Job ID = 6366528 SRX = SRX1769983 Genome = ce11 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-15T22:53:11 prefetch.2.10.7: 1) Downloading 'SRR3535760'... 2020-06-15T22:53:11 prefetch.2.10.7: Downloading via HTTPS... 2020-06-15T22:54:30 prefetch.2.10.7: HTTPS download succeed 2020-06-15T22:54:31 prefetch.2.10.7: 'SRR3535760' is valid 2020-06-15T22:54:31 prefetch.2.10.7: 1) 'SRR3535760' was downloaded successfully Read 19445923 spots for SRR3535760/SRR3535760.sra Written 19445923 spots for SRR3535760/SRR3535760.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: 00:01:52 19445923 reads; of these: 19445923 (100.00%) were unpaired; of these: 15410490 (79.25%) aligned 0 times 3356368 (17.26%) aligned exactly 1 time 679065 (3.49%) aligned >1 times 20.75% overall alignment rate Time searching: 00:01:52 Overall time: 00:01:52 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] 828959 / 4035433 = 0.2054 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 07:58:55: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX1769983/SRX1769983.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX1769983/SRX1769983.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX1769983/SRX1769983.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX1769983/SRX1769983.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 07:58:55: #1 read tag files... INFO @ Tue, 16 Jun 2020 07:58:55: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 07:59:01: 1000000 INFO @ Tue, 16 Jun 2020 07:59:07: 2000000 INFO @ Tue, 16 Jun 2020 07:59:13: 3000000 INFO @ Tue, 16 Jun 2020 07:59:14: #1 tag size is determined as 51 bps INFO @ Tue, 16 Jun 2020 07:59:14: #1 tag size = 51 INFO @ Tue, 16 Jun 2020 07:59:14: #1 total tags in treatment: 3206474 INFO @ Tue, 16 Jun 2020 07:59:14: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 07:59:14: #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 07:59:14: #1 tags after filtering in treatment: 3206474 INFO @ Tue, 16 Jun 2020 07:59:14: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 07:59:14: #1 finished! INFO @ Tue, 16 Jun 2020 07:59:14: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 07:59:14: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 07:59:15: #2 number of paired peaks: 878 WARNING @ Tue, 16 Jun 2020 07:59:15: Fewer paired peaks (878) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 878 pairs to build model! INFO @ Tue, 16 Jun 2020 07:59:15: start model_add_line... INFO @ Tue, 16 Jun 2020 07:59:15: start X-correlation... INFO @ Tue, 16 Jun 2020 07:59:15: end of X-cor INFO @ Tue, 16 Jun 2020 07:59:15: #2 finished! INFO @ Tue, 16 Jun 2020 07:59:15: #2 predicted fragment length is 172 bps INFO @ Tue, 16 Jun 2020 07:59:15: #2 alternative fragment length(s) may be 172 bps INFO @ Tue, 16 Jun 2020 07:59:15: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX1769983/SRX1769983.05_model.r INFO @ Tue, 16 Jun 2020 07:59:15: #3 Call peaks... INFO @ Tue, 16 Jun 2020 07:59:15: #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 07:59:23: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 07:59:25: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX1769983/SRX1769983.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX1769983/SRX1769983.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX1769983/SRX1769983.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX1769983/SRX1769983.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 07:59:25: #1 read tag files... INFO @ Tue, 16 Jun 2020 07:59:25: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 07:59:28: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX1769983/SRX1769983.05_peaks.xls INFO @ Tue, 16 Jun 2020 07:59:28: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX1769983/SRX1769983.05_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 07:59:28: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX1769983/SRX1769983.05_summits.bed INFO @ Tue, 16 Jun 2020 07:59:28: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (1716 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 07:59:30: 1000000 INFO @ Tue, 16 Jun 2020 07:59:36: 2000000 INFO @ Tue, 16 Jun 2020 07:59:42: 3000000 INFO @ Tue, 16 Jun 2020 07:59:43: #1 tag size is determined as 51 bps INFO @ Tue, 16 Jun 2020 07:59:43: #1 tag size = 51 INFO @ Tue, 16 Jun 2020 07:59:43: #1 total tags in treatment: 3206474 INFO @ Tue, 16 Jun 2020 07:59:43: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 