Job ID = 6367110 SRX = SRX277067 Genome = ce11 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-15T23:32:35 prefetch.2.10.7: 1) Downloading 'SRR849743'... 2020-06-15T23:32:35 prefetch.2.10.7: Downloading via HTTPS... 2020-06-15T23:33:15 prefetch.2.10.7: HTTPS download succeed 2020-06-15T23:33:16 prefetch.2.10.7: 'SRR849743' is valid 2020-06-15T23:33:16 prefetch.2.10.7: 1) 'SRR849743' was downloaded successfully Read 6872898 spots for SRR849743/SRR849743.sra Written 6872898 spots for SRR849743/SRR849743.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: 00:01:01 6872898 reads; of these: 6872898 (100.00%) were unpaired; of these: 943084 (13.72%) aligned 0 times 4898366 (71.27%) aligned exactly 1 time 1031448 (15.01%) aligned >1 times 86.28% overall alignment rate Time searching: 00:01:01 Overall time: 00:01:01 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] 574716 / 5929814 = 0.0969 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 08:36:32: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX277067/SRX277067.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX277067/SRX277067.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX277067/SRX277067.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX277067/SRX277067.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 08:36:32: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:36:32: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:36:37: 1000000 INFO @ Tue, 16 Jun 2020 08:36:43: 2000000 INFO @ Tue, 16 Jun 2020 08:36:49: 3000000 INFO @ Tue, 16 Jun 2020 08:36:54: 4000000 INFO @ Tue, 16 Jun 2020 08:36:59: 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 08:37:01: #1 tag size is determined as 32 bps INFO @ Tue, 16 Jun 2020 08:37:01: #1 tag size = 32 INFO @ Tue, 16 Jun 2020 08:37:01: #1 total tags in treatment: 5355098 INFO @ Tue, 16 Jun 2020 08:37:01: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:37:01: #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 08:37:01: #1 tags after filtering in treatment: 5355098 INFO @ Tue, 16 Jun 2020 08:37:01: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:37:01: #1 finished! INFO @ Tue, 16 Jun 2020 08:37:01: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:37:01: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:37:02: #2 number of paired peaks: 1126 INFO @ Tue, 16 Jun 2020 08:37:02: start model_add_line... INFO @ Tue, 16 Jun 2020 08:37:02: start X-correlation... INFO @ Tue, 16 Jun 2020 08:37:02: end of X-cor INFO @ Tue, 16 Jun 2020 08:37:02: #2 finished! INFO @ Tue, 16 Jun 2020 08:37:02: #2 predicted fragment length is 139 bps INFO @ Tue, 16 Jun 2020 08:37:02: #2 alternative fragment length(s) may be 139 bps INFO @ Tue, 16 Jun 2020 08:37:02: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX277067/SRX277067.05_model.r INFO @ Tue, 16 Jun 2020 08:37:02: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:37:02: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 08:37:02: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX277067/SRX277067.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX277067/SRX277067.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX277067/SRX277067.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX277067/SRX277067.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 08:37:02: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:37:02: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:37:07: 1000000 INFO @ Tue, 16 Jun 2020 08:37:12: 2000000 INFO @ Tue, 16 Jun 2020 08:37:14: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 08:37:18: 3000000 INFO @ Tue, 16 Jun 2020 08:37:20: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX277067/SRX277067.05_peaks.xls INFO @ Tue, 16 Jun 2020 08:37:20: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX277067/SRX277067.05_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:37:20: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX277067/SRX277067.05_summits.bed INFO @ Tue, 16 Jun 2020 08:37:20: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (2351 records, 4 fields): 4 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 08:37:23: 4000000 INFO @ Tue, 16 Jun 2020 08:37:28: 5000000 BedGraph に変換中... INFO @ Tue, 16 Jun 2020 08:37:30: #1 tag size is determined as 32 bps INFO @ Tue, 16 Jun 2020 08:37:30: #1 tag size = 32 INFO @ Tue, 16 Jun 2020 08:37:30: #1 total tags in treatment: 5355098 