Job ID = 6368999 SRX = SRX982065 Genome = ce11 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-16T00:39:16 prefetch.2.10.7: 1) Downloading 'SRR1956541'... 2020-06-16T00:39:16 prefetch.2.10.7: Downloading via HTTPS... 2020-06-16T00:42:07 prefetch.2.10.7: HTTPS download succeed 2020-06-16T00:42:07 prefetch.2.10.7: 1) 'SRR1956541' was downloaded successfully Read 20608259 spots for SRR1956541/SRR1956541.sra Written 20608259 spots for SRR1956541/SRR1956541.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: 00:04:29 20608259 reads; of these: 20608259 (100.00%) were unpaired; of these: 1441660 (7.00%) aligned 0 times 16363897 (79.40%) aligned exactly 1 time 2802702 (13.60%) aligned >1 times 93.00% overall alignment rate Time searching: 00:04:29 Overall time: 00:04:29 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] 2799717 / 19166599 = 0.1461 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 09:52:42: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX982065/SRX982065.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX982065/SRX982065.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX982065/SRX982065.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX982065/SRX982065.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 09:52:42: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:52:42: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:52:48: 1000000 INFO @ Tue, 16 Jun 2020 09:52:53: 2000000 INFO @ Tue, 16 Jun 2020 09:52:59: 3000000 INFO @ Tue, 16 Jun 2020 09:53:05: 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 09:53:11: 5000000 INFO @ Tue, 16 Jun 2020 09:53:12: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX982065/SRX982065.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX982065/SRX982065.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX982065/SRX982065.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX982065/SRX982065.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 09:53:12: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:53:12: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:53:17: 6000000 INFO @ Tue, 16 Jun 2020 09:53:19: 1000000 INFO @ Tue, 16 Jun 2020 09:53:23: 7000000 INFO @ Tue, 16 Jun 2020 09:53:25: 2000000 INFO @ Tue, 16 Jun 2020 09:53:29: 8000000 INFO @ Tue, 16 Jun 2020 09:53:32: 3000000 INFO @ Tue, 16 Jun 2020 09:53:36: 9000000 INFO @ Tue, 16 Jun 2020 09:53:38: 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 09:53:42: 10000000 INFO @ Tue, 16 Jun 2020 09:53:42: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX982065/SRX982065.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX982065/SRX982065.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX982065/SRX982065.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX982065/SRX982065.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 09:53:42: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:53:42: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:53:45: 5000000 INFO @ Tue, 16 Jun 2020 09:53:49: 11000000 INFO @ Tue, 16 Jun 2020 09:53:49: 1000000 INFO @ Tue, 16 Jun 2020 09:53:51: 6000000 INFO @ Tue, 16 Jun 2020 09:53:55: 12000000 INFO @ Tue, 16 Jun 2020 09:53:55: 2000000 INFO @ Tue, 16 Jun 2020 09:53:57: 7000000 INFO @ Tue, 16 Jun 2020 09:54:02: 13000000 INFO @ Tue, 16 Jun 2020 09:54:02: 3000000 INFO @ Tue, 16 Jun 2020 09:54:04: 8000000 INFO @ Tue, 16 Jun 2020 09:54:08: 14000000 INFO @ Tue, 16 Jun 2020 09:54:08: 4000000 INFO @ Tue, 16 Jun 2020 09:54:10: 9000000 INFO @ Tue, 16 Jun 2020 09:54:15: 15000000 INFO @ Tue, 16 Jun 2020 09:54:15: 5000000 INFO @ Tue, 16 Jun 2020 09:54:17: 10000000 INFO @ Tue, 16 Jun 2020 09:54:21: 6000000 INFO @ Tue, 16 Jun 2020 09:54:21: 16000000 INFO @ Tue, 16 Jun 2020 09:54:23: 11000000 INFO @ Tue, 16 Jun 2020 09:54:23: #1 tag size is determined as 51 bps INFO @ Tue, 16 Jun 2020 09:54:23: #1 tag size = 51 INFO @ Tue, 16 Jun 2020 09:54:23: #1 total tags in treatment: 16366882 INFO @ Tue, 16 Jun 2020 09:54:23: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:54:23: #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 09:54:24: #1 tags after filtering in treatment: 16366882 INFO @ Tue, 16 Jun 2020 09:54:24: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 09:54:24: #1 finished! INFO @ Tue, 16 Jun 2020 09:54:24: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:54:24: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:54:25: #2 number of paired peaks: 518 WARNING @ Tue, 16 Jun 2020 09:54:25: Fewer paired peaks (518) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 518 pairs to build model! INFO @ Tue, 16 Jun 2020 09:54:25: start model_add_line... INFO @ Tue, 16 Jun 2020 09:54:25: start X-correlation... INFO @ Tue, 16 Jun 2020 09:54:25: end of X-cor INFO @ Tue, 16 Jun 2020 09:54:25: #2 finished! INFO @ Tue, 16 Jun 2020 09:54:25: #2 predicted fragment length is 122 bps INFO @ Tue, 16 Jun 2020 09:54:25: #2 alternative fragment length(s) may be 4,122 bps INFO @ Tue, 16 Jun 2020 09:54:25: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX982065/SRX982065.05_model.r INFO @ Tue, 16 Jun 2020 09:54:25: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:54:25: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 09:54:27: 7000000 INFO @ Tue, 16 