Job ID = 6366539 SRX = SRX1769994 Genome = ce11 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-15T22:53:41 prefetch.2.10.7: 1) Downloading 'SRR3535773'... 2020-06-15T22:53:41 prefetch.2.10.7: Downloading via HTTPS... 2020-06-15T22:58:51 prefetch.2.10.7: HTTPS download succeed 2020-06-15T22:58:51 prefetch.2.10.7: 1) 'SRR3535773' was downloaded successfully Read 54569107 spots for SRR3535773/SRR3535773.sra Written 54569107 spots for SRR3535773/SRR3535773.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: 00:12:18 54569107 reads; of these: 54569107 (100.00%) were unpaired; of these: 3421752 (6.27%) aligned 0 times 43668783 (80.02%) aligned exactly 1 time 7478572 (13.70%) aligned >1 times 93.73% overall alignment rate Time searching: 00:12:18 Overall time: 00:12:18 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 24 files... [bam_rmdupse_core] 23957663 / 51147355 = 0.4684 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 08:25:22: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX1769994/SRX1769994.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX1769994/SRX1769994.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX1769994/SRX1769994.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX1769994/SRX1769994.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 08:25:22: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:25:22: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:25:28: 1000000 INFO @ Tue, 16 Jun 2020 08:25:34: 2000000 INFO @ Tue, 16 Jun 2020 08:25:40: 3000000 INFO @ Tue, 16 Jun 2020 08:25:46: 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 08:25:52: 5000000 INFO @ Tue, 16 Jun 2020 08:25:52: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX1769994/SRX1769994.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX1769994/SRX1769994.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX1769994/SRX1769994.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX1769994/SRX1769994.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 08:25:52: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:25:52: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:25:58: 6000000 INFO @ Tue, 16 Jun 2020 08:25:58: 1000000 INFO @ Tue, 16 Jun 2020 08:26:05: 7000000 INFO @ Tue, 16 Jun 2020 08:26:05: 2000000 INFO @ Tue, 16 Jun 2020 08:26:11: 8000000 INFO @ Tue, 16 Jun 2020 08:26:12: 3000000 INFO @ Tue, 16 Jun 2020 08:26:18: 9000000 INFO @ Tue, 16 Jun 2020 08:26:18: 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 08:26:22: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX1769994/SRX1769994.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX1769994/SRX1769994.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX1769994/SRX1769994.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX1769994/SRX1769994.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 08:26:22: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:26:22: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:26:25: 10000000 INFO @ Tue, 16 Jun 2020 08:26:25: 5000000 INFO @ Tue, 16 Jun 2020 08:26:29: 1000000 INFO @ Tue, 16 Jun 2020 08:26:31: 11000000 INFO @ Tue, 16 Jun 2020 08:26:32: 6000000 INFO @ Tue, 16 Jun 2020 08:26:36: 2000000 INFO @ Tue, 16 Jun 2020 08:26:38: 12000000 INFO @ Tue, 16 Jun 2020 08:26:38: 7000000 INFO @ Tue, 16 Jun 2020 08:26:42: 3000000 INFO @ Tue, 16 Jun 2020 08:26:45: 8000000 INFO @ Tue, 16 Jun 2020 08:26:45: 13000000 INFO @ Tue, 16 Jun 2020 08:26:50: 4000000 INFO @ Tue, 16 Jun 2020 08:26:52: 9000000 INFO @ Tue, 16 Jun 2020 08:26:52: 14000000 INFO @ Tue, 16 Jun 2020 08:26:57: 5000000 INFO @ Tue, 16 Jun 2020 08:26:59: 10000000 INFO @ Tue, 16 Jun 2020 08:26:59: 15000000 INFO @ Tue, 16 Jun 2020 08:27:04: 6000000 INFO @ Tue, 16 Jun 2020 08:27:05: 11000000 INFO @ Tue, 16 Jun 2020 08:27:06: 16000000 INFO @ Tue, 16 Jun 2020 08:27:11: 7000000 INFO @ Tue, 16 Jun 2020 08:27:12: 12000000 INFO @ Tue, 16 Jun 2020 08:27:13: 17000000 INFO @ Tue, 16 Jun 2020 08:27:17: 8000000 INFO @ Tue, 16 Jun 2020 08:27:19: 13000000 INFO @ Tue, 16 Jun 2020 08:27:20: 18000000 INFO @ Tue, 16 Jun 2020 08:27:24: 9000000 INFO @ Tue, 16 Jun 2020 08:27:26: 14000000 INFO @ Tue, 16 Jun 2020 08:27:27: 19000000 INFO @ Tue, 16 Jun 2020 08:27:31: 10000000 INFO @ Tue, 16 Jun 2020 08:27:32: 15000000 INFO @ Tue, 16 Jun 2020 08:27:34: 20000000 INFO @ Tue, 16 Jun 2020 08:27:38: 11000000 INFO @ Tue, 16 Jun 2020 08:27:39: 16000000 INFO @ Tue, 16 Jun 2020 08:27:41: 21000000 INFO @ Tue, 16 Jun 2020 08:27:45: 12000000 INFO @ Tue, 16 Jun 2020 08:27:46: 17000000 INFO @ Tue, 16 Jun 2020 08:27:48: 22000000 INFO @ Tue, 16 Jun 2020 08:27:52: 13000000 INFO @ Tue, 16 Jun 2020 08:27:53: 18000000 INFO @ Tue, 16 Jun 2020 08:27:54: 23000000 INFO @ Tue, 16 Jun 2020 08:27:59: 14000000 INFO @ Tue, 16 Jun 2020 08:27:59: 19000000 INFO @ Tue, 16 Jun 2020 08:28:01: 24000000 INFO @ Tue, 16 Jun 2020 08:28:06: 15000000 INFO @ Tue, 16 Jun 2020 08:28:06: 20000000 INFO @ Tue, 16 Jun 2020 08:28:08: 25000000 INFO @ Tue, 16 Jun 2020 08:28:13: 16000000 INFO @ Tue, 16 Jun 2020 08:28:13: 21000000 INFO @ Tue, 16 Jun 2020 08:28:15: 26000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 16 Jun 2020 08:28:19: 17000000 INFO @ Tue, 16 Jun 2020 08:28:20: 22000000 INFO @ Tue, 16 Jun 2020 08:28:22: 27000000 INFO @ Tue, 16 Jun 2020 08:28:23: #1 tag size is determined as 50 bps INFO @ Tue, 16 Jun 2020 08:28:23: #1 tag size = 50 INFO @ Tue, 16 Jun 2020 08:28:23: #1 total tags in treatment: 27189692 INFO @ Tue, 16 Jun 2020 08:28:23: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:28:23: #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 08:28:24: #1 tags after filtering in treatment: 27189692 INFO @ Tue, 16 Jun 2020 08:28:24: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:28:24: #1 finished! INFO @ Tue, 16 Jun 2020 08:28:24: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:28:24: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:28:25: #2 number of paired peaks: 466 WARNING @ Tue, 16 Jun 2020 08:28:25: Fewer paired peaks (466) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 466 pairs to build model! INFO @ Tue, 16 Jun 2020 08:28:25: start model_add_line... INFO @ Tue, 16 Jun 2020 08:28:26: start X-correlation... INFO @ Tue, 16 Jun 2020 08:28:26: end of X-cor INFO @ Tue, 16 Jun 2020 08:28:26: #2 finished! INFO @ Tue, 16 Jun 2020 08:28:26: #2 predicted fragment length is 245 bps INFO @ Tue, 16 Jun 2020 08:28:26: #2 alternative fragment length(s) may be 4,241,245 bps INFO @ Tue, 16 Jun 2020 08:28:26: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX1769994/SRX1769994.05_model.r INFO @ Tue, 16 Jun 2020 08:28:26: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:28:26: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 08:28:26: 18000000 INFO @ Tue, 16 Jun 2020 08:28:26: 23000000 INFO @ Tue, 16 Jun 2020 08:28:33: 24000000 INFO @ Tue, 16 Jun 2020 08:28:33: 19000000 INFO @ Tue, 16 Jun 2020 08:28:39: 25000000 INFO @ Tue, 16 Jun 2020 08:28:39: 20000000 INFO @ Tue, 16 Jun 2020 08:28:46: 26000000 INFO @ Tue, 16 Jun 2020 08:28:46: 21000000 INFO @ Tue, 16 Jun 2020 08:28:52: 27000000 INFO @ Tue, 16 Jun 2020 08:28:52: 22000000 INFO @ Tue, 16 Jun 2020 08:28:53: #1 tag size is determined as 50 bps INFO @ Tue, 16 Jun 2020 08:28:53: #1 tag size = 50 INFO @ Tue, 16 Jun 2020 08:28:53: #1 total tags in treatment: 27189692 INFO @ Tue, 16 Jun 2020 08:28:53: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:28:53: #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 08:28:54: #1 tags after filtering in treatment: 27189692 INFO @ Tue, 16 Jun 2020 08:28:54: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:28:54: #1 finished! INFO @ Tue, 16 Jun 2020 08:28:54: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:28:54: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:28:56: #2 number of paired peaks: 466 WARNING @ Tue, 16 Jun 2020 08:28:56: Fewer paired peaks (466) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 466 pairs to build model! INFO @ Tue, 16 Jun 2020 08:28:56: start model_add_line... INFO @ Tue, 