Job ID = 6366398 SRX = SRX1388772 Genome = ce11 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-15T22:48:07 prefetch.2.10.7: 1) Downloading 'SRR2832488'... 2020-06-15T22:48:07 prefetch.2.10.7: Downloading via HTTPS... 2020-06-15T22:48:47 prefetch.2.10.7: HTTPS download succeed 2020-06-15T22:48:48 prefetch.2.10.7: 'SRR2832488' is valid 2020-06-15T22:48:48 prefetch.2.10.7: 1) 'SRR2832488' was downloaded successfully Read 6307347 spots for SRR2832488/SRR2832488.sra Written 6307347 spots for SRR2832488/SRR2832488.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: 00:01:32 6307347 reads; of these: 6307347 (100.00%) were unpaired; of these: 174312 (2.76%) aligned 0 times 4631163 (73.42%) aligned exactly 1 time 1501872 (23.81%) aligned >1 times 97.24% overall alignment rate Time searching: 00:01:32 Overall time: 00:01:32 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] 520095 / 6133035 = 0.0848 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 07:52:31: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX1388772/SRX1388772.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX1388772/SRX1388772.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX1388772/SRX1388772.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX1388772/SRX1388772.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 07:52:31: #1 read tag files... INFO @ Tue, 16 Jun 2020 07:52:31: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 07:52:37: 1000000 INFO @ Tue, 16 Jun 2020 07:52:43: 2000000 INFO @ Tue, 16 Jun 2020 07:52:49: 3000000 INFO @ Tue, 16 Jun 2020 07:52:55: 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 07:53:01: 5000000 INFO @ Tue, 16 Jun 2020 07:53:01: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX1388772/SRX1388772.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX1388772/SRX1388772.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX1388772/SRX1388772.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX1388772/SRX1388772.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 07:53:01: #1 read tag files... INFO @ Tue, 16 Jun 2020 07:53:01: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 07:53:05: #1 tag size is determined as 50 bps INFO @ Tue, 16 Jun 2020 07:53:05: #1 tag size = 50 INFO @ Tue, 16 Jun 2020 07:53:05: #1 total tags in treatment: 5612940 INFO @ Tue, 16 Jun 2020 07:53:05: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 07:53:05: #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 07:53:05: #1 tags after filtering in treatment: 5612940 INFO @ Tue, 16 Jun 2020 07:53:05: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 07:53:05: #1 finished! INFO @ Tue, 16 Jun 2020 07:53:05: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 07:53:05: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 07:53:05: #2 number of paired peaks: 629 WARNING @ Tue, 16 Jun 2020 07:53:05: Fewer paired peaks (629) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 629 pairs to build model! INFO @ Tue, 16 Jun 2020 07:53:05: start model_add_line... INFO @ Tue, 16 Jun 2020 07:53:05: start X-correlation... INFO @ Tue, 16 Jun 2020 07:53:05: end of X-cor INFO @ Tue, 16 Jun 2020 07:53:05: #2 finished! INFO @ Tue, 16 Jun 2020 07:53:05: #2 predicted fragment length is 47 bps INFO @ Tue, 16 Jun 2020 07:53:05: #2 alternative fragment length(s) may be 4,47,565 bps INFO @ Tue, 16 Jun 2020 07:53:05: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX1388772/SRX1388772.05_model.r WARNING @ Tue, 16 Jun 2020 07:53:05: #2 Since the d (47) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 07:53:05: #2 You may need to consider one of the other alternative d(s): 4,47,565 WARNING @ Tue, 16 Jun 2020 07:53:05: #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 07:53:05: #3 Call peaks... INFO @ Tue, 16 Jun 2020 07:53:05: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 07:53:08: 1000000 INFO @ Tue, 16 Jun 2020 07:53:14: 2000000 INFO @ Tue, 16 Jun 2020 07:53:18: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 07:53:21: 3000000 INFO @ Tue, 16 Jun 2020 07:53:25: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX1388772/SRX1388772.05_peaks.xls INFO @ Tue, 16 Jun 2020 07:53:25: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX1388772/SRX1388772.05_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 07:53:25: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX1388772/SRX1388772.05_summits.bed INFO @ Tue, 16 Jun 2020 07:53:25: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (606 records, 4 fields): 1 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 07:53:27: 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 07:53:31: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX1388772/SRX1388772.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX1388772/SRX1388772.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX1388772/SRX1388772.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX1388772/SRX1388772.