Job ID = 6366412 SRX = SRX146419 Genome = ce11 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-15T22:38:36 prefetch.2.10.7: 1) Downloading 'SRR494580'... 2020-06-15T22:38:36 prefetch.2.10.7: Downloading via HTTPS... 2020-06-15T22:39:07 prefetch.2.10.7: HTTPS download succeed 2020-06-15T22:39:07 prefetch.2.10.7: 'SRR494580' is valid 2020-06-15T22:39:07 prefetch.2.10.7: 1) 'SRR494580' was downloaded successfully Read 4285635 spots for SRR494580/SRR494580.sra Written 4285635 spots for SRR494580/SRR494580.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: 00:00:45 4285635 reads; of these: 4285635 (100.00%) were unpaired; of these: 186328 (4.35%) aligned 0 times 3447259 (80.44%) aligned exactly 1 time 652048 (15.21%) aligned >1 times 95.65% overall alignment rate Time searching: 00:00:45 Overall time: 00:00:45 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] 324013 / 4099307 = 0.0790 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 07:41:20: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX146419/SRX146419.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX146419/SRX146419.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX146419/SRX146419.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX146419/SRX146419.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 07:41:20: #1 read tag files... INFO @ Tue, 16 Jun 2020 07:41:20: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 07:41:24: 1000000 INFO @ Tue, 16 Jun 2020 07:41:29: 2000000 INFO @ Tue, 16 Jun 2020 07:41:34: 3000000 INFO @ Tue, 16 Jun 2020 07:41:37: #1 tag size is determined as 32 bps INFO @ Tue, 16 Jun 2020 07:41:37: #1 tag size = 32 INFO @ Tue, 16 Jun 2020 07:41:37: #1 total tags in treatment: 3775294 INFO @ Tue, 16 Jun 2020 07:41:37: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 07:41:37: #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 07:41:37: #1 tags after filtering in treatment: 3775294 INFO @ Tue, 16 Jun 2020 07:41:37: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 07:41:37: #1 finished! INFO @ Tue, 16 Jun 2020 07:41:37: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 07:41:37: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 07:41:37: #2 number of paired peaks: 827 WARNING @ Tue, 16 Jun 2020 07:41:37: Fewer paired peaks (827) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 827 pairs to build model! INFO @ Tue, 16 Jun 2020 07:41:37: start model_add_line... INFO @ Tue, 16 Jun 2020 07:41:37: start X-correlation... INFO @ Tue, 16 Jun 2020 07:41:37: end of X-cor INFO @ Tue, 16 Jun 2020 07:41:37: #2 finished! INFO @ Tue, 16 Jun 2020 07:41:37: #2 predicted fragment length is 146 bps INFO @ Tue, 16 Jun 2020 07:41:37: #2 alternative fragment length(s) may be 146 bps INFO @ Tue, 16 Jun 2020 07:41:37: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX146419/SRX146419.05_model.r INFO @ Tue, 16 Jun 2020 07:41:37: #3 Call peaks... INFO @ Tue, 16 Jun 2020 07:41:37: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 07:41:46: #3 Call peaks for each chromosome... 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 07:41:50: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX146419/SRX146419.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX146419/SRX146419.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX146419/SRX146419.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX146419/SRX146419.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 07:41:50: #1 read tag files... INFO @ Tue, 16 Jun 2020 07:41:50: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 07:41:50: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX146419/SRX146419.05_peaks.xls INFO @ Tue, 16 Jun 2020 07:41:50: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX146419/SRX146419.05_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 07:41:50: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX146419/SRX146419.05_summits.bed INFO @ Tue, 16 Jun 2020 07:41:50: Done! pass1 - making usageList (7 chroms): 0 millis pass2 - checking and writing primary data (1672 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 07:41:54: 1000000 INFO @ Tue, 16 Jun 2020 07:41:59: 2000000 INFO @ Tue, 16 Jun 2020 07:42:04: 3000000 INFO @ Tue, 16 Jun 2020 07:42:07: #1 tag size is determined as 32 bps INFO @ Tue, 16 Jun 2020 07:42:07: #1 tag size = 32 INFO @ Tue, 16 Jun 2020 07:42:07: #1 total tags in treatment: 3775294 INFO @ Tue, 16 Jun 2020 