Job ID = 6507926 SRX = SRX495021 Genome = ce11 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-26T14:15:26 prefetch.2.10.7: 1) Downloading 'SRR1198553'... 2020-06-26T14:15:27 prefetch.2.10.7: Downloading via HTTPS... 2020-06-26T14:17:19 prefetch.2.10.7: HTTPS download succeed 2020-06-26T14:17:20 prefetch.2.10.7: 'SRR1198553' is valid 2020-06-26T14:17:20 prefetch.2.10.7: 1) 'SRR1198553' was downloaded successfully Read 18854814 spots for SRR1198553/SRR1198553.sra Written 18854814 spots for SRR1198553/SRR1198553.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: 00:04:48 18854814 reads; of these: 18854814 (100.00%) were unpaired; of these: 288219 (1.53%) aligned 0 times 14954413 (79.31%) aligned exactly 1 time 3612182 (19.16%) aligned >1 times 98.47% overall alignment rate Time searching: 00:04:48 Overall time: 00:04:48 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] 3521715 / 18566595 = 0.1897 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 @ Fri, 26 Jun 2020 23:29:36: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX495021/SRX495021.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX495021/SRX495021.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX495021/SRX495021.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX495021/SRX495021.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 @ Fri, 26 Jun 2020 23:29:36: #1 read tag files... INFO @ Fri, 26 Jun 2020 23:29:36: #1 read treatment tags... INFO @ Fri, 26 Jun 2020 23:29:42: 1000000 INFO @ Fri, 26 Jun 2020 23:29:49: 2000000 INFO @ Fri, 26 Jun 2020 23:29:54: 3000000 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 @ Fri, 26 Jun 2020 23:29:59: 4000000 INFO @ Fri, 26 Jun 2020 23:30:00: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX495021/SRX495021.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX495021/SRX495021.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX495021/SRX495021.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX495021/SRX495021.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 @ Fri, 26 Jun 2020 23:30:00: #1 read tag files... INFO @ Fri, 26 Jun 2020 23:30:00: #1 read treatment tags... INFO @ Fri, 26 Jun 2020 23:30:04: 5000000 INFO @ Fri, 26 Jun 2020 23:30:10: 1000000 INFO @ Fri, 26 Jun 2020 23:30:11: 6000000 INFO @ Fri, 26 Jun 2020 23:30:17: 2000000 INFO @ Fri, 26 Jun 2020 23:30:18: 7000000 INFO @ Fri, 26 Jun 2020 23:30:23: 3000000 INFO @ Fri, 26 Jun 2020 23:30:24: 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 @ Fri, 26 Jun 2020 23:30:29: 4000000 INFO @ Fri, 26 Jun 2020 23:30:29: 9000000 INFO @ Fri, 26 Jun 2020 23:30:30: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX495021/SRX495021.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX495021/SRX495021.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX495021/SRX495021.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX495021/SRX495021.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 @ Fri, 26 Jun 2020 23:30:30: #1 read tag files... INFO @ Fri, 26 Jun 2020 23:30:30: #1 read treatment tags... INFO @ Fri, 26 Jun 2020 23:30:34: 10000000 INFO @ Fri, 26 Jun 2020 23:30:35: 1000000 INFO @ Fri, 26 Jun 2020 23:30:35: 5000000 INFO @ Fri, 26 Jun 2020 23:30:39: 11000000 INFO @ Fri, 26 Jun 2020 23:30:40: 2000000 INFO @ Fri, 26 Jun 2020 23:30:41: 6000000 INFO @ Fri, 26 Jun 2020 23:30:45: 12000000 INFO @ Fri, 26 Jun 2020 23:30:46: 3000000 INFO @ Fri, 26 Jun 2020 23:30:47: 7000000 INFO @ Fri, 26 Jun 2020 23:30:50: 13000000 INFO @ Fri, 26 Jun 2020 23:30:51: 4000000 INFO @ Fri, 26 Jun 2020 23:30:53: 8000000 INFO @ Fri, 26 Jun 2020 23:30:56: 14000000 INFO @ Fri, 26 Jun 2020 23:30:56: 5000000 INFO @ Fri, 26 Jun 2020 23:31:00: 9000000 INFO @ Fri, 26 Jun 2020 23:31:01: 15000000 INFO @ Fri, 26 Jun 2020 23:31:02: #1 tag size is determined as 42 bps INFO @ Fri, 26 Jun 2020 23:31:02: #1 tag size = 42 