Job ID = 6366662 SRX = SRX216763 Genome = ce11 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-15T23:03:53 prefetch.2.10.7: 1) Downloading 'SRR648397'... 2020-06-15T23:03:53 prefetch.2.10.7: Downloading via HTTPS... 2020-06-15T23:05:18 prefetch.2.10.7: HTTPS download succeed 2020-06-15T23:05:18 prefetch.2.10.7: 1) 'SRR648397' was downloaded successfully Read 20221757 spots for SRR648397/SRR648397.sra Written 20221757 spots for SRR648397/SRR648397.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: 00:04:38 20221757 reads; of these: 20221757 (100.00%) were unpaired; of these: 1113334 (5.51%) aligned 0 times 16222018 (80.22%) aligned exactly 1 time 2886405 (14.27%) aligned >1 times 94.49% overall alignment rate Time searching: 00:04:38 Overall time: 00:04:38 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] 1960815 / 19108423 = 0.1026 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 08:15:50: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX216763/SRX216763.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX216763/SRX216763.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX216763/SRX216763.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX216763/SRX216763.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 08:15:50: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:15:50: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:15:56: 1000000 INFO @ Tue, 16 Jun 2020 08:16:02: 2000000 INFO @ Tue, 16 Jun 2020 08:16:09: 3000000 INFO @ Tue, 16 Jun 2020 08:16:15: 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 08:16:20: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX216763/SRX216763.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX216763/SRX216763.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX216763/SRX216763.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX216763/SRX216763.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 08:16:20: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:16:20: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:16:21: 5000000 INFO @ Tue, 16 Jun 2020 08:16:26: 1000000 INFO @ Tue, 16 Jun 2020 08:16:28: 6000000 INFO @ Tue, 16 Jun 2020 08:16:33: 2000000 INFO @ Tue, 16 Jun 2020 08:16:34: 7000000 INFO @ Tue, 16 Jun 2020 08:16:39: 3000000 INFO @ Tue, 16 Jun 2020 08:16:41: 8000000 INFO @ Tue, 16 Jun 2020 08:16:45: 4000000 INFO @ Tue, 16 Jun 2020 08:16:47: 9000000 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 08:16:50: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX216763/SRX216763.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX216763/SRX216763.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX216763/SRX216763.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX216763/SRX216763.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 08:16:50: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:16:50: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:16:51: 5000000 INFO @ Tue, 16 Jun 2020 08:16:53: 10000000 INFO @ Tue, 16 Jun 2020 08:16:57: 1000000 INFO @ Tue, 16 Jun 2020 08:16:58: 6000000 INFO @ Tue, 16 Jun 2020 08:17:00: 11000000 INFO @ Tue, 16 Jun 2020 08:17:04: 2000000 INFO @ Tue, 16 Jun 2020 08:17:04: 7000000 INFO @ Tue, 16 Jun 2020 08:17:06: 12000000 INFO @ Tue, 16 Jun 2020 08:17:10: 3000000 INFO @ Tue, 16 Jun 2020 08:17:11: 8000000 INFO @ Tue, 16 Jun 2020 08:17:12: 13000000 INFO @ Tue, 16 Jun 2020 08:17:17: 4000000 INFO @ Tue, 16 Jun 2020 08:17:17: 9000000 INFO @ Tue, 16 Jun 2020 08:17:19: 14000000 INFO @ Tue, 16 Jun 2020 08:17:23: 10000000 INFO @ Tue, 16 Jun 2020 08:17:24: 5000000 INFO @ Tue, 16 Jun 2020 08:17:25: 15000000 INFO @ Tue, 16 Jun 2020 08:17:30: 11000000 INFO @ Tue, 16 Jun 2020 08:17:30: 6000000 INFO @ Tue, 16 Jun 2020 08:17:32: 16000000 INFO @ Tue, 16 Jun 2020 08:17:36: 12000000 INFO @ Tue, 16 Jun 2020 08:17:37: 7000000 INFO @ Tue, 16 Jun 2020 08:17:38: 17000000 INFO @ Tue, 16 Jun 2020 08:17:39: #1 tag size is determined as 50 bps INFO @ Tue, 16 Jun 2020 08:17:39: #1 tag size = 50 INFO @ Tue, 16 Jun 2020 08:17:39: #1 total tags in treatment: 17147608 INFO @ Tue, 16 Jun 2020 08:17:39: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:17:39: #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 08:17:39: #1 tags after filtering in treatment: 17147608 INFO @ Tue, 16 Jun 2020 08:17:39: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:17:39: #1 finished! INFO @ Tue, 16 Jun 2020 08:17:39: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:17:39: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:17:40: #2 number of paired peaks: 229 WARNING @ Tue, 16 Jun 2020 08:17:40: Fewer paired peaks (229) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 229 pairs to build model! INFO @ Tue, 16 Jun 2020 08:17:40: start model_add_line... INFO @ Tue, 16 Jun 2020 08:17:40: start X-correlation... INFO @ Tue, 16 Jun 2020 08:17:41: end of X-cor INFO @ Tue, 16 Jun 2020 08:17:41: #2 finished! INFO @ Tue, 16 Jun 2020 08:17:41: #2 predicted fragment length is 43 bps INFO @ Tue, 16 Jun 2020 08:17:41: #2 alternative fragment length(s) may be 1,43,574,588 bps INFO @ Tue, 16 Jun 2020 08:17:41: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX216763/SRX216763.05_model.r WARNING @ Tue, 16 Jun 2020 08:17:41: #2 Since the d (43) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 08:17:41: #2 You may need to consider one of the other alternative d(s): 1,43,574,588 WARNING @ Tue, 16 Jun 2020 08:17:41: #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 08:17:41: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:17:41: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 08:17:42: 13000000 INFO @ Tue, 16 Jun 2020 08:17:43: 8000000 INFO @ Tue, 16 Jun 2020 08:17:49: 14000000 INFO @ Tue, 16 Jun 