Job ID = 6367428 SRX = SRX331186 Genome = ce11 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-15T23:29:20 prefetch.2.10.7: 1) Downloading 'SRR947418'... 2020-06-15T23:29:20 prefetch.2.10.7: Downloading via HTTPS... 2020-06-15T23:30:17 prefetch.2.10.7: HTTPS download succeed 2020-06-15T23:30:17 prefetch.2.10.7: 'SRR947418' is valid 2020-06-15T23:30:17 prefetch.2.10.7: 1) 'SRR947418' was downloaded successfully Read 8042136 spots for SRR947418/SRR947418.sra Written 8042136 spots for SRR947418/SRR947418.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: 00:01:17 8042136 reads; of these: 8042136 (100.00%) were unpaired; of these: 1095138 (13.62%) aligned 0 times 5805319 (72.19%) aligned exactly 1 time 1141679 (14.20%) aligned >1 times 86.38% overall alignment rate Time searching: 00:01:17 Overall time: 00:01:17 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] 1236375 / 6946998 = 0.1780 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 08:33:38: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX331186/SRX331186.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX331186/SRX331186.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX331186/SRX331186.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX331186/SRX331186.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 08:33:38: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:33:38: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:33:43: 1000000 INFO @ Tue, 16 Jun 2020 08:33:48: 2000000 INFO @ Tue, 16 Jun 2020 08:33:53: 3000000 INFO @ Tue, 16 Jun 2020 08:33:58: 4000000 INFO @ Tue, 16 Jun 2020 08:34:03: 5000000 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 08:34:06: #1 tag size is determined as 32 bps INFO @ Tue, 16 Jun 2020 08:34:06: #1 tag size = 32 INFO @ Tue, 16 Jun 2020 08:34:06: #1 total tags in treatment: 5710623 INFO @ Tue, 16 Jun 2020 08:34:06: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:34:06: #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 08:34:06: #1 tags after filtering in treatment: 5710623 INFO @ Tue, 16 Jun 2020 08:34:06: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:34:06: #1 finished! INFO @ Tue, 16 Jun 2020 08:34:06: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:34:06: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:34:07: #2 number of paired peaks: 489 WARNING @ Tue, 16 Jun 2020 08:34:07: Fewer paired peaks (489) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 489 pairs to build model! INFO @ Tue, 16 Jun 2020 08:34:07: start model_add_line... INFO @ Tue, 16 Jun 2020 08:34:07: start X-correlation... INFO @ Tue, 16 Jun 2020 08:34:07: end of X-cor INFO @ Tue, 16 Jun 2020 08:34:07: #2 finished! INFO @ Tue, 16 Jun 2020 08:34:07: #2 predicted fragment length is 89 bps INFO @ Tue, 16 Jun 2020 08:34:07: #2 alternative fragment length(s) may be 4,37,67,89 bps INFO @ Tue, 16 Jun 2020 08:34:07: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX331186/SRX331186.05_model.r INFO @ Tue, 16 Jun 2020 08:34:07: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:34:07: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 08:34:07: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX331186/SRX331186.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX331186/SRX331186.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX331186/SRX331186.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX331186/SRX331186.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 08:34:07: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:34:07: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:34:12: 1000000 INFO @ Tue, 16 Jun 2020 08:34:17: 2000000 INFO @ Tue, 16 Jun 2020 08:34:19: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 08:34:21: 3000000 INFO @ Tue, 16 Jun 2020 08:34:26: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX331186/SRX331186.05_peaks.xls INFO @ Tue, 16 Jun 2020 08:34:26: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX331186/SRX331186.05_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:34:26: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX331186/SRX331186.05_summits.bed INFO @ Tue, 16 Jun 2020 08:34:26: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (1225 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 08:34:26: 4000000 INFO @ Tue, 16 Jun 2020 08:34:31: 5000000 INFO @ Tue, 16 Jun 2020 08:34:34: #1 tag size is determined as 32 bps INFO @ Tue, 16 Jun 2020 08:34:34: #1 tag size = 32 INFO @ Tue, 16 Jun 2020 08:34:34: #1 total tags in treatment: 5710623 INFO @ Tue, 16 Jun 2020 