Job ID = 6366370 SRX = SRX1388744 Genome = ce11 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-15T22:41:52 prefetch.2.10.7: 1) Downloading 'SRR2832460'... 2020-06-15T22:41:52 prefetch.2.10.7: Downloading via HTTPS... 2020-06-15T22:42:14 prefetch.2.10.7: HTTPS download succeed 2020-06-15T22:42:14 prefetch.2.10.7: 'SRR2832460' is valid 2020-06-15T22:42:14 prefetch.2.10.7: 1) 'SRR2832460' was downloaded successfully Read 566269 spots for SRR2832460/SRR2832460.sra Written 566269 spots for SRR2832460/SRR2832460.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: 00:00:07 566269 reads; of these: 566269 (100.00%) were unpaired; of these: 159903 (28.24%) aligned 0 times 316982 (55.98%) aligned exactly 1 time 89384 (15.78%) aligned >1 times 71.76% overall alignment rate Time searching: 00:00:07 Overall time: 00:00:07 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] 15203 / 406366 = 0.0374 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 07:43:02: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX1388744/SRX1388744.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX1388744/SRX1388744.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX1388744/SRX1388744.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX1388744/SRX1388744.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 07:43:02: #1 read tag files... INFO @ Tue, 16 Jun 2020 07:43:02: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 07:43:05: #1 tag size is determined as 50 bps INFO @ Tue, 16 Jun 2020 07:43:05: #1 tag size = 50 INFO @ Tue, 16 Jun 2020 07:43:05: #1 total tags in treatment: 391163 INFO @ Tue, 16 Jun 2020 07:43:05: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 07:43:05: #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 07:43:05: #1 tags after filtering in treatment: 391163 INFO @ Tue, 16 Jun 2020 07:43:05: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 07:43:05: #1 finished! INFO @ Tue, 16 Jun 2020 07:43:05: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 07:43:05: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 07:43:05: #2 number of paired peaks: 629 WARNING @ Tue, 16 Jun 2020 07:43:05: 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 07:43:05: start model_add_line... INFO @ Tue, 16 Jun 2020 07:43:05: start X-correlation... INFO @ Tue, 16 Jun 2020 07:43:05: end of X-cor INFO @ Tue, 16 Jun 2020 07:43:05: #2 finished! INFO @ Tue, 16 Jun 2020 07:43:05: #2 predicted fragment length is 49 bps INFO @ Tue, 16 Jun 2020 07:43:05: #2 alternative fragment length(s) may be 49,580 bps INFO @ Tue, 16 Jun 2020 07:43:05: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX1388744/SRX1388744.05_model.r WARNING @ Tue, 16 Jun 2020 07:43:05: #2 Since the d (49) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 07:43:05: #2 You may need to consider one of the other alternative d(s): 49,580 WARNING @ Tue, 16 Jun 2020 07:43:05: #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 07:43:05: #3 Call peaks... INFO @ Tue, 16 Jun 2020 07:43:05: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 07:43:06: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 07:43:06: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX1388744/SRX1388744.05_peaks.xls INFO @ Tue, 16 Jun 2020 07:43:06: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX1388744/SRX1388744.05_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 07:43:06: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX1388744/SRX1388744.05_summits.bed INFO @ Tue, 16 Jun 2020 07:43:06: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (108 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 07:43:32: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX1388744/SRX1388744.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX1388744/SRX1388744.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX1388744/SRX1388744.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX1388744/SRX1388744.