Job ID = 6366709 SRX = SRX2228864 Genome = ce11 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-15T22:59:53 prefetch.2.10.7: 1) Downloading 'SRR4380320'... 2020-06-15T22:59:53 prefetch.2.10.7: Downloading via HTTPS... 2020-06-15T23:00:42 prefetch.2.10.7: HTTPS download succeed 2020-06-15T23:00:42 prefetch.2.10.7: 'SRR4380320' is valid 2020-06-15T23:00:42 prefetch.2.10.7: 1) 'SRR4380320' was downloaded successfully Read 10064622 spots for SRR4380320/SRR4380320.sra Written 10064622 spots for SRR4380320/SRR4380320.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: 00:01:58 10064622 reads; of these: 10064622 (100.00%) were unpaired; of these: 2079638 (20.66%) aligned 0 times 6653188 (66.10%) aligned exactly 1 time 1331796 (13.23%) aligned >1 times 79.34% overall alignment rate Time searching: 00:01:58 Overall time: 00:01:58 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] 1051598 / 7984984 = 0.1317 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 08:05:33: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX2228864/SRX2228864.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX2228864/SRX2228864.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX2228864/SRX2228864.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX2228864/SRX2228864.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 08:05:33: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:05:33: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:05:39: 1000000 INFO @ Tue, 16 Jun 2020 08:05:45: 2000000 INFO @ Tue, 16 Jun 2020 08:05:51: 3000000 INFO @ Tue, 16 Jun 2020 08:05:57: 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 08:06:03: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX2228864/SRX2228864.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX2228864/SRX2228864.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX2228864/SRX2228864.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX2228864/SRX2228864.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 08:06:03: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:06:03: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:06:04: 5000000 INFO @ Tue, 16 Jun 2020 08:06:08: 1000000 INFO @ Tue, 16 Jun 2020 08:06:10: 6000000 INFO @ Tue, 16 Jun 2020 08:06:13: 2000000 INFO @ Tue, 16 Jun 2020 08:06:16: #1 tag size is determined as 51 bps INFO @ Tue, 16 Jun 2020 08:06:16: #1 tag size = 51 INFO @ Tue, 16 Jun 2020 08:06:16: #1 total tags in treatment: 6933386 INFO @ Tue, 16 Jun 2020 08:06:16: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:06:16: #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 08:06:16: #1 tags after filtering in treatment: 6933386 INFO @ Tue, 16 Jun 2020 08:06:16: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:06:16: #1 finished! INFO @ Tue, 16 Jun 2020 08:06:16: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:06:16: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:06:16: #2 number of paired peaks: 704 WARNING @ Tue, 16 Jun 2020 08:06:16: Fewer paired peaks (704) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 704 pairs to build model! INFO @ Tue, 16 Jun 2020 08:06:16: start model_add_line... INFO @ Tue, 16 Jun 2020 08:06:16: start X-correlation... INFO @ Tue, 16 Jun 2020 08:06:16: end of X-cor INFO @ Tue, 16 Jun 2020 08:06:16: #2 finished! INFO @ Tue, 16 Jun 2020 08:06:16: #2 predicted fragment length is 115 bps INFO @ Tue, 16 Jun 2020 08:06:16: #2 alternative fragment length(s) may be 115 bps INFO @ Tue, 16 Jun 2020 08:06:16: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX2228864/SRX2228864.05_model.r INFO @ Tue, 16 Jun 2020 08:06:16: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:06:16: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 08:06:18: 3000000 INFO @ Tue, 16 Jun 2020 08:06:23: 4000000 INFO @ Tue, 16 Jun 2020 08:06:28: 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 08:06:32: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 08:06:33: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX2228864/SRX2228864.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX2228864/SRX2228864.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX2228864/SRX2228864.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX2228864/SRX2228864.