Job ID = 6367981 SRX = SRX4626833 Genome = ce11 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-15T23:44:29 prefetch.2.10.7: 1) Downloading 'SRR7771416'... 2020-06-15T23:44:29 prefetch.2.10.7: Downloading via HTTPS... 2020-06-15T23:46:35 prefetch.2.10.7: HTTPS download succeed 2020-06-15T23:46:36 prefetch.2.10.7: 'SRR7771416' is valid 2020-06-15T23:46:36 prefetch.2.10.7: 1) 'SRR7771416' was downloaded successfully Read 13386168 spots for SRR7771416/SRR7771416.sra Written 13386168 spots for SRR7771416/SRR7771416.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: 00:01:29 13386168 reads; of these: 13386168 (100.00%) were unpaired; of these: 8129902 (60.73%) aligned 0 times 4426848 (33.07%) aligned exactly 1 time 829418 (6.20%) aligned >1 times 39.27% overall alignment rate Time searching: 00:01:29 Overall time: 00:01:29 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_rmdupse_core] 2084441 / 5256266 = 0.3966 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 08:50:05: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX4626833/SRX4626833.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX4626833/SRX4626833.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX4626833/SRX4626833.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX4626833/SRX4626833.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 08:50:05: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:50:05: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:50:10: 1000000 INFO @ Tue, 16 Jun 2020 08:50:15: 2000000 INFO @ Tue, 16 Jun 2020 08:50:19: 3000000 INFO @ Tue, 16 Jun 2020 08:50:20: #1 tag size is determined as 40 bps INFO @ Tue, 16 Jun 2020 08:50:20: #1 tag size = 40 INFO @ Tue, 16 Jun 2020 08:50:20: #1 total tags in treatment: 3171825 INFO @ Tue, 16 Jun 2020 08:50:20: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:50:20: #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 08:50:20: #1 tags after filtering in treatment: 3171825 INFO @ Tue, 16 Jun 2020 08:50:20: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:50:20: #1 finished! INFO @ Tue, 16 Jun 2020 08:50:20: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:50:20: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:50:20: #2 number of paired peaks: 581 WARNING @ Tue, 16 Jun 2020 08:50:20: Fewer paired peaks (581) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 581 pairs to build model! INFO @ Tue, 16 Jun 2020 08:50:20: start model_add_line... INFO @ Tue, 16 Jun 2020 08:50:20: start X-correlation... INFO @ Tue, 16 Jun 2020 08:50:20: end of X-cor INFO @ Tue, 16 Jun 2020 08:50:20: #2 finished! INFO @ Tue, 16 Jun 2020 08:50:20: #2 predicted fragment length is 97 bps INFO @ Tue, 16 Jun 2020 08:50:20: #2 alternative fragment length(s) may be 48,97 bps INFO @ Tue, 16 Jun 2020 08:50:20: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX4626833/SRX4626833.05_model.r INFO @ Tue, 16 Jun 2020 08:50:20: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:50:20: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 08:50:27: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 08:50:30: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX4626833/SRX4626833.05_peaks.xls INFO @ Tue, 16 Jun 2020 08:50:30: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX4626833/SRX4626833.05_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:50:30: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX4626833/SRX4626833.05_summits.bed INFO @ Tue, 16 Jun 2020 08:50:30: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (896 records, 4 fields): 3 millis CompletedMACS2peakCalling 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 08:50:35: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX4626833/SRX4626833.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX4626833/SRX4626833.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX4626833/SRX4626833.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX4626833/SRX4626833.