Job ID = 6365907 SRX = SRX027098 Genome = ce11 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-15T22:29:44 prefetch.2.10.7: 1) Downloading 'SRR066370'... 2020-06-15T22:29:44 prefetch.2.10.7: Downloading via HTTPS... 2020-06-15T22:30:25 prefetch.2.10.7: HTTPS download succeed 2020-06-15T22:30:26 prefetch.2.10.7: 'SRR066370' is valid 2020-06-15T22:30:26 prefetch.2.10.7: 1) 'SRR066370' was downloaded successfully Read 10435718 spots for SRR066370/SRR066370.sra Written 10435718 spots for SRR066370/SRR066370.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: 00:01:30 10435718 reads; of these: 10435718 (100.00%) were unpaired; of these: 2655673 (25.45%) aligned 0 times 6046371 (57.94%) aligned exactly 1 time 1733674 (16.61%) aligned >1 times 74.55% overall alignment rate Time searching: 00:01:30 Overall time: 00:01:30 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] 1056196 / 7780045 = 0.1358 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 07:34:41: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX027098/SRX027098.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX027098/SRX027098.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX027098/SRX027098.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX027098/SRX027098.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 07:34:41: #1 read tag files... INFO @ Tue, 16 Jun 2020 07:34:41: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 07:34:47: 1000000 INFO @ Tue, 16 Jun 2020 07:34:52: 2000000 INFO @ Tue, 16 Jun 2020 07:34:58: 3000000 INFO @ Tue, 16 Jun 2020 07:35:04: 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 07:35:09: 5000000 INFO @ Tue, 16 Jun 2020 07:35:11: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX027098/SRX027098.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX027098/SRX027098.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX027098/SRX027098.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX027098/SRX027098.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 07:35:11: #1 read tag files... INFO @ Tue, 16 Jun 2020 07:35:11: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 07:35:15: 6000000 INFO @ Tue, 16 Jun 2020 07:35:17: 1000000 INFO @ Tue, 16 Jun 2020 07:35:20: #1 tag size is determined as 36 bps INFO @ Tue, 16 Jun 2020 07:35:20: #1 tag size = 36 INFO @ Tue, 16 Jun 2020 07:35:20: #1 total tags in treatment: 6723849 INFO @ Tue, 16 Jun 2020 07:35:20: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 07:35:20: #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 07:35:20: #1 tags after filtering in treatment: 6723849 INFO @ Tue, 16 Jun 2020 07:35:20: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 07:35:20: #1 finished! INFO @ Tue, 16 Jun 2020 07:35:20: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 07:35:20: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 07:35:20: #2 number of paired peaks: 556 WARNING @ Tue, 16 Jun 2020 07:35:20: Fewer paired peaks (556) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 556 pairs to build model! INFO @ Tue, 16 Jun 2020 07:35:20: start model_add_line... INFO @ Tue, 16 Jun 2020 07:35:21: start X-correlation... INFO @ Tue, 16 Jun 2020 07:35:21: end of X-cor INFO @ Tue, 16 Jun 2020 07:35:21: #2 finished! INFO @ Tue, 16 Jun 2020 07:35:21: #2 predicted fragment length is 150 bps INFO @ Tue, 16 Jun 2020 07:35:21: #2 alternative fragment length(s) may be 4,139,150 bps INFO @ Tue, 16 Jun 2020 07:35:21: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX027098/SRX027098.05_model.r INFO @ Tue, 16 Jun 2020 07:35:21: #3 Call peaks... INFO @ Tue, 16 Jun 2020 07:35:21: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 07:35:23: 2000000 INFO @ Tue, 16 Jun 2020 07:35:29: 3000000 INFO @ Tue, 16 Jun 2020 07:35:35: 4000000 INFO @ Tue, 16 Jun 2020 07:35:37: #3 Call peaks for each chromosome... 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 07:35:41: 5000000 INFO @ Tue, 16 Jun 2020 07:35:41: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX027098/SRX027098.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX027098/SRX027098.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX027098/SRX027098.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX027098/SRX027098.