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 07:43:32: #1 read tag files... INFO @ Tue, 16 Jun 2020 07:43:32: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 07:43:35: #1 tag size is determined as 50 bps INFO @ Tue, 16 Jun 2020 07:43:35: #1 tag size = 50 INFO @ Tue, 16 Jun 2020 07:43:35: #1 total tags in treatment: 391163 INFO @ Tue, 16 Jun 2020 07:43:35: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 07:43:35: #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 07:43:35: #1 tags after filtering in treatment: 391163 INFO @ Tue, 16 Jun 2020 07:43:35: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 07:43:35: #1 finished! INFO @ Tue, 16 Jun 2020 07:43:35: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 07:43:35: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 07:43:35: #2 number of paired peaks: 629 WARNING @ Tue, 16 Jun 2020 07:43:35: 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 07:43:35: start model_add_line... INFO @ Tue, 16 Jun 2020 07:43:35: start X-correlation... INFO @ Tue, 16 Jun 2020 07:43:35: end of X-cor INFO @ Tue, 16 Jun 2020 07:43:35: #2 finished! INFO @ Tue, 16 Jun 2020 07:43:35: #2 predicted fragment length is 49 bps INFO @ Tue, 16 Jun 2020 07:43:35: #2 alternative fragment length(s) may be 49,580 bps INFO @ Tue, 16 Jun 2020 07:43:35: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX1388744/SRX1388744.10_model.r WARNING @ Tue, 16 Jun 2020 07:43:35: #2 Since the d (49) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 07:43:35: #2 You may need to consider one of the other alternative d(s): 49,580 WARNING @ Tue, 16 Jun 2020 07:43:35: #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 07:43:35: #3 Call peaks... INFO @ Tue, 16 Jun 2020 07:43:35: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 07:43:36: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 07:43:36: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX1388744/SRX1388744.10_peaks.xls INFO @ Tue, 16 Jun 2020 07:43:36: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX1388744/SRX1388744.10_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 07:43:36: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX1388744/SRX1388744.10_summits.bed INFO @ Tue, 16 Jun 2020 07:43:36: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (65 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 07:44:02: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX1388744/SRX1388744.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX1388744/SRX1388744.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX1388744/SRX1388744.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX1388744/SRX1388744.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 07:44:02: #1 read tag files... INFO @ Tue, 16 Jun 2020 07:44:02: #1 read treatment tags... BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。 INFO @ Tue, 16 Jun 2020 07:44:05: #1 tag size is determined as 50 bps INFO @ Tue, 16 Jun 2020 07:44:05: #1 tag size = 50 INFO @ Tue, 16 Jun 2020 07:44:05: #1 total tags in treatment: 391163 INFO @ Tue, 16 Jun 2020 07:44:05: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 07:44:05: #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 07:44:05: #1 tags after filtering in treatment: 391163 INFO @ Tue, 16 Jun 2020 07:44:05: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 07:44:05: #1 finished! INFO @ Tue, 16 Jun 2020 07:44:05: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 07:44:05: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 07:44:05: #2 number of paired peaks: 629 WARNING @ Tue, 16 Jun 2020 07:44:05: 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 07:44:05: start model_add_line... INFO @ Tue, 16 Jun 2020 07:44:05: start X-correlation... INFO @ Tue, 16 Jun 2020 07:44:05: end of X-cor INFO @ Tue, 16 Jun 2020 07:44:05: #2 finished! INFO @ Tue, 16 Jun 2020 07:44:05: #2 predicted fragment length is 49 bps INFO @ Tue, 16 Jun 2020 07:44:05: #2 alternative fragment length(s) may be 49,580 bps INFO @ Tue, 16 Jun 2020 07:44:05: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX1388744/SRX1388744.20_model.r WARNING @ Tue, 16 Jun 2020 07:44:05: #2 Since the d (49) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 07:44:05: #2 You may need to consider one of the other alternative d(s): 49,580 WARNING @ Tue, 16 Jun 2020 07:44:05: #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 07:44:05: #3 Call peaks... INFO @ Tue, 16 Jun 2020 07:44:05: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 07:44:06: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 07:44:06: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX1388744/SRX1388744.20_peaks.xls INFO @ Tue, 16 Jun 2020 07:44:06: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX1388744/SRX1388744.20_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 07:44:06: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX1388744/SRX1388744.20_summits.bed INFO @ Tue, 16 Jun 2020 07:44:06: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (33 records, 4 fields): 1 millis CompletedMACS2peakCalling