Job ID = 6368397 SRX = SRX495076 Genome = ce11 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-16T00:43:42 prefetch.2.10.7: 1) Downloading 'SRR1198608'... 2020-06-16T00:43:42 prefetch.2.10.7: Downloading via HTTPS... 2020-06-16T00:48:49 prefetch.2.10.7: HTTPS download succeed 2020-06-16T00:48:49 prefetch.2.10.7: 1) 'SRR1198608' was downloaded successfully Read 18930018 spots for SRR1198608/SRR1198608.sra Written 18930018 spots for SRR1198608/SRR1198608.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: 00:03:26 18930018 reads; of these: 18930018 (100.00%) were unpaired; of these: 2654982 (14.03%) aligned 0 times 13796626 (72.88%) aligned exactly 1 time 2478410 (13.09%) aligned >1 times 85.97% overall alignment rate Time searching: 00:03:26 Overall time: 00:03:26 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_sort_core] merging from 8 files... [bam_rmdupse_core] 5323992 / 16275036 = 0.3271 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 09:57:13: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX495076/SRX495076.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX495076/SRX495076.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX495076/SRX495076.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX495076/SRX495076.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 09:57:13: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:57:13: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:57:20: 1000000 INFO @ Tue, 16 Jun 2020 09:57:26: 2000000 INFO @ Tue, 16 Jun 2020 09:57:32: 3000000 INFO @ Tue, 16 Jun 2020 09:57:39: 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 09:57:43: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX495076/SRX495076.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX495076/SRX495076.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX495076/SRX495076.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX495076/SRX495076.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 09:57:43: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:57:43: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:57:45: 5000000 INFO @ Tue, 16 Jun 2020 09:57:51: 1000000 INFO @ Tue, 16 Jun 2020 09:57:52: 6000000 INFO @ Tue, 16 Jun 2020 09:57:58: 2000000 INFO @ Tue, 16 Jun 2020 09:58:00: 7000000 INFO @ Tue, 16 Jun 2020 09:58:05: 3000000 INFO @ Tue, 16 Jun 2020 09:58:07: 8000000 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 09:58:12: 4000000 INFO @ Tue, 16 Jun 2020 09:58:13: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX495076/SRX495076.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX495076/SRX495076.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX495076/SRX495076.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX495076/SRX495076.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 09:58:13: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:58:13: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:58:14: 9000000 INFO @ Tue, 16 Jun 2020 09:58:19: 5000000 INFO @ Tue, 16 Jun 2020 09:58:21: 1000000 INFO @ Tue, 16 Jun 2020 09:58:21: 10000000 INFO @ Tue, 16 Jun 2020 09:58:26: 6000000 INFO @ Tue, 16 Jun 2020 09:58:28: #1 tag size is determined as 42 bps INFO @ Tue, 16 Jun 2020 09:58:28: #1 tag size = 42 INFO @ Tue, 16 Jun 2020 09:58:28: #1 total tags in treatment: 10951044 INFO @ Tue, 16 Jun 2020 09:58:28: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:58:28: #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 09:58:28: #1 tags after filtering in treatment: 10951044 INFO @ Tue, 16 Jun 2020 09:58:28: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 09:58:28: #1 finished! INFO @ Tue, 16 Jun 2020 09:58:28: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:58:28: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:58:28: 2000000 INFO @ Tue, 16 Jun 2020 09:58:29: #2 number of paired peaks: 695 WARNING @ Tue, 16 Jun 2020 09:58:29: Fewer paired peaks (695) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 695 pairs to build model! INFO @ Tue, 16 Jun 2020 09:58:29: start model_add_line... INFO @ Tue, 16 Jun 2020 09:58:29: start X-correlation... INFO @ Tue, 16 Jun 2020 09:58:29: end of X-cor INFO @ Tue, 16 Jun 2020 09:58:29: #2 finished! INFO @ Tue, 16 Jun 2020 09:58:29: #2 predicted fragment length is 221 bps INFO @ Tue, 16 Jun 2020 09:58:29: #2 alternative fragment length(s) may be 221 bps INFO @ Tue, 16 Jun 2020 09:58:29: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX495076/SRX495076.05_model.r INFO @ Tue, 16 Jun 2020 09:58:29: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:58:29: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 09:58:33: 7000000 INFO @ Tue, 16 Jun 2020 09:58:36: 3000000 INFO @ Tue, 16 Jun 2020 09:58:39: 8000000 INFO @ Tue, 16 Jun 2020 09:58:42: 4000000 INFO @ Tue, 16 Jun 2020 09:58:46: 9000000 INFO @ Tue, 16 Jun 2020 09:58:49: 5000000 INFO @ Tue, 16 Jun 2020 