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 07:35:41: #1 read tag files... INFO @ Tue, 16 Jun 2020 07:35:41: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 07:35:45: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX027098/SRX027098.05_peaks.xls INFO @ Tue, 16 Jun 2020 07:35:45: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX027098/SRX027098.05_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 07:35:45: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX027098/SRX027098.05_summits.bed INFO @ Tue, 16 Jun 2020 07:35:45: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (4243 records, 4 fields): 5 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 07:35:48: 1000000 INFO @ Tue, 16 Jun 2020 07:35:48: 6000000 INFO @ Tue, 16 Jun 2020 07:35:53: #1 tag size is determined as 36 bps INFO @ Tue, 16 Jun 2020 07:35:54: #1 tag size = 36 INFO @ Tue, 16 Jun 2020 07:35:54: #1 total tags in treatment: 6723849 INFO @ Tue, 16 Jun 2020 07:35:54: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 07:35:54: #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 07:35:54: #1 tags after filtering in treatment: 6723849 INFO @ Tue, 16 Jun 2020 07:35:54: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 07:35:54: #1 finished! INFO @ Tue, 16 Jun 2020 07:35:54: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 07:35:54: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 07:35:54: #2 number of paired peaks: 556 WARNING @ Tue, 16 Jun 2020 07:35:54: Fewer paired peaks (556) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 556 pairs to build model! INFO @ Tue, 16 Jun 2020 07:35:54: start model_add_line... INFO @ Tue, 16 Jun 2020 07:35:54: start X-correlation... INFO @ Tue, 16 Jun 2020 07:35:54: end of X-cor INFO @ Tue, 16 Jun 2020 07:35:54: #2 finished! INFO @ Tue, 16 Jun 2020 07:35:54: #2 predicted fragment length is 150 bps INFO @ Tue, 16 Jun 2020 07:35:54: #2 alternative fragment length(s) may be 4,139,150 bps INFO @ Tue, 16 Jun 2020 07:35:54: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX027098/SRX027098.10_model.r INFO @ Tue, 16 Jun 2020 07:35:54: #3 Call peaks... INFO @ Tue, 16 Jun 2020 07:35:54: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 07:35:55: 2000000 INFO @ Tue, 16 Jun 2020 07:36:02: 3000000 INFO @ Tue, 16 Jun 2020 07:36:09: 4000000 INFO @ Tue, 16 Jun 2020 07:36:09: #3 Call peaks for each chromosome... BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 16 Jun 2020 07:36:15: 5000000 INFO @ Tue, 16 Jun 2020 07:36:17: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX027098/SRX027098.10_peaks.xls INFO @ Tue, 16 Jun 2020 07:36:17: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX027098/SRX027098.10_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 07:36:17: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX027098/SRX027098.10_summits.bed INFO @ Tue, 16 Jun 2020 07:36:17: Done! pass1 - making usageList (7 chroms): 0 millis pass2 - checking and writing primary data (1113 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 07:36:22: 6000000 INFO @ Tue, 16 Jun 2020 07:36:27: #1 tag size is determined as 36 bps INFO @ Tue, 16 Jun 2020 07:36:27: #1 tag size = 36 INFO @ Tue, 16 Jun 2020 07:36:27: #1 total tags in treatment: 6723849 INFO @ Tue, 16 Jun 2020 07:36:27: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 07:36:27: #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 07:36:27: #1 tags after filtering in treatment: 6723849 INFO @ Tue, 16 Jun 2020 07:36:27: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 07:36:27: #1 finished! INFO @ Tue, 16 Jun 2020 07:36:27: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 07:36:27: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 07:36:27: #2 number of paired peaks: 556 WARNING @ Tue, 16 Jun 2020 07:36:27: Fewer paired peaks (556) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 556 pairs to build model! INFO @ Tue, 16 Jun 2020 07:36:27: start model_add_line... INFO @ Tue, 16 Jun 2020 07:36:27: start X-correlation... INFO @ Tue, 16 Jun 2020 07:36:28: end of X-cor INFO @ Tue, 16 Jun 2020 07:36:28: #2 finished! INFO @ Tue, 16 Jun 2020 07:36:28: #2 predicted fragment length is 150 bps INFO @ Tue, 16 Jun 2020 07:36:28: #2 alternative fragment length(s) may be 4,139,150 bps INFO @ Tue, 16 Jun 2020 07:36:28: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX027098/SRX027098.20_model.r INFO @ Tue, 16 Jun 2020 07:36:28: #3 Call peaks... INFO @ Tue, 16 Jun 2020 07:36:28: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Tue, 16 Jun 2020 07:36:43: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 07:36:51: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX027098/SRX027098.20_peaks.xls INFO @ Tue, 16 Jun 2020 07:36:51: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX027098/SRX027098.20_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 07:36:51: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX027098/SRX027098.20_summits.bed INFO @ Tue, 16 Jun 2020 07:36:51: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (210 records, 4 fields): 1 millis CompletedMACS2peakCalling