16 Jun 2020 08:28:56: start X-correlation... INFO @ Tue, 16 Jun 2020 08:28:56: end of X-cor INFO @ Tue, 16 Jun 2020 08:28:56: #2 finished! INFO @ Tue, 16 Jun 2020 08:28:56: #2 predicted fragment length is 245 bps INFO @ Tue, 16 Jun 2020 08:28:56: #2 alternative fragment length(s) may be 4,241,245 bps INFO @ Tue, 16 Jun 2020 08:28:56: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX1769994/SRX1769994.10_model.r INFO @ Tue, 16 Jun 2020 08:28:56: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:28:56: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 08:28:58: 23000000 INFO @ Tue, 16 Jun 2020 08:29:05: 24000000 BigWig に変換しました。 INFO @ Tue, 16 Jun 2020 08:29:11: 25000000 INFO @ Tue, 16 Jun 2020 08:29:17: 26000000 INFO @ Tue, 16 Jun 2020 08:29:23: 27000000 INFO @ Tue, 16 Jun 2020 08:29:24: #1 tag size is determined as 50 bps INFO @ Tue, 16 Jun 2020 08:29:24: #1 tag size = 50 INFO @ Tue, 16 Jun 2020 08:29:24: #1 total tags in treatment: 27189692 INFO @ Tue, 16 Jun 2020 08:29:24: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:29:24: #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 08:29:24: #1 tags after filtering in treatment: 27189692 INFO @ Tue, 16 Jun 2020 08:29:24: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:29:24: #1 finished! INFO @ Tue, 16 Jun 2020 08:29:24: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:29:24: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:29:26: #2 number of paired peaks: 466 WARNING @ Tue, 16 Jun 2020 08:29:26: Fewer paired peaks (466) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 466 pairs to build model! INFO @ Tue, 16 Jun 2020 08:29:26: start model_add_line... INFO @ Tue, 16 Jun 2020 08:29:26: start X-correlation... INFO @ Tue, 16 Jun 2020 08:29:26: end of X-cor INFO @ Tue, 16 Jun 2020 08:29:26: #2 finished! INFO @ Tue, 16 Jun 2020 08:29:26: #2 predicted fragment length is 245 bps INFO @ Tue, 16 Jun 2020 08:29:26: #2 alternative fragment length(s) may be 4,241,245 bps INFO @ Tue, 16 Jun 2020 08:29:26: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX1769994/SRX1769994.20_model.r INFO @ Tue, 16 Jun 2020 08:29:26: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:29:26: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 08:29:33: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 08:30:02: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX1769994/SRX1769994.05_peaks.xls INFO @ Tue, 16 Jun 2020 08:30:02: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX1769994/SRX1769994.05_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:30:02: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX1769994/SRX1769994.05_summits.bed INFO @ Tue, 16 Jun 2020 08:30:02: Done! pass1 - making usageList (7 chroms): 2 millis pass2 - checking and writing primary data (8481 records, 4 fields): 9 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 08:30:03: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 08:30:29: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX1769994/SRX1769994.10_peaks.xls INFO @ Tue, 16 Jun 2020 08:30:30: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX1769994/SRX1769994.10_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:30:30: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX1769994/SRX1769994.10_summits.bed INFO @ Tue, 16 Jun 2020 08:30:30: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (6359 records, 4 fields): 7 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 08:30:32: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 08:30:59: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX1769994/SRX1769994.20_peaks.xls INFO @ Tue, 16 Jun 2020 08:30:59: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX1769994/SRX1769994.20_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:30:59: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX1769994/SRX1769994.20_summits.bed INFO @ Tue, 16 Jun 2020 08:30:59: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (4038 records, 4 fields): 5 millis CompletedMACS2peakCalling