Job ID = 6366909 SRX = SRX257654 Genome = ce11 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-15T23:12:01 prefetch.2.10.7: 1) Downloading 'SRR800665'... 2020-06-15T23:12:01 prefetch.2.10.7: Downloading via HTTPS... 2020-06-15T23:13:48 prefetch.2.10.7: HTTPS download succeed 2020-06-15T23:13:49 prefetch.2.10.7: 'SRR800665' is valid 2020-06-15T23:13:49 prefetch.2.10.7: 1) 'SRR800665' was downloaded successfully Read 18930018 spots for SRR800665/SRR800665.sra Written 18930018 spots for SRR800665/SRR800665.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: 00:03:20 18930018 reads; of these: 18930018 (100.00%) were unpaired; of these: 2654963 (14.03%) aligned 0 times 13796615 (72.88%) aligned exactly 1 time 2478440 (13.09%) aligned >1 times 85.97% overall alignment rate Time searching: 00:03:20 Overall time: 00:03:20 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] 5323780 / 16275055 = 0.3271 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 08:22:14: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX257654/SRX257654.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX257654/SRX257654.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX257654/SRX257654.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX257654/SRX257654.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 08:22:14: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:22:14: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:22:21: 1000000 INFO @ Tue, 16 Jun 2020 08:22:28: 2000000 INFO @ Tue, 16 Jun 2020 08:22:36: 3000000 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 08:22:43: 4000000 INFO @ Tue, 16 Jun 2020 08:22:44: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX257654/SRX257654.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX257654/SRX257654.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX257654/SRX257654.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX257654/SRX257654.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 08:22:44: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:22:44: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:22:51: 1000000 INFO @ Tue, 16 Jun 2020 08:22:51: 5000000 INFO @ Tue, 16 Jun 2020 08:22:58: 2000000 INFO @ Tue, 16 Jun 2020 08:23:00: 6000000 INFO @ Tue, 16 Jun 2020 08:23:06: 3000000 INFO @ Tue, 16 Jun 2020 08:23:08: 7000000 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 08:23:13: 4000000 INFO @ Tue, 16 Jun 2020 08:23:14: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX257654/SRX257654.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX257654/SRX257654.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX257654/SRX257654.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX257654/SRX257654.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 08:23:14: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:23:14: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:23:16: 8000000 INFO @ Tue, 16 Jun 2020 08:23:20: 5000000 INFO @ Tue, 16 Jun 2020 08:23:21: 1000000 INFO @ Tue, 16 Jun 2020 08:23:24: 9000000 INFO @ Tue, 16 Jun 2020 08:23:28: 6000000 INFO @ Tue, 16 Jun 2020 08:23:28: 2000000 INFO @ Tue, 16 Jun 2020 08:23:32: 10000000 INFO @ Tue, 16 Jun 2020 08:23:35: 7000000 INFO @ Tue, 16 Jun 2020 08:23:36: 3000000 INFO @ Tue, 16 Jun 2020 08:23:40: #1 tag size is determined as 42 bps INFO @ Tue, 16 Jun 2020 08:23:40: #1 tag size = 42 INFO @ Tue, 16 Jun 2020 08:23:40: #1 total tags in treatment: 10951275 INFO @ Tue, 16 Jun 2020 08:23:40: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:23:40: #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 08:23:40: #1 tags after filtering in treatment: 10951275 INFO @ Tue, 16 Jun 2020 08:23:40: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:23:40: #1 finished! INFO @ Tue, 16 Jun 2020 08:23:40: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:23:40: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:23:41: #2 number of paired peaks: 719 WARNING @ Tue, 16 Jun 2020 08:23:41: Fewer paired peaks (719) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 719 pairs to build model! INFO @ Tue, 16 Jun 2020 08:23:41: start model_add_line... INFO @ Tue, 16 Jun 2020 08:23:41: start X-correlation... INFO @ Tue, 16 Jun 2020 08:23:41: end of X-cor INFO @ Tue, 16 Jun 2020 08:23:41: #2 finished! INFO @ Tue, 16 Jun 2020 08:23:41: #2 predicted fragment length is 218 bps INFO @ Tue, 16 Jun 2020 08:23:41: #2 alternative fragment length(s) may be 218 bps INFO @ Tue, 16 Jun 2020 08:23:41: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX257654/SRX257654.05_model.r INFO @ Tue, 16 Jun 2020 08:23:41: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:23:41: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 08:23:43: 8000000 INFO @ Tue, 16 Jun 2020 08:23:43: 4000000 INFO @ Tue, 16 Jun 2020 08:23:49: 9000000 INFO @ Tue, 16 Jun 2020 08:23:50: 5000000 INFO @ Tue, 16 Jun 2020 08:23:56: 