Job ID = 6366352 SRX = SRX120284 Genome = ce11 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-15T22:38:51 prefetch.2.10.7: 1) Downloading 'SRR408770'... 2020-06-15T22:38:51 prefetch.2.10.7: Downloading via HTTPS... 2020-06-15T22:39:24 prefetch.2.10.7: HTTPS download succeed 2020-06-15T22:39:24 prefetch.2.10.7: 'SRR408770' is valid 2020-06-15T22:39:24 prefetch.2.10.7: 1) 'SRR408770' was downloaded successfully Read 4425317 spots for SRR408770/SRR408770.sra Written 4425317 spots for SRR408770/SRR408770.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 4425317 reads; of these: 4425317 (100.00%) were unpaired; of these: 1104518 (24.96%) aligned 0 times 2791519 (63.08%) aligned exactly 1 time 529280 (11.96%) aligned >1 times 75.04% 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] 179659 / 3320799 = 0.0541 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 07:41:28: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX120284/SRX120284.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX120284/SRX120284.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX120284/SRX120284.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX120284/SRX120284.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 07:41:28: #1 read tag files... INFO @ Tue, 16 Jun 2020 07:41:28: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 07:41:33: 1000000 INFO @ Tue, 16 Jun 2020 07:41:38: 2000000 INFO @ Tue, 16 Jun 2020 07:41:43: 3000000 INFO @ Tue, 16 Jun 2020 07:41:44: #1 tag size is determined as 32 bps INFO @ Tue, 16 Jun 2020 07:41:44: #1 tag size = 32 INFO @ Tue, 16 Jun 2020 07:41:44: #1 total tags in treatment: 3141140 INFO @ Tue, 16 Jun 2020 07:41:44: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 07:41:44: #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 07:41:44: #1 tags after filtering in treatment: 3141140 INFO @ Tue, 16 Jun 2020 07:41:44: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 07:41:44: #1 finished! INFO @ Tue, 16 Jun 2020 07:41:44: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 07:41:44: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 07:41:44: #2 number of paired peaks: 398 WARNING @ Tue, 16 Jun 2020 07:41:44: Fewer paired peaks (398) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 398 pairs to build model! INFO @ Tue, 16 Jun 2020 07:41:44: start model_add_line... INFO @ Tue, 16 Jun 2020 07:41:44: start X-correlation... INFO @ Tue, 16 Jun 2020 07:41:44: end of X-cor INFO @ Tue, 16 Jun 2020 07:41:44: #2 finished! INFO @ Tue, 16 Jun 2020 07:41:44: #2 predicted fragment length is 40 bps INFO @ Tue, 16 Jun 2020 07:41:44: #2 alternative fragment length(s) may be 3,40,542,568,595 bps INFO @ Tue, 16 Jun 2020 07:41:44: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX120284/SRX120284.05_model.r WARNING @ Tue, 16 Jun 2020 07:41:44: #2 Since the d (40) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 07:41:44: #2 You may need to consider one of the other alternative d(s): 3,40,542,568,595 WARNING @ Tue, 16 Jun 2020 07:41:44: #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 07:41:44: #3 Call peaks... INFO @ Tue, 16 Jun 2020 07:41:44: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 07:41:51: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 07:41:54: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX120284/SRX120284.05_peaks.xls INFO @ Tue, 16 Jun 2020 07:41:54: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX120284/SRX120284.05_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 07:41:54: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX120284/SRX120284.05_summits.bed INFO @ Tue, 16 Jun 2020 07:41:54: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (237 records, 4 fields): 1 millis CompletedMACS2peakCalling 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 07:41:58: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX120284/SRX120284.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX120284/SRX120284.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX120284/SRX120284.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX120284/SRX120284.