Job ID = 6367139 SRX = SRX277097 Genome = ce11 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-15T23:33:20 prefetch.2.10.7: 1) Downloading 'SRR849773'... 2020-06-15T23:33:20 prefetch.2.10.7: Downloading via HTTPS... 2020-06-15T23:34:05 prefetch.2.10.7: HTTPS download succeed 2020-06-15T23:34:06 prefetch.2.10.7: 'SRR849773' is valid 2020-06-15T23:34:06 prefetch.2.10.7: 1) 'SRR849773' was downloaded successfully Read 5551777 spots for SRR849773/SRR849773.sra Written 5551777 spots for SRR849773/SRR849773.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: 00:00:36 5551777 reads; of these: 5551777 (100.00%) were unpaired; of these: 2828350 (50.94%) aligned 0 times 2247634 (40.48%) aligned exactly 1 time 475793 (8.57%) aligned >1 times 49.06% overall alignment rate Time searching: 00:00:36 Overall time: 00:00:36 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] 298683 / 2723427 = 0.1097 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 08:36:09: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX277097/SRX277097.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX277097/SRX277097.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX277097/SRX277097.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX277097/SRX277097.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 08:36:09: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:36:09: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:36:14: 1000000 INFO @ Tue, 16 Jun 2020 08:36:18: 2000000 INFO @ Tue, 16 Jun 2020 08:36:20: #1 tag size is determined as 32 bps INFO @ Tue, 16 Jun 2020 08:36:20: #1 tag size = 32 INFO @ Tue, 16 Jun 2020 08:36:20: #1 total tags in treatment: 2424744 INFO @ Tue, 16 Jun 2020 08:36:20: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:36:20: #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 08:36:20: #1 tags after filtering in treatment: 2424744 INFO @ Tue, 16 Jun 2020 08:36:20: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:36:20: #1 finished! INFO @ Tue, 16 Jun 2020 08:36:20: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:36:20: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:36:20: #2 number of paired peaks: 833 WARNING @ Tue, 16 Jun 2020 08:36:20: Fewer paired peaks (833) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 833 pairs to build model! INFO @ Tue, 16 Jun 2020 08:36:20: start model_add_line... INFO @ Tue, 16 Jun 2020 08:36:21: start X-correlation... INFO @ Tue, 16 Jun 2020 08:36:21: end of X-cor INFO @ Tue, 16 Jun 2020 08:36:21: #2 finished! INFO @ Tue, 16 Jun 2020 08:36:21: #2 predicted fragment length is 107 bps INFO @ Tue, 16 Jun 2020 08:36:21: #2 alternative fragment length(s) may be 107 bps INFO @ Tue, 16 Jun 2020 08:36:21: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX277097/SRX277097.05_model.r INFO @ Tue, 16 Jun 2020 08:36:21: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:36:21: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 08:36:26: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 08:36:29: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX277097/SRX277097.05_peaks.xls INFO @ Tue, 16 Jun 2020 08:36:29: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX277097/SRX277097.05_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:36:29: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX277097/SRX277097.05_summits.bed INFO @ Tue, 16 Jun 2020 08:36:29: Done! pass1 - making usageList (7 chroms): 0 millis pass2 - checking and writing primary data (1786 records, 4 fields): 4 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 08:36:39: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX277097/SRX277097.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX277097/SRX277097.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX277097/SRX277097.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX277097/SRX277097.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 08:36:39: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:36:39: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:36:45: 1000000 INFO @ Tue, 16 Jun 2020 08:36:50: 2000000 INFO @ Tue, 16 Jun 2020 08:36:52: #1 tag size is determined as 32 bps INFO @ Tue, 16 Jun 2020 08:36:52: #1 tag size = 32 INFO @ Tue, 16 Jun 2020 08:36:52: #1 total tags in treatment: 2424744 INFO @ Tue, 16 Jun 2020 08:36:52: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:36:52: #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 08:36:52: #1 tags after filtering in treatment: 2424744 INFO @ Tue, 16 Jun 2020 08:36:52: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:36:52: #1 finished! INFO @ Tue, 16 Jun 2020 08:36:52: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:36:52: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:36:52: #2 number of paired peaks: 833 WARNING @ Tue, 16 Jun 2020 08:36:52: Fewer paired peaks (833) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 833 pairs to build model! INFO @ Tue, 16 Jun 2020 08:36:52: start model_add_line... INFO @ Tue, 16 Jun 2020 08:36:52: start X-correlation... INFO @ Tue, 16 Jun 2020 08:36:52: end of X-cor INFO @ Tue, 16 Jun 2020 08:36:52: #2 finished! INFO @ Tue, 16 Jun 2020 08:36:52: #2 predicted fragment length is 107 bps INFO @ Tue, 16 Jun 2020 08:36:52: #2 alternative fragment length(s) may be 107 bps INFO @ Tue, 16 Jun 2020 08:36:52: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX277097/SRX277097.10_model.r INFO @ Tue, 16 Jun 2020 08:36:52: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:36:52: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 08:36:57: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 08:37:00: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX277097/SRX277097.10_peaks.xls INFO @ Tue, 16 Jun 2020 08:37:00: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX277097/SRX277097.10_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:37:00: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX277097/SRX277097.10_summits.bed INFO @ Tue, 16 Jun 2020 08:37:00: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (708 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 08:37:09: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX277097/SRX277097.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX277097/SRX277097.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX277097/SRX277097.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX277097/SRX277097.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 08:37:09: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:37:09: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:37:14: 1000000 INFO @ Tue, 16 Jun 2020 08:37:19: 2000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 16 Jun 2020 08:37:21: #1 tag size is determined as 32 bps INFO @ Tue, 16 Jun 2020 08:37:21: #1 tag size = 32 INFO @ Tue, 16 Jun 2020 08:37:21: #1 total tags in treatment: 2424744 INFO @ Tue, 16 Jun 2020 08:37:21: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:37:21: #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 08:37:21: #1 tags after filtering in treatment: 2424744 INFO @ Tue, 16 Jun 2020 08:37:21: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:37:21: #1 finished! INFO @ Tue, 16 Jun 2020 08:37:21: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:37:21: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:37:21: #2 number of paired peaks: 833 WARNING @ Tue, 16 Jun 2020 08:37:21: Fewer paired peaks (833) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 833 pairs to build model! INFO @ Tue, 16 Jun 2020 08:37:21: start model_add_line... INFO @ Tue, 16 Jun 2020 08:37:21: start X-correlation... INFO @ Tue, 16 Jun 2020 08:37:21: end of X-cor INFO @ Tue, 16 Jun 2020 08:37:21: #2 finished! INFO @ Tue, 16 Jun 2020 08:37:21: #2 predicted fragment length is 107 bps INFO @ Tue, 16 Jun 2020 08:37:21: #2 alternative fragment length(s) may be 107 bps INFO @ Tue, 16 Jun 2020 08:37:21: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX277097/SRX277097.20_model.r INFO @ Tue, 16 Jun 2020 08:37:21: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:37:21: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 08:37:26: #3 Call peaks for each chromosome... BigWig に変換しました。 INFO @ Tue, 16 Jun 2020 08:37:29: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX277097/SRX277097.20_peaks.xls INFO @ Tue, 16 Jun 2020 08:37:29: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX277097/SRX277097.20_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:37:29: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX277097/SRX277097.20_summits.bed INFO @ Tue, 16 Jun 2020 08:37:29: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (228 records, 4 fields): 1 millis CompletedMACS2peakCalling