INFO @ Fri, 26 Jun 2020 23:31:02: #1 total tags in treatment: 15044880 INFO @ Fri, 26 Jun 2020 23:31:02: #1 user defined the maximum tags... INFO @ Fri, 26 Jun 2020 23:31:02: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 26 Jun 2020 23:31:02: #1 tags after filtering in treatment: 15044880 INFO @ Fri, 26 Jun 2020 23:31:02: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 26 Jun 2020 23:31:02: #1 finished! INFO @ Fri, 26 Jun 2020 23:31:02: #2 Build Peak Model... INFO @ Fri, 26 Jun 2020 23:31:02: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 26 Jun 2020 23:31:02: 6000000 INFO @ Fri, 26 Jun 2020 23:31:03: #2 number of paired peaks: 439 WARNING @ Fri, 26 Jun 2020 23:31:03: Fewer paired peaks (439) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 439 pairs to build model! INFO @ Fri, 26 Jun 2020 23:31:03: start model_add_line... INFO @ Fri, 26 Jun 2020 23:31:03: start X-correlation... INFO @ Fri, 26 Jun 2020 23:31:03: end of X-cor INFO @ Fri, 26 Jun 2020 23:31:03: #2 finished! INFO @ Fri, 26 Jun 2020 23:31:03: #2 predicted fragment length is 48 bps INFO @ Fri, 26 Jun 2020 23:31:03: #2 alternative fragment length(s) may be 2,48 bps INFO @ Fri, 26 Jun 2020 23:31:03: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX495021/SRX495021.05_model.r WARNING @ Fri, 26 Jun 2020 23:31:03: #2 Since the d (48) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 26 Jun 2020 23:31:03: #2 You may need to consider one of the other alternative d(s): 2,48 WARNING @ Fri, 26 Jun 2020 23:31:03: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Fri, 26 Jun 2020 23:31:03: #3 Call peaks... INFO @ Fri, 26 Jun 2020 23:31:03: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 26 Jun 2020 23:31:06: 10000000 INFO @ Fri, 26 Jun 2020 23:31:07: 7000000 INFO @ Fri, 26 Jun 2020 23:31:11: 11000000 INFO @ Fri, 26 Jun 2020 23:31:13: 8000000 INFO @ Fri, 26 Jun 2020 23:31:18: 12000000 INFO @ Fri, 26 Jun 2020 23:31:19: 9000000 INFO @ Fri, 26 Jun 2020 23:31:24: 13000000 INFO @ Fri, 26 Jun 2020 23:31:24: 10000000 INFO @ Fri, 26 Jun 2020 23:31:30: 11000000 INFO @ Fri, 26 Jun 2020 23:31:30: 14000000 INFO @ Fri, 26 Jun 2020 23:31:33: #3 Call peaks for each chromosome... INFO @ Fri, 26 Jun 2020 23:31:35: 12000000 INFO @ Fri, 26 Jun 2020 23:31:36: 15000000 INFO @ Fri, 26 Jun 2020 23:31:37: #1 tag size is determined as 42 bps INFO @ Fri, 26 Jun 2020 23:31:37: #1 tag size = 42 INFO @ Fri, 26 Jun 2020 23:31:37: #1 total tags in treatment: 15044880 INFO @ Fri, 26 Jun 2020 23:31:37: #1 user defined the maximum tags... INFO @ Fri, 26 Jun 2020 23:31:37: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 26 Jun 2020 23:31:37: #1 tags after filtering in treatment: 15044880 INFO @ Fri, 26 Jun 2020 23:31:37: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 26 Jun 2020 23:31:37: #1 finished! INFO @ Fri, 26 Jun 2020 23:31:37: #2 Build Peak Model... INFO @ Fri, 26 Jun 2020 23:31:37: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 26 Jun 2020 23:31:38: #2 number of paired peaks: 439 WARNING @ Fri, 26 Jun 2020 23:31:38: Fewer paired peaks (439) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 439 pairs to build model! INFO @ Fri, 26 Jun 2020 23:31:38: start model_add_line... INFO @ Fri, 26 Jun 2020 23:31:38: start X-correlation... INFO @ Fri, 26 Jun 2020 23:31:38: end of X-cor INFO @ Fri, 26 Jun 2020 23:31:38: #2 finished! INFO @ Fri, 26 Jun 2020 23:31:38: #2 predicted fragment length is 48 bps INFO @ Fri, 26 Jun 2020 23:31:38: #2 alternative fragment length(s) may be 2,48 bps INFO @ Fri, 26 Jun 2020 23:31:38: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX495021/SRX495021.10_model.r WARNING @ Fri, 26 Jun 2020 23:31:38: #2 Since the d (48) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 26 Jun 2020 23:31:38: #2 You may need to consider one of the other alternative d(s): 2,48 WARNING @ Fri, 26 