jun 2020 08:34:35: #2 alternative fragment length(s) may be 161 bps INFO @ Tue, 16 Jun 2020 08:34:35: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX331074/SRX331074.20_model.r INFO @ Tue, 16 Jun 2020 08:34:35: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:34:35: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Tue, 16 Jun 2020 08:34:49: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 08:34:55: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX331074/SRX331074.20_peaks.xls INFO @ Tue, 16 Jun 2020 08:34:55: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX331074/SRX331074.20_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:34:55: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX331074/SRX331074.20_summits.bed INFO @ Tue, 16 Jun 2020 08:34:55: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (2030 records, 4 fields): 4 millis CompletedMACS2peakCalling