Job ID = 6366282 SRX = SRX1078707 Genome = ce11 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-15T22:31:59 prefetch.2.10.7: 1) Downloading 'SRR2084314'... 2020-06-15T22:31:59 prefetch.2.10.7: Downloading via HTTPS... 2020-06-15T22:34:37 prefetch.2.10.7: HTTPS download succeed 2020-06-15T22:34:37 prefetch.2.10.7: 1) 'SRR2084314' was downloaded successfully Read 22046643 spots for SRR2084314/SRR2084314.sra Written 22046643 spots for SRR2084314/SRR2084314.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: 00:04:13 22046643 reads; of these: 22046643 (100.00%) were unpaired; of these: 7559422 (34.29%) aligned 0 times 11976669 (54.32%) aligned exactly 1 time 2510552 (11.39%) aligned >1 times 65.71% overall alignment rate Time searching: 00:04:13 Overall time: 00:04:13 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] 7296961 / 14487221 = 0.5037 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 07:43:36: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX1078707/SRX1078707.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX1078707/SRX1078707.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX1078707/SRX1078707.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX1078707/SRX1078707.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 07:43:36: #1 read tag files... INFO @ Tue, 16 Jun 2020 07:43:36: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 07:43:41: 1000000 INFO @ Tue, 16 Jun 2020 07:43:47: 2000000 INFO @ Tue, 16 Jun 2020 07:43:52: 3000000 INFO @ Tue, 16 Jun 2020 07:43:57: 4000000 INFO @ Tue, 16 Jun 2020 07:44:02: 5000000 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 07:44:06: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX1078707/SRX1078707.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX1078707/SRX1078707.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX1078707/SRX1078707.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX1078707/SRX1078707.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 07:44:06: #1 read tag files... INFO @ Tue, 16 Jun 2020 07:44:06: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 07:44:08: 6000000 INFO @ Tue, 16 Jun 2020 07:44:11: 1000000 INFO @ Tue, 16 Jun 2020 07:44:13: 7000000 INFO @ Tue, 16 Jun 2020 07:44:14: #1 tag size is determined as 51 bps INFO @ Tue, 16 Jun 2020 07:44:14: #1 tag size = 51 INFO @ Tue, 16 Jun 2020 07:44:14: #1 total tags in treatment: 7190260 INFO @ Tue, 16 Jun 2020 07:44:14: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 07:44:14: #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 07:44:14: #1 tags after filtering in treatment: 7190260 INFO @ Tue, 16 Jun 2020 07:44:14: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 07:44:14: #1 finished! INFO @ Tue, 16 Jun 2020 07:44:14: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 07:44:14: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 07:44:15: #2 number of paired peaks: 565 WARNING @ Tue, 16 Jun 2020 07:44:15: Fewer paired peaks (565) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 565 pairs to build model! INFO @ Tue, 16 Jun 2020 07:44:15: start model_add_line... INFO @ Tue, 16 Jun 2020 07:44:15: start X-correlation... INFO @ Tue, 16 Jun 2020 07:44:15: end of X-cor INFO @ Tue, 16 Jun 2020 07:44:15: #2 finished! INFO @ Tue, 16 Jun 2020 07:44:15: #2 predicted fragment length is 48 bps INFO @ Tue, 16 Jun 2020 07:44:15: #2 alternative fragment length(s) may be 3,48 bps INFO @ Tue, 16 Jun 2020 07:44:15: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX1078707/SRX1078707.05_model.r WARNING @ Tue, 16 Jun 2020 07:44:15: #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 07:44:15: #2 You may need to consider one of the other alternative d(s): 3,48 WARNING @ Tue, 16 Jun 2020 07:44:15: #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 07:44:15: #3 Call peaks... INFO @ Tue, 16 Jun 2020 07:44:15: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 07:44:17: 2000000 INFO @ Tue, 16 Jun 2020 07:44:22: 3000000 INFO @ Tue, 16 Jun 2020 07:44:28: 4000000 INFO @ Tue, 16 Jun 2020 07:44:29: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 07:44:33: 5000000 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 07:44:36: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX1078707/SRX1078707.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX1078707/SRX1078707.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX1078707/SRX1078707.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX1078707/SRX1078707.