Jun 2020 23:31:38: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Fri, 26 Jun 2020 23:31:38: #3 Call peaks... INFO @ Fri, 26 Jun 2020 23:31:38: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 26 Jun 2020 23:31:41: 13000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Fri, 26 Jun 2020 23:31:46: 14000000 INFO @ Fri, 26 Jun 2020 23:31:50: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX495021/SRX495021.05_peaks.xls INFO @ Fri, 26 Jun 2020 23:31:50: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX495021/SRX495021.05_peaks.narrowPeak INFO @ Fri, 26 Jun 2020 23:31:50: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX495021/SRX495021.05_summits.bed INFO @ Fri, 26 Jun 2020 23:31:50: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (4183 records, 4 fields): 16 millis CompletedMACS2peakCalling INFO @ Fri, 26 Jun 2020 23:31:51: 15000000 INFO @ Fri, 26 Jun 2020 23:31:51: #1 tag size is determined as 42 bps INFO @ Fri, 26 Jun 2020 23:31:51: #1 tag size = 42 INFO @ Fri, 26 Jun 2020 23:31:51: #1 total tags in treatment: 15044880 INFO @ Fri, 26 Jun 2020 23:31:51: #1 user defined the maximum tags... INFO @ Fri, 26 Jun 2020 23:31:51: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 26 Jun 2020 23:31:52: #1 tags after filtering in treatment: 15044880 INFO @ Fri, 26 Jun 2020 23:31:52: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 26 Jun 2020 23:31:52: #1 finished! INFO @ Fri, 26 Jun 2020 23:31:52: #2 Build Peak Model... INFO @ Fri, 26 Jun 2020 23:31:52: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 26 Jun 2020 23:31:53: #2 number of paired peaks: 439 WARNING @ Fri, 26 Jun 2020 23:31:53: Fewer paired peaks (439) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 439 pairs to build model! INFO @ Fri, 26 Jun 2020 23:31:53: start model_add_line... INFO @ Fri, 26 Jun 2020 23:31:53: start X-correlation... INFO @ Fri, 26 Jun 2020 23:31:53: end of X-cor INFO @ Fri, 26 Jun 2020 23:31:53: #2 finished! INFO @ Fri, 26 Jun 2020 23:31:53: #2 predicted fragment length is 48 bps INFO @ Fri, 26 Jun 2020 23:31:53: #2 alternative fragment length(s) may be 2,48 bps INFO @ Fri, 26 Jun 2020 23:31:53: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX495021/SRX495021.20_model.r WARNING @ Fri, 26 Jun 2020 23:31:53: #2 Since the d (48) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 26 Jun 2020 23:31:53: #2 You may need to consider one of the other alternative d(s): 2,48 WARNING @ Fri, 26 Jun 2020 23:31:53: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Fri, 26 Jun 2020 23:31:53: #3 Call peaks... INFO @ Fri, 26 Jun 2020 23:31:53: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 26 Jun 2020 23:32:10: #3 Call peaks for each chromosome... BigWig に変換しました。 INFO @ Fri, 26 Jun 2020 23:32:23: #3 Call peaks for each chromosome... INFO @ Fri, 26 Jun 2020 23:32:27: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX495021/SRX495021.10_peaks.xls INFO @ Fri, 26 Jun 2020 23:32:27: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX495021/SRX495021.10_peaks.narrowPeak INFO @ Fri, 26 Jun 2020 23:32:27: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX495021/SRX495021.10_summits.bed INFO @ Fri, 26 Jun 2020 23:32:27: Done! pass1 - making usageList (7 chroms): 2 millis pass2 - checking and writing primary data (1022 records, 4 fields): 5 millis CompletedMACS2peakCalling INFO @ Fri, 26 Jun 2020 23:32:38: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX495021/SRX495021.20_peaks.xls INFO @ Fri, 26 Jun 2020 23:32:38: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX495021/SRX495021.20_peaks.narrowPeak INFO @ Fri, 26 Jun 2020 23:32:38: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX495021/SRX495021.20_summits.bed INFO @ Fri, 26 Jun 2020 23:32:38: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (280 records, 4 fields): 1 millis CompletedMACS2peakCalling