Job ID = 6368690 SRX = SRX5402716 Genome = ce11 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-16T00:23:48 prefetch.2.10.7: 1) Downloading 'SRR8602950'... 2020-06-16T00:23:48 prefetch.2.10.7: Downloading via HTTPS... 2020-06-16T00:27:18 prefetch.2.10.7: HTTPS download succeed 2020-06-16T00:27:18 prefetch.2.10.7: 1) 'SRR8602950' was downloaded successfully Read 34323165 spots for SRR8602950/SRR8602950.sra Written 34323165 spots for SRR8602950/SRR8602950.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: 00:05:32 34323165 reads; of these: 34323165 (100.00%) were unpaired; of these: 14691375 (42.80%) aligned 0 times 16969878 (49.44%) aligned exactly 1 time 2661912 (7.76%) aligned >1 times 57.20% overall alignment rate Time searching: 00:05:32 Overall time: 00:05:32 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] 4710041 / 19631790 = 0.2399 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 09:39:18: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX5402716/SRX5402716.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX5402716/SRX5402716.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX5402716/SRX5402716.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX5402716/SRX5402716.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 09:39:18: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:39:18: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:39:24: 1000000 INFO @ Tue, 16 Jun 2020 09:39:30: 2000000 INFO @ Tue, 16 Jun 2020 09:39:37: 3000000 INFO @ Tue, 16 Jun 2020 09:39:43: 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 09:39:48: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX5402716/SRX5402716.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX5402716/SRX5402716.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX5402716/SRX5402716.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX5402716/SRX5402716.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 09:39:48: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:39:48: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:39:49: 5000000 INFO @ Tue, 16 Jun 2020 09:39:54: 1000000 INFO @ Tue, 16 Jun 2020 09:39:55: 6000000 INFO @ Tue, 16 Jun 2020 09:40:01: 2000000 INFO @ Tue, 16 Jun 2020 09:40:02: 7000000 INFO @ Tue, 16 Jun 2020 09:40:08: 3000000 INFO @ Tue, 16 Jun 2020 09:40:08: 8000000 INFO @ Tue, 16 Jun 2020 09:40:15: 9000000 INFO @ Tue, 16 Jun 2020 09:40:15: 4000000 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 09:40:17: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX5402716/SRX5402716.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX5402716/SRX5402716.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX5402716/SRX5402716.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX5402716/SRX5402716.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 09:40:17: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:40:17: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:40:21: 10000000 INFO @ Tue, 16 Jun 2020 09:40:22: 5000000 INFO @ Tue, 16 Jun 2020 09:40:23: 1000000 INFO @ Tue, 16 Jun 2020 09:40:28: 11000000 INFO @ Tue, 16 Jun 2020 09:40:28: 6000000 INFO @ Tue, 16 Jun 2020 09:40:29: 2000000 INFO @ Tue, 16 Jun 2020 09:40:34: 12000000 INFO @ Tue, 16 Jun 2020 09:40:35: 7000000 INFO @ Tue, 16 Jun 2020 09:40:35: 3000000 INFO @ Tue, 16 Jun 2020 09:40:40: 13000000 INFO @ Tue, 16 Jun 2020 09:40:41: 4000000 INFO @ Tue, 16 Jun 2020 09:40:41: 8000000 INFO @ Tue, 16 Jun 2020 09:40:47: 14000000 INFO @ Tue, 16 Jun 2020 09:40:47: 5000000 INFO @ Tue, 16 Jun 2020 09:40:48: 9000000 INFO @ Tue, 16 Jun 2020 09:40:53: #1 tag size is determined as 50 bps INFO @ Tue, 16 Jun 2020 09:40:53: #1 tag size = 50 INFO @ Tue, 16 Jun 2020 09:40:53: #1 total tags in treatment: 14921749 INFO @ Tue, 16 Jun 2020 09:40:53: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:40:53: #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 09:40:53: #1 tags after filtering in treatment: 14921749 INFO @ Tue, 16 Jun 2020 09:40:53: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 09:40:53: #1 finished! INFO @ Tue, 16 Jun 2020 09:40:53: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:40:53: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:40:53: 6000000 INFO @ Tue, 16 Jun 2020 09:40:54: #2 number of paired peaks: 719 WARNING @ Tue, 16 Jun 2020 09:40:54: Fewer paired peaks (719) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 719 pairs to build model! INFO @ Tue, 16 Jun 2020 09:40:54: start model_add_line... INFO @ Tue, 16 Jun 2020 09:40:54: start X-correlation... INFO @ Tue, 16 Jun 2020 09:40:54: end of X-cor INFO @ Tue, 16 Jun 2020 09:40:54: #2 finished! INFO @ Tue, 16 Jun 2020 09:40:54: #2 predicted fragment length is 48 bps INFO @ Tue, 16 Jun 2020 09:40:54: #2 alternative fragment length(s) may be 2,48 bps INFO @ Tue, 16 Jun 2020 09:40:54: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX5402716/SRX5402716.05_model.r WARNING @ Tue, 16 Jun 2020 09:40:54: #2 Since the d (48) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 09:40:54: #2 You may need to consider one of the other alternative d(s): 2,48 WARNING @ Tue, 16 Jun 2020 09:40:54: #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 09:40:54: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:40:54: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 09:40:54: 10000000 INFO @ Tue, 16 Jun 2020 09:40:59: 7000000 INFO @ Tue, 16 Jun 2020 09:41:01: 11000000 INFO @ Tue, 16 Jun 2020 09:41:05: 8000000 INFO @ Tue, 16 Jun 2020 09:41:07: 12000000 INFO @ Tue, 16 