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 07:53:31: #1 read tag files... INFO @ Tue, 16 Jun 2020 07:53:31: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 07:53:33: 5000000 INFO @ Tue, 16 Jun 2020 07:53:37: #1 tag size is determined as 50 bps INFO @ Tue, 16 Jun 2020 07:53:37: #1 tag size = 50 INFO @ Tue, 16 Jun 2020 07:53:37: #1 total tags in treatment: 5612940 INFO @ Tue, 16 Jun 2020 07:53:37: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 07:53:37: #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 07:53:37: #1 tags after filtering in treatment: 5612940 INFO @ Tue, 16 Jun 2020 07:53:37: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 07:53:37: #1 finished! INFO @ Tue, 16 Jun 2020 07:53:37: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 07:53:37: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 07:53:37: #2 number of paired peaks: 629 WARNING @ Tue, 16 Jun 2020 07:53:37: Fewer paired peaks (629) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 629 pairs to build model! INFO @ Tue, 16 Jun 2020 07:53:37: start model_add_line... INFO @ Tue, 16 Jun 2020 07:53:38: start X-correlation... INFO @ Tue, 16 Jun 2020 07:53:38: end of X-cor INFO @ Tue, 16 Jun 2020 07:53:38: #2 finished! INFO @ Tue, 16 Jun 2020 07:53:38: #2 predicted fragment length is 47 bps INFO @ Tue, 16 Jun 2020 07:53:38: #2 alternative fragment length(s) may be 4,47,565 bps INFO @ Tue, 16 Jun 2020 07:53:38: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX1388772/SRX1388772.10_model.r WARNING @ Tue, 16 Jun 2020 07:53:38: #2 Since the d (47) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 07:53:38: #2 You may need to consider one of the other alternative d(s): 4,47,565 WARNING @ Tue, 16 Jun 2020 07:53:38: #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 07:53:38: #3 Call peaks... INFO @ Tue, 16 Jun 2020 07:53:38: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 07:53:38: 1000000 INFO @ Tue, 16 Jun 2020 07:53:44: 2000000 INFO @ Tue, 16 Jun 2020 07:53:50: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 07:53:51: 3000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 16 Jun 2020 07:53:57: 4000000 INFO @ Tue, 16 Jun 2020 07:53:57: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX1388772/SRX1388772.10_peaks.xls INFO @ Tue, 16 Jun 2020 07:53:57: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX1388772/SRX1388772.10_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 07:53:57: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX1388772/SRX1388772.10_summits.bed INFO @ Tue, 16 Jun 2020 07:53:57: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (393 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 07:54:03: 5000000 INFO @ Tue, 16 Jun 2020 07:54:07: #1 tag size is determined as 50 bps INFO @ Tue, 16 Jun 2020 07:54:07: #1 tag size = 50 INFO @ Tue, 16 Jun 2020 07:54:07: #1 total tags in treatment: 5612940 INFO @ Tue, 16 Jun 2020 07:54:07: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 07:54:07: #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 07:54:07: #1 tags after filtering in treatment: 5612940 INFO @ Tue, 16 Jun 2020 07:54:07: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 07:54:07: #1 finished! INFO @ Tue, 16 Jun 2020 07:54:07: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 07:54:07: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 07:54:07: #2 number of paired peaks: 629 WARNING @ Tue, 16 Jun 2020 07:54:07: Fewer paired peaks (629) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 629 pairs to build model! INFO @ Tue, 16 Jun 2020 07:54:07: start model_add_line... INFO @ Tue, 16 Jun 2020 07:54:07: start X-correlation... INFO @ Tue, 16 Jun 2020 07:54:07: end of X-cor INFO @ Tue, 16 Jun 2020 07:54:07: #2 finished! INFO @ Tue, 16 Jun 2020 07:54:07: #2 predicted fragment length is 47 bps INFO @ Tue, 16 Jun 2020 07:54:07: #2 alternative fragment length(s) may be 4,47,565 bps INFO @ Tue, 16 Jun 2020 07:54:07: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX1388772/SRX1388772.20_model.r WARNING @ Tue, 16 Jun 2020 07:54:07: #2 Since the d (47) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 07:54:07: #2 You may need to consider one of the other alternative d(s): 4,47,565 WARNING @ Tue, 16 Jun 2020 07:54:07: #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 07:54:07: #3 Call peaks... INFO @ Tue, 16 Jun 2020 07:54:07: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Tue, 16 Jun 2020 07:54:20: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 07:54:27: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX1388772/SRX1388772.20_peaks.xls INFO @ Tue, 16 Jun 2020 07:54:27: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX1388772/SRX1388772.20_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 07:54:27: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX1388772/SRX1388772.20_summits.bed INFO @ Tue, 16 Jun 2020 07:54:27: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (157 records, 4 fields): 1 millis CompletedMACS2peakCalling