Job ID = 6366080 SRX = SRX059252 Genome = ce11 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-15T22:38:51 prefetch.2.10.7: 1) Downloading 'SRR190692'... 2020-06-15T22:38:51 prefetch.2.10.7: Downloading via HTTPS... 2020-06-15T22:40:38 prefetch.2.10.7: HTTPS download succeed 2020-06-15T22:40:39 prefetch.2.10.7: 'SRR190692' is valid 2020-06-15T22:40:39 prefetch.2.10.7: 1) 'SRR190692' was downloaded successfully Read 15991314 spots for SRR190692/SRR190692.sra Written 15991314 spots for SRR190692/SRR190692.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: 00:02:56 15991314 reads; of these: 15991314 (100.00%) were unpaired; of these: 1056337 (6.61%) aligned 0 times 12427608 (77.71%) aligned exactly 1 time 2507369 (15.68%) aligned >1 times 93.39% overall alignment rate Time searching: 00:02:56 Overall time: 00:02:56 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] 3468074 / 14934977 = 0.2322 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 07:48:26: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX059252/SRX059252.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX059252/SRX059252.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX059252/SRX059252.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX059252/SRX059252.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 07:48:26: #1 read tag files... INFO @ Tue, 16 Jun 2020 07:48:26: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 07:48:31: 1000000 INFO @ Tue, 16 Jun 2020 07:48:36: 2000000 INFO @ Tue, 16 Jun 2020 07:48:42: 3000000 INFO @ Tue, 16 Jun 2020 07:48:47: 4000000 INFO @ Tue, 16 Jun 2020 07:48:52: 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 07:48:56: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX059252/SRX059252.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX059252/SRX059252.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX059252/SRX059252.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX059252/SRX059252.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 07:48:56: #1 read tag files... INFO @ Tue, 16 Jun 2020 07:48:56: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 07:48:58: 6000000 INFO @ Tue, 16 Jun 2020 07:49:01: 1000000 INFO @ Tue, 16 Jun 2020 07:49:04: 7000000 INFO @ Tue, 16 Jun 2020 07:49:07: 2000000 INFO @ Tue, 16 Jun 2020 07:49:09: 8000000 INFO @ Tue, 16 Jun 2020 07:49:13: 3000000 INFO @ Tue, 16 Jun 2020 07:49:15: 9000000 INFO @ Tue, 16 Jun 2020 07:49:18: 4000000 INFO @ Tue, 16 Jun 2020 07:49:20: 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 07:49:24: 5000000 INFO @ Tue, 16 Jun 2020 07:49:25: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX059252/SRX059252.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX059252/SRX059252.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX059252/SRX059252.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX059252/SRX059252.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 07:49:25: #1 read tag files... INFO @ Tue, 16 Jun 2020 07:49:25: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 07:49:26: 11000000 INFO @ Tue, 16 Jun 2020 07:49:29: #1 tag size is determined as 42 bps INFO @ Tue, 16 Jun 2020 07:49:29: #1 tag size = 42 INFO @ Tue, 16 Jun 2020 07:49:29: #1 total tags in treatment: 11466903 INFO @ Tue, 16 Jun 2020 07:49:29: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 07:49:29: #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 07:49:29: #1 tags after filtering in treatment: 11466903 INFO @ Tue, 16 Jun 2020 07:49:29: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 07:49:29: #1 finished! INFO @ Tue, 16 Jun 2020 07:49:29: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 07:49:29: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 07:49:30: 6000000 INFO @ Tue, 16 Jun 2020 07:49:30: #2 number of paired peaks: 575 WARNING @ Tue, 16 Jun 2020 07:49:30: Fewer paired peaks (575) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 575 pairs to build model! INFO @ Tue, 16 Jun 2020 07:49:30: start model_add_line... INFO @ Tue, 16 Jun 2020 07:49:30: start X-correlation... INFO @ Tue, 16 Jun 2020 07:49:30: end of X-cor INFO @ Tue, 16 Jun 2020 07:49:30: #2 finished! INFO @ Tue, 16 Jun 2020 07:49:30: #2 predicted fragment length is 131 bps INFO @ Tue, 16 Jun 2020 07:49:30: #2 alternative fragment length(s) may be 131 bps INFO @ Tue, 16 Jun 2020 07:49:30: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX059252/SRX059252.05_model.r INFO @ Tue, 16 Jun 2020 07:49:30: #3 Call peaks... INFO @ Tue, 16 Jun 2020 07:49:30: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 07:49:31: 1000000 INFO @ Tue, 16 Jun 2020 07:49:35: 7000000 INFO @ Tue, 16 Jun 2020 07:49:37: 2000000 INFO @ Tue, 16 Jun 2020 07:49:41: 8000000 INFO @ Tue, 16 Jun 2020 07:49:43: 3000000 INFO @ Tue, 16 Jun 2020 07:49:47: 9000000 INFO @ Tue, 16 Jun 2020 07:49:48: 4000000 INFO @ Tue, 16 Jun 2020 07:49:53: 10000000 INFO @ Tue, 16 Jun 2020 07:49:54: 5000000 INFO @ Tue, 16 Jun 2020 