08:34:34: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:34:34: #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 08:34:34: #1 tags after filtering in treatment: 5710623 INFO @ Tue, 16 Jun 2020 08:34:34: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:34:34: #1 finished! INFO @ Tue, 16 Jun 2020 08:34:34: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:34:34: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:34:34: #2 number of paired peaks: 489 WARNING @ Tue, 16 Jun 2020 08:34:34: Fewer paired peaks (489) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 489 pairs to build model! INFO @ Tue, 16 Jun 2020 08:34:34: start model_add_line... INFO @ Tue, 16 Jun 2020 08:34:35: start X-correlation... INFO @ Tue, 16 Jun 2020 08:34:35: end of X-cor INFO @ Tue, 16 Jun 2020 08:34:35: #2 finished! INFO @ Tue, 16 Jun 2020 08:34:35: #2 predicted fragment length is 89 bps INFO @ Tue, 16 Jun 2020 08:34:35: #2 alternative fragment length(s) may be 4,37,67,89 bps INFO @ Tue, 16 Jun 2020 08:34:35: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX331186/SRX331186.10_model.r INFO @ Tue, 16 Jun 2020 08:34:35: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:34:35: #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 08:34:37: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX331186/SRX331186.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX331186/SRX331186.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX331186/SRX331186.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX331186/SRX331186.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 08:34:37: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:34:37: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:34:43: 1000000 INFO @ Tue, 16 Jun 2020 08:34:46: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 08:34:48: 2000000 INFO @ Tue, 16 Jun 2020 08:34:52: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX331186/SRX331186.10_peaks.xls INFO @ Tue, 16 Jun 2020 08:34:52: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX331186/SRX331186.10_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:34:52: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX331186/SRX331186.10_summits.bed INFO @ Tue, 16 Jun 2020 08:34:52: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (601 records, 4 fields): 5 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 08:34:53: 3000000 INFO @ Tue, 16 Jun 2020 08:34:58: 4000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 16 Jun 2020 08:35:04: 5000000 INFO @ Tue, 16 Jun 2020 08:35:08: #1 tag size is determined as 32 bps INFO @ Tue, 16 Jun 2020 08:35:08: #1 tag size = 32 INFO @ Tue, 16 Jun 2020 08:35:08: #1 total tags in treatment: 5710623 INFO @ Tue, 16 Jun 2020 08:35:08: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:35:08: #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 08:35:08: #1 tags after filtering in treatment: 5710623 INFO @ Tue, 16 Jun 2020 08:35:08: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:35:08: #1 finished! INFO @ Tue, 16 Jun 2020 08:35:08: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:35:08: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:35:08: #2 number of paired peaks: 489 WARNING @ Tue, 16 Jun 2020 08:35:08: Fewer paired peaks (489) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 489 pairs to build model! INFO @ Tue, 16 Jun 2020 08:35:08: start model_add_line... INFO @ Tue, 16 Jun 2020 08:35:08: start X-correlation... INFO @ Tue, 16 Jun 2020 08:35:08: end of X-cor INFO @ Tue, 16 Jun 2020 08:35:08: #2 finished! INFO @ Tue, 16 Jun 2020 08:35:08: #2 predicted fragment length is 89 bps INFO @ Tue, 16 Jun 2020 08:35:08: #2 alternative fragment length(s) may be 4,37,67,89 bps INFO @ Tue, 16 Jun 2020 08:35:08: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX331186/SRX331186.20_model.r INFO @ Tue, 16 Jun 2020 08:35:08: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:35:08: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Tue, 16 Jun 2020 08:35:20: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 08:35:25: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX331186/SRX331186.20_peaks.xls INFO @ Tue, 16 Jun 2020 08:35:25: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX331186/SRX331186.20_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:35:25: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX331186/SRX331186.20_summits.bed INFO @ Tue, 16 Jun 2020 08:35:25: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (202 records, 4 fields): 1 millis CompletedMACS2peakCalling