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 07:44:36: #1 read tag files... INFO @ Tue, 16 Jun 2020 07:44:36: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 07:44:37: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX1078707/SRX1078707.05_peaks.xls INFO @ Tue, 16 Jun 2020 07:44:37: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX1078707/SRX1078707.05_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 07:44:37: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX1078707/SRX1078707.05_summits.bed INFO @ Tue, 16 Jun 2020 07:44:37: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (767 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 07:44:39: 6000000 INFO @ Tue, 16 Jun 2020 07:44:42: 1000000 INFO @ Tue, 16 Jun 2020 07:44:45: 7000000 INFO @ Tue, 16 Jun 2020 07:44:46: #1 tag size is determined as 51 bps INFO @ Tue, 16 Jun 2020 07:44:46: #1 tag size = 51 INFO @ Tue, 16 Jun 2020 07:44:46: #1 total tags in treatment: 7190260 INFO @ Tue, 16 Jun 2020 07:44:46: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 07:44:46: #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 07:44:46: #1 tags after filtering in treatment: 7190260 INFO @ Tue, 16 Jun 2020 07:44:46: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 07:44:46: #1 finished! INFO @ Tue, 16 Jun 2020 07:44:46: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 07:44:46: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 07:44:47: #2 number of paired peaks: 565 WARNING @ Tue, 16 Jun 2020 07:44:47: Fewer paired peaks (565) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 565 pairs to build model! INFO @ Tue, 16 Jun 2020 07:44:47: start model_add_line... INFO @ Tue, 16 Jun 2020 07:44:47: start X-correlation... INFO @ Tue, 16 Jun 2020 07:44:47: end of X-cor INFO @ Tue, 16 Jun 2020 07:44:47: #2 finished! INFO @ Tue, 16 Jun 2020 07:44:47: #2 predicted fragment length is 48 bps INFO @ Tue, 16 Jun 2020 07:44:47: #2 alternative fragment length(s) may be 3,48 bps INFO @ Tue, 16 Jun 2020 07:44:47: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX1078707/SRX1078707.10_model.r WARNING @ Tue, 16 Jun 2020 07:44:47: #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 07:44:47: #2 You may need to consider one of the other alternative d(s): 3,48 WARNING @ Tue, 16 Jun 2020 07:44:47: #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 07:44:47: #3 Call peaks... INFO @ Tue, 16 Jun 2020 07:44:47: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 07:44:48: 2000000 INFO @ Tue, 16 Jun 2020 07:44:53: 3000000 INFO @ Tue, 16 Jun 2020 07:44:59: 4000000 INFO @ Tue, 16 Jun 2020 07:45:03: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 07:45:04: 5000000 INFO @ Tue, 16 Jun 2020 07:45:10: 6000000 INFO @ Tue, 16 Jun 2020 07:45:11: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX1078707/SRX1078707.10_peaks.xls INFO @ Tue, 16 Jun 2020 07:45:11: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX1078707/SRX1078707.10_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 07:45:11: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX1078707/SRX1078707.10_summits.bed INFO @ Tue, 16 Jun 2020 07:45:11: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (589 records, 4 fields): 2 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 16 Jun 2020 07:45:15: 7000000 INFO @ Tue, 16 Jun 2020 07:45:16: #1 tag size is determined as 51 bps INFO @ Tue, 16 Jun 2020 07:45:16: #1 tag size = 51 INFO @ Tue, 16 Jun 2020 07:45:16: #1 total tags in treatment: 7190260 INFO @ Tue, 16 Jun 2020 07:45:16: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 07:45:16: #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 07:45:17: #1 tags after filtering in treatment: 7190260 INFO @ Tue, 16 Jun 2020 07:45:17: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 07:45:17: #1 finished! INFO @ Tue, 16 Jun 2020 07:45:17: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 07:45:17: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 07:45:17: #2 number of paired peaks: 565 WARNING @ Tue, 16 Jun 2020 07:45:17: Fewer paired peaks (565) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 565 pairs to build model! INFO @ Tue, 16 Jun 2020 07:45:17: start model_add_line... INFO @ Tue, 16 Jun 2020 07:45:17: start X-correlation... INFO @ Tue, 16 Jun 2020 07:45:17: end of X-cor INFO @ Tue, 16 Jun 2020 07:45:17: #2 finished! INFO @ Tue, 16 Jun 2020 07:45:17: #2 predicted fragment length is 48 bps INFO @ Tue, 16 Jun 2020 07:45:17: #2 alternative fragment length(s) may be 3,48 bps INFO @ Tue, 16 Jun 2020 07:45:17: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX1078707/SRX1078707.20_model.r WARNING @ Tue, 16 Jun 2020 07:45:17: #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 07:45:17: #2 You may need to consider one of the other alternative d(s): 3,48 WARNING @ Tue, 16 Jun 2020 07:45:17: #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 07:45:17: #3 Call peaks... INFO @ Tue, 16 Jun 2020 07:45:17: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Tue, 16 Jun 2020 07:45:33: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 07:45:41: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX1078707/SRX1078707.20_peaks.xls INFO @ Tue, 16 Jun 2020 07:45:41: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX1078707/SRX1078707.20_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 07:45:41: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX1078707/SRX1078707.20_summits.bed INFO @ Tue, 16 Jun 2020 07:45:41: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (243 records, 4 fields): 2 millis CompletedMACS2peakCalling