Job ID = 6366399 SRX = SRX1388773 Genome = ce11 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-15T22:46:37 prefetch.2.10.7: 1) Downloading 'SRR2832489'... 2020-06-15T22:46:37 prefetch.2.10.7: Downloading via HTTPS... 2020-06-15T22:47:12 prefetch.2.10.7: HTTPS download succeed 2020-06-15T22:47:12 prefetch.2.10.7: 'SRR2832489' is valid 2020-06-15T22:47:12 prefetch.2.10.7: 1) 'SRR2832489' was downloaded successfully Read 6497093 spots for SRR2832489/SRR2832489.sra Written 6497093 spots for SRR2832489/SRR2832489.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: 00:01:35 6497093 reads; of these: 6497093 (100.00%) were unpaired; of these: 176901 (2.72%) aligned 0 times 4761245 (73.28%) aligned exactly 1 time 1558947 (23.99%) aligned >1 times 97.28% overall alignment rate Time searching: 00:01:35 Overall time: 00:01:35 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_rmdupse_core] 540138 / 6320192 = 0.0855 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 07:51:02: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX1388773/SRX1388773.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX1388773/SRX1388773.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX1388773/SRX1388773.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX1388773/SRX1388773.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 07:51:02: #1 read tag files... INFO @ Tue, 16 Jun 2020 07:51:02: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 07:51:08: 1000000 INFO @ Tue, 16 Jun 2020 07:51:13: 2000000 INFO @ Tue, 16 Jun 2020 07:51:19: 3000000 INFO @ Tue, 16 Jun 2020 07:51:25: 4000000 INFO @ Tue, 16 Jun 2020 07:51:30: 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 07:51:32: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX1388773/SRX1388773.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX1388773/SRX1388773.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX1388773/SRX1388773.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX1388773/SRX1388773.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 07:51:32: #1 read tag files... INFO @ Tue, 16 Jun 2020 07:51:32: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 07:51:35: #1 tag size is determined as 50 bps INFO @ Tue, 16 Jun 2020 07:51:35: #1 tag size = 50 INFO @ Tue, 16 Jun 2020 07:51:35: #1 total tags in treatment: 5780054 INFO @ Tue, 16 Jun 2020 07:51:35: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 07:51:35: #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 07:51:35: #1 tags after filtering in treatment: 5780054 INFO @ Tue, 16 Jun 2020 07:51:35: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 07:51:35: #1 finished! INFO @ Tue, 16 Jun 2020 07:51:35: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 07:51:35: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 07:51:35: #2 number of paired peaks: 877 WARNING @ Tue, 16 Jun 2020 07:51:35: Fewer paired peaks (877) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 877 pairs to build model! INFO @ Tue, 16 Jun 2020 07:51:35: start model_add_line... INFO @ Tue, 16 Jun 2020 07:51:35: start X-correlation... INFO @ Tue, 16 Jun 2020 07:51:35: end of X-cor INFO @ Tue, 16 Jun 2020 07:51:35: #2 finished! INFO @ Tue, 16 Jun 2020 07:51:35: #2 predicted fragment length is 55 bps INFO @ Tue, 16 Jun 2020 07:51:35: #2 alternative fragment length(s) may be 3,55,575,591 bps INFO @ Tue, 16 Jun 2020 07:51:35: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX1388773/SRX1388773.05_model.r WARNING @ Tue, 16 Jun 2020 07:51:35: #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 07:51:35: #2 You may need to consider one of the other alternative d(s): 3,55,575,591 WARNING @ Tue, 16 Jun 2020 07:51:35: #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 07:51:35: #3 Call peaks... INFO @ Tue, 16 Jun 2020 07:51:35: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 07:51:38: 1000000 INFO @ Tue, 16 Jun 2020 07:51:44: 2000000 INFO @ Tue, 16 Jun 2020 07:51:49: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 07:51:50: 3000000 INFO @ Tue, 16 Jun 2020 07:51:56: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX1388773/SRX1388773.05_peaks.xls INFO @ Tue, 16 Jun 2020 07:51:56: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX1388773/SRX1388773.05_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 07:51:56: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX1388773/SRX1388773.05_summits.bed INFO @ Tue, 16 Jun 2020 07:51:56: Done! INFO @ Tue, 16 Jun 2020 07:51:56: 4000000 pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (600 records, 4 fields): 2 millis CompletedMACS2peakCalling 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 07:52:01: 5000000 INFO @ Tue, 16 Jun 2020 07:52:02: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX1388773/SRX1388773.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX1388773/SRX1388773.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX1388773/SRX1388773.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX1388773/SRX1388773.