Job ID = 6368498 SRX = SRX5020728 Genome = ce11 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-16T00:21:51 prefetch.2.10.7: 1) Downloading 'SRR8201351'... 2020-06-16T00:21:51 prefetch.2.10.7: Downloading via HTTPS... 2020-06-16T00:24:54 prefetch.2.10.7: HTTPS download succeed 2020-06-16T00:24:54 prefetch.2.10.7: 1) 'SRR8201351' was downloaded successfully Read 15967421 spots for SRR8201351/SRR8201351.sra Written 15967421 spots for SRR8201351/SRR8201351.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: 00:03:43 15967421 reads; of these: 15967421 (100.00%) were unpaired; of these: 487629 (3.05%) aligned 0 times 13057985 (81.78%) aligned exactly 1 time 2421807 (15.17%) aligned >1 times 96.95% overall alignment rate Time searching: 00:03:43 Overall time: 00:03:43 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] 1447507 / 15479792 = 0.0935 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 09:34:01: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX5020728/SRX5020728.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX5020728/SRX5020728.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX5020728/SRX5020728.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX5020728/SRX5020728.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 09:34:01: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:34:01: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:34:08: 1000000 INFO @ Tue, 16 Jun 2020 09:34:14: 2000000 INFO @ Tue, 16 Jun 2020 09:34:20: 3000000 INFO @ Tue, 16 Jun 2020 09:34:27: 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 09:34:31: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX5020728/SRX5020728.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX5020728/SRX5020728.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX5020728/SRX5020728.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX5020728/SRX5020728.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 09:34:31: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:34:31: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:34:33: 5000000 INFO @ Tue, 16 Jun 2020 09:34:38: 1000000 INFO @ Tue, 16 Jun 2020 09:34:41: 6000000 INFO @ Tue, 16 Jun 2020 09:34:45: 2000000 INFO @ Tue, 16 Jun 2020 09:34:48: 7000000 INFO @ Tue, 16 Jun 2020 09:34:52: 3000000 INFO @ Tue, 16 Jun 2020 09:34:55: 8000000 INFO @ Tue, 16 Jun 2020 09:34:59: 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 09:35:01: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX5020728/SRX5020728.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX5020728/SRX5020728.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX5020728/SRX5020728.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX5020728/SRX5020728.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 09:35:01: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:35:01: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:35:02: 9000000 INFO @ Tue, 16 Jun 2020 09:35:06: 5000000 INFO @ Tue, 16 Jun 2020 09:35:08: 1000000 INFO @ Tue, 16 Jun 2020 09:35:09: 10000000 INFO @ Tue, 16 Jun 2020 09:35:13: 6000000 INFO @ Tue, 16 Jun 2020 09:35:15: 2000000 INFO @ Tue, 16 Jun 2020 09:35:16: 11000000 INFO @ Tue, 16 Jun 2020 09:35:20: 7000000 INFO @ Tue, 16 Jun 2020 09:35:22: 3000000 INFO @ Tue, 16 Jun 2020 09:35:24: 12000000 INFO @ Tue, 16 Jun 2020 09:35:28: 8000000 INFO @ Tue, 16 Jun 2020 09:35:29: 4000000 INFO @ Tue, 16 Jun 2020 09:35:31: 13000000 INFO @ Tue, 16 Jun 2020 09:35:35: 9000000 INFO @ Tue, 16 Jun 2020 09:35:37: 5000000 INFO @ Tue, 16 Jun 2020 09:35:38: 14000000 INFO @ Tue, 16 Jun 2020 09:35:38: #1 tag size is determined as 51 bps INFO @ Tue, 16 Jun 2020 09:35:38: #1 tag size = 51 INFO @ Tue, 16 Jun 2020 09:35:38: #1 total tags in treatment: 14032285 INFO @ Tue, 16 Jun 2020 09:35:38: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:35:38: #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 09:35:38: #1 tags after filtering in treatment: 14032285 INFO @ Tue, 16 Jun 2020 09:35:38: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 09:35:38: #1 finished! INFO @ Tue, 16 Jun 2020 09:35:38: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:35:38: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:35:39: #2 number of paired peaks: 238 WARNING @ Tue, 16 Jun 2020 09:35:39: Fewer paired peaks (238) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 238 pairs to build model! INFO @ Tue, 16 Jun 2020 09:35:39: start model_add_line... INFO @ Tue, 16 Jun 2020 09:35:39: start X-correlation... INFO @ Tue, 16 Jun 2020 09:35:40: end of X-cor INFO @ Tue, 16 Jun 2020 09:35:40: #2 finished! INFO @ Tue, 16 Jun 2020 09:35:40: #2 predicted fragment length is 55 bps INFO @ Tue, 16 Jun 2020 09:35:40: #2 alternative fragment length(s) may be 3,55,559,573 bps INFO @ Tue, 16 Jun 2020 09:35:40: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX5020728/SRX5020728.05_model.r WARNING @ Tue, 16 Jun 2020 09:35:40: #2 Since the d (55) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 09:35:40: #2 You may need to consider one of the other alternative d(s): 3,55,559,573 WARNING @ Tue, 16 Jun 2020 09:35:40: #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 09:35:40: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:35:40: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 09:35:42: 10000000 INFO @ Tue, 16 Jun 2020 09:35:44: 6000000 INFO @ Tue, 16 Jun 2020 09:35:49: 11000000 INFO @ Tue, 16 Jun 2020 09:35:51: 7000000 INFO @ Tue, 16 Jun 2020 09:35:56: 12000000 INFO @ Tue, 16 Jun 2020 09:35:58: 8000000 INFO @ Tue, 16 Jun 2020 09:36:03: 