Job ID = 6367251 SRX = SRX312080 Genome = ce11 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-15T23:23:01 prefetch.2.10.7: 1) Downloading 'SRR915704'... 2020-06-15T23:23:01 prefetch.2.10.7: Downloading via HTTPS... 2020-06-15T23:24:03 prefetch.2.10.7: HTTPS download succeed 2020-06-15T23:24:04 prefetch.2.10.7: 'SRR915704' is valid 2020-06-15T23:24:04 prefetch.2.10.7: 1) 'SRR915704' was downloaded successfully Read 14572174 spots for SRR915704/SRR915704.sra Written 14572174 spots for SRR915704/SRR915704.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 14572174 reads; of these: 14572174 (100.00%) were unpaired; of these: 3363899 (23.08%) aligned 0 times 9168658 (62.92%) aligned exactly 1 time 2039617 (14.00%) aligned >1 times 76.92% 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_sort_core] merging from 8 files... [bam_rmdupse_core] 1269170 / 11208275 = 0.1132 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 08:30:39: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX312080/SRX312080.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX312080/SRX312080.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX312080/SRX312080.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX312080/SRX312080.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 08:30:39: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:30:39: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:30:46: 1000000 INFO @ Tue, 16 Jun 2020 08:30:52: 2000000 INFO @ Tue, 16 Jun 2020 08:30:59: 3000000 INFO @ Tue, 16 Jun 2020 08:31:06: 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 08:31:09: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX312080/SRX312080.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX312080/SRX312080.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX312080/SRX312080.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX312080/SRX312080.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 08:31:09: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:31:09: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:31:13: 5000000 INFO @ Tue, 16 Jun 2020 08:31:16: 1000000 INFO @ Tue, 16 Jun 2020 08:31:21: 6000000 INFO @ Tue, 16 Jun 2020 08:31:23: 2000000 INFO @ Tue, 16 Jun 2020 08:31:29: 7000000 INFO @ Tue, 16 Jun 2020 08:31:30: 3000000 INFO @ Tue, 16 Jun 2020 08:31:37: 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 08:31:37: 4000000 INFO @ Tue, 16 Jun 2020 08:31:39: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX312080/SRX312080.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX312080/SRX312080.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX312080/SRX312080.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX312080/SRX312080.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 08:31:39: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:31:39: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:31:45: 9000000 INFO @ Tue, 16 Jun 2020 08:31:45: 5000000 INFO @ Tue, 16 Jun 2020 08:31:46: 1000000 INFO @ Tue, 16 Jun 2020 08:31:52: 6000000 INFO @ Tue, 16 Jun 2020 08:31:52: #1 tag size is determined as 51 bps INFO @ Tue, 16 Jun 2020 08:31:52: #1 tag size = 51 INFO @ Tue, 16 Jun 2020 08:31:52: #1 total tags in treatment: 9939105 INFO @ Tue, 16 Jun 2020 08:31:52: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:31:52: #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 08:31:52: #1 tags after filtering in treatment: 9939105 INFO @ Tue, 16 Jun 2020 08:31:52: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:31:52: #1 finished! INFO @ Tue, 16 Jun 2020 08:31:52: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:31:52: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:31:53: #2 number of paired peaks: 341 WARNING @ Tue, 16 Jun 2020 08:31:53: Fewer paired peaks (341) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 341 pairs to build model! INFO @ Tue, 16 Jun 2020 08:31:53: start model_add_line... INFO @ Tue, 16 Jun 2020 08:31:53: start X-correlation... INFO @ Tue, 16 Jun 2020 08:31:53: end of X-cor INFO @ Tue, 16 Jun 2020 08:31:53: #2 finished! INFO @ Tue, 16 Jun 2020 08:31:53: #2 predicted fragment length is 50 bps INFO @ Tue, 16 Jun 2020 08:31:53: #2 alternative fragment length(s) may be 4,50 bps INFO @ Tue, 16 Jun 2020 08:31:53: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX312080/SRX312080.05_model.r WARNING @ Tue, 16 Jun 2020 08:31:53: #2 Since the d (50) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 08:31:53: #2 You may need to consider one of the other alternative d(s): 4,50 WARNING @ Tue, 16 Jun 2020 08:31:53: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 16 Jun 2020 08:31:53: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:31:53: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 08:31:53: 2000000 INFO @ Tue, 16 Jun 2020 08:31:59: 7000000 INFO @ Tue, 16 Jun 2020 08:32:00: 3000000 INFO @ Tue, 16 Jun 2020 08:32:05: 8000000 INFO @ Tue, 16 Jun 2020 08:32:07: 4000000 INFO @ Tue, 16 Jun 2020 08:32:12: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 08:32:12: 9000000 INFO @ Tue, 16 Jun 2020 08:32:14: 5000000 INFO @ Tue, 16 Jun 2020 08:32:18: #1 tag size is determined as 51 bps INFO @ Tue, 16 Jun 2020 