07:59:43: #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 07:59:43: #1 tags after filtering in treatment: 3206474 INFO @ Tue, 16 Jun 2020 07:59:43: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 07:59:43: #1 finished! INFO @ Tue, 16 Jun 2020 07:59:43: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 07:59:43: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 07:59:43: #2 number of paired peaks: 878 WARNING @ Tue, 16 Jun 2020 07:59:43: Fewer paired peaks (878) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 878 pairs to build model! INFO @ Tue, 16 Jun 2020 07:59:43: start model_add_line... INFO @ Tue, 16 Jun 2020 07:59:43: start X-correlation... INFO @ Tue, 16 Jun 2020 07:59:43: end of X-cor INFO @ Tue, 16 Jun 2020 07:59:43: #2 finished! INFO @ Tue, 16 Jun 2020 07:59:43: #2 predicted fragment length is 172 bps INFO @ Tue, 16 Jun 2020 07:59:43: #2 alternative fragment length(s) may be 172 bps INFO @ Tue, 16 Jun 2020 07:59:43: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX1769983/SRX1769983.10_model.r INFO @ Tue, 16 Jun 2020 07:59:43: #3 Call peaks... INFO @ Tue, 16 Jun 2020 07:59:43: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 07:59:52: #3 Call peaks for each chromosome... 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 07:59:55: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX1769983/SRX1769983.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX1769983/SRX1769983.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX1769983/SRX1769983.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX1769983/SRX1769983.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 07:59:55: #1 read tag files... INFO @ Tue, 16 Jun 2020 07:59:55: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 07:59:56: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX1769983/SRX1769983.10_peaks.xls INFO @ Tue, 16 Jun 2020 07:59:56: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX1769983/SRX1769983.10_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 07:59:56: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX1769983/SRX1769983.10_summits.bed INFO @ Tue, 16 Jun 2020 07:59:56: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (929 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 08:00:01: 1000000 INFO @ Tue, 16 Jun 2020 08:00:06: 2000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 16 Jun 2020 08:00:12: 3000000 INFO @ Tue, 16 Jun 2020 08:00:13: #1 tag size is determined as 51 bps INFO @ Tue, 16 Jun 2020 08:00:13: #1 tag size = 51 INFO @ Tue, 16 Jun 2020 08:00:13: #1 total tags in treatment: 3206474 INFO @ Tue, 16 Jun 2020 08:00:13: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:00:13: #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 08:00:13: #1 tags after filtering in treatment: 3206474 INFO @ Tue, 16 Jun 2020 08:00:13: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:00:13: #1 finished! INFO @ Tue, 16 Jun 2020 08:00:13: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:00:13: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:00:14: #2 number of paired peaks: 878 WARNING @ Tue, 16 Jun 2020 08:00:14: Fewer paired peaks (878) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 878 pairs to build model! INFO @ Tue, 16 Jun 2020 08:00:14: start model_add_line... INFO @ Tue, 16 Jun 2020 08:00:14: start X-correlation... INFO @ Tue, 16 Jun 2020 08:00:14: end of X-cor INFO @ Tue, 16 Jun 2020 08:00:14: #2 finished! INFO @ Tue, 16 Jun 2020 08:00:14: #2 predicted fragment length is 172 bps INFO @ Tue, 16 Jun 2020 08:00:14: #2 alternative fragment length(s) may be 172 bps INFO @ Tue, 16 Jun 2020 08:00:14: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX1769983/SRX1769983.20_model.r INFO @ Tue, 16 Jun 2020 08:00:14: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:00:14: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Tue, 16 Jun 2020 08:00:22: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 08:00:26: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX1769983/SRX1769983.20_peaks.xls INFO @ Tue, 16 Jun 2020 08:00:26: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX1769983/SRX1769983.20_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:00:26: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX1769983/SRX1769983.20_summits.bed INFO @ Tue, 16 Jun 2020 08:00:26: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (480 records, 4 fields): 1 millis CompletedMACS2peakCalling