Job ID = 6366634 SRX = SRX2144181 Genome = ce11 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-15T22:51:56 prefetch.2.10.7: 1) Downloading 'SRR4188785'... 2020-06-15T22:51:56 prefetch.2.10.7: Downloading via HTTPS... 2020-06-15T22:52:43 prefetch.2.10.7: HTTPS download succeed 2020-06-15T22:52:44 prefetch.2.10.7: 'SRR4188785' is valid 2020-06-15T22:52:44 prefetch.2.10.7: 1) 'SRR4188785' was downloaded successfully Read 8842349 spots for SRR4188785/SRR4188785.sra Written 8842349 spots for SRR4188785/SRR4188785.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: 00:01:27 8842349 reads; of these: 8842349 (100.00%) were unpaired; of these: 3823017 (43.24%) aligned 0 times 4326026 (48.92%) aligned exactly 1 time 693306 (7.84%) aligned >1 times 56.76% overall alignment rate Time searching: 00:01:27 Overall time: 00:01:27 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] 1279596 / 5019332 = 0.2549 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 07:56:38: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX2144181/SRX2144181.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX2144181/SRX2144181.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX2144181/SRX2144181.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX2144181/SRX2144181.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 07:56:38: #1 read tag files... INFO @ Tue, 16 Jun 2020 07:56:38: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 07:56:43: 1000000 INFO @ Tue, 16 Jun 2020 07:56:48: 2000000 INFO @ Tue, 16 Jun 2020 07:56:54: 3000000 INFO @ Tue, 16 Jun 2020 07:56:58: #1 tag size is determined as 50 bps INFO @ Tue, 16 Jun 2020 07:56:58: #1 tag size = 50 INFO @ Tue, 16 Jun 2020 07:56:58: #1 total tags in treatment: 3739736 INFO @ Tue, 16 Jun 2020 07:56:58: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 07:56:58: #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 07:56:58: #1 tags after filtering in treatment: 3739736 INFO @ Tue, 16 Jun 2020 07:56:58: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 07:56:58: #1 finished! INFO @ Tue, 16 Jun 2020 07:56:58: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 07:56:58: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 07:56:58: #2 number of paired peaks: 2807 INFO @ Tue, 16 Jun 2020 07:56:58: start model_add_line... INFO @ Tue, 16 Jun 2020 07:56:59: start X-correlation... INFO @ Tue, 16 Jun 2020 07:56:59: end of X-cor INFO @ Tue, 16 Jun 2020 07:56:59: #2 finished! INFO @ Tue, 16 Jun 2020 07:56:59: #2 predicted fragment length is 131 bps INFO @ Tue, 16 Jun 2020 07:56:59: #2 alternative fragment length(s) may be 131 bps INFO @ Tue, 16 Jun 2020 07:56:59: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX2144181/SRX2144181.05_model.r INFO @ Tue, 16 Jun 2020 07:56:59: #3 Call peaks... INFO @ Tue, 16 Jun 2020 07:56:59: #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 07:57:08: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX2144181/SRX2144181.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX2144181/SRX2144181.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX2144181/SRX2144181.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX2144181/SRX2144181.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 07:57:08: #1 read tag files... INFO @ Tue, 16 Jun 2020 07:57:08: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 07:57:09: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 07:57:14: 1000000 INFO @ Tue, 16 Jun 2020 07:57:14: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX2144181/SRX2144181.05_peaks.xls INFO @ Tue, 16 Jun 2020 07:57:14: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX2144181/SRX2144181.05_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 07:57:14: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX2144181/SRX2144181.05_summits.bed INFO @ Tue, 16 Jun 2020 07:57:14: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (3057 records, 4 fields): 6 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 07:57:19: 2000000 INFO @ Tue, 16 Jun 2020 07:57:25: 3000000 INFO @ Tue, 16 Jun 2020 07:57:30: #1 tag size is determined as 50 bps INFO @ Tue, 16 Jun 2020 07:57:30: #1 tag size = 50 INFO @ Tue, 16 Jun 2020 07:57:30: #1 total tags in treatment: 