Job ID = 6365991 SRX = SRX044002 Genome = ce11 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-15T22:27:44 prefetch.2.10.7: 1) Downloading 'SRR107584'... 2020-06-15T22:27:44 prefetch.2.10.7: Downloading via HTTPS... 2020-06-15T22:28:14 prefetch.2.10.7: HTTPS download succeed 2020-06-15T22:28:14 prefetch.2.10.7: 'SRR107584' is valid 2020-06-15T22:28:14 prefetch.2.10.7: 1) 'SRR107584' was downloaded successfully Read 4377247 spots for SRR107584/SRR107584.sra Written 4377247 spots for SRR107584/SRR107584.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: 00:00:01 Time loading mirror index: 00:00:00 Multiseed full-index search: 00:00:40 4377247 reads; of these: 4377247 (100.00%) were unpaired; of these: 547558 (12.51%) aligned 0 times 3237271 (73.96%) aligned exactly 1 time 592418 (13.53%) aligned >1 times 87.49% overall alignment rate Time searching: 00:00:41 Overall time: 00:00:41 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] 262333 / 3829689 = 0.0685 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 07:30:32: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX044002/SRX044002.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX044002/SRX044002.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX044002/SRX044002.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX044002/SRX044002.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 07:30:32: #1 read tag files... INFO @ Tue, 16 Jun 2020 07:30:32: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 07:30:37: 1000000 INFO @ Tue, 16 Jun 2020 07:30:43: 2000000 INFO @ Tue, 16 Jun 2020 07:30:48: 3000000 INFO @ Tue, 16 Jun 2020 07:30:51: #1 tag size is determined as 32 bps INFO @ Tue, 16 Jun 2020 07:30:51: #1 tag size = 32 INFO @ Tue, 16 Jun 2020 07:30:51: #1 total tags in treatment: 3567356 INFO @ Tue, 16 Jun 2020 07:30:51: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 07:30:51: #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 07:30:51: #1 tags after filtering in treatment: 3567356 INFO @ Tue, 16 Jun 2020 07:30:51: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 07:30:51: #1 finished! INFO @ Tue, 16 Jun 2020 07:30:51: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 07:30:51: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 07:30:52: #2 number of paired peaks: 835 WARNING @ Tue, 16 Jun 2020 07:30:52: Fewer paired peaks (835) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 835 pairs to build model! INFO @ Tue, 16 Jun 2020 07:30:52: start model_add_line... INFO @ Tue, 16 Jun 2020 07:30:52: start X-correlation... INFO @ Tue, 16 Jun 2020 07:30:52: end of X-cor INFO @ Tue, 16 Jun 2020 07:30:52: #2 finished! INFO @ Tue, 16 Jun 2020 07:30:52: #2 predicted fragment length is 129 bps INFO @ Tue, 16 Jun 2020 07:30:52: #2 alternative fragment length(s) may be 129 bps INFO @ Tue, 16 Jun 2020 07:30:52: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX044002/SRX044002.05_model.r INFO @ Tue, 16 Jun 2020 07:30:52: #3 Call peaks... INFO @ Tue, 16 Jun 2020 07:30:52: #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 07:31:01: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 07:31:01: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX044002/SRX044002.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX044002/SRX044002.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX044002/SRX044002.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX044002/SRX044002.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 07:31:01: #1 read tag files... INFO @ Tue, 16 Jun 2020 07:31:01: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 07:31:05: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX044002/SRX044002.05_peaks.xls INFO @ Tue, 16 Jun 2020 07:31:05: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX044002/SRX044002.05_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 07:31:05: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX044002/SRX044002.05_summits.bed INFO @ Tue, 16 Jun 2020 07:31:05: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (3036 records, 4 fields): 5 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 07:31:07: 1000000 INFO @ Tue, 16 Jun 2020 07:31:12: 2000000 INFO @ Tue, 16 Jun 2020 07:31:18: 3000000 INFO @ Tue, 16 Jun 2020 07:31:21: #1 tag size is determined as 32 bps INFO @ Tue, 16 Jun 2020 07:31:21: #1 tag size = 32 INFO @ Tue, 16 Jun 2020 07:31:21: #1 total tags in treatment: 3567356 INFO @ Tue, 16 Jun 2020 