Jun 2020 09:54:29: 12000000 INFO @ Tue, 16 Jun 2020 09:54:33: 8000000 INFO @ Tue, 16 Jun 2020 09:54:35: 13000000 INFO @ Tue, 16 Jun 2020 09:54:39: 9000000 INFO @ Tue, 16 Jun 2020 09:54:41: 14000000 INFO @ Tue, 16 Jun 2020 09:54:45: 10000000 INFO @ Tue, 16 Jun 2020 09:54:47: 15000000 INFO @ Tue, 16 Jun 2020 09:54:52: 11000000 INFO @ Tue, 16 Jun 2020 09:54:53: 16000000 INFO @ Tue, 16 Jun 2020 09:54:56: #1 tag size is determined as 51 bps INFO @ Tue, 16 Jun 2020 09:54:56: #1 tag size = 51 INFO @ Tue, 16 Jun 2020 09:54:56: #1 total tags in treatment: 16366882 INFO @ Tue, 16 Jun 2020 09:54:56: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:54:56: #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 09:54:56: #1 tags after filtering in treatment: 16366882 INFO @ Tue, 16 Jun 2020 09:54:56: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 09:54:56: #1 finished! INFO @ Tue, 16 Jun 2020 09:54:56: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:54:56: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:54:57: #2 number of paired peaks: 518 WARNING @ Tue, 16 Jun 2020 09:54:57: Fewer paired peaks (518) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 518 pairs to build model! INFO @ Tue, 16 Jun 2020 09:54:57: start model_add_line... INFO @ Tue, 16 Jun 2020 09:54:57: start X-correlation... INFO @ Tue, 16 Jun 2020 09:54:57: end of X-cor INFO @ Tue, 16 Jun 2020 09:54:57: #2 finished! INFO @ Tue, 16 Jun 2020 09:54:57: #2 predicted fragment length is 122 bps INFO @ Tue, 16 Jun 2020 09:54:57: #2 alternative fragment length(s) may be 4,122 bps INFO @ Tue, 16 Jun 2020 09:54:57: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX982065/SRX982065.10_model.r INFO @ Tue, 16 Jun 2020 09:54:57: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:54:57: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 09:54:58: 12000000 INFO @ Tue, 16 Jun 2020 09:54:58: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 09:55:03: 13000000 INFO @ Tue, 16 Jun 2020 09:55:09: 14000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 16 Jun 2020 09:55:14: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX982065/SRX982065.05_peaks.xls INFO @ Tue, 16 Jun 2020 09:55:14: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX982065/SRX982065.05_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:55:14: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX982065/SRX982065.05_summits.bed INFO @ Tue, 16 Jun 2020 09:55:14: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (1750 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 09:55:15: 15000000 INFO @ Tue, 16 Jun 2020 09:55:20: 16000000 INFO @ Tue, 16 Jun 2020 09:55:22: #1 tag size is determined as 51 bps INFO @ Tue, 16 Jun 2020 09:55:22: #1 tag size = 51 INFO @ Tue, 16 Jun 2020 09:55:22: #1 total tags in treatment: 16366882 INFO @ Tue, 16 Jun 2020 09:55:22: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:55:22: #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 09:55:22: #1 tags after filtering in treatment: 16366882 INFO @ Tue, 16 Jun 2020 09:55:22: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 09:55:22: #1 finished! INFO @ Tue, 16 Jun 2020 09:55:22: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:55:22: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:55:23: #2 number of paired peaks: 518 WARNING @ Tue, 16 Jun 2020 09:55:23: Fewer paired peaks (518) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 518 pairs to build model! INFO @ Tue, 16 Jun 2020 09:55:23: start model_add_line... INFO @ Tue, 16 Jun 2020 09:55:24: start X-correlation... INFO @ Tue, 16 Jun 2020 09:55:24: end of X-cor INFO @ Tue, 16 Jun 2020 09:55:24: #2 finished! INFO @ Tue, 16 Jun 2020 09:55:24: #2 predicted fragment length is 122 bps INFO @ Tue, 16 Jun 2020 09:55:24: #2 alternative fragment length(s) may be 4,122 bps INFO @ Tue, 16 Jun 2020 09:55:24: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX982065/SRX982065.20_model.r INFO @ Tue, 16 Jun 2020 09:55:24: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:55:24: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 09:55:30: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 09:55:46: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX982065/SRX982065.10_peaks.xls INFO @ Tue, 16 Jun 2020 09:55:46: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX982065/SRX982065.10_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:55:46: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX982065/SRX982065.10_summits.bed INFO @ Tue, 16 Jun 2020 09:55:46: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (1068 records, 4 fields): 3 millis CompletedMACS2peakCalling BigWig に変換しました。 INFO @ Tue, 16 Jun 2020 09:55:56: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 09:56:12: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX982065/SRX982065.20_peaks.xls INFO @ Tue, 16 Jun 2020 09:56:12: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX982065/SRX982065.20_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:56:12: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX982065/SRX982065.20_summits.bed INFO @ Tue, 16 Jun 2020 09:56:12: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (590 records, 4 fields): 2 millis CompletedMACS2peakCalling