Job ID = 6366663 SRX = SRX216764 Genome = ce11 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-15T23:00:08 prefetch.2.10.7: 1) Downloading 'SRR648398'... 2020-06-15T23:00:08 prefetch.2.10.7: Downloading via HTTPS... 2020-06-15T23:02:03 prefetch.2.10.7: HTTPS download succeed 2020-06-15T23:02:03 prefetch.2.10.7: 1) 'SRR648398' was downloaded successfully Read 25457393 spots for SRR648398/SRR648398.sra Written 25457393 spots for SRR648398/SRR648398.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: 00:04:30 25457393 reads; of these: 25457393 (100.00%) were unpaired; of these: 5622774 (22.09%) aligned 0 times 17804644 (69.94%) aligned exactly 1 time 2029975 (7.97%) aligned >1 times 77.91% overall alignment rate Time searching: 00:04:30 Overall time: 00:04:30 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 12 files... [bam_rmdupse_core] 5466601 / 19834619 = 0.2756 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 08:12:16: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX216764/SRX216764.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX216764/SRX216764.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX216764/SRX216764.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX216764/SRX216764.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 08:12:16: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:12:16: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:12:22: 1000000 INFO @ Tue, 16 Jun 2020 08:12:27: 2000000 INFO @ Tue, 16 Jun 2020 08:12:32: 3000000 INFO @ Tue, 16 Jun 2020 08:12:37: 4000000 INFO @ Tue, 16 Jun 2020 08:12:42: 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 08:12:46: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX216764/SRX216764.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX216764/SRX216764.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX216764/SRX216764.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX216764/SRX216764.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 08:12:46: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:12:46: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:12:48: 6000000 INFO @ Tue, 16 Jun 2020 08:12:53: 1000000 INFO @ Tue, 16 Jun 2020 08:12:54: 7000000 INFO @ Tue, 16 Jun 2020 08:12:59: 2000000 INFO @ Tue, 16 Jun 2020 08:13:00: 8000000 INFO @ Tue, 16 Jun 2020 08:13:06: 9000000 INFO @ Tue, 16 Jun 2020 08:13:06: 3000000 INFO @ Tue, 16 Jun 2020 08:13:12: 10000000 INFO @ Tue, 16 Jun 2020 08:13:13: 4000000 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 08:13:16: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX216764/SRX216764.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX216764/SRX216764.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX216764/SRX216764.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX216764/SRX216764.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 08:13:16: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:13:16: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:13:17: 11000000 INFO @ Tue, 16 Jun 2020 08:13:20: 5000000 INFO @ Tue, 16 Jun 2020 08:13:22: 1000000 INFO @ Tue, 16 Jun 2020 08:13:23: 12000000 INFO @ Tue, 16 Jun 2020 08:13:27: 6000000 INFO @ Tue, 16 Jun 2020 08:13:28: 2000000 INFO @ Tue, 16 Jun 2020 08:13:29: 13000000 INFO @ Tue, 16 Jun 2020 08:13:34: 3000000 INFO @ Tue, 16 Jun 2020 08:13:34: 7000000 INFO @ Tue, 16 Jun 2020 08:13:36: 14000000 INFO @ Tue, 16 Jun 2020 08:13:38: #1 tag size is determined as 50 bps INFO @ Tue, 16 Jun 2020 08:13:38: #1 tag size = 50 INFO @ Tue, 16 Jun 2020 08:13:38: #1 total tags in treatment: 14368018 INFO @ Tue, 16 Jun 2020 08:13:38: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:13:38: #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 08:13:38: #1 tags after filtering in treatment: 14368018 INFO @ Tue, 16 Jun 2020 08:13:38: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:13:38: #1 finished! INFO @ Tue, 16 Jun 2020 08:13:38: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:13:38: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:13:39: #2 number of paired peaks: 841 WARNING @ Tue, 16 Jun 2020 08:13:39: Fewer paired peaks (841) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 841 pairs to build model! INFO @ Tue, 16 Jun 2020 08:13:39: start model_add_line... INFO @ Tue, 16 Jun 2020 08:13:39: start X-correlation... INFO @ Tue, 16 Jun 2020 08:13:39: end of X-cor INFO @ Tue, 16 Jun 2020 08:13:39: #2 finished! INFO @ Tue, 16 Jun 2020 08:13:39: #2 predicted fragment length is 164 bps INFO @ Tue, 16 Jun 2020 08:13:39: #2 alternative fragment length(s) may be 4,164 bps INFO @ Tue, 16 Jun 2020 08:13:39: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX216764/SRX216764.05_model.r INFO @ Tue, 16 Jun 2020 08:13:39: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:13:39: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 08:13:40: 4000000 INFO @ Tue, 16 Jun 2020 08:13:41: 8000000 INFO @ Tue, 16 Jun 2020 08:13:46: 5000000 INFO @ Tue, 16 Jun 2020 08:13:48: 9000000 INFO @ Tue, 16 Jun 2020 08:13:52: 6000000 INFO @ Tue, 16 Jun 2020 08:13:55: 10000000 INFO @ Tue, 16 Jun 2020 08:13:58: 7000000 INFO @ Tue, 