2020 08:17:50: 9000000 INFO @ Tue, 16 Jun 2020 08:17:55: 15000000 INFO @ Tue, 16 Jun 2020 08:17:56: 10000000 INFO @ Tue, 16 Jun 2020 08:18:01: 16000000 INFO @ Tue, 16 Jun 2020 08:18:03: 11000000 INFO @ Tue, 16 Jun 2020 08:18:07: 17000000 INFO @ Tue, 16 Jun 2020 08:18:08: #1 tag size is determined as 50 bps INFO @ Tue, 16 Jun 2020 08:18:08: #1 tag size = 50 INFO @ Tue, 16 Jun 2020 08:18:08: #1 total tags in treatment: 17147608 INFO @ Tue, 16 Jun 2020 08:18:08: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:18:08: #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 08:18:08: #1 tags after filtering in treatment: 17147608 INFO @ Tue, 16 Jun 2020 08:18:08: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:18:08: #1 finished! INFO @ Tue, 16 Jun 2020 08:18:08: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:18:08: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:18:09: 12000000 INFO @ Tue, 16 Jun 2020 08:18:09: #2 number of paired peaks: 229 WARNING @ Tue, 16 Jun 2020 08:18:09: Fewer paired peaks (229) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 229 pairs to build model! INFO @ Tue, 16 Jun 2020 08:18:09: start model_add_line... INFO @ Tue, 16 Jun 2020 08:18:10: start X-correlation... INFO @ Tue, 16 Jun 2020 08:18:10: end of X-cor INFO @ Tue, 16 Jun 2020 08:18:10: #2 finished! INFO @ Tue, 16 Jun 2020 08:18:10: #2 predicted fragment length is 43 bps INFO @ Tue, 16 Jun 2020 08:18:10: #2 alternative fragment length(s) may be 1,43,574,588 bps INFO @ Tue, 16 Jun 2020 08:18:10: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX216763/SRX216763.10_model.r WARNING @ Tue, 16 Jun 2020 08:18:10: #2 Since the d (43) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 08:18:10: #2 You may need to consider one of the other alternative d(s): 1,43,574,588 WARNING @ Tue, 16 Jun 2020 08:18:10: #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 08:18:10: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:18:10: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 08:18:11: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 08:18:16: 13000000 INFO @ Tue, 16 Jun 2020 08:18:22: 14000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 16 Jun 2020 08:18:26: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX216763/SRX216763.05_peaks.xls INFO @ Tue, 16 Jun 2020 08:18:26: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX216763/SRX216763.05_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:18:26: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX216763/SRX216763.05_summits.bed INFO @ Tue, 16 Jun 2020 08:18:26: Done! pass1 - making usageList (7 chroms): 0 millis pass2 - checking and writing primary data (672 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 08:18:28: 15000000 INFO @ Tue, 16 Jun 2020 08:18:34: 16000000 INFO @ Tue, 16 Jun 2020 08:18:39: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 08:18:40: 17000000 INFO @ Tue, 16 Jun 2020 08:18:41: #1 tag size is determined as 50 bps INFO @ Tue, 16 Jun 2020 08:18:41: #1 tag size = 50 INFO @ Tue, 16 Jun 2020 08:18:41: #1 total tags in treatment: 17147608 INFO @ Tue, 16 Jun 2020 08:18:41: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:18:41: #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 08:18:41: #1 tags after filtering in treatment: 17147608 INFO @ Tue, 16 Jun 2020 08:18:41: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:18:41: #1 finished! INFO @ Tue, 16 Jun 2020 08:18:41: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:18:41: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:18:43: #2 number of paired peaks: 229 WARNING @ Tue, 16 Jun 2020 08:18:43: Fewer paired peaks (229) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 229 pairs to build model! INFO @ Tue, 16 Jun 2020 08:18:43: start model_add_line... INFO @ Tue, 16 Jun 2020 08:18:43: start X-correlation... INFO @ Tue, 16 Jun 2020 08:18:43: end of X-cor INFO @ Tue, 16 Jun 2020 08:18:43: #2 finished! INFO @ Tue, 16 Jun 2020 08:18:43: #2 predicted fragment length is 43 bps INFO @ Tue, 16 Jun 2020 08:18:43: #2 alternative fragment length(s) may be 1,43,574,588 bps INFO @ Tue, 16 Jun 2020 08:18:43: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX216763/SRX216763.20_model.r WARNING @ Tue, 16 Jun 2020 08:18:43: #2 Since the d (43) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 08:18:43: #2 You may need to consider one of the other alternative d(s): 1,43,574,588 WARNING @ Tue, 16 Jun 2020 08:18:43: #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 08:18:43: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:18:43: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 08:18:53: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX216763/SRX216763.10_peaks.xls INFO @ Tue, 16 Jun 2020 08:18:53: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX216763/SRX216763.10_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:18:53: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX216763/SRX216763.10_summits.bed INFO @ Tue, 16 Jun 2020 08:18:53: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (408 records, 4 fields): 1 millis CompletedMACS2peakCalling BigWig に変換しました。 INFO @ Tue, 16 Jun 2020 08:19:12: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 08:19:27: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX216763/SRX216763.20_peaks.xls INFO @ Tue, 16 Jun 2020 08:19:27: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX216763/SRX216763.20_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:19:27: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX216763/SRX216763.20_summits.bed INFO @ Tue, 16 Jun 2020 08:19:27: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (142 records, 4 fields): 1 millis CompletedMACS2peakCalling