Job ID = 6368126 SRX = SRX467091 Genome = ce11 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-16T00:04:45 prefetch.2.10.7: 1) Downloading 'SRR1164515'... 2020-06-16T00:04:45 prefetch.2.10.7: Downloading via HTTPS... 2020-06-16T00:05:14 prefetch.2.10.7: HTTPS download succeed 2020-06-16T00:05:14 prefetch.2.10.7: 'SRR1164515' is valid 2020-06-16T00:05:14 prefetch.2.10.7: 1) 'SRR1164515' was downloaded successfully Read 4387804 spots for SRR1164515/SRR1164515.sra Written 4387804 spots for SRR1164515/SRR1164515.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: 00:00:38 4387804 reads; of these: 4387804 (100.00%) were unpaired; of these: 283058 (6.45%) aligned 0 times 3401451 (77.52%) aligned exactly 1 time 703295 (16.03%) aligned >1 times 93.55% overall alignment rate Time searching: 00:00:38 Overall time: 00:00:38 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] 174937 / 4104746 = 0.0426 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 09:07:27: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX467091/SRX467091.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX467091/SRX467091.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX467091/SRX467091.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX467091/SRX467091.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 09:07:27: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:07:27: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:07:32: 1000000 INFO @ Tue, 16 Jun 2020 09:07:37: 2000000 INFO @ Tue, 16 Jun 2020 09:07:43: 3000000 INFO @ Tue, 16 Jun 2020 09:07:47: #1 tag size is determined as 32 bps INFO @ Tue, 16 Jun 2020 09:07:47: #1 tag size = 32 INFO @ Tue, 16 Jun 2020 09:07:47: #1 total tags in treatment: 3929809 INFO @ Tue, 16 Jun 2020 09:07:47: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:07:47: #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 09:07:47: #1 tags after filtering in treatment: 3929809 INFO @ Tue, 16 Jun 2020 09:07:47: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 09:07:47: #1 finished! INFO @ Tue, 16 Jun 2020 09:07:47: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:07:47: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:07:48: #2 number of paired peaks: 380 WARNING @ Tue, 16 Jun 2020 09:07:48: Fewer paired peaks (380) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 380 pairs to build model! INFO @ Tue, 16 Jun 2020 09:07:48: start model_add_line... INFO @ Tue, 16 Jun 2020 09:07:48: start X-correlation... INFO @ Tue, 16 Jun 2020 09:07:48: end of X-cor INFO @ Tue, 16 Jun 2020 09:07:48: #2 finished! INFO @ Tue, 16 Jun 2020 09:07:48: #2 predicted fragment length is 33 bps INFO @ Tue, 16 Jun 2020 09:07:48: #2 alternative fragment length(s) may be 4,33,463,573 bps INFO @ Tue, 16 Jun 2020 09:07:48: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX467091/SRX467091.05_model.r WARNING @ Tue, 16 Jun 2020 09:07:48: #2 Since the d (33) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 09:07:48: #2 You may need to consider one of the other alternative d(s): 4,33,463,573 WARNING @ Tue, 16 Jun 2020 09:07:48: #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 09:07:48: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:07:48: #3 Pre-compute pvalue-qvalue table... 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 09:07:56: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 09:07:57: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX467091/SRX467091.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX467091/SRX467091.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX467091/SRX467091.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX467091/SRX467091.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 09:07:57: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:07:57: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:08:00: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX467091/SRX467091.05_peaks.xls INFO @ Tue, 16 Jun 2020 09:08:00: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX467091/SRX467091.05_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:08:00: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX467091/SRX467091.05_summits.bed INFO @ Tue, 16 Jun 2020 09:08:00: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (363 records, 4 fields): 1 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 09:08:02: 1000000 INFO @ Tue, 16 Jun 2020 09:08:08: 2000000 INFO @ Tue, 16 Jun 2020 09:08:13: 3000000 INFO @ Tue, 16 Jun 2020 09:08:17: #1 tag size is determined as 32 bps INFO @ Tue, 16 Jun 2020 09:08:17: #1 tag size = 32 INFO @ Tue, 16 Jun 2020 09:08:17: #1 total tags in treatment: 3929809 INFO @ Tue, 16 Jun 2020 09:08:17: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:08:17: #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 09:08:17: #1 tags after filtering in treatment: 3929809 INFO @ Tue, 16 Jun 2020 09:08:17: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 09:08:17: #1 finished! INFO @ Tue, 16 Jun 2020 09:08:17: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:08:17: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:08:18: #2 number of paired peaks: 380 WARNING @ Tue, 16 Jun 2020 09:08:18: Fewer paired peaks (380) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 380 pairs to build model! INFO @ Tue, 16 Jun 2020 09:08:18: start model_add_line... INFO @ Tue, 16 Jun 2020 09:08:18: start X-correlation... INFO @ Tue, 16 Jun 2020 09:08:18: end of X-cor INFO @ Tue, 16 Jun 2020 09:08:18: #2 finished! INFO @ Tue, 16 Jun 2020 09:08:18: #2 predicted fragment length is 33 bps INFO @ Tue, 16 Jun 2020 09:08:18: #2 alternative fragment length(s) may be 4,33,463,573 bps INFO @ Tue, 16 Jun 2020 09:08:18: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX467091/SRX467091.10_model.r WARNING @ Tue, 16 Jun 2020 09:08:18: #2 Since the d (33) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 09:08:18: #2 You may need to consider one of the other alternative d(s): 4,33,463,573 WARNING @ Tue, 16 Jun 2020 09:08:18: #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 09:08:18: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:08:18: #3 Pre-compute pvalue-qvalue table... 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 09:08:26: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 09:08:27: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX467091/SRX467091.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX467091/SRX467091.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX467091/SRX467091.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX467091/SRX467091.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 09:08:27: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:08:27: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:08:30: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX467091/SRX467091.10_peaks.xls INFO @ Tue, 16 Jun 2020 09:08:30: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX467091/SRX467091.10_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:08:30: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX467091/SRX467091.10_summits.bed INFO @ Tue, 16 Jun 2020 09:08:30: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (178 records, 4 fields): 1 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 09:08:32: 1000000 INFO @ Tue, 16 Jun 2020 09:08:37: 2000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 16 Jun 2020 09:08:42: 3000000 INFO @ Tue, 16 Jun 2020 09:08:47: #1 tag size is determined as 32 bps INFO @ Tue, 16 Jun 2020 09:08:47: #1 tag size = 32 INFO @ Tue, 16 Jun 2020 09:08:47: #1 total tags in treatment: 3929809 INFO @ Tue, 16 Jun 2020 09:08:47: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:08:47: #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 09:08:47: #1 tags after filtering in treatment: 3929809 INFO @ Tue, 16 Jun 2020 09:08:47: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 09:08:47: #1 finished! INFO @ Tue, 16 Jun 2020 09:08:47: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:08:47: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:08:48: #2 number of paired peaks: 380 WARNING @ Tue, 16 Jun 2020 09:08:48: Fewer paired peaks (380) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 380 pairs to build model! INFO @ Tue, 16 Jun 2020 09:08:48: start model_add_line... INFO @ Tue, 16 Jun 2020 09:08:48: start X-correlation... INFO @ Tue, 16 Jun 2020 09:08:48: end of X-cor INFO @ Tue, 16 Jun 2020 09:08:48: #2 finished! INFO @ Tue, 16 Jun 2020 09:08:48: #2 predicted fragment length is 33 bps INFO @ Tue, 16 Jun 2020 09:08:48: #2 alternative fragment length(s) may be 4,33,463,573 bps INFO @ Tue, 16 Jun 2020 09:08:48: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX467091/SRX467091.20_model.r WARNING @ Tue, 16 Jun 2020 09:08:48: #2 Since the d (33) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 09:08:48: #2 You may need to consider one of the other alternative d(s): 4,33,463,573 WARNING @ Tue, 16 Jun 2020 09:08:48: #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 09:08:48: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:08:48: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Tue, 16 Jun 2020 09:08:56: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 09:09:00: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX467091/SRX467091.20_peaks.xls INFO @ Tue, 16 Jun 2020 09:09:00: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX467091/SRX467091.20_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:09:00: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX467091/SRX467091.20_summits.bed INFO @ Tue, 16 Jun 2020 09:09:00: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (45 records, 4 fields): 1 millis CompletedMACS2peakCalling