Job ID = 6366885 SRX = SRX2543053 Genome = ce11 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-15T22:58:23 prefetch.2.10.7: 1) Downloading 'SRR5235989'... 2020-06-15T22:58:23 prefetch.2.10.7: Downloading via HTTPS... 2020-06-15T22:59:25 prefetch.2.10.7: HTTPS download succeed 2020-06-15T22:59:25 prefetch.2.10.7: 'SRR5235989' is valid 2020-06-15T22:59:25 prefetch.2.10.7: 1) 'SRR5235989' was downloaded successfully 2020-06-15T22:59:25 prefetch.2.10.7: 'SRR5235989' has 0 unresolved dependencies Read 16580230 spots for SRR5235989/SRR5235989.sra Written 16580230 spots for SRR5235989/SRR5235989.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: 00:06:06 16580230 reads; of these: 16580230 (100.00%) were unpaired; of these: 295963 (1.79%) aligned 0 times 13442934 (81.08%) aligned exactly 1 time 2841333 (17.14%) aligned >1 times 98.21% overall alignment rate Time searching: 00:06:06 Overall time: 00:06:06 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] 2195912 / 16284267 = 0.1348 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 08:10:47: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX2543053/SRX2543053.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX2543053/SRX2543053.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX2543053/SRX2543053.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX2543053/SRX2543053.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 08:10:47: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:10:47: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:10:53: 1000000 INFO @ Tue, 16 Jun 2020 08:10:59: 2000000 INFO @ Tue, 16 Jun 2020 08:11:05: 3000000 INFO @ Tue, 16 Jun 2020 08:11:10: 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 08:11:16: 5000000 INFO @ Tue, 16 Jun 2020 08:11:17: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX2543053/SRX2543053.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX2543053/SRX2543053.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX2543053/SRX2543053.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX2543053/SRX2543053.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 08:11:17: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:11:17: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:11:23: 6000000 INFO @ Tue, 16 Jun 2020 08:11:24: 1000000 INFO @ Tue, 16 Jun 2020 08:11:29: 7000000 INFO @ Tue, 16 Jun 2020 08:11:30: 2000000 INFO @ Tue, 16 Jun 2020 08:11:35: 8000000 INFO @ Tue, 16 Jun 2020 08:11:36: 3000000 INFO @ Tue, 16 Jun 2020 08:11:42: 9000000 INFO @ Tue, 16 Jun 2020 08:11:42: 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 08:11:47: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX2543053/SRX2543053.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX2543053/SRX2543053.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX2543053/SRX2543053.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX2543053/SRX2543053.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 08:11:47: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:11:47: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:11:48: 10000000 INFO @ Tue, 16 Jun 2020 08:11:49: 5000000 INFO @ Tue, 16 Jun 2020 08:11:54: 1000000 INFO @ Tue, 16 Jun 2020 08:11:54: 11000000 INFO @ Tue, 16 Jun 2020 08:11:55: 6000000 INFO @ Tue, 16 Jun 2020 08:12:00: 2000000 INFO @ Tue, 16 Jun 2020 08:12:01: 12000000 INFO @ Tue, 16 Jun 2020 08:12:02: 7000000 INFO @ Tue, 16 Jun 2020 08:12:07: 3000000 INFO @ Tue, 16 Jun 2020 08:12:07: 13000000 INFO @ Tue, 16 Jun 2020 08:12:08: 8000000 INFO @ Tue, 16 Jun 2020 08:12:13: 4000000 INFO @ Tue, 16 Jun 2020 08:12:14: 14000000 INFO @ Tue, 16 Jun 2020 08:12:14: 9000000 INFO @ Tue, 16 Jun 2020 08:12:15: #1 tag size is determined as 75 bps INFO @ Tue, 16 Jun 2020 08:12:15: #1 tag size = 75 INFO @ Tue, 16 Jun 2020 08:12:15: #1 total tags in treatment: 14088355 INFO @ Tue, 16 Jun 2020 08:12:15: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:12:15: #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 08:12:15: #1 tags after filtering in treatment: 14088355 INFO @ Tue, 16 Jun 2020 08:12:15: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:12:15: #1 finished! INFO @ Tue, 16 Jun 2020 08:12:15: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:12:15: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:12:16: #2 number of paired peaks: 233 WARNING @ Tue, 16 Jun 2020 08:12:16: Fewer paired peaks (233) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 233 pairs to build model! INFO @ Tue, 16 Jun 2020 08:12:16: start model_add_line... INFO @ Tue, 16 Jun 2020 08:12:16: start X-correlation... INFO @ Tue, 16 Jun 2020 08:12:16: end of X-cor INFO @ Tue, 16 Jun 2020 08:12:16: #2 finished! INFO @ Tue, 16 Jun 2020 08:12:16: #2 predicted fragment length is 69 bps INFO @ Tue, 16 Jun 2020 08:12:16: #2 alternative fragment length(s) may be 3,69,578 bps INFO @ Tue, 16 Jun 2020 08:12:16: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX2543053/SRX2543053.05_model.r WARNING @ Tue, 16 Jun 2020 08:12:16: #2 Since the d (69) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 08:12:16: #2 You may need to consider one of the other alternative d(s): 3,69,578 WARNING @ Tue, 16 Jun 2020 08:12:16: #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 08:12:16: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:12:16: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 08:12:20: 5000000 INFO @ Tue, 16 Jun 2020 08:12:21: 10000000 INFO @ Tue, 16 Jun 2020 08:12:27: 6000000 INFO @ Tue, 16 Jun 2020 08:12:27: 11000000 INFO @ Tue, 16 Jun 2020 08:12:33: 7000000 INFO @ Tue, 16 Jun 2020 08:12:34: 12000000 INFO @ Tue, 16 