Job ID = 6366888 SRX = SRX2543056 Genome = ce11 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-15T23:10:16 prefetch.2.10.7: 1) Downloading 'SRR5235992'... 2020-06-15T23:10:16 prefetch.2.10.7: Downloading via HTTPS... 2020-06-15T23:11:44 prefetch.2.10.7: HTTPS download succeed 2020-06-15T23:11:45 prefetch.2.10.7: 'SRR5235992' is valid 2020-06-15T23:11:45 prefetch.2.10.7: 1) 'SRR5235992' was downloaded successfully 2020-06-15T23:11:45 prefetch.2.10.7: 'SRR5235992' has 0 unresolved dependencies Read 15812347 spots for SRR5235992/SRR5235992.sra Written 15812347 spots for SRR5235992/SRR5235992.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: 00:05:20 15812347 reads; of these: 15812347 (100.00%) were unpaired; of these: 3262336 (20.63%) aligned 0 times 10511972 (66.48%) aligned exactly 1 time 2038039 (12.89%) aligned >1 times 79.37% overall alignment rate Time searching: 00:05:20 Overall time: 00:05:20 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] 3061832 / 12550011 = 0.2440 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 08:21:30: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX2543056/SRX2543056.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX2543056/SRX2543056.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX2543056/SRX2543056.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX2543056/SRX2543056.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 08:21:30: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:21:30: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:21:36: 1000000 INFO @ Tue, 16 Jun 2020 08:21:42: 2000000 INFO @ Tue, 16 Jun 2020 08:21:48: 3000000 INFO @ Tue, 16 Jun 2020 08:21:55: 4000000 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 08:22:00: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX2543056/SRX2543056.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX2543056/SRX2543056.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX2543056/SRX2543056.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX2543056/SRX2543056.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 08:22:00: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:22:00: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:22:01: 5000000 INFO @ Tue, 16 Jun 2020 08:22:06: 1000000 INFO @ Tue, 16 Jun 2020 08:22:08: 6000000 INFO @ Tue, 16 Jun 2020 08:22:12: 2000000 INFO @ Tue, 16 Jun 2020 08:22:14: 7000000 INFO @ Tue, 16 Jun 2020 08:22:17: 3000000 INFO @ Tue, 16 Jun 2020 08:22:21: 8000000 INFO @ Tue, 16 Jun 2020 08:22:23: 4000000 INFO @ Tue, 16 Jun 2020 08:22:28: 9000000 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 08:22:29: 5000000 INFO @ Tue, 16 Jun 2020 08:22:30: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX2543056/SRX2543056.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX2543056/SRX2543056.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX2543056/SRX2543056.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX2543056/SRX2543056.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 08:22:30: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:22:30: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:22:31: #1 tag size is determined as 75 bps INFO @ Tue, 16 Jun 2020 08:22:31: #1 tag size = 75 INFO @ Tue, 16 Jun 2020 08:22:31: #1 total tags in treatment: 9488179 INFO @ Tue, 16 Jun 2020 08:22:31: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:22:31: #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 08:22:31: #1 tags after filtering in treatment: 9488179 INFO @ Tue, 16 Jun 2020 08:22:31: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:22:31: #1 finished! INFO @ Tue, 16 Jun 2020 08:22:31: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:22:31: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:22:32: #2 number of paired peaks: 572 WARNING @ Tue, 16 Jun 2020 08:22:32: Fewer paired peaks (572) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 572 pairs to build model! INFO @ Tue, 16 Jun 2020 08:22:32: start model_add_line... INFO @ Tue, 16 Jun 2020 08:22:32: start X-correlation... INFO @ Tue, 16 Jun 2020 08:22:32: end of X-cor INFO @ Tue, 16 Jun 2020 08:22:32: #2 finished! INFO @ Tue, 16 Jun 2020 08:22:32: #2 predicted fragment length is 180 bps INFO @ Tue, 16 Jun 2020 08:22:32: #2 alternative fragment length(s) may be 4,167,180 bps INFO @ Tue, 16 Jun 2020 08:22:32: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX2543056/SRX2543056.05_model.r INFO @ Tue, 16 Jun 2020 08:22:32: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:22:32: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 08:22:35: 6000000 INFO @ Tue, 16 Jun 2020 08:22:36: 1000000 INFO @ Tue, 16 Jun 2020 08:22:41: 7000000 INFO @ Tue, 16 Jun 2020 08:22:41: 2000000 INFO @ Tue, 16 Jun 2020 08:22:47: 8000000 INFO @ Tue, 16 Jun 2020 08:22:47: 3000000 INFO @ Tue, 16 Jun 2020 08:22:53: 9000000 INFO @ Tue, 16 Jun 2020 08:22:53: 4000000 INFO @ Tue, 16 Jun 2020 08:22:55: #1 tag size is determined as 75 bps INFO @ Tue, 16 Jun 2020 08:22:55: #1 tag size = 75 INFO @ Tue, 16 Jun 2020 08:22:55: #1 total tags in treatment: 9488179 INFO @ Tue, 16 Jun 2020 08:22:55: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:22:55: #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 08:22:56: #1 tags after filtering in treatment: 9488179 INFO @ Tue, 16 Jun 2020 08:22:56: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:22:56: #1 finished! INFO @ Tue, 16 Jun 2020 08:22:56: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:22:56: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:22:56: #2 number of paired peaks: 572 WARNING @ Tue, 16 Jun 2020 08:22:56: Fewer paired peaks (572) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 572 pairs to build model! INFO @ Tue, 16 Jun 2020 08:22:56: start model_add_line... INFO @ Tue, 16 Jun 2020 08:22:56: start X-correlation... INFO @ Tue, 16 Jun 2020 08:22:56: end of X-cor INFO @ Tue, 16 Jun 2020 08:22:56: #2 finished! INFO @ Tue, 16 Jun 2020 08:22:56: #2 predicted fragment length is 180 bps INFO @ Tue, 16 Jun 2020 08:22:56: #2 alternative fragment length(s) may be 4,167,180 bps INFO @ Tue, 16 Jun 2020 08:22:56: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX2543056/SRX2543056.10_model.r INFO @ Tue, 16 Jun 2020 08:22:56: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:22:56: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 08:22:57: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 08:22:58: 5000000 INFO @ Tue, 16 Jun 2020 08:23:04: 6000000 INFO @ Tue, 16 Jun 2020 08:23:08: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX2543056/SRX2543056.05_peaks.xls INFO @ Tue, 16 Jun 2020 08:23:08: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX2543056/SRX2543056.05_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:23:08: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX2543056/SRX2543056.05_summits.bed INFO @ Tue, 16 Jun 2020 08:23:08: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (2004 records, 4 fields): 4 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 08:23:09: 7000000 INFO @ Tue, 16 Jun 2020 08:23:15: 8000000 INFO @ Tue, 16 Jun 2020 08:23:20: 9000000 INFO @ Tue, 16 Jun 2020 08:23:20: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 08:23:23: #1 tag size is determined as 75 bps INFO @ Tue, 16 Jun 2020 08:23:23: #1 tag size = 75 INFO @ Tue, 16 Jun 2020 08:23:23: #1 total tags in treatment: 9488179 INFO @ Tue, 16 Jun 2020 08:23:23: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:23:23: #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 08:23:23: #1 tags after filtering in treatment: 9488179 INFO @ Tue, 16 Jun 2020 08:23:23: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:23:23: #1 finished! INFO @ Tue, 16 Jun 2020 08:23:23: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:23:23: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:23:24: #2 number of paired peaks: 572 WARNING @ Tue, 16 Jun 2020 08:23:24: Fewer paired peaks (572) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 572 pairs to build model! INFO @ Tue, 16 Jun 2020 08:23:24: start model_add_line... INFO @ Tue, 16 Jun 2020 08:23:24: start X-correlation... INFO @ Tue, 16 Jun 2020 08:23:24: end of X-cor INFO @ Tue, 16 Jun 2020 08:23:24: #2 finished! INFO @ Tue, 16 Jun 2020 08:23:24: #2 predicted fragment length is 180 bps INFO @ Tue, 16 Jun 2020 08:23:24: #2 alternative fragment length(s) may be 4,167,180 bps INFO @ Tue, 16 Jun 2020 08:23:24: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX2543056/SRX2543056.20_model.r INFO @ Tue, 16 Jun 2020 08:23:24: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:23:24: #3 Pre-compute pvalue-qvalue table... BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 16 Jun 2020 08:23:32: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX2543056/SRX2543056.10_peaks.xls INFO @ Tue, 16 Jun 2020 08:23:32: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX2543056/SRX2543056.10_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:23:32: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX2543056/SRX2543056.10_summits.bed INFO @ Tue, 16 Jun 2020 08:23:32: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (911 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 08:23:46: #3 Call peaks for each chromosome... BigWig に変換しました。 INFO @ Tue, 16 Jun 2020 08:23:57: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX2543056/SRX2543056.20_peaks.xls INFO @ Tue, 16 Jun 2020 08:23:57: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX2543056/SRX2543056.20_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:23:57: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX2543056/SRX2543056.20_summits.bed INFO @ Tue, 16 Jun 2020 08:23:57: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (389 records, 4 fields): 2 millis CompletedMACS2peakCalling