08:32:18: #1 tag size = 51 INFO @ Tue, 16 Jun 2020 08:32:18: #1 total tags in treatment: 9939105 INFO @ Tue, 16 Jun 2020 08:32:18: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:32:18: #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 08:32:18: #1 tags after filtering in treatment: 9939105 INFO @ Tue, 16 Jun 2020 08:32:18: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:32:18: #1 finished! INFO @ Tue, 16 Jun 2020 08:32:18: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:32:18: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:32:19: #2 number of paired peaks: 341 WARNING @ Tue, 16 Jun 2020 08:32:19: Fewer paired peaks (341) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 341 pairs to build model! INFO @ Tue, 16 Jun 2020 08:32:19: start model_add_line... INFO @ Tue, 16 Jun 2020 08:32:19: start X-correlation... INFO @ Tue, 16 Jun 2020 08:32:19: end of X-cor INFO @ Tue, 16 Jun 2020 08:32:19: #2 finished! INFO @ Tue, 16 Jun 2020 08:32:19: #2 predicted fragment length is 50 bps INFO @ Tue, 16 Jun 2020 08:32:19: #2 alternative fragment length(s) may be 4,50 bps INFO @ Tue, 16 Jun 2020 08:32:19: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX312080/SRX312080.10_model.r WARNING @ Tue, 16 Jun 2020 08:32:19: #2 Since the d (50) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 08:32:19: #2 You may need to consider one of the other alternative d(s): 4,50 WARNING @ Tue, 16 Jun 2020 08:32:19: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 16 Jun 2020 08:32:19: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:32:19: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 08:32:20: 6000000 INFO @ Tue, 16 Jun 2020 08:32:21: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX312080/SRX312080.05_peaks.xls INFO @ Tue, 16 Jun 2020 08:32:21: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX312080/SRX312080.05_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:32:21: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX312080/SRX312080.05_summits.bed INFO @ Tue, 16 Jun 2020 08:32:21: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (736 records, 4 fields): 2 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 16 Jun 2020 08:32:26: 7000000 INFO @ Tue, 16 Jun 2020 08:32:33: 8000000 INFO @ Tue, 16 Jun 2020 08:32:38: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 08:32:39: 9000000 INFO @ Tue, 16 Jun 2020 08:32:44: #1 tag size is determined as 51 bps INFO @ Tue, 16 Jun 2020 08:32:44: #1 tag size = 51 INFO @ Tue, 16 Jun 2020 08:32:44: #1 total tags in treatment: 9939105 INFO @ Tue, 16 Jun 2020 08:32:44: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:32:44: #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 08:32:45: #1 tags after filtering in treatment: 9939105 INFO @ Tue, 16 Jun 2020 08:32:45: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:32:45: #1 finished! INFO @ Tue, 16 Jun 2020 08:32:45: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:32:45: #2 looking for paired plus/minus strand peaks... BigWig に変換しました。 INFO @ Tue, 16 Jun 2020 08:32:45: #2 number of paired peaks: 341 WARNING @ Tue, 16 Jun 2020 08:32:45: Fewer paired peaks (341) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 341 pairs to build model! INFO @ Tue, 16 Jun 2020 08:32:45: start model_add_line... INFO @ Tue, 16 Jun 2020 08:32:45: start X-correlation... INFO @ Tue, 16 Jun 2020 08:32:45: end of X-cor INFO @ Tue, 16 Jun 2020 08:32:45: #2 finished! INFO @ Tue, 16 Jun 2020 08:32:45: #2 predicted fragment length is 50 bps INFO @ Tue, 16 Jun 2020 08:32:45: #2 alternative fragment length(s) may be 4,50 bps INFO @ Tue, 16 Jun 2020 08:32:45: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX312080/SRX312080.20_model.r WARNING @ Tue, 16 Jun 2020 08:32:45: #2 Since the d (50) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 08:32:45: #2 You may need to consider one of the other alternative d(s): 4,50 WARNING @ Tue, 16 Jun 2020 08:32:45: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 16 Jun 2020 08:32:45: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:32:45: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 08:32:47: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX312080/SRX312080.10_peaks.xls INFO @ Tue, 16 Jun 2020 08:32:47: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX312080/SRX312080.10_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:32:47: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX312080/SRX312080.10_summits.bed INFO @ Tue, 16 Jun 2020 08:32:47: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (461 records, 4 fields): 1 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 08:33:03: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 08:33:13: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX312080/SRX312080.20_peaks.xls INFO @ Tue, 16 Jun 2020 08:33:13: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX312080/SRX312080.20_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:33:13: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX312080/SRX312080.20_summits.bed INFO @ Tue, 16 Jun 2020 08:33:13: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (229 records, 4 fields): 1 millis CompletedMACS2peakCalling