13000000 INFO @ Tue, 16 Jun 2020 09:36:05: 9000000 INFO @ Tue, 16 Jun 2020 09:36:06: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 09:36:11: 14000000 INFO @ Tue, 16 Jun 2020 09:36:11: #1 tag size is determined as 51 bps INFO @ Tue, 16 Jun 2020 09:36:11: #1 tag size = 51 INFO @ Tue, 16 Jun 2020 09:36:11: #1 total tags in treatment: 14032285 INFO @ Tue, 16 Jun 2020 09:36:11: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:36:11: #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 09:36:11: #1 tags after filtering in treatment: 14032285 INFO @ Tue, 16 Jun 2020 09:36:11: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 09:36:11: #1 finished! INFO @ Tue, 16 Jun 2020 09:36:11: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:36:11: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:36:12: 10000000 INFO @ Tue, 16 Jun 2020 09:36:12: #2 number of paired peaks: 238 WARNING @ Tue, 16 Jun 2020 09:36:12: Fewer paired peaks (238) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 238 pairs to build model! INFO @ Tue, 16 Jun 2020 09:36:12: start model_add_line... INFO @ Tue, 16 Jun 2020 09:36:12: start X-correlation... INFO @ Tue, 16 Jun 2020 09:36:12: end of X-cor INFO @ Tue, 16 Jun 2020 09:36:12: #2 finished! INFO @ Tue, 16 Jun 2020 09:36:12: #2 predicted fragment length is 55 bps INFO @ Tue, 16 Jun 2020 09:36:12: #2 alternative fragment length(s) may be 3,55,559,573 bps INFO @ Tue, 16 Jun 2020 09:36:12: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX5020728/SRX5020728.10_model.r WARNING @ Tue, 16 Jun 2020 09:36:12: #2 Since the d (55) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 09:36:12: #2 You may need to consider one of the other alternative d(s): 3,55,559,573 WARNING @ Tue, 16 Jun 2020 09:36:12: #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 09:36:12: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:36:12: #3 Pre-compute pvalue-qvalue table... BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 16 Jun 2020 09:36:19: 11000000 INFO @ Tue, 16 Jun 2020 09:36:20: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX5020728/SRX5020728.05_peaks.xls INFO @ Tue, 16 Jun 2020 09:36:20: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX5020728/SRX5020728.05_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:36:20: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX5020728/SRX5020728.05_summits.bed INFO @ Tue, 16 Jun 2020 09:36:20: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (605 records, 4 fields): 1 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 09:36:25: 12000000 INFO @ Tue, 16 Jun 2020 09:36:31: 13000000 INFO @ Tue, 16 Jun 2020 09:36:38: 14000000 INFO @ Tue, 16 Jun 2020 09:36:38: #1 tag size is determined as 51 bps INFO @ Tue, 16 Jun 2020 09:36:38: #1 tag size = 51 INFO @ Tue, 16 Jun 2020 09:36:38: #1 total tags in treatment: 14032285 INFO @ Tue, 16 Jun 2020 09:36:38: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:36:38: #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 09:36:38: #1 tags after filtering in treatment: 14032285 INFO @ Tue, 16 Jun 2020 09:36:38: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 09:36:38: #1 finished! INFO @ Tue, 16 Jun 2020 09:36:38: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:36:38: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:36:39: #2 number of paired peaks: 238 WARNING @ Tue, 16 Jun 2020 09:36:39: Fewer paired peaks (238) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 238 pairs to build model! INFO @ Tue, 16 Jun 2020 09:36:39: start model_add_line... INFO @ Tue, 16 Jun 2020 09:36:39: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 09:36:39: start X-correlation... INFO @ Tue, 16 Jun 2020 09:36:39: end of X-cor INFO @ Tue, 16 Jun 2020 09:36:39: #2 finished! INFO @ Tue, 16 Jun 2020 09:36:39: #2 predicted fragment length is 55 bps INFO @ Tue, 16 Jun 2020 09:36:39: #2 alternative fragment length(s) may be 3,55,559,573 bps INFO @ Tue, 16 Jun 2020 09:36:39: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX5020728/SRX5020728.20_model.r WARNING @ Tue, 16 Jun 2020 09:36:39: #2 Since the d (55) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 09:36:39: #2 You may need to consider one of the other alternative d(s): 3,55,559,573 WARNING @ Tue, 16 Jun 2020 09:36:39: #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 09:36:39: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:36:39: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Tue, 16 Jun 2020 09:36:53: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX5020728/SRX5020728.10_peaks.xls INFO @ Tue, 16 Jun 2020 09:36:53: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX5020728/SRX5020728.10_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:36:53: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX5020728/SRX5020728.10_summits.bed INFO @ Tue, 16 Jun 2020 09:36:53: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (338 records, 4 fields): 1 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 09:37:05: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 09:37:19: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX5020728/SRX5020728.20_peaks.xls INFO @ Tue, 16 Jun 2020 09:37:19: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX5020728/SRX5020728.20_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:37:19: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX5020728/SRX5020728.20_summits.bed INFO @ Tue, 16 Jun 2020 09:37:19: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (155 records, 4 fields): 1 millis CompletedMACS2peakCalling