Job ID = 6368536 SRX = SRX5020764 Genome = ce11 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-16T00:18:06 prefetch.2.10.7: 1) Downloading 'SRR8201387'... 2020-06-16T00:18:06 prefetch.2.10.7: Downloading via HTTPS... 2020-06-16T00:19:59 prefetch.2.10.7: HTTPS download succeed 2020-06-16T00:20:00 prefetch.2.10.7: 'SRR8201387' is valid 2020-06-16T00:20:00 prefetch.2.10.7: 1) 'SRR8201387' was downloaded successfully Read 16732587 spots for SRR8201387/SRR8201387.sra Written 16732587 spots for SRR8201387/SRR8201387.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: 00:03:48 16732587 reads; of these: 16732587 (100.00%) were unpaired; of these: 1332306 (7.96%) aligned 0 times 12892612 (77.05%) aligned exactly 1 time 2507669 (14.99%) aligned >1 times 92.04% overall alignment rate Time searching: 00:03:48 Overall time: 00:03:48 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_sort_core] merging from 8 files... [bam_rmdupse_core] 8434603 / 15400281 = 0.5477 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 09:28:14: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX5020764/SRX5020764.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX5020764/SRX5020764.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX5020764/SRX5020764.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX5020764/SRX5020764.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 09:28:14: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:28:14: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:28:20: 1000000 INFO @ Tue, 16 Jun 2020 09:28:25: 2000000 INFO @ Tue, 16 Jun 2020 09:28:30: 3000000 INFO @ Tue, 16 Jun 2020 09:28:35: 4000000 INFO @ Tue, 16 Jun 2020 09:28:40: 5000000 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 09:28:44: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX5020764/SRX5020764.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX5020764/SRX5020764.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX5020764/SRX5020764.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX5020764/SRX5020764.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 09:28:44: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:28:44: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:28:45: 6000000 INFO @ Tue, 16 Jun 2020 09:28:50: #1 tag size is determined as 51 bps INFO @ Tue, 16 Jun 2020 09:28:50: #1 tag size = 51 INFO @ Tue, 16 Jun 2020 09:28:50: #1 total tags in treatment: 6965678 INFO @ Tue, 16 Jun 2020 09:28:50: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:28:50: #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 09:28:50: #1 tags after filtering in treatment: 6965678 INFO @ Tue, 16 Jun 2020 09:28:50: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 09:28:50: #1 finished! INFO @ Tue, 16 Jun 2020 09:28:50: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:28:50: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:28:51: 1000000 INFO @ Tue, 16 Jun 2020 09:28:51: #2 number of paired peaks: 1067 INFO @ Tue, 16 Jun 2020 09:28:51: start model_add_line... INFO @ Tue, 16 Jun 2020 09:28:51: start X-correlation... INFO @ Tue, 16 Jun 2020 09:28:51: end of X-cor INFO @ Tue, 16 Jun 2020 09:28:51: #2 finished! INFO @ Tue, 16 Jun 2020 09:28:51: #2 predicted fragment length is 116 bps INFO @ Tue, 16 Jun 2020 09:28:51: #2 alternative fragment length(s) may be 4,116 bps INFO @ Tue, 16 Jun 2020 09:28:51: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX5020764/SRX5020764.05_model.r INFO @ Tue, 16 Jun 2020 09:28:51: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:28:51: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 09:28:57: 2000000 INFO @ Tue, 16 Jun 2020 09:29:03: 3000000 INFO @ Tue, 16 Jun 2020 09:29:07: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 09:29:09: 4000000 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 09:29:14: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX5020764/SRX5020764.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX5020764/SRX5020764.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX5020764/SRX5020764.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX5020764/SRX5020764.