Job ID = 6367060 SRX = SRX276918 Genome = ce11 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-15T23:09:01 prefetch.2.10.7: 1) Downloading 'SRR849524'... 2020-06-15T23:09:01 prefetch.2.10.7: Downloading via HTTPS... 2020-06-15T23:09:28 prefetch.2.10.7: HTTPS download succeed 2020-06-15T23:09:28 prefetch.2.10.7: 'SRR849524' is valid 2020-06-15T23:09:28 prefetch.2.10.7: 1) 'SRR849524' was downloaded successfully Read 5638235 spots for SRR849524/SRR849524.sra Written 5638235 spots for SRR849524/SRR849524.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: 00:00:48 5638235 reads; of these: 5638235 (100.00%) were unpaired; of these: 715644 (12.69%) aligned 0 times 4148546 (73.58%) aligned exactly 1 time 774045 (13.73%) aligned >1 times 87.31% overall alignment rate Time searching: 00:00:48 Overall time: 00:00:48 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] 331718 / 4922591 = 0.0674 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 08:12:13: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX276918/SRX276918.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX276918/SRX276918.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX276918/SRX276918.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX276918/SRX276918.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 08:12:13: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:12:13: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:12:18: 1000000 INFO @ Tue, 16 Jun 2020 08:12:24: 2000000 INFO @ Tue, 16 Jun 2020 08:12:29: 3000000 INFO @ Tue, 16 Jun 2020 08:12:34: 4000000 INFO @ Tue, 16 Jun 2020 08:12:37: #1 tag size is determined as 32 bps INFO @ Tue, 16 Jun 2020 08:12:37: #1 tag size = 32 INFO @ Tue, 16 Jun 2020 08:12:37: #1 total tags in treatment: 4590873 INFO @ Tue, 16 Jun 2020 08:12:37: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:12:37: #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 08:12:37: #1 tags after filtering in treatment: 4590873 INFO @ Tue, 16 Jun 2020 08:12:37: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:12:37: #1 finished! INFO @ Tue, 16 Jun 2020 08:12:37: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:12:37: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:12:38: #2 number of paired peaks: 357 WARNING @ Tue, 16 Jun 2020 08:12:38: Fewer paired peaks (357) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 357 pairs to build model! INFO @ Tue, 16 Jun 2020 08:12:38: start model_add_line... INFO @ Tue, 16 Jun 2020 08:12:38: start X-correlation... INFO @ Tue, 16 Jun 2020 08:12:38: end of X-cor INFO @ Tue, 16 Jun 2020 08:12:38: #2 finished! INFO @ Tue, 16 Jun 2020 08:12:38: #2 predicted fragment length is 30 bps INFO @ Tue, 16 Jun 2020 08:12:38: #2 alternative fragment length(s) may be 4,30,477,549,581 bps INFO @ Tue, 16 Jun 2020 08:12:38: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX276918/SRX276918.05_model.r WARNING @ Tue, 16 Jun 2020 08:12:38: #2 Since the d (30) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 08:12:38: #2 You may need to consider one of the other alternative d(s): 4,30,477,549,581 WARNING @ Tue, 16 Jun 2020 08:12:38: #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 08:12:38: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:12:38: #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 08:12:43: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX276918/SRX276918.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX276918/SRX276918.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX276918/SRX276918.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX276918/SRX276918.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 08:12:43: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:12:43: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:12:46: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 08:12:49: 1000000 INFO @ Tue, 16 Jun 2020 08:12:51: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX276918/SRX276918.05_peaks.xls INFO @ Tue, 16 Jun 2020 08:12:51: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX276918/SRX276918.05_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:12:51: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX276918/SRX276918.05_summits.bed INFO @ Tue, 16 Jun 2020 08:12:51: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (366 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 08:12:54: 2000000 INFO @ Tue, 16 Jun 2020 08:12:59: 3000000 INFO @ Tue, 16 Jun 2020 08:13:04: 4000000 INFO @ Tue, 16 Jun 2020 08:13:07: #1 tag size is determined as 32 bps INFO @ Tue, 16 Jun 2020 08:13:07: #1 tag size = 32 INFO @ Tue, 16 Jun 2020 08:13:07: #1 total tags in treatment: 4590873 INFO @ Tue, 16 Jun 2020 08:13:07: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:13:07: #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 08:13:07: #1 tags after filtering in treatment: 4590873 INFO @ Tue, 16 Jun 2020 08:13:07: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:13:07: #1 finished! INFO @ Tue, 16 Jun 2020 08:13:07: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:13:07: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:13:07: #2 number of paired peaks: 357 WARNING @ Tue, 16 Jun 2020 08:13:07: Fewer paired peaks (357) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 357 pairs to build model! INFO @ Tue, 16 Jun 2020 08:13:07: start model_add_line... INFO @ Tue, 16 Jun 2020 08:13:07: start X-correlation... INFO @ Tue, 16 Jun 2020 08:13:07: end of X-cor INFO @ Tue, 16 Jun 2020 08:13:07: #2 finished! INFO @ Tue, 16 Jun 2020 08:13:07: #2 predicted fragment length is 30 bps INFO @ Tue, 16 Jun 2020 08:13:07: #2 alternative fragment length(s) may be 4,30,477,549,581 bps INFO @ Tue, 16 Jun 2020 08:13:07: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX276918/SRX276918.10_model.r WARNING @ Tue, 16 Jun 2020 08:13:07: #2 Since the d (30) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 08:13:07: #2 You may need to consider one of the other alternative d(s): 4,30,477,549,581 WARNING @ Tue, 16 Jun 2020 08:13:07: #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 08:13:07: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:13:07: #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 08:13:13: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX276918/SRX276918.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX276918/SRX276918.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX276918/SRX276918.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX276918/SRX276918.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 08:13:13: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:13:13: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:13:16: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 08:13:18: 1000000 INFO @ Tue, 16 Jun 2020 08:13:20: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX276918/SRX276918.10_peaks.xls INFO @ Tue, 16 Jun 2020 08:13:20: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX276918/SRX276918.10_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:13:20: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX276918/SRX276918.10_summits.bed INFO @ Tue, 16 Jun 2020 08:13:20: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (151 records, 4 fields): 1 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 08:13:24: 2000000 INFO @ Tue, 16 Jun 2020 08:13:29: 3000000 INFO @ Tue, 16 Jun 2020 08:13:34: 4000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 16 Jun 2020 08:13:37: #1 tag size is determined as 32 bps INFO @ Tue, 16 Jun 2020 08:13:37: #1 tag size = 32 INFO @ Tue, 16 Jun 2020 08:13:37: #1 total tags in treatment: 4590873 INFO @ Tue, 16 Jun 2020 08:13:37: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:13:37: #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 08:13:37: #1 tags after filtering in treatment: 4590873 INFO @ Tue, 16 Jun 2020 08:13:37: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:13:37: #1 finished! INFO @ Tue, 16 Jun 2020 08:13:37: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:13:37: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:13:37: #2 number of paired peaks: 357 WARNING @ Tue, 16 Jun 2020 08:13:37: Fewer paired peaks (357) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 357 pairs to build model! INFO @ Tue, 16 Jun 2020 08:13:37: start model_add_line... INFO @ Tue, 16 Jun 2020 08:13:37: start X-correlation... INFO @ Tue, 16 Jun 2020 08:13:37: end of X-cor INFO @ Tue, 16 Jun 2020 08:13:37: #2 finished! INFO @ Tue, 16 Jun 2020 08:13:37: #2 predicted fragment length is 30 bps INFO @ Tue, 16 Jun 2020 08:13:37: #2 alternative fragment length(s) may be 4,30,477,549,581 bps INFO @ Tue, 16 Jun 2020 08:13:37: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX276918/SRX276918.20_model.r WARNING @ Tue, 16 Jun 2020 08:13:37: #2 Since the d (30) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 08:13:37: #2 You may need to consider one of the other alternative d(s): 4,30,477,549,581 WARNING @ Tue, 16 Jun 2020 08:13:37: #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 08:13:37: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:13:37: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 08:13:46: #3 Call peaks for each chromosome... BigWig に変換しました。 INFO @ Tue, 16 Jun 2020 08:13:50: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX276918/SRX276918.20_peaks.xls INFO @ Tue, 16 Jun 2020 08:13:50: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX276918/SRX276918.20_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:13:50: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX276918/SRX276918.20_summits.bed INFO @ Tue, 16 Jun 2020 08:13:50: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (46 records, 4 fields): 1 millis CompletedMACS2peakCalling