Job ID = 6368316 SRX = SRX494999 Genome = ce11 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-16T00:09:54 prefetch.2.10.7: 1) Downloading 'SRR1198531'... 2020-06-16T00:09:54 prefetch.2.10.7: Downloading via HTTPS... 2020-06-16T00:12:20 prefetch.2.10.7: HTTPS download succeed 2020-06-16T00:12:20 prefetch.2.10.7: 'SRR1198531' is valid 2020-06-16T00:12:20 prefetch.2.10.7: 1) 'SRR1198531' was downloaded successfully Read 15778723 spots for SRR1198531/SRR1198531.sra Written 15778723 spots for SRR1198531/SRR1198531.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: 00:02:46 15778723 reads; of these: 15778723 (100.00%) were unpaired; of these: 2296635 (14.56%) aligned 0 times 10954453 (69.43%) aligned exactly 1 time 2527635 (16.02%) aligned >1 times 85.44% overall alignment rate Time searching: 00:02:46 Overall time: 00:02:46 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] 7351263 / 13482088 = 0.5453 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 09:18:44: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX494999/SRX494999.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX494999/SRX494999.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX494999/SRX494999.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX494999/SRX494999.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 09:18:44: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:18:44: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:18:50: 1000000 INFO @ Tue, 16 Jun 2020 09:18:57: 2000000 INFO @ Tue, 16 Jun 2020 09:19:04: 3000000 INFO @ Tue, 16 Jun 2020 09:19:10: 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 09:19:14: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX494999/SRX494999.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX494999/SRX494999.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX494999/SRX494999.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX494999/SRX494999.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 09:19:14: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:19:14: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:19:17: 5000000 INFO @ Tue, 16 Jun 2020 09:19:21: 1000000 INFO @ Tue, 16 Jun 2020 09:19:24: 6000000 INFO @ Tue, 16 Jun 2020 09:19:25: #1 tag size is determined as 42 bps INFO @ Tue, 16 Jun 2020 09:19:25: #1 tag size = 42 INFO @ Tue, 16 Jun 2020 09:19:25: #1 total tags in treatment: 6130825 INFO @ Tue, 16 Jun 2020 09:19:25: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:19:25: #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 09:19:25: #1 tags after filtering in treatment: 6130825 INFO @ Tue, 16 Jun 2020 09:19:25: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 09:19:25: #1 finished! INFO @ Tue, 16 Jun 2020 09:19:25: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:19:25: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:19:25: #2 number of paired peaks: 996 WARNING @ Tue, 16 Jun 2020 09:19:25: Fewer paired peaks (996) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 996 pairs to build model! INFO @ Tue, 16 Jun 2020 09:19:25: start model_add_line... INFO @ Tue, 16 Jun 2020 09:19:25: start X-correlation... INFO @ Tue, 16 Jun 2020 09:19:25: end of X-cor INFO @ Tue, 16 Jun 2020 09:19:25: #2 finished! INFO @ Tue, 16 Jun 2020 09:19:25: #2 predicted fragment length is 207 bps INFO @ Tue, 16 Jun 2020 09:19:25: #2 alternative fragment length(s) may be 207 bps INFO @ Tue, 16 Jun 2020 09:19:25: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX494999/SRX494999.05_model.r INFO @ Tue, 16 Jun 2020 09:19:25: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:19:25: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 09:19:27: 2000000 INFO @ Tue, 16 Jun 2020 09:19:33: 3000000 INFO @ Tue, 16 Jun 2020 09:19:39: 4000000 INFO @ Tue, 16 Jun 2020 09:19:41: #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 09:19:44: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX494999/SRX494999.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX494999/SRX494999.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX494999/SRX494999.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX494999/SRX494999.