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 08:06:33: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:06:33: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:06:33: 6000000 INFO @ Tue, 16 Jun 2020 08:06:38: #1 tag size is determined as 51 bps INFO @ Tue, 16 Jun 2020 08:06:38: #1 tag size = 51 INFO @ Tue, 16 Jun 2020 08:06:38: #1 total tags in treatment: 6933386 INFO @ Tue, 16 Jun 2020 08:06:38: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:06:38: #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 08:06:38: 1000000 INFO @ Tue, 16 Jun 2020 08:06:38: #1 tags after filtering in treatment: 6933386 INFO @ Tue, 16 Jun 2020 08:06:38: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:06:38: #1 finished! INFO @ Tue, 16 Jun 2020 08:06:38: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:06:38: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:06:39: #2 number of paired peaks: 704 WARNING @ Tue, 16 Jun 2020 08:06:39: Fewer paired peaks (704) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 704 pairs to build model! INFO @ Tue, 16 Jun 2020 08:06:39: start model_add_line... INFO @ Tue, 16 Jun 2020 08:06:39: start X-correlation... INFO @ Tue, 16 Jun 2020 08:06:39: end of X-cor INFO @ Tue, 16 Jun 2020 08:06:39: #2 finished! INFO @ Tue, 16 Jun 2020 08:06:39: #2 predicted fragment length is 115 bps INFO @ Tue, 16 Jun 2020 08:06:39: #2 alternative fragment length(s) may be 115 bps INFO @ Tue, 16 Jun 2020 08:06:39: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX2228864/SRX2228864.10_model.r INFO @ Tue, 16 Jun 2020 08:06:39: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:06:39: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 08:06:40: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX2228864/SRX2228864.05_peaks.xls INFO @ Tue, 16 Jun 2020 08:06:40: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX2228864/SRX2228864.05_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:06:40: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX2228864/SRX2228864.05_summits.bed INFO @ Tue, 16 Jun 2020 08:06:40: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (1747 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 08:06:43: 2000000 INFO @ Tue, 16 Jun 2020 08:06:48: 3000000 INFO @ Tue, 16 Jun 2020 08:06:53: 4000000 INFO @ Tue, 16 Jun 2020 08:06:53: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 08:06:59: 5000000 INFO @ Tue, 16 Jun 2020 08:07:01: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX2228864/SRX2228864.10_peaks.xls INFO @ Tue, 16 Jun 2020 08:07:01: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX2228864/SRX2228864.10_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:07:01: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX2228864/SRX2228864.10_summits.bed INFO @ Tue, 16 Jun 2020 08:07:01: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (1095 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 08:07:04: 6000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 16 Jun 2020 08:07:09: #1 tag size is determined as 51 bps INFO @ Tue, 16 Jun 2020 08:07:09: #1 tag size = 51 INFO @ Tue, 16 Jun 2020 08:07:09: #1 total tags in treatment: 6933386 INFO @ Tue, 16 Jun 2020 08:07:09: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:07:09: #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 08:07:09: #1 tags after filtering in treatment: 6933386 INFO @ Tue, 16 Jun 2020 08:07:09: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:07:09: #1 finished! INFO @ Tue, 16 Jun 2020 08:07:09: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:07:09: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:07:09: #2 number of paired peaks: 704 WARNING @ Tue, 16 Jun 2020 08:07:09: Fewer paired peaks (704) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 704 pairs to build model! INFO @ Tue, 16 Jun 2020 08:07:09: start model_add_line... INFO @ Tue, 16 Jun 2020 08:07:09: start X-correlation... INFO @ Tue, 16 Jun 2020 08:07:09: end of X-cor INFO @ Tue, 16 Jun 2020 08:07:09: #2 finished! INFO @ Tue, 16 Jun 2020 08:07:09: #2 predicted fragment length is 115 bps INFO @ Tue, 16 Jun 2020 08:07:09: #2 alternative fragment length(s) may be 115 bps INFO @ Tue, 16 Jun 2020 08:07:09: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX2228864/SRX2228864.20_model.r INFO @ Tue, 16 Jun 2020 08:07:09: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:07:09: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Tue, 16 Jun 2020 08:07:25: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 08:07:32: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX2228864/SRX2228864.20_peaks.xls INFO @ Tue, 16 Jun 2020 08:07:32: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX2228864/SRX2228864.20_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:07:32: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX2228864/SRX2228864.20_summits.bed INFO @ Tue, 16 Jun 2020 08:07:32: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (630 records, 4 fields): 1 millis CompletedMACS2peakCalling