Job ID = 6366568 SRX = SRX1949397 Genome = ce11 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-15T22:57:23 prefetch.2.10.7: 1) Downloading 'SRR3922837'... 2020-06-15T22:57:23 prefetch.2.10.7: Downloading via HTTPS... 2020-06-15T22:58:11 prefetch.2.10.7: HTTPS download succeed 2020-06-15T22:58:11 prefetch.2.10.7: 'SRR3922837' is valid 2020-06-15T22:58:11 prefetch.2.10.7: 1) 'SRR3922837' was downloaded successfully Read 12492161 spots for SRR3922837/SRR3922837.sra Written 12492161 spots for SRR3922837/SRR3922837.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: 00:02:36 12492161 reads; of these: 12492161 (100.00%) were unpaired; of these: 2829106 (22.65%) aligned 0 times 8110485 (64.92%) aligned exactly 1 time 1552570 (12.43%) aligned >1 times 77.35% overall alignment rate Time searching: 00:02:36 Overall time: 00:02:36 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] 2258582 / 9663055 = 0.2337 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 08:04:16: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX1949397/SRX1949397.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX1949397/SRX1949397.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX1949397/SRX1949397.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX1949397/SRX1949397.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 08:04:16: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:04:16: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:04:22: 1000000 INFO @ Tue, 16 Jun 2020 08:04:28: 2000000 INFO @ Tue, 16 Jun 2020 08:04:34: 3000000 INFO @ Tue, 16 Jun 2020 08:04:41: 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 08:04:46: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX1949397/SRX1949397.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX1949397/SRX1949397.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX1949397/SRX1949397.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX1949397/SRX1949397.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 08:04:46: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:04:46: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:04:47: 5000000 INFO @ Tue, 16 Jun 2020 08:04:53: 1000000 INFO @ Tue, 16 Jun 2020 08:04:53: 6000000 INFO @ Tue, 16 Jun 2020 08:04:59: 2000000 INFO @ Tue, 16 Jun 2020 08:05:00: 7000000 INFO @ Tue, 16 Jun 2020 08:05:03: #1 tag size is determined as 49 bps INFO @ Tue, 16 Jun 2020 08:05:03: #1 tag size = 49 INFO @ Tue, 16 Jun 2020 08:05:03: #1 total tags in treatment: 7404473 INFO @ Tue, 16 Jun 2020 08:05:03: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:05:03: #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 08:05:03: #1 tags after filtering in treatment: 7404473 INFO @ Tue, 16 Jun 2020 08:05:03: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:05:03: #1 finished! INFO @ Tue, 16 Jun 2020 08:05:03: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:05:03: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:05:04: #2 number of paired peaks: 500 WARNING @ Tue, 16 Jun 2020 08:05:04: Fewer paired peaks (500) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 500 pairs to build model! INFO @ Tue, 16 Jun 2020 08:05:04: start model_add_line... INFO @ Tue, 16 Jun 2020 08:05:04: start X-correlation... INFO @ Tue, 16 Jun 2020 08:05:04: end of X-cor INFO @ Tue, 16 Jun 2020 08:05:04: #2 finished! INFO @ Tue, 16 Jun 2020 08:05:04: #2 predicted fragment length is 145 bps INFO @ Tue, 16 Jun 2020 08:05:04: #2 alternative fragment length(s) may be 145 bps INFO @ Tue, 16 Jun 2020 08:05:04: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX1949397/SRX1949397.05_model.r INFO @ Tue, 16 Jun 2020 08:05:04: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:05:04: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 08:05:06: 3000000 INFO @ Tue, 16 Jun 2020 08:05:12: 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 08:05:16: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX1949397/SRX1949397.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX1949397/SRX1949397.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX1949397/SRX1949397.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX1949397/SRX1949397.