07:42:07: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 07:42:07: #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 07:42:07: #1 tags after filtering in treatment: 3775294 INFO @ Tue, 16 Jun 2020 07:42:07: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 07:42:07: #1 finished! INFO @ Tue, 16 Jun 2020 07:42:07: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 07:42:07: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 07:42:08: #2 number of paired peaks: 827 WARNING @ Tue, 16 Jun 2020 07:42:08: Fewer paired peaks (827) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 827 pairs to build model! INFO @ Tue, 16 Jun 2020 07:42:08: start model_add_line... INFO @ Tue, 16 Jun 2020 07:42:08: start X-correlation... INFO @ Tue, 16 Jun 2020 07:42:08: end of X-cor INFO @ Tue, 16 Jun 2020 07:42:08: #2 finished! INFO @ Tue, 16 Jun 2020 07:42:08: #2 predicted fragment length is 146 bps INFO @ Tue, 16 Jun 2020 07:42:08: #2 alternative fragment length(s) may be 146 bps INFO @ Tue, 16 Jun 2020 07:42:08: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX146419/SRX146419.10_model.r INFO @ Tue, 16 Jun 2020 07:42:08: #3 Call peaks... INFO @ Tue, 16 Jun 2020 07:42:08: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 07:42:16: #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 07:42:20: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX146419/SRX146419.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX146419/SRX146419.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX146419/SRX146419.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX146419/SRX146419.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 07:42:20: #1 read tag files... INFO @ Tue, 16 Jun 2020 07:42:20: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 07:42:20: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX146419/SRX146419.10_peaks.xls INFO @ Tue, 16 Jun 2020 07:42:20: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX146419/SRX146419.10_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 07:42:20: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX146419/SRX146419.10_summits.bed INFO @ Tue, 16 Jun 2020 07:42:20: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (1096 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 07:42:24: 1000000 INFO @ Tue, 16 Jun 2020 07:42:29: 2000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 16 Jun 2020 07:42:34: 3000000 INFO @ Tue, 16 Jun 2020 07:42:38: #1 tag size is determined as 32 bps INFO @ Tue, 16 Jun 2020 07:42:38: #1 tag size = 32 INFO @ Tue, 16 Jun 2020 07:42:38: #1 total tags in treatment: 3775294 INFO @ Tue, 16 Jun 2020 07:42:38: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 07:42:38: #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 07:42:38: #1 tags after filtering in treatment: 3775294 INFO @ Tue, 16 Jun 2020 07:42:38: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 07:42:38: #1 finished! INFO @ Tue, 16 Jun 2020 07:42:38: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 07:42:38: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 07:42:38: #2 number of paired peaks: 827 WARNING @ Tue, 16 Jun 2020 07:42:38: Fewer paired peaks (827) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 827 pairs to build model! INFO @ Tue, 16 Jun 2020 07:42:38: start model_add_line... INFO @ Tue, 16 Jun 2020 07:42:38: start X-correlation... INFO @ Tue, 16 Jun 2020 07:42:38: end of X-cor INFO @ Tue, 16 Jun 2020 07:42:38: #2 finished! INFO @ Tue, 16 Jun 2020 07:42:38: #2 predicted fragment length is 146 bps INFO @ Tue, 16 Jun 2020 07:42:38: #2 alternative fragment length(s) may be 146 bps INFO @ Tue, 16 Jun 2020 07:42:38: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX146419/SRX146419.20_model.r INFO @ Tue, 16 Jun 2020 07:42:38: #3 Call peaks... INFO @ Tue, 16 Jun 2020 07:42:38: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Tue, 16 Jun 2020 07:42:46: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 07:42:50: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX146419/SRX146419.20_peaks.xls INFO @ Tue, 16 Jun 2020 07:42:50: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX146419/SRX146419.20_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 07:42:50: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX146419/SRX146419.20_summits.bed INFO @ Tue, 16 Jun 2020 07:42:50: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (685 records, 4 fields): 2 millis CompletedMACS2peakCalling