3739736 INFO @ Tue, 16 Jun 2020 07:57:30: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 07:57:30: #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 07:57:30: #1 tags after filtering in treatment: 3739736 INFO @ Tue, 16 Jun 2020 07:57:30: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 07:57:30: #1 finished! INFO @ Tue, 16 Jun 2020 07:57:30: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 07:57:30: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 07:57:30: #2 number of paired peaks: 2807 INFO @ Tue, 16 Jun 2020 07:57:30: start model_add_line... INFO @ Tue, 16 Jun 2020 07:57:30: start X-correlation... INFO @ Tue, 16 Jun 2020 07:57:30: end of X-cor INFO @ Tue, 16 Jun 2020 07:57:30: #2 finished! INFO @ Tue, 16 Jun 2020 07:57:30: #2 predicted fragment length is 131 bps INFO @ Tue, 16 Jun 2020 07:57:30: #2 alternative fragment length(s) may be 131 bps INFO @ Tue, 16 Jun 2020 07:57:30: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX2144181/SRX2144181.10_model.r INFO @ Tue, 16 Jun 2020 07:57:30: #3 Call peaks... INFO @ Tue, 16 Jun 2020 07:57:30: #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 07:57:38: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX2144181/SRX2144181.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX2144181/SRX2144181.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX2144181/SRX2144181.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX2144181/SRX2144181.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 07:57:38: #1 read tag files... INFO @ Tue, 16 Jun 2020 07:57:38: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 07:57:40: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 07:57:43: 1000000 INFO @ Tue, 16 Jun 2020 07:57:46: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX2144181/SRX2144181.10_peaks.xls INFO @ Tue, 16 Jun 2020 07:57:46: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX2144181/SRX2144181.10_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 07:57:46: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX2144181/SRX2144181.10_summits.bed INFO @ Tue, 16 Jun 2020 07:57:46: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (1453 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 07:57:49: 2000000 INFO @ Tue, 16 Jun 2020 07:57:54: 3000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 16 Jun 2020 07:57:58: #1 tag size is determined as 50 bps INFO @ Tue, 16 Jun 2020 07:57:58: #1 tag size = 50 INFO @ Tue, 16 Jun 2020 07:57:58: #1 total tags in treatment: 3739736 INFO @ Tue, 16 Jun 2020 07:57:58: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 07:57:58: #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 07:57:58: #1 tags after filtering in treatment: 3739736 INFO @ Tue, 16 Jun 2020 07:57:58: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 07:57:58: #1 finished! INFO @ Tue, 16 Jun 2020 07:57:58: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 07:57:58: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 07:57:59: #2 number of paired peaks: 2807 INFO @ Tue, 16 Jun 2020 07:57:59: start model_add_line... INFO @ Tue, 16 Jun 2020 07:57:59: start X-correlation... INFO @ Tue, 16 Jun 2020 07:57:59: end of X-cor INFO @ Tue, 16 Jun 2020 07:57:59: #2 finished! INFO @ Tue, 16 Jun 2020 07:57:59: #2 predicted fragment length is 131 bps INFO @ Tue, 16 Jun 2020 07:57:59: #2 alternative fragment length(s) may be 131 bps INFO @ Tue, 16 Jun 2020 07:57:59: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX2144181/SRX2144181.20_model.r INFO @ Tue, 16 Jun 2020 07:57:59: #3 Call peaks... INFO @ Tue, 16 Jun 2020 07:57:59: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Tue, 16 Jun 2020 07:58:09: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 07:58:15: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX2144181/SRX2144181.20_peaks.xls INFO @ Tue, 16 Jun 2020 07:58:15: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX2144181/SRX2144181.20_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 07:58:15: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX2144181/SRX2144181.20_summits.bed INFO @ Tue, 16 Jun 2020 07:58:15: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (474 records, 4 fields): 1 millis CompletedMACS2peakCalling