Job ID = 6365916 SRX = SRX043849 Genome = ce11 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-15T22:32:36 prefetch.2.10.7: 1) Downloading 'SRR107306'... 2020-06-15T22:32:36 prefetch.2.10.7: Downloading via HTTPS... 2020-06-15T22:33:01 prefetch.2.10.7: HTTPS download succeed 2020-06-15T22:33:01 prefetch.2.10.7: 'SRR107306' is valid 2020-06-15T22:33:01 prefetch.2.10.7: 1) 'SRR107306' was downloaded successfully Read 3514796 spots for SRR107306/SRR107306.sra Written 3514796 spots for SRR107306/SRR107306.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: 00:00:31 3514796 reads; of these: 3514796 (100.00%) were unpaired; of these: 995167 (28.31%) aligned 0 times 2212686 (62.95%) aligned exactly 1 time 306943 (8.73%) aligned >1 times 71.69% overall alignment rate Time searching: 00:00:31 Overall time: 00:00:31 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] 183471 / 2519629 = 0.0728 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 07:34:57: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX043849/SRX043849.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX043849/SRX043849.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX043849/SRX043849.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX043849/SRX043849.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 07:34:57: #1 read tag files... INFO @ Tue, 16 Jun 2020 07:34:57: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 07:35:03: 1000000 INFO @ Tue, 16 Jun 2020 07:35:10: 2000000 INFO @ Tue, 16 Jun 2020 07:35:12: #1 tag size is determined as 34 bps INFO @ Tue, 16 Jun 2020 07:35:12: #1 tag size = 34 INFO @ Tue, 16 Jun 2020 07:35:12: #1 total tags in treatment: 2336158 INFO @ Tue, 16 Jun 2020 07:35:12: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 07:35:12: #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 07:35:12: #1 tags after filtering in treatment: 2336158 INFO @ Tue, 16 Jun 2020 07:35:12: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 07:35:12: #1 finished! INFO @ Tue, 16 Jun 2020 07:35:12: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 07:35:12: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 07:35:12: #2 number of paired peaks: 327 WARNING @ Tue, 16 Jun 2020 07:35:12: Fewer paired peaks (327) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 327 pairs to build model! INFO @ Tue, 16 Jun 2020 07:35:12: start model_add_line... INFO @ Tue, 16 Jun 2020 07:35:12: start X-correlation... INFO @ Tue, 16 Jun 2020 07:35:12: end of X-cor INFO @ Tue, 16 Jun 2020 07:35:12: #2 finished! INFO @ Tue, 16 Jun 2020 07:35:12: #2 predicted fragment length is 96 bps INFO @ Tue, 16 Jun 2020 07:35:12: #2 alternative fragment length(s) may be 96,574 bps INFO @ Tue, 16 Jun 2020 07:35:12: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX043849/SRX043849.05_model.r INFO @ Tue, 16 Jun 2020 07:35:12: #3 Call peaks... INFO @ Tue, 16 Jun 2020 07:35:12: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 07:35:18: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 07:35:21: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX043849/SRX043849.05_peaks.xls INFO @ Tue, 16 Jun 2020 07:35:21: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX043849/SRX043849.05_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 07:35:21: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX043849/SRX043849.05_summits.bed INFO @ Tue, 16 Jun 2020 07:35:21: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (1076 records, 4 fields): 3 millis CompletedMACS2peakCalling 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 07:35:26: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX043849/SRX043849.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX043849/SRX043849.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX043849/SRX043849.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX043849/SRX043849.