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 08:50:35: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:50:35: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:50:40: 1000000 INFO @ Tue, 16 Jun 2020 08:50:45: 2000000 INFO @ Tue, 16 Jun 2020 08:50:49: 3000000 INFO @ Tue, 16 Jun 2020 08:50:50: #1 tag size is determined as 40 bps INFO @ Tue, 16 Jun 2020 08:50:50: #1 tag size = 40 INFO @ Tue, 16 Jun 2020 08:50:50: #1 total tags in treatment: 3171825 INFO @ Tue, 16 Jun 2020 08:50:50: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:50:50: #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 08:50:50: #1 tags after filtering in treatment: 3171825 INFO @ Tue, 16 Jun 2020 08:50:50: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:50:50: #1 finished! INFO @ Tue, 16 Jun 2020 08:50:50: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:50:50: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:50:50: #2 number of paired peaks: 581 WARNING @ Tue, 16 Jun 2020 08:50:50: Fewer paired peaks (581) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 581 pairs to build model! INFO @ Tue, 16 Jun 2020 08:50:50: start model_add_line... INFO @ Tue, 16 Jun 2020 08:50:50: start X-correlation... INFO @ Tue, 16 Jun 2020 08:50:50: end of X-cor INFO @ Tue, 16 Jun 2020 08:50:50: #2 finished! INFO @ Tue, 16 Jun 2020 08:50:50: #2 predicted fragment length is 97 bps INFO @ Tue, 16 Jun 2020 08:50:50: #2 alternative fragment length(s) may be 48,97 bps INFO @ Tue, 16 Jun 2020 08:50:50: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX4626833/SRX4626833.10_model.r INFO @ Tue, 16 Jun 2020 08:50:50: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:50:50: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 08:50:57: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 08:51:01: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX4626833/SRX4626833.10_peaks.xls INFO @ Tue, 16 Jun 2020 08:51:01: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX4626833/SRX4626833.10_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:51:01: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX4626833/SRX4626833.10_summits.bed INFO @ Tue, 16 Jun 2020 08:51:01: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (454 records, 4 fields): 1 millis CompletedMACS2peakCalling 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 08:51:05: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX4626833/SRX4626833.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX4626833/SRX4626833.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX4626833/SRX4626833.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX4626833/SRX4626833.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 08:51:05: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:51:05: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:51:10: 1000000 INFO @ Tue, 16 Jun 2020 08:51:15: 2000000 INFO @ Tue, 16 Jun 2020 08:51:19: 3000000 INFO @ Tue, 16 Jun 2020 08:51:20: #1 tag size is determined as 40 bps INFO @ Tue, 16 Jun 2020 08:51:20: #1 tag size = 40 INFO @ Tue, 16 Jun 2020 08:51:20: #1 total tags in treatment: 3171825 INFO @ Tue, 16 Jun 2020 08:51:20: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:51:20: #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 08:51:20: #1 tags after filtering in treatment: 3171825 INFO @ Tue, 16 Jun 2020 08:51:20: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:51:20: #1 finished! INFO @ Tue, 16 Jun 2020 08:51:20: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:51:20: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:51:20: #2 number of paired peaks: 581 WARNING @ Tue, 16 Jun 2020 08:51:20: Fewer paired peaks (581) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 581 pairs to build model! INFO @ Tue, 16 Jun 2020 08:51:20: start model_add_line... INFO @ Tue, 16 Jun 2020 08:51:20: start X-correlation... INFO @ Tue, 16 Jun 2020 08:51:20: end of X-cor INFO @ Tue, 16 Jun 2020 08:51:20: #2 finished! INFO @ Tue, 16 Jun 2020 08:51:20: #2 predicted fragment length is 97 bps INFO @ Tue, 16 Jun 2020 08:51:20: #2 alternative fragment length(s) may be 48,97 bps INFO @ Tue, 16 Jun 2020 08:51:20: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX4626833/SRX4626833.20_model.r INFO @ Tue, 16 Jun 2020 08:51:20: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:51:20: #3 Pre-compute pvalue-qvalue table... BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 16 Jun 2020 08:51:27: #3 Call peaks for each chromosome... BigWig に変換しました。 INFO @ Tue, 16 Jun 2020 08:51:31: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX4626833/SRX4626833.20_peaks.xls INFO @ Tue, 16 Jun 2020 08:51:31: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX4626833/SRX4626833.20_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:51:31: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX4626833/SRX4626833.20_summits.bed INFO @ Tue, 16 Jun 2020 08:51:31: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (172 records, 4 fields): 1 millis CompletedMACS2peakCalling