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 09:19:44: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:19:44: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:19:45: 5000000 INFO @ Tue, 16 Jun 2020 09:19:49: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX494999/SRX494999.05_peaks.xls INFO @ Tue, 16 Jun 2020 09:19:49: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX494999/SRX494999.05_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:19:49: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX494999/SRX494999.05_summits.bed INFO @ Tue, 16 Jun 2020 09:19:49: Done! pass1 - making usageList (7 chroms): 0 millis pass2 - checking and writing primary data (1737 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 09:19:50: 1000000 INFO @ Tue, 16 Jun 2020 09:19:51: 6000000 INFO @ Tue, 16 Jun 2020 09:19:52: #1 tag size is determined as 42 bps INFO @ Tue, 16 Jun 2020 09:19:52: #1 tag size = 42 INFO @ Tue, 16 Jun 2020 09:19:52: #1 total tags in treatment: 6130825 INFO @ Tue, 16 Jun 2020 09:19:52: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:19:52: #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 09:19:52: #1 tags after filtering in treatment: 6130825 INFO @ Tue, 16 Jun 2020 09:19:52: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 09:19:52: #1 finished! INFO @ Tue, 16 Jun 2020 09:19:52: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:19:52: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:19:52: #2 number of paired peaks: 996 WARNING @ Tue, 16 Jun 2020 09:19:52: Fewer paired peaks (996) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 996 pairs to build model! INFO @ Tue, 16 Jun 2020 09:19:52: start model_add_line... INFO @ Tue, 16 Jun 2020 09:19:52: start X-correlation... INFO @ Tue, 16 Jun 2020 09:19:52: end of X-cor INFO @ Tue, 16 Jun 2020 09:19:52: #2 finished! INFO @ Tue, 16 Jun 2020 09:19:52: #2 predicted fragment length is 207 bps INFO @ Tue, 16 Jun 2020 09:19:52: #2 alternative fragment length(s) may be 207 bps INFO @ Tue, 16 Jun 2020 09:19:52: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX494999/SRX494999.10_model.r INFO @ Tue, 16 Jun 2020 09:19:52: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:19:52: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 09:19:56: 2000000 INFO @ Tue, 16 Jun 2020 09:20:02: 3000000 INFO @ Tue, 16 Jun 2020 09:20:08: 4000000 INFO @ Tue, 16 Jun 2020 09:20:09: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 09:20:14: 5000000 INFO @ Tue, 16 Jun 2020 09:20:16: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX494999/SRX494999.10_peaks.xls INFO @ Tue, 16 Jun 2020 09:20:16: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX494999/SRX494999.10_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:20:16: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX494999/SRX494999.10_summits.bed INFO @ Tue, 16 Jun 2020 09:20:16: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (1173 records, 4 fields): 2 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 16 Jun 2020 09:20:20: 6000000 INFO @ Tue, 16 Jun 2020 09:20:21: #1 tag size is determined as 42 bps INFO @ Tue, 16 Jun 2020 09:20:21: #1 tag size = 42 INFO @ Tue, 16 Jun 2020 09:20:21: #1 total tags in treatment: 6130825 INFO @ Tue, 16 Jun 2020 09:20:21: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:20:21: #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 09:20:21: #1 tags after filtering in treatment: 6130825 INFO @ Tue, 16 Jun 2020 09:20:21: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 09:20:21: #1 finished! INFO @ Tue, 16 Jun 2020 09:20:21: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:20:21: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:20:21: #2 number of paired peaks: 996 WARNING @ Tue, 16 Jun 2020 09:20:21: Fewer paired peaks (996) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 996 pairs to build model! INFO @ Tue, 16 Jun 2020 09:20:21: start model_add_line... INFO @ Tue, 16 Jun 2020 09:20:21: start X-correlation... INFO @ Tue, 16 Jun 2020 09:20:21: end of X-cor INFO @ Tue, 16 Jun 2020 09:20:21: #2 finished! INFO @ Tue, 16 Jun 2020 09:20:21: #2 predicted fragment length is 207 bps INFO @ Tue, 16 Jun 2020 09:20:21: #2 alternative fragment length(s) may be 207 bps INFO @ Tue, 16 Jun 2020 09:20:21: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX494999/SRX494999.20_model.r INFO @ Tue, 16 Jun 2020 09:20:21: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:20:21: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Tue, 16 Jun 2020 09:20:37: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 09:20:45: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX494999/SRX494999.20_peaks.xls INFO @ Tue, 16 Jun 2020 09:20:45: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX494999/SRX494999.20_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:20:45: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX494999/SRX494999.20_summits.bed INFO @ Tue, 16 Jun 2020 09:20:45: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (818 records, 4 fields): 2 millis CompletedMACS2peakCalling