Job ID = 6365987 SRX = SRX043998 Genome = ce11 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-15T22:37:21 prefetch.2.10.7: 1) Downloading 'SRR107578'... 2020-06-15T22:37:21 prefetch.2.10.7: Downloading via HTTPS... 2020-06-15T22:38:05 prefetch.2.10.7: HTTPS download succeed 2020-06-15T22:38:05 prefetch.2.10.7: 'SRR107578' is valid 2020-06-15T22:38:05 prefetch.2.10.7: 1) 'SRR107578' was downloaded successfully Read 4850547 spots for SRR107578/SRR107578.sra Written 4850547 spots for SRR107578/SRR107578.sra 2020-06-15T22:38:29 prefetch.2.10.7: 1) Downloading 'SRR107579'... 2020-06-15T22:38:29 prefetch.2.10.7: Downloading via HTTPS... 2020-06-15T22:39:08 prefetch.2.10.7: HTTPS download succeed 2020-06-15T22:39:08 prefetch.2.10.7: 'SRR107579' is valid 2020-06-15T22:39:08 prefetch.2.10.7: 1) 'SRR107579' was downloaded successfully Read 4952599 spots for SRR107579/SRR107579.sra Written 4952599 spots for SRR107579/SRR107579.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: 00:01:03 9803146 reads; of these: 9803146 (100.00%) were unpaired; of these: 5788217 (59.04%) aligned 0 times 3256110 (33.21%) aligned exactly 1 time 758819 (7.74%) aligned >1 times 40.96% overall alignment rate Time searching: 00:01:03 Overall time: 00:01:03 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] 604874 / 4014929 = 0.1507 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 07:41:55: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX043998/SRX043998.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX043998/SRX043998.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX043998/SRX043998.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX043998/SRX043998.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 07:41:55: #1 read tag files... INFO @ Tue, 16 Jun 2020 07:41:55: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 07:42:02: 1000000 INFO @ Tue, 16 Jun 2020 07:42:09: 2000000 INFO @ Tue, 16 Jun 2020 07:42:16: 3000000 INFO @ Tue, 16 Jun 2020 07:42:18: #1 tag size is determined as 32 bps INFO @ Tue, 16 Jun 2020 07:42:18: #1 tag size = 32 INFO @ Tue, 16 Jun 2020 07:42:18: #1 total tags in treatment: 3410055 INFO @ Tue, 16 Jun 2020 07:42:18: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 07:42:18: #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 07:42:18: #1 tags after filtering in treatment: 3410055 INFO @ Tue, 16 Jun 2020 07:42:18: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 07:42:18: #1 finished! INFO @ Tue, 16 Jun 2020 07:42:18: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 07:42:18: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 07:42:19: #2 number of paired peaks: 552 WARNING @ Tue, 16 Jun 2020 07:42:19: Fewer paired peaks (552) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 552 pairs to build model! INFO @ Tue, 16 Jun 2020 07:42:19: start model_add_line... INFO @ Tue, 16 Jun 2020 07:42:19: start X-correlation... INFO @ Tue, 16 Jun 2020 07:42:19: end of X-cor INFO @ Tue, 16 Jun 2020 07:42:19: #2 finished! INFO @ Tue, 16 Jun 2020 07:42:19: #2 predicted fragment length is 87 bps INFO @ Tue, 16 Jun 2020 07:42:19: #2 alternative fragment length(s) may be 87 bps INFO @ Tue, 16 Jun 2020 07:42:19: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX043998/SRX043998.05_model.r INFO @ Tue, 16 Jun 2020 07:42:19: #3 Call peaks... INFO @ Tue, 16 Jun 2020 07:42:19: #3 Pre-compute pvalue-qvalue table... 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 07:42:25: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX043998/SRX043998.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX043998/SRX043998.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX043998/SRX043998.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX043998/SRX043998.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 07:42:25: #1 read tag files... INFO @ Tue, 16 Jun 2020 07:42:25: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 07:42:27: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 07:42:31: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX043998/SRX043998.05_peaks.xls INFO @ Tue, 16 Jun 2020 07:42:31: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX043998/SRX043998.05_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 07:42:31: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX043998/SRX043998.05_summits.bed INFO @ Tue, 16 Jun 2020 07:42:31: Done! pass1 - making usageList (7 chroms): 0 millis pass2 - checking and writing primary data (1274 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 07:42:31: 1000000 INFO @ Tue, 16 Jun 2020 07:42:38: 2000000 INFO @ Tue, 16 Jun 2020 07:42:45: 3000000 INFO @ Tue, 16 Jun 2020 07:42:48: #1 tag size is determined as 32 bps INFO @ Tue, 16 Jun 