Jun 2020 08:12:40: 8000000 INFO @ Tue, 16 Jun 2020 08:12:40: 13000000 INFO @ Tue, 16 Jun 2020 08:12:43: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 08:12:46: 9000000 INFO @ Tue, 16 Jun 2020 08:12:47: 14000000 INFO @ Tue, 16 Jun 2020 08:12:47: #1 tag size is determined as 75 bps INFO @ Tue, 16 Jun 2020 08:12:47: #1 tag size = 75 INFO @ Tue, 16 Jun 2020 08:12:47: #1 total tags in treatment: 14088355 INFO @ Tue, 16 Jun 2020 08:12:47: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:12:47: #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 08:12:48: #1 tags after filtering in treatment: 14088355 INFO @ Tue, 16 Jun 2020 08:12:48: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:12:48: #1 finished! INFO @ Tue, 16 Jun 2020 08:12:48: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:12:48: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:12:48: #2 number of paired peaks: 233 WARNING @ Tue, 16 Jun 2020 08:12:48: Fewer paired peaks (233) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 233 pairs to build model! INFO @ Tue, 16 Jun 2020 08:12:48: start model_add_line... INFO @ Tue, 16 Jun 2020 08:12:49: start X-correlation... INFO @ Tue, 16 Jun 2020 08:12:49: end of X-cor INFO @ Tue, 16 Jun 2020 08:12:49: #2 finished! INFO @ Tue, 16 Jun 2020 08:12:49: #2 predicted fragment length is 69 bps INFO @ Tue, 16 Jun 2020 08:12:49: #2 alternative fragment length(s) may be 3,69,578 bps INFO @ Tue, 16 Jun 2020 08:12:49: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX2543053/SRX2543053.10_model.r WARNING @ Tue, 16 Jun 2020 08:12:49: #2 Since the d (69) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 08:12:49: #2 You may need to consider one of the other alternative d(s): 3,69,578 WARNING @ Tue, 16 Jun 2020 08:12:49: #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 08:12:49: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:12:49: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 08:12:52: 10000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 16 Jun 2020 08:12:56: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX2543053/SRX2543053.05_peaks.xls INFO @ Tue, 16 Jun 2020 08:12:56: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX2543053/SRX2543053.05_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:12:56: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX2543053/SRX2543053.05_summits.bed INFO @ Tue, 16 Jun 2020 08:12:56: Done! pass1 - making usageList (7 chroms): 0 millis pass2 - checking and writing primary data (651 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 08:12:58: 11000000 INFO @ Tue, 16 Jun 2020 08:13:04: 12000000 INFO @ Tue, 16 Jun 2020 08:13:10: 13000000 INFO @ Tue, 16 Jun 2020 08:13:15: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 08:13:16: 14000000 INFO @ Tue, 16 Jun 2020 08:13:16: #1 tag size is determined as 75 bps INFO @ Tue, 16 Jun 2020 08:13:16: #1 tag size = 75 INFO @ Tue, 16 Jun 2020 08:13:16: #1 total tags in treatment: 14088355 INFO @ Tue, 16 Jun 2020 08:13:16: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:13:16: #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 08:13:16: #1 tags after filtering in treatment: 14088355 INFO @ Tue, 16 Jun 2020 08:13:16: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:13:16: #1 finished! INFO @ Tue, 16 Jun 2020 08:13:16: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:13:16: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:13:17: #2 number of paired peaks: 233 WARNING @ Tue, 16 Jun 2020 08:13:17: Fewer paired peaks (233) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 233 pairs to build model! INFO @ Tue, 16 Jun 2020 08:13:17: start model_add_line... INFO @ Tue, 16 Jun 2020 08:13:18: start X-correlation... INFO @ Tue, 16 Jun 2020 08:13:18: end of X-cor INFO @ Tue, 16 Jun 2020 08:13:18: #2 finished! INFO @ Tue, 16 Jun 2020 08:13:18: #2 predicted fragment length is 69 bps INFO @ Tue, 16 Jun 2020 08:13:18: #2 alternative fragment length(s) may be 3,69,578 bps INFO @ Tue, 16 Jun 2020 08:13:18: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX2543053/SRX2543053.20_model.r WARNING @ Tue, 16 Jun 2020 08:13:18: #2 Since the d (69) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 08:13:18: #2 You may need to consider one of the other alternative d(s): 3,69,578 WARNING @ Tue, 16 Jun 2020 08:13:18: #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 08:13:18: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:13:18: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Tue, 16 Jun 2020 08:13:28: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX2543053/SRX2543053.10_peaks.xls INFO @ Tue, 16 Jun 2020 08:13:28: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX2543053/SRX2543053.10_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:13:28: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX2543053/SRX2543053.10_summits.bed INFO @ Tue, 16 Jun 2020 08:13:28: Done! pass1 - making usageList (7 chroms): 0 millis pass2 - checking and writing primary data (399 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 08:13:44: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 08:13:57: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX2543053/SRX2543053.20_peaks.xls INFO @ Tue, 16 Jun 2020 08:13:57: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX2543053/SRX2543053.20_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:13:57: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX2543053/SRX2543053.20_summits.bed INFO @ Tue, 16 Jun 2020 08:13:57: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (197 records, 4 fields): 1 millis CompletedMACS2peakCalling