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 07:35:26: #1 read tag files... INFO @ Tue, 16 Jun 2020 07:35:26: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 07:35:32: 1000000 INFO @ Tue, 16 Jun 2020 07:35:38: 2000000 INFO @ Tue, 16 Jun 2020 07:35:40: #1 tag size is determined as 34 bps INFO @ Tue, 16 Jun 2020 07:35:40: #1 tag size = 34 INFO @ Tue, 16 Jun 2020 07:35:40: #1 total tags in treatment: 2336158 INFO @ Tue, 16 Jun 2020 07:35:40: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 07:35:40: #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 07:35:40: #1 tags after filtering in treatment: 2336158 INFO @ Tue, 16 Jun 2020 07:35:40: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 07:35:40: #1 finished! INFO @ Tue, 16 Jun 2020 07:35:40: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 07:35:40: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 07:35:40: #2 number of paired peaks: 327 WARNING @ Tue, 16 Jun 2020 07:35:40: Fewer paired peaks (327) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 327 pairs to build model! INFO @ Tue, 16 Jun 2020 07:35:40: start model_add_line... INFO @ Tue, 16 Jun 2020 07:35:40: start X-correlation... INFO @ Tue, 16 Jun 2020 07:35:40: end of X-cor INFO @ Tue, 16 Jun 2020 07:35:40: #2 finished! INFO @ Tue, 16 Jun 2020 07:35:40: #2 predicted fragment length is 96 bps INFO @ Tue, 16 Jun 2020 07:35:40: #2 alternative fragment length(s) may be 96,574 bps INFO @ Tue, 16 Jun 2020 07:35:40: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX043849/SRX043849.10_model.r INFO @ Tue, 16 Jun 2020 07:35:40: #3 Call peaks... INFO @ Tue, 16 Jun 2020 07:35:40: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 07:35:46: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 07:35:49: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX043849/SRX043849.10_peaks.xls INFO @ Tue, 16 Jun 2020 07:35:49: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX043849/SRX043849.10_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 07:35:49: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX043849/SRX043849.10_summits.bed INFO @ Tue, 16 Jun 2020 07:35:49: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (222 records, 4 fields): 2 millis CompletedMACS2peakCalling 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 07:35:56: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX043849/SRX043849.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX043849/SRX043849.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX043849/SRX043849.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX043849/SRX043849.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 07:35:56: #1 read tag files... INFO @ Tue, 16 Jun 2020 07:35:56: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 07:36:02: 1000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 16 Jun 2020 07:36:08: 2000000 INFO @ Tue, 16 Jun 2020 07:36:10: #1 tag size is determined as 34 bps INFO @ Tue, 16 Jun 2020 07:36:10: #1 tag size = 34 INFO @ Tue, 16 Jun 2020 07:36:10: #1 total tags in treatment: 2336158 INFO @ Tue, 16 Jun 2020 07:36:10: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 07:36:10: #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 07:36:10: #1 tags after filtering in treatment: 2336158 INFO @ Tue, 16 Jun 2020 07:36:10: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 07:36:10: #1 finished! INFO @ Tue, 16 Jun 2020 07:36:10: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 07:36:10: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 07:36:10: #2 number of paired peaks: 327 WARNING @ Tue, 16 Jun 2020 07:36:10: Fewer paired peaks (327) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 327 pairs to build model! INFO @ Tue, 16 Jun 2020 07:36:10: start model_add_line... INFO @ Tue, 16 Jun 2020 07:36:10: start X-correlation... INFO @ Tue, 16 Jun 2020 07:36:10: end of X-cor INFO @ Tue, 16 Jun 2020 07:36:10: #2 finished! INFO @ Tue, 16 Jun 2020 07:36:10: #2 predicted fragment length is 96 bps INFO @ Tue, 16 Jun 2020 07:36:10: #2 alternative fragment length(s) may be 96,574 bps INFO @ Tue, 16 Jun 2020 07:36:10: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX043849/SRX043849.20_model.r INFO @ Tue, 16 Jun 2020 07:36:10: #3 Call peaks... INFO @ Tue, 16 Jun 2020 07:36:10: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Tue, 16 Jun 2020 07:36:16: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 07:36:19: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX043849/SRX043849.20_peaks.xls INFO @ Tue, 16 Jun 2020 07:36:19: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX043849/SRX043849.20_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 07:36:19: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX043849/SRX043849.20_summits.bed INFO @ Tue, 16 Jun 2020 07:36:19: Done! pass1 - making usageList (7 chroms): 0 millis pass2 - checking and writing primary data (13 records, 4 fields): 1 millis CompletedMACS2peakCalling