Job ID = 6366608 SRX = SRX208772 Genome = ce11 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-15T22:45:07 prefetch.2.10.7: 1) Downloading 'SRR628906'... 2020-06-15T22:45:07 prefetch.2.10.7: Downloading via HTTPS... 2020-06-15T22:46:43 prefetch.2.10.7: HTTPS download succeed 2020-06-15T22:46:44 prefetch.2.10.7: 'SRR628906' is valid 2020-06-15T22:46:44 prefetch.2.10.7: 1) 'SRR628906' was downloaded successfully Read 13827258 spots for SRR628906/SRR628906.sra Written 13827258 spots for SRR628906/SRR628906.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: 00:00:01 Time loading mirror index: 00:00:00 Multiseed full-index search: 00:04:07 13827258 reads; of these: 13827258 (100.00%) were unpaired; of these: 1119663 (8.10%) aligned 0 times 10073733 (72.85%) aligned exactly 1 time 2633862 (19.05%) aligned >1 times 91.90% overall alignment rate Time searching: 00:04:08 Overall time: 00:04:08 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] 9088988 / 12707595 = 0.7152 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 07:54:23: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX208772/SRX208772.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX208772/SRX208772.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX208772/SRX208772.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX208772/SRX208772.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 07:54:23: #1 read tag files... INFO @ Tue, 16 Jun 2020 07:54:23: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 07:54:29: 1000000 INFO @ Tue, 16 Jun 2020 07:54:34: 2000000 INFO @ Tue, 16 Jun 2020 07:54:40: 3000000 INFO @ Tue, 16 Jun 2020 07:54:44: #1 tag size is determined as 50 bps INFO @ Tue, 16 Jun 2020 07:54:44: #1 tag size = 50 INFO @ Tue, 16 Jun 2020 07:54:44: #1 total tags in treatment: 3618607 INFO @ Tue, 16 Jun 2020 07:54:44: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 07:54:44: #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 07:54:44: #1 tags after filtering in treatment: 3618607 INFO @ Tue, 16 Jun 2020 07:54:44: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 07:54:44: #1 finished! INFO @ Tue, 16 Jun 2020 07:54:44: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 07:54:44: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 07:54:44: #2 number of paired peaks: 1755 INFO @ Tue, 16 Jun 2020 07:54:44: start model_add_line... INFO @ Tue, 16 Jun 2020 07:54:44: start X-correlation... INFO @ Tue, 16 Jun 2020 07:54:44: end of X-cor INFO @ Tue, 16 Jun 2020 07:54:44: #2 finished! INFO @ Tue, 16 Jun 2020 07:54:44: #2 predicted fragment length is 318 bps INFO @ Tue, 16 Jun 2020 07:54:44: #2 alternative fragment length(s) may be 318 bps INFO @ Tue, 16 Jun 2020 07:54:44: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX208772/SRX208772.05_model.r INFO @ Tue, 16 Jun 2020 07:54:44: #3 Call peaks... INFO @ Tue, 16 Jun 2020 07:54:44: #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 07:54:53: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX208772/SRX208772.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX208772/SRX208772.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX208772/SRX208772.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX208772/SRX208772.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 07:54:53: #1 read tag files... INFO @ Tue, 16 Jun 2020 07:54:53: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 07:54:53: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 07:54:57: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX208772/SRX208772.05_peaks.xls INFO @ Tue, 16 Jun 2020 07:54:57: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX208772/SRX208772.05_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 07:54:57: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX208772/SRX208772.05_summits.bed INFO @ Tue, 16 Jun 2020 07:54:57: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (1777 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 07:54:59: 1000000 INFO @ Tue, 16 Jun 2020 07:55:04: 2000000 INFO @ Tue, 16 Jun 2020 07:55:10: 3000000 INFO @ Tue, 16 Jun 2020 07:55:14: #1 tag size is determined as 50 bps INFO @ Tue, 16 Jun 2020 07:55:14: #1 tag size = 50 INFO @ Tue, 16 Jun 2020 07:55:14: #1 