07:31:21: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 07:31:21: #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 07:31:21: #1 tags after filtering in treatment: 3567356 INFO @ Tue, 16 Jun 2020 07:31:21: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 07:31:21: #1 finished! INFO @ Tue, 16 Jun 2020 07:31:21: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 07:31:21: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 07:31:21: #2 number of paired peaks: 835 WARNING @ Tue, 16 Jun 2020 07:31:21: Fewer paired peaks (835) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 835 pairs to build model! INFO @ Tue, 16 Jun 2020 07:31:21: start model_add_line... INFO @ Tue, 16 Jun 2020 07:31:21: start X-correlation... INFO @ Tue, 16 Jun 2020 07:31:21: end of X-cor INFO @ Tue, 16 Jun 2020 07:31:21: #2 finished! INFO @ Tue, 16 Jun 2020 07:31:21: #2 predicted fragment length is 129 bps INFO @ Tue, 16 Jun 2020 07:31:21: #2 alternative fragment length(s) may be 129 bps INFO @ Tue, 16 Jun 2020 07:31:21: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX044002/SRX044002.10_model.r INFO @ Tue, 16 Jun 2020 07:31:21: #3 Call peaks... INFO @ Tue, 16 Jun 2020 07:31:21: #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 07:31:30: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 07:31:31: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX044002/SRX044002.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX044002/SRX044002.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX044002/SRX044002.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX044002/SRX044002.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 07:31:31: #1 read tag files... INFO @ Tue, 16 Jun 2020 07:31:31: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 07:31:35: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX044002/SRX044002.10_peaks.xls INFO @ Tue, 16 Jun 2020 07:31:35: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX044002/SRX044002.10_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 07:31:35: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX044002/SRX044002.10_summits.bed INFO @ Tue, 16 Jun 2020 07:31:35: Done! pass1 - making usageList (7 chroms): 0 millis pass2 - checking and writing primary data (1356 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 07:31:37: 1000000 INFO @ Tue, 16 Jun 2020 07:31:42: 2000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 16 Jun 2020 07:31:47: 3000000 INFO @ Tue, 16 Jun 2020 07:31:50: #1 tag size is determined as 32 bps INFO @ Tue, 16 Jun 2020 07:31:50: #1 tag size = 32 INFO @ Tue, 16 Jun 2020 07:31:50: #1 total tags in treatment: 3567356 INFO @ Tue, 16 Jun 2020 07:31:50: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 07:31:50: #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 07:31:50: #1 tags after filtering in treatment: 3567356 INFO @ Tue, 16 Jun 2020 07:31:50: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 07:31:50: #1 finished! INFO @ Tue, 16 Jun 2020 07:31:50: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 07:31:50: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 07:31:51: #2 number of paired peaks: 835 WARNING @ Tue, 16 Jun 2020 07:31:51: Fewer paired peaks (835) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 835 pairs to build model! INFO @ Tue, 16 Jun 2020 07:31:51: start model_add_line... INFO @ Tue, 16 Jun 2020 07:31:51: start X-correlation... INFO @ Tue, 16 Jun 2020 07:31:51: end of X-cor INFO @ Tue, 16 Jun 2020 07:31:51: #2 finished! INFO @ Tue, 16 Jun 2020 07:31:51: #2 predicted fragment length is 129 bps INFO @ Tue, 16 Jun 2020 07:31:51: #2 alternative fragment length(s) may be 129 bps INFO @ Tue, 16 Jun 2020 07:31:51: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX044002/SRX044002.20_model.r INFO @ Tue, 16 Jun 2020 07:31:51: #3 Call peaks... INFO @ Tue, 16 Jun 2020 07:31:51: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Tue, 16 Jun 2020 07:31:59: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 07:32:04: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX044002/SRX044002.20_peaks.xls INFO @ Tue, 16 Jun 2020 07:32:04: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX044002/SRX044002.20_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 07:32:04: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX044002/SRX044002.20_summits.bed INFO @ Tue, 16 Jun 2020 07:32:04: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (369 records, 4 fields): 1 millis CompletedMACS2peakCalling