Jun 2020 09:41:10: 9000000 INFO @ Tue, 16 Jun 2020 09:41:14: 13000000 INFO @ Tue, 16 Jun 2020 09:41:16: 10000000 INFO @ Tue, 16 Jun 2020 09:41:20: 14000000 INFO @ Tue, 16 Jun 2020 09:41:21: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 09:41:22: 11000000 INFO @ Tue, 16 Jun 2020 09:41:26: #1 tag size is determined as 50 bps INFO @ Tue, 16 Jun 2020 09:41:26: #1 tag size = 50 INFO @ Tue, 16 Jun 2020 09:41:26: #1 total tags in treatment: 14921749 INFO @ Tue, 16 Jun 2020 09:41:26: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:41:26: #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 09:41:26: #1 tags after filtering in treatment: 14921749 INFO @ Tue, 16 Jun 2020 09:41:26: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 09:41:26: #1 finished! INFO @ Tue, 16 Jun 2020 09:41:26: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:41:26: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:41:28: #2 number of paired peaks: 719 WARNING @ Tue, 16 Jun 2020 09:41:28: Fewer paired peaks (719) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 719 pairs to build model! INFO @ Tue, 16 Jun 2020 09:41:28: start model_add_line... INFO @ Tue, 16 Jun 2020 09:41:28: 12000000 INFO @ Tue, 16 Jun 2020 09:41:28: start X-correlation... INFO @ Tue, 16 Jun 2020 09:41:28: end of X-cor INFO @ Tue, 16 Jun 2020 09:41:28: #2 finished! INFO @ Tue, 16 Jun 2020 09:41:28: #2 predicted fragment length is 48 bps INFO @ Tue, 16 Jun 2020 09:41:28: #2 alternative fragment length(s) may be 2,48 bps INFO @ Tue, 16 Jun 2020 09:41:28: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX5402716/SRX5402716.10_model.r WARNING @ Tue, 16 Jun 2020 09:41:28: #2 Since the d (48) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 09:41:28: #2 You may need to consider one of the other alternative d(s): 2,48 WARNING @ Tue, 16 Jun 2020 09:41:28: #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 09:41:28: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:41:28: #3 Pre-compute pvalue-qvalue table... BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 16 Jun 2020 09:41:33: 13000000 INFO @ Tue, 16 Jun 2020 09:41:35: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX5402716/SRX5402716.05_peaks.xls INFO @ Tue, 16 Jun 2020 09:41:35: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX5402716/SRX5402716.05_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:41:35: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX5402716/SRX5402716.05_summits.bed INFO @ Tue, 16 Jun 2020 09:41:35: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (7154 records, 4 fields): 8 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 09:41:39: 14000000 INFO @ Tue, 16 Jun 2020 09:41:44: #1 tag size is determined as 50 bps INFO @ Tue, 16 Jun 2020 09:41:44: #1 tag size = 50 INFO @ Tue, 16 Jun 2020 09:41:44: #1 total tags in treatment: 14921749 INFO @ Tue, 16 Jun 2020 09:41:44: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:41:44: #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 09:41:44: #1 tags after filtering in treatment: 14921749 INFO @ Tue, 16 Jun 2020 09:41:44: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 09:41:44: #1 finished! INFO @ Tue, 16 Jun 2020 09:41:44: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:41:44: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:41:45: #2 number of paired peaks: 719 WARNING @ Tue, 16 Jun 2020 09:41:45: Fewer paired peaks (719) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 719 pairs to build model! INFO @ Tue, 16 Jun 2020 09:41:45: start model_add_line... INFO @ Tue, 16 Jun 2020 09:41:45: start X-correlation... INFO @ Tue, 16 Jun 2020 09:41:45: end of X-cor INFO @ Tue, 16 Jun 2020 09:41:45: #2 finished! INFO @ Tue, 16 Jun 2020 09:41:45: #2 predicted fragment length is 48 bps INFO @ Tue, 16 Jun 2020 09:41:45: #2 alternative fragment length(s) may be 2,48 bps INFO @ Tue, 16 Jun 2020 09:41:45: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX5402716/SRX5402716.20_model.r WARNING @ Tue, 16 Jun 2020 09:41:45: #2 Since the d (48) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 09:41:45: #2 You may need to consider one of the other alternative d(s): 2,48 WARNING @ Tue, 16 Jun 2020 09:41:45: #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 09:41:45: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:41:45: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 09:41:55: #3 Call peaks for each chromosome... BigWig に変換しました。 INFO @ Tue, 16 Jun 2020 09:42:11: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX5402716/SRX5402716.10_peaks.xls INFO @ Tue, 16 Jun 2020 09:42:11: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX5402716/SRX5402716.10_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:42:11: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX5402716/SRX5402716.10_summits.bed INFO @ Tue, 16 Jun 2020 09:42:11: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (1482 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 09:42:13: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 09:42:27: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX5402716/SRX5402716.20_peaks.xls INFO @ Tue, 16 Jun 2020 09:42:27: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX5402716/SRX5402716.20_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:42:27: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX5402716/SRX5402716.20_summits.bed INFO @ Tue, 16 Jun 2020 09:42:27: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (204 records, 4 fields): 1 millis CompletedMACS2peakCalling