07:49:55: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 07:49:59: 11000000 INFO @ Tue, 16 Jun 2020 07:50:00: 6000000 INFO @ Tue, 16 Jun 2020 07:50:02: #1 tag size is determined as 42 bps INFO @ Tue, 16 Jun 2020 07:50:02: #1 tag size = 42 INFO @ Tue, 16 Jun 2020 07:50:02: #1 total tags in treatment: 11466903 INFO @ Tue, 16 Jun 2020 07:50:02: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 07:50:02: #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 07:50:02: #1 tags after filtering in treatment: 11466903 INFO @ Tue, 16 Jun 2020 07:50:02: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 07:50:02: #1 finished! INFO @ Tue, 16 Jun 2020 07:50:02: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 07:50:02: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 07:50:03: #2 number of paired peaks: 575 WARNING @ Tue, 16 Jun 2020 07:50:03: Fewer paired peaks (575) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 575 pairs to build model! INFO @ Tue, 16 Jun 2020 07:50:03: start model_add_line... INFO @ Tue, 16 Jun 2020 07:50:03: start X-correlation... INFO @ Tue, 16 Jun 2020 07:50:03: end of X-cor INFO @ Tue, 16 Jun 2020 07:50:03: #2 finished! INFO @ Tue, 16 Jun 2020 07:50:03: #2 predicted fragment length is 131 bps INFO @ Tue, 16 Jun 2020 07:50:03: #2 alternative fragment length(s) may be 131 bps INFO @ Tue, 16 Jun 2020 07:50:03: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX059252/SRX059252.10_model.r INFO @ Tue, 16 Jun 2020 07:50:03: #3 Call peaks... INFO @ Tue, 16 Jun 2020 07:50:03: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 07:50:06: 7000000 INFO @ Tue, 16 Jun 2020 07:50:08: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX059252/SRX059252.05_peaks.xls INFO @ Tue, 16 Jun 2020 07:50:08: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX059252/SRX059252.05_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 07:50:08: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX059252/SRX059252.05_summits.bed INFO @ Tue, 16 Jun 2020 07:50:08: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (4933 records, 4 fields): 5 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 07:50:11: 8000000 INFO @ Tue, 16 Jun 2020 07:50:16: 9000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 16 Jun 2020 07:50:22: 10000000 INFO @ Tue, 16 Jun 2020 07:50:27: 11000000 INFO @ Tue, 16 Jun 2020 07:50:29: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 07:50:30: #1 tag size is determined as 42 bps INFO @ Tue, 16 Jun 2020 07:50:30: #1 tag size = 42 INFO @ Tue, 16 Jun 2020 07:50:30: #1 total tags in treatment: 11466903 INFO @ Tue, 16 Jun 2020 07:50:30: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 07:50:30: #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 07:50:30: #1 tags after filtering in treatment: 11466903 INFO @ Tue, 16 Jun 2020 07:50:30: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 07:50:30: #1 finished! INFO @ Tue, 16 Jun 2020 07:50:30: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 07:50:30: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 07:50:31: #2 number of paired peaks: 575 WARNING @ Tue, 16 Jun 2020 07:50:31: Fewer paired peaks (575) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 575 pairs to build model! INFO @ Tue, 16 Jun 2020 07:50:31: start model_add_line... INFO @ Tue, 16 Jun 2020 07:50:31: start X-correlation... INFO @ Tue, 16 Jun 2020 07:50:31: end of X-cor INFO @ Tue, 16 Jun 2020 07:50:31: #2 finished! INFO @ Tue, 16 Jun 2020 07:50:31: #2 predicted fragment length is 131 bps INFO @ Tue, 16 Jun 2020 07:50:31: #2 alternative fragment length(s) may be 131 bps INFO @ Tue, 16 Jun 2020 07:50:31: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX059252/SRX059252.20_model.r INFO @ Tue, 16 Jun 2020 07:50:31: #3 Call peaks... INFO @ Tue, 16 Jun 2020 07:50:31: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 07:50:41: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX059252/SRX059252.10_peaks.xls INFO @ Tue, 16 Jun 2020 07:50:41: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX059252/SRX059252.10_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 07:50:41: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX059252/SRX059252.10_summits.bed INFO @ Tue, 16 Jun 2020 07:50:41: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (2531 records, 4 fields): 4 millis CompletedMACS2peakCalling BigWig に変換しました。 INFO @ Tue, 16 Jun 2020 07:50:54: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 07:51:07: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX059252/SRX059252.20_peaks.xls INFO @ Tue, 16 Jun 2020 07:51:07: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX059252/SRX059252.20_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 07:51:07: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX059252/SRX059252.20_summits.bed INFO @ Tue, 16 Jun 2020 07:51:07: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (1643 records, 4 fields): 3 millis CompletedMACS2peakCalling