09:58:53: 10000000 INFO @ Tue, 16 Jun 2020 09:58:55: 6000000 INFO @ Tue, 16 Jun 2020 09:58:58: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 09:58:59: #1 tag size is determined as 42 bps INFO @ Tue, 16 Jun 2020 09:58:59: #1 tag size = 42 INFO @ Tue, 16 Jun 2020 09:58:59: #1 total tags in treatment: 10951044 INFO @ Tue, 16 Jun 2020 09:58:59: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:58:59: #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 09:58:59: #1 tags after filtering in treatment: 10951044 INFO @ Tue, 16 Jun 2020 09:58:59: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 09:58:59: #1 finished! INFO @ Tue, 16 Jun 2020 09:58:59: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:58:59: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:59:00: #2 number of paired peaks: 695 WARNING @ Tue, 16 Jun 2020 09:59:00: Fewer paired peaks (695) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 695 pairs to build model! INFO @ Tue, 16 Jun 2020 09:59:00: start model_add_line... INFO @ Tue, 16 Jun 2020 09:59:00: start X-correlation... INFO @ Tue, 16 Jun 2020 09:59:00: end of X-cor INFO @ Tue, 16 Jun 2020 09:59:00: #2 finished! INFO @ Tue, 16 Jun 2020 09:59:00: #2 predicted fragment length is 221 bps INFO @ Tue, 16 Jun 2020 09:59:00: #2 alternative fragment length(s) may be 221 bps INFO @ Tue, 16 Jun 2020 09:59:00: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX495076/SRX495076.10_model.r INFO @ Tue, 16 Jun 2020 09:59:00: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:59:00: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 09:59:02: 7000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 16 Jun 2020 09:59:08: 8000000 INFO @ Tue, 16 Jun 2020 09:59:11: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX495076/SRX495076.05_peaks.xls INFO @ Tue, 16 Jun 2020 09:59:11: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX495076/SRX495076.05_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:59:11: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX495076/SRX495076.05_summits.bed INFO @ Tue, 16 Jun 2020 09:59:11: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (3177 records, 4 fields): 4 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 09:59:15: 9000000 INFO @ Tue, 16 Jun 2020 09:59:21: 10000000 INFO @ Tue, 16 Jun 2020 09:59:27: #1 tag size is determined as 42 bps INFO @ Tue, 16 Jun 2020 09:59:27: #1 tag size = 42 INFO @ Tue, 16 Jun 2020 09:59:27: #1 total tags in treatment: 10951044 INFO @ Tue, 16 Jun 2020 09:59:27: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:59:27: #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 09:59:27: #1 tags after filtering in treatment: 10951044 INFO @ Tue, 16 Jun 2020 09:59:27: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 09:59:27: #1 finished! INFO @ Tue, 16 Jun 2020 09:59:27: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:59:27: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:59:28: #2 number of paired peaks: 695 WARNING @ Tue, 16 Jun 2020 09:59:28: Fewer paired peaks (695) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 695 pairs to build model! INFO @ Tue, 16 Jun 2020 09:59:28: start model_add_line... INFO @ Tue, 16 Jun 2020 09:59:28: start X-correlation... INFO @ Tue, 16 Jun 2020 09:59:28: end of X-cor INFO @ Tue, 16 Jun 2020 09:59:28: #2 finished! INFO @ Tue, 16 Jun 2020 09:59:28: #2 predicted fragment length is 221 bps INFO @ Tue, 16 Jun 2020 09:59:28: #2 alternative fragment length(s) may be 221 bps INFO @ Tue, 16 Jun 2020 09:59:28: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX495076/SRX495076.20_model.r INFO @ Tue, 16 Jun 2020 09:59:28: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:59:28: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 09:59:28: #3 Call peaks for each chromosome... BigWig に変換しました。 INFO @ Tue, 16 Jun 2020 09:59:40: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX495076/SRX495076.10_peaks.xls INFO @ Tue, 16 Jun 2020 09:59:40: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX495076/SRX495076.10_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:59:40: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX495076/SRX495076.10_summits.bed INFO @ Tue, 16 Jun 2020 09:59:40: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (1783 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 09:59:55: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 10:00:08: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX495076/SRX495076.20_peaks.xls INFO @ Tue, 16 Jun 2020 10:00:08: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX495076/SRX495076.20_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 10:00:08: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX495076/SRX495076.20_summits.bed INFO @ Tue, 16 Jun 2020 10:00:08: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (954 records, 4 fields): 3 millis CompletedMACS2peakCalling