INFO @ Tue, 16 Jun 2020 08:37:30: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:37:30: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) 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 08:37:30: #1 tags after filtering in treatment: 5355098 INFO @ Tue, 16 Jun 2020 08:37:30: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:37:30: #1 finished! INFO @ Tue, 16 Jun 2020 08:37:30: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:37:30: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:37:30: #2 number of paired peaks: 1126 INFO @ Tue, 16 Jun 2020 08:37:30: start model_add_line... INFO @ Tue, 16 Jun 2020 08:37:30: start X-correlation... INFO @ Tue, 16 Jun 2020 08:37:30: end of X-cor INFO @ Tue, 16 Jun 2020 08:37:30: #2 finished! INFO @ Tue, 16 Jun 2020 08:37:30: #2 predicted fragment length is 139 bps INFO @ Tue, 16 Jun 2020 08:37:30: #2 alternative fragment length(s) may be 139 bps INFO @ Tue, 16 Jun 2020 08:37:30: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX277067/SRX277067.10_model.r INFO @ Tue, 16 Jun 2020 08:37:30: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:37:30: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 08:37:32: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX277067/SRX277067.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX277067/SRX277067.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX277067/SRX277067.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX277067/SRX277067.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 08:37:32: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:37:32: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:37:38: 1000000 INFO @ Tue, 16 Jun 2020 08:37:43: 2000000 INFO @ Tue, 16 Jun 2020 08:37:43: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 08:37:48: 3000000 INFO @ Tue, 16 Jun 2020 08:37:49: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX277067/SRX277067.10_peaks.xls INFO @ Tue, 16 Jun 2020 08:37:49: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX277067/SRX277067.10_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:37:49: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX277067/SRX277067.10_summits.bed INFO @ Tue, 16 Jun 2020 08:37:49: Done! pass1 - making usageList (7 chroms): 0 millis pass2 - checking and writing primary data (1354 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 08:37:54: 4000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 16 Jun 2020 08:37:59: 5000000 INFO @ Tue, 16 Jun 2020 08:38:01: #1 tag size is determined as 32 bps INFO @ Tue, 16 Jun 2020 08:38:01: #1 tag size = 32 INFO @ Tue, 16 Jun 2020 08:38:01: #1 total tags in treatment: 5355098 INFO @ Tue, 16 Jun 2020 08:38:01: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:38:01: #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 08:38:01: #1 tags after filtering in treatment: 5355098 INFO @ Tue, 16 Jun 2020 08:38:01: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:38:01: #1 finished! INFO @ Tue, 16 Jun 2020 08:38:01: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:38:01: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:38:01: #2 number of paired peaks: 1126 INFO @ Tue, 16 Jun 2020 08:38:01: start model_add_line... INFO @ Tue, 16 Jun 2020 08:38:01: start X-correlation... INFO @ Tue, 16 Jun 2020 08:38:01: end of X-cor INFO @ Tue, 16 Jun 2020 08:38:01: #2 finished! INFO @ Tue, 16 Jun 2020 08:38:01: #2 predicted fragment length is 139 bps INFO @ Tue, 16 Jun 2020 08:38:01: #2 alternative fragment length(s) may be 139 bps INFO @ Tue, 16 Jun 2020 08:38:01: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX277067/SRX277067.20_model.r INFO @ Tue, 16 Jun 2020 08:38:02: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:38:02: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Tue, 16 Jun 2020 08:38:14: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 08:38:20: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX277067/SRX277067.20_peaks.xls INFO @ Tue, 16 Jun 2020 08:38:20: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX277067/SRX277067.20_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:38:20: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX277067/SRX277067.20_summits.bed INFO @ Tue, 16 Jun 2020 08:38:20: Done! pass1 - making usageList (7 chroms): 0 millis pass2 - checking and writing primary data (699 records, 4 fields): 3 millis CompletedMACS2peakCalling