10000000 INFO @ Tue, 16 Jun 2020 08:23:57: 6000000 INFO @ Tue, 16 Jun 2020 08:24:03: #1 tag size is determined as 42 bps INFO @ Tue, 16 Jun 2020 08:24:03: #1 tag size = 42 INFO @ Tue, 16 Jun 2020 08:24:03: #1 total tags in treatment: 10951275 INFO @ Tue, 16 Jun 2020 08:24:03: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:24:03: #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 08:24:03: #1 tags after filtering in treatment: 10951275 INFO @ Tue, 16 Jun 2020 08:24:03: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:24:03: #1 finished! INFO @ Tue, 16 Jun 2020 08:24:03: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:24:03: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:24:03: 7000000 INFO @ Tue, 16 Jun 2020 08:24:04: #2 number of paired peaks: 719 WARNING @ Tue, 16 Jun 2020 08:24:04: Fewer paired peaks (719) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 719 pairs to build model! INFO @ Tue, 16 Jun 2020 08:24:04: start model_add_line... BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 16 Jun 2020 08:24:04: start X-correlation... INFO @ Tue, 16 Jun 2020 08:24:04: end of X-cor INFO @ Tue, 16 Jun 2020 08:24:04: #2 finished! INFO @ Tue, 16 Jun 2020 08:24:04: #2 predicted fragment length is 218 bps INFO @ Tue, 16 Jun 2020 08:24:04: #2 alternative fragment length(s) may be 218 bps INFO @ Tue, 16 Jun 2020 08:24:04: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX257654/SRX257654.10_model.r INFO @ Tue, 16 Jun 2020 08:24:04: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:24:04: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 08:24:09: 8000000 INFO @ Tue, 16 Jun 2020 08:24:10: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 08:24:15: 9000000 INFO @ Tue, 16 Jun 2020 08:24:21: 10000000 INFO @ Tue, 16 Jun 2020 08:24:23: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX257654/SRX257654.05_peaks.xls INFO @ Tue, 16 Jun 2020 08:24:23: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX257654/SRX257654.05_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:24:23: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX257654/SRX257654.05_summits.bed INFO @ Tue, 16 Jun 2020 08:24:23: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (3159 records, 4 fields): 4 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 08:24:27: #1 tag size is determined as 42 bps INFO @ Tue, 16 Jun 2020 08:24:27: #1 tag size = 42 INFO @ Tue, 16 Jun 2020 08:24:27: #1 total tags in treatment: 10951275 INFO @ Tue, 16 Jun 2020 08:24:27: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:24:27: #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 08:24:27: #1 tags after filtering in treatment: 10951275 INFO @ Tue, 16 Jun 2020 08:24:27: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:24:27: #1 finished! INFO @ Tue, 16 Jun 2020 08:24:27: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:24:27: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:24:28: #2 number of paired peaks: 719 WARNING @ Tue, 16 Jun 2020 08:24:28: Fewer paired peaks (719) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 719 pairs to build model! INFO @ Tue, 16 Jun 2020 08:24:28: start model_add_line... INFO @ Tue, 16 Jun 2020 08:24:28: start X-correlation... INFO @ Tue, 16 Jun 2020 08:24:28: end of X-cor INFO @ Tue, 16 Jun 2020 08:24:28: #2 finished! INFO @ Tue, 16 Jun 2020 08:24:28: #2 predicted fragment length is 218 bps INFO @ Tue, 16 Jun 2020 08:24:28: #2 alternative fragment length(s) may be 218 bps INFO @ Tue, 16 Jun 2020 08:24:28: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX257654/SRX257654.20_model.r INFO @ Tue, 16 Jun 2020 08:24:28: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:24:28: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Tue, 16 Jun 2020 08:24:33: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 08:24:46: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX257654/SRX257654.10_peaks.xls INFO @ Tue, 16 Jun 2020 08:24:46: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX257654/SRX257654.10_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:24:46: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX257654/SRX257654.10_summits.bed INFO @ Tue, 16 Jun 2020 08:24:46: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (1799 records, 4 fields): 4 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 08:24:58: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 08:25:11: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX257654/SRX257654.20_peaks.xls INFO @ Tue, 16 Jun 2020 08:25:11: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX257654/SRX257654.20_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:25:11: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX257654/SRX257654.20_summits.bed INFO @ Tue, 16 Jun 2020 08:25:11: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (977 records, 4 fields): 3 millis CompletedMACS2peakCalling