Job ID = 6366289 SRX = SRX1078713 Genome = ce11 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-15T22:33:36 prefetch.2.10.7: 1) Downloading 'SRR2084320'... 2020-06-15T22:33:36 prefetch.2.10.7: Downloading via HTTPS... 2020-06-15T22:36:24 prefetch.2.10.7: HTTPS download succeed 2020-06-15T22:36:24 prefetch.2.10.7: 1) 'SRR2084320' was downloaded successfully Read 24816727 spots for SRR2084320/SRR2084320.sra Written 24816727 spots for SRR2084320/SRR2084320.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: 00:04:58 24816727 reads; of these: 24816727 (100.00%) were unpaired; of these: 2480037 (9.99%) aligned 0 times 18575075 (74.85%) aligned exactly 1 time 3761615 (15.16%) aligned >1 times 90.01% overall alignment rate Time searching: 00:04:58 Overall time: 00:04:58 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_sort_core] merging from 12 files... [bam_rmdupse_core] 12111915 / 22336690 = 0.5422 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 07:47:12: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX1078713/SRX1078713.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX1078713/SRX1078713.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX1078713/SRX1078713.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX1078713/SRX1078713.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 07:47:12: #1 read tag files... INFO @ Tue, 16 Jun 2020 07:47:12: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 07:47:17: 1000000 INFO @ Tue, 16 Jun 2020 07:47:23: 2000000 INFO @ Tue, 16 Jun 2020 07:47:29: 3000000 INFO @ Tue, 16 Jun 2020 07:47:34: 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 07:47:40: 5000000 INFO @ Tue, 16 Jun 2020 07:47:42: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX1078713/SRX1078713.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX1078713/SRX1078713.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX1078713/SRX1078713.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX1078713/SRX1078713.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 07:47:42: #1 read tag files... INFO @ Tue, 16 Jun 2020 07:47:42: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 07:47:46: 6000000 INFO @ Tue, 16 Jun 2020 07:47:47: 1000000 INFO @ Tue, 16 Jun 2020 07:47:52: 7000000 INFO @ Tue, 16 Jun 2020 07:47:53: 2000000 INFO @ Tue, 16 Jun 2020 07:47:58: 8000000 INFO @ Tue, 16 Jun 2020 07:47:59: 3000000 INFO @ Tue, 16 Jun 2020 07:48:04: 9000000 INFO @ Tue, 16 Jun 2020 07:48:05: 4000000 INFO @ Tue, 16 Jun 2020 07:48:09: 10000000 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 07:48:10: 5000000 INFO @ Tue, 16 Jun 2020 07:48:11: #1 tag size is determined as 51 bps INFO @ Tue, 16 Jun 2020 07:48:11: #1 tag size = 51 INFO @ Tue, 16 Jun 2020 07:48:11: #1 total tags in treatment: 10224775 INFO @ Tue, 16 Jun 2020 07:48:11: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 07:48:11: #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 07:48:11: #1 tags after filtering in treatment: 10224775 INFO @ Tue, 16 Jun 2020 07:48:11: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 07:48:11: #1 finished! INFO @ Tue, 16 Jun 2020 07:48:11: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 07:48:11: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 07:48:12: #2 number of paired peaks: 705 WARNING @ Tue, 16 Jun 2020 07:48:12: Fewer paired peaks (705) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 705 pairs to build model! INFO @ Tue, 16 Jun 2020 07:48:12: start model_add_line... INFO @ Tue, 16 Jun 2020 07:48:12: start X-correlation... INFO @ Tue, 16 Jun 2020 07:48:12: end of X-cor INFO @ Tue, 16 Jun 2020 07:48:12: #2 finished! INFO @ Tue, 16 Jun 2020 07:48:12: #2 predicted fragment length is 123 bps INFO @ Tue, 16 Jun 2020 07:48:12: #2 alternative fragment length(s) may be 123 bps INFO @ Tue, 16 Jun 2020 07:48:12: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX1078713/SRX1078713.05_model.r INFO @ Tue, 16 Jun 2020 07:48:12: #3 Call peaks... INFO @ Tue, 16 Jun 2020 07:48:12: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 07:48:12: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX1078713/SRX1078713.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX1078713/SRX1078713.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX1078713/SRX1078713.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX1078713/SRX1078713.