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 07:41:58: #1 read tag files... INFO @ Tue, 16 Jun 2020 07:41:58: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 07:42:03: 1000000 INFO @ Tue, 16 Jun 2020 07:42:08: 2000000 INFO @ Tue, 16 Jun 2020 07:42:13: 3000000 INFO @ Tue, 16 Jun 2020 07:42:14: #1 tag size is determined as 32 bps INFO @ Tue, 16 Jun 2020 07:42:14: #1 tag size = 32 INFO @ Tue, 16 Jun 2020 07:42:14: #1 total tags in treatment: 3141140 INFO @ Tue, 16 Jun 2020 07:42:14: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 07:42:14: #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 07:42:14: #1 tags after filtering in treatment: 3141140 INFO @ Tue, 16 Jun 2020 07:42:14: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 07:42:14: #1 finished! INFO @ Tue, 16 Jun 2020 07:42:14: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 07:42:14: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 07:42:14: #2 number of paired peaks: 398 WARNING @ Tue, 16 Jun 2020 07:42:14: Fewer paired peaks (398) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 398 pairs to build model! INFO @ Tue, 16 Jun 2020 07:42:14: start model_add_line... INFO @ Tue, 16 Jun 2020 07:42:14: start X-correlation... INFO @ Tue, 16 Jun 2020 07:42:14: end of X-cor INFO @ Tue, 16 Jun 2020 07:42:14: #2 finished! INFO @ Tue, 16 Jun 2020 07:42:14: #2 predicted fragment length is 40 bps INFO @ Tue, 16 Jun 2020 07:42:14: #2 alternative fragment length(s) may be 3,40,542,568,595 bps INFO @ Tue, 16 Jun 2020 07:42:14: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX120284/SRX120284.10_model.r WARNING @ Tue, 16 Jun 2020 07:42:14: #2 Since the d (40) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 07:42:14: #2 You may need to consider one of the other alternative d(s): 3,40,542,568,595 WARNING @ Tue, 16 Jun 2020 07:42:14: #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 07:42:14: #3 Call peaks... INFO @ Tue, 16 Jun 2020 07:42:14: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 07:42:21: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 07:42:24: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX120284/SRX120284.10_peaks.xls INFO @ Tue, 16 Jun 2020 07:42:24: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX120284/SRX120284.10_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 07:42:24: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX120284/SRX120284.10_summits.bed INFO @ Tue, 16 Jun 2020 07:42:24: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (114 records, 4 fields): 1 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 07:42:28: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX120284/SRX120284.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX120284/SRX120284.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX120284/SRX120284.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX120284/SRX120284.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 07:42:28: #1 read tag files... INFO @ Tue, 16 Jun 2020 07:42:28: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 07:42:34: 1000000 INFO @ Tue, 16 Jun 2020 07:42:40: 2000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 16 Jun 2020 07:42:46: 3000000 INFO @ Tue, 16 Jun 2020 07:42:47: #1 tag size is determined as 32 bps INFO @ Tue, 16 Jun 2020 07:42:47: #1 tag size = 32 INFO @ Tue, 16 Jun 2020 07:42:47: #1 total tags in treatment: 3141140 INFO @ Tue, 16 Jun 2020 07:42:47: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 07:42:47: #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 07:42:47: #1 tags after filtering in treatment: 3141140 INFO @ Tue, 16 Jun 2020 07:42:47: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 07:42:47: #1 finished! INFO @ Tue, 16 Jun 2020 07:42:47: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 07:42:47: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 07:42:47: #2 number of paired peaks: 398 WARNING @ Tue, 16 Jun 2020 07:42:47: Fewer paired peaks (398) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 398 pairs to build model! INFO @ Tue, 16 Jun 2020 07:42:47: start model_add_line... INFO @ Tue, 16 Jun 2020 07:42:47: start X-correlation... INFO @ Tue, 16 Jun 2020 07:42:47: end of X-cor INFO @ Tue, 16 Jun 2020 07:42:47: #2 finished! INFO @ Tue, 16 Jun 2020 07:42:47: #2 predicted fragment length is 40 bps INFO @ Tue, 16 Jun 2020 07:42:47: #2 alternative fragment length(s) may be 3,40,542,568,595 bps INFO @ Tue, 16 Jun 2020 07:42:47: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX120284/SRX120284.20_model.r WARNING @ Tue, 16 Jun 2020 07:42:47: #2 Since the d (40) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 07:42:47: #2 You may need to consider one of the other alternative d(s): 3,40,542,568,595 WARNING @ Tue, 16 Jun 2020 07:42:47: #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 07:42:47: #3 Call peaks... INFO @ Tue, 16 Jun 2020 07:42:47: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Tue, 16 Jun 2020 07:42:54: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 07:42:58: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX120284/SRX120284.20_peaks.xls INFO @ Tue, 16 Jun 2020 07:42:58: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX120284/SRX120284.20_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 07:42:58: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX120284/SRX120284.20_summits.bed INFO @ Tue, 16 Jun 2020 07:42:58: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (21 records, 4 fields): 1 millis CompletedMACS2peakCalling