Job ID = 6368301 SRX = SRX494984 Genome = ce11 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-16T00:09:24 prefetch.2.10.7: 1) Downloading 'SRR1198516'... 2020-06-16T00:09:24 prefetch.2.10.7: Downloading via HTTPS... 2020-06-16T00:10:53 prefetch.2.10.7: HTTPS download succeed 2020-06-16T00:10:53 prefetch.2.10.7: 'SRR1198516' is valid 2020-06-16T00:10:53 prefetch.2.10.7: 1) 'SRR1198516' was downloaded successfully Read 10015794 spots for SRR1198516/SRR1198516.sra Written 10015794 spots for SRR1198516/SRR1198516.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: 00:02:11 10015794 reads; of these: 10015794 (100.00%) were unpaired; of these: 133828 (1.34%) aligned 0 times 7608618 (75.97%) aligned exactly 1 time 2273348 (22.70%) aligned >1 times 98.66% overall alignment rate Time searching: 00:02:11 Overall time: 00:02:11 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] 2069100 / 9881966 = 0.2094 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 09:16:07: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX494984/SRX494984.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX494984/SRX494984.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX494984/SRX494984.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX494984/SRX494984.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 09:16:07: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:16:07: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:16:11: 1000000 INFO @ Tue, 16 Jun 2020 09:16:16: 2000000 INFO @ Tue, 16 Jun 2020 09:16:21: 3000000 INFO @ Tue, 16 Jun 2020 09:16:26: 4000000 INFO @ Tue, 16 Jun 2020 09:16:31: 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 09:16:36: 6000000 INFO @ Tue, 16 Jun 2020 09:16:36: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX494984/SRX494984.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX494984/SRX494984.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX494984/SRX494984.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX494984/SRX494984.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 09:16:36: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:16:36: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:16:41: 7000000 INFO @ Tue, 16 Jun 2020 09:16:42: 1000000 INFO @ Tue, 16 Jun 2020 09:16:45: #1 tag size is determined as 42 bps INFO @ Tue, 16 Jun 2020 09:16:45: #1 tag size = 42 INFO @ Tue, 16 Jun 2020 09:16:45: #1 total tags in treatment: 7812866 INFO @ Tue, 16 Jun 2020 09:16:45: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:16:45: #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 09:16:45: #1 tags after filtering in treatment: 7812866 INFO @ Tue, 16 Jun 2020 09:16:45: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 09:16:45: #1 finished! INFO @ Tue, 16 Jun 2020 09:16:45: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:16:45: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:16:46: #2 number of paired peaks: 821 WARNING @ Tue, 16 Jun 2020 09:16:46: Fewer paired peaks (821) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 821 pairs to build model! INFO @ Tue, 16 Jun 2020 09:16:46: start model_add_line... INFO @ Tue, 16 Jun 2020 09:16:46: start X-correlation... INFO @ Tue, 16 Jun 2020 09:16:46: end of X-cor INFO @ Tue, 16 Jun 2020 09:16:46: #2 finished! INFO @ Tue, 16 Jun 2020 09:16:46: #2 predicted fragment length is 147 bps INFO @ Tue, 16 Jun 2020 09:16:46: #2 alternative fragment length(s) may be 147 bps INFO @ Tue, 16 Jun 2020 09:16:46: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX494984/SRX494984.05_model.r INFO @ Tue, 16 Jun 2020 09:16:46: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:16:46: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 09:16:47: 2000000 INFO @ Tue, 16 Jun 2020 09:16:52: 3000000 INFO @ Tue, 16 Jun 2020 09:16:57: 4000000 INFO @ Tue, 16 Jun 2020 09:17:02: 5000000 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 09:17:05: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 09:17:06: 6000000 INFO @ Tue, 16 Jun 2020 09:17:06: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX494984/SRX494984.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX494984/SRX494984.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX494984/SRX494984.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX494984/SRX494984.