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 07:48:12: #1 read tag files... INFO @ Tue, 16 Jun 2020 07:48:12: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 07:48:16: 6000000 INFO @ Tue, 16 Jun 2020 07:48:17: 1000000 INFO @ Tue, 16 Jun 2020 07:48:22: 7000000 INFO @ Tue, 16 Jun 2020 07:48:23: 2000000 INFO @ Tue, 16 Jun 2020 07:48:27: 8000000 INFO @ Tue, 16 Jun 2020 07:48:28: 3000000 INFO @ Tue, 16 Jun 2020 07:48:32: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 07:48:33: 9000000 INFO @ Tue, 16 Jun 2020 07:48:34: 4000000 INFO @ Tue, 16 Jun 2020 07:48:39: 10000000 INFO @ Tue, 16 Jun 2020 07:48:40: 5000000 INFO @ Tue, 16 Jun 2020 07:48:40: #1 tag size is determined as 51 bps INFO @ Tue, 16 Jun 2020 07:48:40: #1 tag size = 51 INFO @ Tue, 16 Jun 2020 07:48:40: #1 total tags in treatment: 10224775 INFO @ Tue, 16 Jun 2020 07:48:40: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 07:48:40: #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 07:48:40: #1 tags after filtering in treatment: 10224775 INFO @ Tue, 16 Jun 2020 07:48:40: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 07:48:40: #1 finished! INFO @ Tue, 16 Jun 2020 07:48:40: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 07:48:40: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 07:48:41: #2 number of paired peaks: 705 WARNING @ Tue, 16 Jun 2020 07:48:41: Fewer paired peaks (705) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 705 pairs to build model! INFO @ Tue, 16 Jun 2020 07:48:41: start model_add_line... INFO @ Tue, 16 Jun 2020 07:48:41: start X-correlation... INFO @ Tue, 16 Jun 2020 07:48:41: end of X-cor INFO @ Tue, 16 Jun 2020 07:48:41: #2 finished! INFO @ Tue, 16 Jun 2020 07:48:41: #2 predicted fragment length is 123 bps INFO @ Tue, 16 Jun 2020 07:48:41: #2 alternative fragment length(s) may be 123 bps INFO @ Tue, 16 Jun 2020 07:48:41: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX1078713/SRX1078713.10_model.r INFO @ Tue, 16 Jun 2020 07:48:41: #3 Call peaks... INFO @ Tue, 16 Jun 2020 07:48:41: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 07:48:43: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX1078713/SRX1078713.05_peaks.xls INFO @ Tue, 16 Jun 2020 07:48:43: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX1078713/SRX1078713.05_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 07:48:43: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX1078713/SRX1078713.05_summits.bed INFO @ Tue, 16 Jun 2020 07:48:43: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (5441 records, 4 fields): 6 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 07:48:46: 6000000 INFO @ Tue, 16 Jun 2020 07:48:51: 7000000 INFO @ Tue, 16 Jun 2020 07:48:57: 8000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 16 Jun 2020 07:49:02: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 07:49:02: 9000000 INFO @ Tue, 16 Jun 2020 07:49:07: 10000000 INFO @ Tue, 16 Jun 2020 07:49:09: #1 tag size is determined as 51 bps INFO @ Tue, 16 Jun 2020 07:49:09: #1 tag size = 51 INFO @ Tue, 16 Jun 2020 07:49:09: #1 total tags in treatment: 10224775 INFO @ Tue, 16 Jun 2020 07:49:09: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 07:49:09: #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 07:49:09: #1 tags after filtering in treatment: 10224775 INFO @ Tue, 16 Jun 2020 07:49:09: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 07:49:09: #1 finished! INFO @ Tue, 16 Jun 2020 07:49:09: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 07:49:09: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 07:49:10: #2 number of paired peaks: 705 WARNING @ Tue, 16 Jun 2020 07:49:10: Fewer paired peaks (705) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 705 pairs to build model! INFO @ Tue, 16 Jun 2020 07:49:10: start model_add_line... INFO @ Tue, 16 Jun 2020 07:49:10: start X-correlation... INFO @ Tue, 16 Jun 2020 07:49:10: end of X-cor INFO @ Tue, 16 Jun 2020 07:49:10: #2 finished! INFO @ Tue, 16 Jun 2020 07:49:10: #2 predicted fragment length is 123 bps INFO @ Tue, 16 Jun 2020 07:49:10: #2 alternative fragment length(s) may be 123 bps INFO @ Tue, 16 Jun 2020 07:49:10: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX1078713/SRX1078713.20_model.r INFO @ Tue, 16 Jun 2020 07:49:10: #3 Call peaks... INFO @ Tue, 16 Jun 2020 07:49:10: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 07:49:12: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX1078713/SRX1078713.10_peaks.xls INFO @ Tue, 16 Jun 2020 07:49:12: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX1078713/SRX1078713.10_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 07:49:12: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX1078713/SRX1078713.10_summits.bed INFO @ Tue, 16 Jun 2020 07:49:12: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (2803 records, 4 fields): 3 millis CompletedMACS2peakCalling BigWig に変換しました。 INFO @ Tue, 16 Jun 2020 07:49:31: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 07:49:42: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX1078713/SRX1078713.20_peaks.xls INFO @ Tue, 16 Jun 2020 07:49:42: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX1078713/SRX1078713.20_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 07:49:43: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX1078713/SRX1078713.20_summits.bed INFO @ Tue, 16 Jun 2020 07:49:43: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (1099 records, 4 fields): 2 millis CompletedMACS2peakCalling