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 09:29:14: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:29:14: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:29:15: 5000000 INFO @ Tue, 16 Jun 2020 09:29:15: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX5020764/SRX5020764.05_peaks.xls INFO @ Tue, 16 Jun 2020 09:29:15: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX5020764/SRX5020764.05_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:29:15: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX5020764/SRX5020764.05_summits.bed INFO @ Tue, 16 Jun 2020 09:29:15: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (2227 records, 4 fields): 4 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 09:29:20: 1000000 INFO @ Tue, 16 Jun 2020 09:29:21: 6000000 INFO @ Tue, 16 Jun 2020 09:29:25: 2000000 INFO @ Tue, 16 Jun 2020 09:29:27: #1 tag size is determined as 51 bps INFO @ Tue, 16 Jun 2020 09:29:27: #1 tag size = 51 INFO @ Tue, 16 Jun 2020 09:29:27: #1 total tags in treatment: 6965678 INFO @ Tue, 16 Jun 2020 09:29:27: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:29:27: #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 09:29:27: #1 tags after filtering in treatment: 6965678 INFO @ Tue, 16 Jun 2020 09:29:27: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 09:29:27: #1 finished! INFO @ Tue, 16 Jun 2020 09:29:27: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:29:27: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:29:28: #2 number of paired peaks: 1067 INFO @ Tue, 16 Jun 2020 09:29:28: start model_add_line... INFO @ Tue, 16 Jun 2020 09:29:28: start X-correlation... INFO @ Tue, 16 Jun 2020 09:29:28: end of X-cor INFO @ Tue, 16 Jun 2020 09:29:28: #2 finished! INFO @ Tue, 16 Jun 2020 09:29:28: #2 predicted fragment length is 116 bps INFO @ Tue, 16 Jun 2020 09:29:28: #2 alternative fragment length(s) may be 4,116 bps INFO @ Tue, 16 Jun 2020 09:29:28: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX5020764/SRX5020764.10_model.r INFO @ Tue, 16 Jun 2020 09:29:28: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:29:28: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 09:29:30: 3000000 INFO @ Tue, 16 Jun 2020 09:29:36: 4000000 INFO @ Tue, 16 Jun 2020 09:29:41: 5000000 INFO @ Tue, 16 Jun 2020 09:29:45: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 09:29:46: 6000000 INFO @ Tue, 16 Jun 2020 09:29:51: #1 tag size is determined as 51 bps INFO @ Tue, 16 Jun 2020 09:29:51: #1 tag size = 51 INFO @ Tue, 16 Jun 2020 09:29:51: #1 total tags in treatment: 6965678 INFO @ Tue, 16 Jun 2020 09:29:51: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:29:51: #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 09:29:51: #1 tags after filtering in treatment: 6965678 INFO @ Tue, 16 Jun 2020 09:29:51: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 09:29:51: #1 finished! INFO @ Tue, 16 Jun 2020 09:29:51: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:29:51: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:29:51: #2 number of paired peaks: 1067 INFO @ Tue, 16 Jun 2020 09:29:51: start model_add_line... INFO @ Tue, 16 Jun 2020 09:29:51: start X-correlation... INFO @ Tue, 16 Jun 2020 09:29:51: end of X-cor INFO @ Tue, 16 Jun 2020 09:29:51: #2 finished! INFO @ Tue, 16 Jun 2020 09:29:51: #2 predicted fragment length is 116 bps INFO @ Tue, 16 Jun 2020 09:29:51: #2 alternative fragment length(s) may be 4,116 bps INFO @ Tue, 16 Jun 2020 09:29:51: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX5020764/SRX5020764.20_model.r INFO @ Tue, 16 Jun 2020 09:29:51: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:29:51: #3 Pre-compute pvalue-qvalue table... BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 16 Jun 2020 09:29:53: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX5020764/SRX5020764.10_peaks.xls INFO @ Tue, 16 Jun 2020 09:29:53: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX5020764/SRX5020764.10_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:29:53: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX5020764/SRX5020764.10_summits.bed INFO @ Tue, 16 Jun 2020 09:29:53: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (1154 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 09:30:07: #3 Call peaks for each chromosome... BigWig に変換しました。 INFO @ Tue, 16 Jun 2020 09:30:14: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX5020764/SRX5020764.20_peaks.xls INFO @ Tue, 16 Jun 2020 09:30:14: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX5020764/SRX5020764.20_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:30:14: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX5020764/SRX5020764.20_summits.bed INFO @ Tue, 16 Jun 2020 09:30:14: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (588 records, 4 fields): 2 millis CompletedMACS2peakCalling