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 09:17:06: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:17:06: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:17:11: 7000000 INFO @ Tue, 16 Jun 2020 09:17:12: 1000000 INFO @ Tue, 16 Jun 2020 09:17:15: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX494984/SRX494984.05_peaks.xls INFO @ Tue, 16 Jun 2020 09:17:15: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX494984/SRX494984.05_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:17:15: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX494984/SRX494984.05_summits.bed INFO @ Tue, 16 Jun 2020 09:17:15: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (8504 records, 4 fields): 10 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 09:17:16: #1 tag size is determined as 42 bps INFO @ Tue, 16 Jun 2020 09:17:16: #1 tag size = 42 INFO @ Tue, 16 Jun 2020 09:17:16: #1 total tags in treatment: 7812866 INFO @ Tue, 16 Jun 2020 09:17:16: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:17:16: #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 09:17:16: #1 tags after filtering in treatment: 7812866 INFO @ Tue, 16 Jun 2020 09:17:16: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 09:17:16: #1 finished! INFO @ Tue, 16 Jun 2020 09:17:16: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:17:16: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:17:16: #2 number of paired peaks: 821 WARNING @ Tue, 16 Jun 2020 09:17:16: Fewer paired peaks (821) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 821 pairs to build model! INFO @ Tue, 16 Jun 2020 09:17:16: start model_add_line... INFO @ Tue, 16 Jun 2020 09:17:16: start X-correlation... INFO @ Tue, 16 Jun 2020 09:17:16: end of X-cor INFO @ Tue, 16 Jun 2020 09:17:16: #2 finished! INFO @ Tue, 16 Jun 2020 09:17:16: #2 predicted fragment length is 147 bps INFO @ Tue, 16 Jun 2020 09:17:16: #2 alternative fragment length(s) may be 147 bps INFO @ Tue, 16 Jun 2020 09:17:16: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX494984/SRX494984.10_model.r INFO @ Tue, 16 Jun 2020 09:17:16: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:17:16: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 09:17:16: 2000000 INFO @ Tue, 16 Jun 2020 09:17:21: 3000000 INFO @ Tue, 16 Jun 2020 09:17:26: 4000000 INFO @ Tue, 16 Jun 2020 09:17:31: 5000000 INFO @ Tue, 16 Jun 2020 09:17:35: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 09:17:36: 6000000 INFO @ Tue, 16 Jun 2020 09:17:41: 7000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 16 Jun 2020 09:17:45: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX494984/SRX494984.10_peaks.xls INFO @ Tue, 16 Jun 2020 09:17:45: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX494984/SRX494984.10_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:17:45: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX494984/SRX494984.10_summits.bed INFO @ Tue, 16 Jun 2020 09:17:45: Done! pass1 - making usageList (7 chroms): 0 millis pass2 - checking and writing primary data (3303 records, 4 fields): 5 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 09:17:45: #1 tag size is determined as 42 bps INFO @ Tue, 16 Jun 2020 09:17:45: #1 tag size = 42 INFO @ Tue, 16 Jun 2020 09:17:45: #1 total tags in treatment: 7812866 INFO @ Tue, 16 Jun 2020 09:17:45: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:17:45: #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 09:17:45: #1 tags after filtering in treatment: 7812866 INFO @ Tue, 16 Jun 2020 09:17:45: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 09:17:45: #1 finished! INFO @ Tue, 16 Jun 2020 09:17:45: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:17:45: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:17:46: #2 number of paired peaks: 821 WARNING @ Tue, 16 Jun 2020 09:17:46: Fewer paired peaks (821) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 821 pairs to build model! INFO @ Tue, 16 Jun 2020 09:17:46: start model_add_line... INFO @ Tue, 16 Jun 2020 09:17:46: start X-correlation... INFO @ Tue, 16 Jun 2020 09:17:46: end of X-cor INFO @ Tue, 16 Jun 2020 09:17:46: #2 finished! INFO @ Tue, 16 Jun 2020 09:17:46: #2 predicted fragment length is 147 bps INFO @ Tue, 16 Jun 2020 09:17:46: #2 alternative fragment length(s) may be 147 bps INFO @ Tue, 16 Jun 2020 09:17:46: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX494984/SRX494984.20_model.r INFO @ Tue, 16 Jun 2020 09:17:46: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:17:46: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Tue, 16 Jun 2020 09:18:04: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 09:18:14: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX494984/SRX494984.20_peaks.xls INFO @ Tue, 16 Jun 2020 09:18:14: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX494984/SRX494984.20_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:18:14: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX494984/SRX494984.20_summits.bed INFO @ Tue, 16 Jun 2020 09:18:14: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (1058 records, 4 fields): 3 millis CompletedMACS2peakCalling