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 08:05:16: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:05:16: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:05:19: 5000000 INFO @ Tue, 16 Jun 2020 08:05:22: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 08:05:23: 1000000 INFO @ Tue, 16 Jun 2020 08:05:26: 6000000 INFO @ Tue, 16 Jun 2020 08:05:30: 2000000 INFO @ Tue, 16 Jun 2020 08:05:31: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX1949397/SRX1949397.05_peaks.xls INFO @ Tue, 16 Jun 2020 08:05:31: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX1949397/SRX1949397.05_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:05:31: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX1949397/SRX1949397.05_summits.bed INFO @ Tue, 16 Jun 2020 08:05:31: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (1740 records, 4 fields): 11 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 08:05:33: 7000000 INFO @ Tue, 16 Jun 2020 08:05:35: #1 tag size is determined as 49 bps INFO @ Tue, 16 Jun 2020 08:05:35: #1 tag size = 49 INFO @ Tue, 16 Jun 2020 08:05:35: #1 total tags in treatment: 7404473 INFO @ Tue, 16 Jun 2020 08:05:35: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:05:35: #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 08:05:36: #1 tags after filtering in treatment: 7404473 INFO @ Tue, 16 Jun 2020 08:05:36: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:05:36: #1 finished! INFO @ Tue, 16 Jun 2020 08:05:36: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:05:36: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:05:36: #2 number of paired peaks: 500 WARNING @ Tue, 16 Jun 2020 08:05:36: Fewer paired peaks (500) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 500 pairs to build model! INFO @ Tue, 16 Jun 2020 08:05:36: start model_add_line... INFO @ Tue, 16 Jun 2020 08:05:36: start X-correlation... INFO @ Tue, 16 Jun 2020 08:05:36: end of X-cor INFO @ Tue, 16 Jun 2020 08:05:36: #2 finished! INFO @ Tue, 16 Jun 2020 08:05:36: #2 predicted fragment length is 145 bps INFO @ Tue, 16 Jun 2020 08:05:36: #2 alternative fragment length(s) may be 145 bps INFO @ Tue, 16 Jun 2020 08:05:36: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX1949397/SRX1949397.10_model.r INFO @ Tue, 16 Jun 2020 08:05:36: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:05:36: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 08:05:36: 3000000 INFO @ Tue, 16 Jun 2020 08:05:43: 4000000 INFO @ Tue, 16 Jun 2020 08:05:50: 5000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 16 Jun 2020 08:05:55: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 08:05:56: 6000000 INFO @ Tue, 16 Jun 2020 08:06:03: 7000000 INFO @ Tue, 16 Jun 2020 08:06:04: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX1949397/SRX1949397.10_peaks.xls INFO @ Tue, 16 Jun 2020 08:06:04: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX1949397/SRX1949397.10_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:06:04: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX1949397/SRX1949397.10_summits.bed INFO @ Tue, 16 Jun 2020 08:06:04: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (866 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 08:06:05: #1 tag size is determined as 49 bps INFO @ Tue, 16 Jun 2020 08:06:05: #1 tag size = 49 INFO @ Tue, 16 Jun 2020 08:06:05: #1 total tags in treatment: 7404473 INFO @ Tue, 16 Jun 2020 08:06:05: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:06:05: #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 08:06:06: #1 tags after filtering in treatment: 7404473 INFO @ Tue, 16 Jun 2020 08:06:06: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:06:06: #1 finished! INFO @ Tue, 16 Jun 2020 08:06:06: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:06:06: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:06:06: #2 number of paired peaks: 500 WARNING @ Tue, 16 Jun 2020 08:06:06: Fewer paired peaks (500) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 500 pairs to build model! INFO @ Tue, 16 Jun 2020 08:06:06: start model_add_line... INFO @ Tue, 16 Jun 2020 08:06:06: start X-correlation... INFO @ Tue, 16 Jun 2020 08:06:06: end of X-cor INFO @ Tue, 16 Jun 2020 08:06:06: #2 finished! INFO @ Tue, 16 Jun 2020 08:06:06: #2 predicted fragment length is 145 bps INFO @ Tue, 16 Jun 2020 08:06:06: #2 alternative fragment length(s) may be 145 bps INFO @ Tue, 16 Jun 2020 08:06:06: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX1949397/SRX1949397.20_model.r INFO @ Tue, 16 Jun 2020 08:06:06: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:06:06: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Tue, 16 Jun 2020 08:06:25: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 08:06:34: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX1949397/SRX1949397.20_peaks.xls INFO @ Tue, 16 Jun 2020 08:06:34: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX1949397/SRX1949397.20_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:06:34: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX1949397/SRX1949397.20_summits.bed INFO @ Tue, 16 Jun 2020 08:06:34: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (409 records, 4 fields): 1 millis CompletedMACS2peakCalling