total tags in treatment: 3618607 INFO @ Tue, 16 Jun 2020 07:55:14: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 07:55:14: #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 07:55:14: #1 tags after filtering in treatment: 3618607 INFO @ Tue, 16 Jun 2020 07:55:14: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 07:55:14: #1 finished! INFO @ Tue, 16 Jun 2020 07:55:14: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 07:55:14: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 07:55:14: #2 number of paired peaks: 1755 INFO @ Tue, 16 Jun 2020 07:55:14: start model_add_line... INFO @ Tue, 16 Jun 2020 07:55:14: start X-correlation... INFO @ Tue, 16 Jun 2020 07:55:14: end of X-cor INFO @ Tue, 16 Jun 2020 07:55:14: #2 finished! INFO @ Tue, 16 Jun 2020 07:55:14: #2 predicted fragment length is 318 bps INFO @ Tue, 16 Jun 2020 07:55:14: #2 alternative fragment length(s) may be 318 bps INFO @ Tue, 16 Jun 2020 07:55:14: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX208772/SRX208772.10_model.r INFO @ Tue, 16 Jun 2020 07:55:14: #3 Call peaks... INFO @ Tue, 16 Jun 2020 07:55:14: #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 07:55:23: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 07:55:23: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX208772/SRX208772.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX208772/SRX208772.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX208772/SRX208772.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX208772/SRX208772.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 07:55:23: #1 read tag files... INFO @ Tue, 16 Jun 2020 07:55:23: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 07:55:27: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX208772/SRX208772.10_peaks.xls INFO @ Tue, 16 Jun 2020 07:55:27: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX208772/SRX208772.10_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 07:55:27: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX208772/SRX208772.10_summits.bed INFO @ Tue, 16 Jun 2020 07:55:27: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (1410 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 07:55:29: 1000000 INFO @ Tue, 16 Jun 2020 07:55:35: 2000000 INFO @ Tue, 16 Jun 2020 07:55:40: 3000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 16 Jun 2020 07:55:44: #1 tag size is determined as 50 bps INFO @ Tue, 16 Jun 2020 07:55:44: #1 tag size = 50 INFO @ Tue, 16 Jun 2020 07:55:44: #1 total tags in treatment: 3618607 INFO @ Tue, 16 Jun 2020 07:55:44: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 07:55:44: #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 07:55:44: #1 tags after filtering in treatment: 3618607 INFO @ Tue, 16 Jun 2020 07:55:44: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 07:55:44: #1 finished! INFO @ Tue, 16 Jun 2020 07:55:44: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 07:55:44: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 07:55:44: #2 number of paired peaks: 1755 INFO @ Tue, 16 Jun 2020 07:55:44: start model_add_line... INFO @ Tue, 16 Jun 2020 07:55:44: start X-correlation... INFO @ Tue, 16 Jun 2020 07:55:44: end of X-cor INFO @ Tue, 16 Jun 2020 07:55:44: #2 finished! INFO @ Tue, 16 Jun 2020 07:55:44: #2 predicted fragment length is 318 bps INFO @ Tue, 16 Jun 2020 07:55:44: #2 alternative fragment length(s) may be 318 bps INFO @ Tue, 16 Jun 2020 07:55:44: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX208772/SRX208772.20_model.r INFO @ Tue, 16 Jun 2020 07:55:44: #3 Call peaks... INFO @ Tue, 16 Jun 2020 07:55:44: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Tue, 16 Jun 2020 07:55:53: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 07:55:58: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX208772/SRX208772.20_peaks.xls INFO @ Tue, 16 Jun 2020 07:55:58: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX208772/SRX208772.20_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 07:55:58: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX208772/SRX208772.20_summits.bed INFO @ Tue, 16 Jun 2020 07:55:58: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (1104 records, 4 fields): 4 millis CompletedMACS2peakCalling