2020 07:42:48: #1 tag size = 32 INFO @ Tue, 16 Jun 2020 07:42:48: #1 total tags in treatment: 3410055 INFO @ Tue, 16 Jun 2020 07:42:48: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 07:42:48: #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 07:42:48: #1 tags after filtering in treatment: 3410055 INFO @ Tue, 16 Jun 2020 07:42:48: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 07:42:48: #1 finished! INFO @ Tue, 16 Jun 2020 07:42:48: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 07:42:48: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 07:42:48: #2 number of paired peaks: 552 WARNING @ Tue, 16 Jun 2020 07:42:48: Fewer paired peaks (552) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 552 pairs to build model! INFO @ Tue, 16 Jun 2020 07:42:48: start model_add_line... INFO @ Tue, 16 Jun 2020 07:42:48: start X-correlation... INFO @ Tue, 16 Jun 2020 07:42:48: end of X-cor INFO @ Tue, 16 Jun 2020 07:42:48: #2 finished! INFO @ Tue, 16 Jun 2020 07:42:48: #2 predicted fragment length is 87 bps INFO @ Tue, 16 Jun 2020 07:42:48: #2 alternative fragment length(s) may be 87 bps INFO @ Tue, 16 Jun 2020 07:42:48: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX043998/SRX043998.10_model.r INFO @ Tue, 16 Jun 2020 07:42:48: #3 Call peaks... INFO @ Tue, 16 Jun 2020 07:42:48: #3 Pre-compute pvalue-qvalue table... 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 07:42:56: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX043998/SRX043998.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX043998/SRX043998.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX043998/SRX043998.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX043998/SRX043998.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 07:42:56: #1 read tag files... INFO @ Tue, 16 Jun 2020 07:42:56: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 07:42:57: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 07:43:01: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX043998/SRX043998.10_peaks.xls INFO @ Tue, 16 Jun 2020 07:43:01: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX043998/SRX043998.10_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 07:43:01: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX043998/SRX043998.10_summits.bed INFO @ Tue, 16 Jun 2020 07:43:01: Done! INFO @ Tue, 16 Jun 2020 07:43:03: 1000000 pass1 - making usageList (7 chroms): 0 millis pass2 - checking and writing primary data (570 records, 4 fields): 4 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 07:43:10: 2000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 16 Jun 2020 07:43:17: 3000000 INFO @ Tue, 16 Jun 2020 07:43:20: #1 tag size is determined as 32 bps INFO @ Tue, 16 Jun 2020 07:43:20: #1 tag size = 32 INFO @ Tue, 16 Jun 2020 07:43:20: #1 total tags in treatment: 3410055 INFO @ Tue, 16 Jun 2020 07:43:20: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 07:43:20: #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 07:43:20: #1 tags after filtering in treatment: 3410055 INFO @ Tue, 16 Jun 2020 07:43:20: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 07:43:20: #1 finished! INFO @ Tue, 16 Jun 2020 07:43:20: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 07:43:20: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 07:43:20: #2 number of paired peaks: 552 WARNING @ Tue, 16 Jun 2020 07:43:20: Fewer paired peaks (552) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 552 pairs to build model! INFO @ Tue, 16 Jun 2020 07:43:20: start model_add_line... INFO @ Tue, 16 Jun 2020 07:43:20: start X-correlation... INFO @ Tue, 16 Jun 2020 07:43:20: end of X-cor INFO @ Tue, 16 Jun 2020 07:43:20: #2 finished! INFO @ Tue, 16 Jun 2020 07:43:20: #2 predicted fragment length is 87 bps INFO @ Tue, 16 Jun 2020 07:43:20: #2 alternative fragment length(s) may be 87 bps INFO @ Tue, 16 Jun 2020 07:43:20: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX043998/SRX043998.20_model.r INFO @ Tue, 16 Jun 2020 07:43:20: #3 Call peaks... INFO @ Tue, 16 Jun 2020 07:43:20: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Tue, 16 Jun 2020 07:43:28: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 07:43:32: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX043998/SRX043998.20_peaks.xls INFO @ Tue, 16 Jun 2020 07:43:32: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX043998/SRX043998.20_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 07:43:32: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX043998/SRX043998.20_summits.bed INFO @ Tue, 16 Jun 2020 07:43:32: Done! pass1 - making usageList (7 chroms): 0 millis pass2 - checking and writing primary data (204 records, 4 fields): 2 millis CompletedMACS2peakCalling