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 07:52:02: #1 read tag files... INFO @ Tue, 16 Jun 2020 07:52:02: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 07:52:06: #1 tag size is determined as 50 bps INFO @ Tue, 16 Jun 2020 07:52:06: #1 tag size = 50 INFO @ Tue, 16 Jun 2020 07:52:06: #1 total tags in treatment: 5780054 INFO @ Tue, 16 Jun 2020 07:52:06: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 07:52:06: #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 07:52:06: #1 tags after filtering in treatment: 5780054 INFO @ Tue, 16 Jun 2020 07:52:06: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 07:52:06: #1 finished! INFO @ Tue, 16 Jun 2020 07:52:06: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 07:52:06: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 07:52:07: #2 number of paired peaks: 877 WARNING @ Tue, 16 Jun 2020 07:52:07: Fewer paired peaks (877) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 877 pairs to build model! INFO @ Tue, 16 Jun 2020 07:52:07: start model_add_line... INFO @ Tue, 16 Jun 2020 07:52:07: start X-correlation... INFO @ Tue, 16 Jun 2020 07:52:07: end of X-cor INFO @ Tue, 16 Jun 2020 07:52:07: #2 finished! INFO @ Tue, 16 Jun 2020 07:52:07: #2 predicted fragment length is 55 bps INFO @ Tue, 16 Jun 2020 07:52:07: #2 alternative fragment length(s) may be 3,55,575,591 bps INFO @ Tue, 16 Jun 2020 07:52:07: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX1388773/SRX1388773.10_model.r WARNING @ Tue, 16 Jun 2020 07:52:07: #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 07:52:07: #2 You may need to consider one of the other alternative d(s): 3,55,575,591 WARNING @ Tue, 16 Jun 2020 07:52:07: #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 07:52:07: #3 Call peaks... INFO @ Tue, 16 Jun 2020 07:52:07: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 07:52:08: 1000000 INFO @ Tue, 16 Jun 2020 07:52:14: 2000000 INFO @ Tue, 16 Jun 2020 07:52:20: 3000000 INFO @ Tue, 16 Jun 2020 07:52:20: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 07:52:26: 4000000 INFO @ Tue, 16 Jun 2020 07:52:27: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX1388773/SRX1388773.10_peaks.xls INFO @ Tue, 16 Jun 2020 07:52:27: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX1388773/SRX1388773.10_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 07:52:27: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX1388773/SRX1388773.10_summits.bed INFO @ Tue, 16 Jun 2020 07:52:27: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (375 records, 4 fields): 2 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 16 Jun 2020 07:52:31: 5000000 INFO @ Tue, 16 Jun 2020 07:52:36: #1 tag size is determined as 50 bps INFO @ Tue, 16 Jun 2020 07:52:36: #1 tag size = 50 INFO @ Tue, 16 Jun 2020 07:52:36: #1 total tags in treatment: 5780054 INFO @ Tue, 16 Jun 2020 07:52:36: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 07:52:36: #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 07:52:36: #1 tags after filtering in treatment: 5780054 INFO @ Tue, 16 Jun 2020 07:52:36: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 07:52:36: #1 finished! INFO @ Tue, 16 Jun 2020 07:52:36: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 07:52:36: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 07:52:36: #2 number of paired peaks: 877 WARNING @ Tue, 16 Jun 2020 07:52:36: Fewer paired peaks (877) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 877 pairs to build model! INFO @ Tue, 16 Jun 2020 07:52:36: start model_add_line... INFO @ Tue, 16 Jun 2020 07:52:36: start X-correlation... INFO @ Tue, 16 Jun 2020 07:52:36: end of X-cor INFO @ Tue, 16 Jun 2020 07:52:36: #2 finished! INFO @ Tue, 16 Jun 2020 07:52:36: #2 predicted fragment length is 55 bps INFO @ Tue, 16 Jun 2020 07:52:36: #2 alternative fragment length(s) may be 3,55,575,591 bps INFO @ Tue, 16 Jun 2020 07:52:36: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX1388773/SRX1388773.20_model.r WARNING @ Tue, 16 Jun 2020 07:52:36: #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 07:52:36: #2 You may need to consider one of the other alternative d(s): 3,55,575,591 WARNING @ Tue, 16 Jun 2020 07:52:36: #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 07:52:36: #3 Call peaks... INFO @ Tue, 16 Jun 2020 07:52:36: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Tue, 16 Jun 2020 07:52:49: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 07:52:57: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX1388773/SRX1388773.20_peaks.xls INFO @ Tue, 16 Jun 2020 07:52:57: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX1388773/SRX1388773.20_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 07:52:57: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX1388773/SRX1388773.20_summits.bed INFO @ Tue, 16 Jun 2020 07:52:57: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (163 records, 4 fields): 1 millis CompletedMACS2peakCalling