16 Jun 2020 08:14:02: 11000000 INFO @ Tue, 16 Jun 2020 08:14:04: 8000000 INFO @ Tue, 16 Jun 2020 08:14:09: 12000000 INFO @ Tue, 16 Jun 2020 08:14:10: 9000000 INFO @ Tue, 16 Jun 2020 08:14:14: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 08:14:16: 13000000 INFO @ Tue, 16 Jun 2020 08:14:16: 10000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 16 Jun 2020 08:14:22: 11000000 INFO @ Tue, 16 Jun 2020 08:14:23: 14000000 INFO @ Tue, 16 Jun 2020 08:14:25: #1 tag size is determined as 50 bps INFO @ Tue, 16 Jun 2020 08:14:25: #1 tag size = 50 INFO @ Tue, 16 Jun 2020 08:14:25: #1 total tags in treatment: 14368018 INFO @ Tue, 16 Jun 2020 08:14:25: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:14:25: #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 08:14:25: #1 tags after filtering in treatment: 14368018 INFO @ Tue, 16 Jun 2020 08:14:25: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:14:25: #1 finished! INFO @ Tue, 16 Jun 2020 08:14:25: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:14:25: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:14:26: #2 number of paired peaks: 841 WARNING @ Tue, 16 Jun 2020 08:14:26: Fewer paired peaks (841) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 841 pairs to build model! INFO @ Tue, 16 Jun 2020 08:14:26: start model_add_line... INFO @ Tue, 16 Jun 2020 08:14:26: start X-correlation... INFO @ Tue, 16 Jun 2020 08:14:27: end of X-cor INFO @ Tue, 16 Jun 2020 08:14:27: #2 finished! INFO @ Tue, 16 Jun 2020 08:14:27: #2 predicted fragment length is 164 bps INFO @ Tue, 16 Jun 2020 08:14:27: #2 alternative fragment length(s) may be 4,164 bps INFO @ Tue, 16 Jun 2020 08:14:27: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX216764/SRX216764.10_model.r INFO @ Tue, 16 Jun 2020 08:14:27: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:14:27: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 08:14:28: 12000000 INFO @ Tue, 16 Jun 2020 08:14:32: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX216764/SRX216764.05_peaks.xls INFO @ Tue, 16 Jun 2020 08:14:32: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX216764/SRX216764.05_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:14:32: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX216764/SRX216764.05_summits.bed INFO @ Tue, 16 Jun 2020 08:14:32: Done! INFO @ Tue, 16 Jun 2020 08:14:33: 13000000 pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (5941 records, 4 fields): 6 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 08:14:38: 14000000 INFO @ Tue, 16 Jun 2020 08:14:40: #1 tag size is determined as 50 bps INFO @ Tue, 16 Jun 2020 08:14:40: #1 tag size = 50 INFO @ Tue, 16 Jun 2020 08:14:40: #1 total tags in treatment: 14368018 INFO @ Tue, 16 Jun 2020 08:14:40: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:14:40: #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 08:14:40: #1 tags after filtering in treatment: 14368018 INFO @ Tue, 16 Jun 2020 08:14:40: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:14:40: #1 finished! INFO @ Tue, 16 Jun 2020 08:14:40: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:14:40: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:14:41: #2 number of paired peaks: 841 WARNING @ Tue, 16 Jun 2020 08:14:41: Fewer paired peaks (841) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 841 pairs to build model! INFO @ Tue, 16 Jun 2020 08:14:41: start model_add_line... INFO @ Tue, 16 Jun 2020 08:14:41: start X-correlation... INFO @ Tue, 16 Jun 2020 08:14:41: end of X-cor INFO @ Tue, 16 Jun 2020 08:14:41: #2 finished! INFO @ Tue, 16 Jun 2020 08:14:41: #2 predicted fragment length is 164 bps INFO @ Tue, 16 Jun 2020 08:14:41: #2 alternative fragment length(s) may be 4,164 bps INFO @ Tue, 16 Jun 2020 08:14:41: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX216764/SRX216764.20_model.r INFO @ Tue, 16 Jun 2020 08:14:42: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:14:42: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Tue, 16 Jun 2020 08:14:59: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 08:15:13: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 08:15:16: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX216764/SRX216764.10_peaks.xls INFO @ Tue, 16 Jun 2020 08:15:16: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX216764/SRX216764.10_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:15:16: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX216764/SRX216764.10_summits.bed INFO @ Tue, 16 Jun 2020 08:15:16: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (3587 records, 4 fields): 4 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 08:15:28: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX216764/SRX216764.20_peaks.xls INFO @ Tue, 16 Jun 2020 08:15:28: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX216764/SRX216764.20_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:15:28: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX216764/SRX216764.20_summits.bed INFO @ Tue, 16 Jun 2020 08:15:28: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (1688 records, 4 fields): 2 millis CompletedMACS2peakCalling