Job ID = 6366447 SRX = SRX146511 Genome = ce11 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-15T23:12:31 prefetch.2.10.7: 1) Downloading 'SRR494679'... 2020-06-15T23:12:31 prefetch.2.10.7: Downloading via HTTPS... 2020-06-15T23:12:50 prefetch.2.10.7: HTTPS download succeed 2020-06-15T23:12:51 prefetch.2.10.7: 'SRR494679' is valid 2020-06-15T23:12:51 prefetch.2.10.7: 1) 'SRR494679' was downloaded successfully Read 3578655 spots for SRR494679/SRR494679.sra Written 3578655 spots for SRR494679/SRR494679.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: 00:00:39 3578655 reads; of these: 3578655 (100.00%) were unpaired; of these: 254041 (7.10%) aligned 0 times 2739619 (76.55%) aligned exactly 1 time 584995 (16.35%) aligned >1 times 92.90% overall alignment rate Time searching: 00:00:39 Overall time: 00:00:39 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] 131136 / 3324614 = 0.0394 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 08:14:50: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX146511/SRX146511.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX146511/SRX146511.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX146511/SRX146511.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX146511/SRX146511.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 08:14:50: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:14:50: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:14:56: 1000000 INFO @ Tue, 16 Jun 2020 08:15:01: 2000000 INFO @ Tue, 16 Jun 2020 08:15:07: 3000000 INFO @ Tue, 16 Jun 2020 08:15:08: #1 tag size is determined as 32 bps INFO @ Tue, 16 Jun 2020 08:15:08: #1 tag size = 32 INFO @ Tue, 16 Jun 2020 08:15:08: #1 total tags in treatment: 3193478 INFO @ Tue, 16 Jun 2020 08:15:08: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:15:08: #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 08:15:08: #1 tags after filtering in treatment: 3193478 INFO @ Tue, 16 Jun 2020 08:15:08: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:15:08: #1 finished! INFO @ Tue, 16 Jun 2020 08:15:08: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:15:08: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:15:08: #2 number of paired peaks: 417 WARNING @ Tue, 16 Jun 2020 08:15:08: Fewer paired peaks (417) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 417 pairs to build model! INFO @ Tue, 16 Jun 2020 08:15:08: start model_add_line... INFO @ Tue, 16 Jun 2020 08:15:08: start X-correlation... INFO @ Tue, 16 Jun 2020 08:15:08: end of X-cor INFO @ Tue, 16 Jun 2020 08:15:08: #2 finished! INFO @ Tue, 16 Jun 2020 08:15:08: #2 predicted fragment length is 31 bps INFO @ Tue, 16 Jun 2020 08:15:08: #2 alternative fragment length(s) may be 4,31,194,213,407,459,481,542 bps INFO @ Tue, 16 Jun 2020 08:15:08: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX146511/SRX146511.05_model.r WARNING @ Tue, 16 Jun 2020 08:15:08: #2 Since the d (31) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 08:15:08: #2 You may need to consider one of the other alternative d(s): 4,31,194,213,407,459,481,542 WARNING @ Tue, 16 Jun 2020 08:15:08: #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 08:15:08: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:15:08: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 08:15:16: #3 Call peaks for each chromosome... 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 08:15:19: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX146511/SRX146511.05_peaks.xls INFO @ Tue, 16 Jun 2020 08:15:19: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX146511/SRX146511.05_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:15:19: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX146511/SRX146511.05_summits.bed INFO @ Tue, 16 Jun 2020 08:15:19: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (361 records, 4 fields): 1 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 08:15:20: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX146511/SRX146511.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX146511/SRX146511.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX146511/SRX146511.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX146511/SRX146511.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 08:15:20: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:15:20: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:15:25: 1000000 INFO @ Tue, 16 Jun 2020 08:15:31: 2000000 INFO @ Tue, 16 Jun 2020 08:15:36: 3000000 INFO @ Tue, 16 Jun 2020 08:15:37: #1 tag size is determined as 32 bps INFO @ Tue, 16 Jun 2020 08:15:37: #1 tag size = 32 INFO @ Tue, 16 Jun 2020 08:15:37: #1 total tags in treatment: 3193478 INFO @ Tue, 16 Jun 2020 08:15:37: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:15:37: #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 08:15:37: #1 tags after filtering in treatment: 3193478 INFO @ Tue, 16 Jun 2020 08:15:37: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:15:37: #1 finished! INFO @ Tue, 16 Jun 2020 08:15:37: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:15:37: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:15:38: #2 number of paired peaks: 417 WARNING @ Tue, 16 Jun 2020 08:15:38: Fewer paired peaks (417) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 417 pairs to build model! INFO @ Tue, 16 Jun 2020 08:15:38: start model_add_line... INFO @ Tue, 16 Jun 2020 08:15:38: start X-correlation... INFO @ Tue, 16 Jun 2020 08:15:38: end of X-cor INFO @ Tue, 16 Jun 2020 08:15:38: #2 finished! INFO @ Tue, 16 Jun 2020 08:15:38: #2 predicted fragment length is 31 bps INFO @ Tue, 16 Jun 2020 08:15:38: #2 alternative fragment length(s) may be 4,31,194,213,407,459,481,542 bps INFO @ Tue, 16 Jun 2020 08:15:38: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX146511/SRX146511.10_model.r WARNING @ Tue, 16 Jun 2020 08:15:38: #2 Since the d (31) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 08:15:38: #2 You may need to consider one of the other alternative d(s): 4,31,194,213,407,459,481,542 WARNING @ Tue, 16 Jun 2020 08:15:38: #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 08:15:38: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:15:38: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 08:15:45: #3 Call peaks for each chromosome... 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 08:15:49: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX146511/SRX146511.10_peaks.xls INFO @ Tue, 16 Jun 2020 08:15:49: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX146511/SRX146511.10_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:15:49: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX146511/SRX146511.10_summits.bed INFO @ Tue, 16 Jun 2020 08:15:49: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (153 records, 4 fields): 1 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 08:15:50: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX146511/SRX146511.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX146511/SRX146511.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX146511/SRX146511.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX146511/SRX146511.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 08:15:50: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:15:50: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:15:56: 1000000 INFO @ Tue, 16 Jun 2020 08:16:01: 2000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 16 Jun 2020 08:16:07: 3000000 INFO @ Tue, 16 Jun 2020 08:16:08: #1 tag size is determined as 32 bps INFO @ Tue, 16 Jun 2020 08:16:08: #1 tag size = 32 INFO @ Tue, 16 Jun 2020 08:16:08: #1 total tags in treatment: 3193478 INFO @ Tue, 16 Jun 2020 08:16:08: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:16:08: #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 08:16:08: #1 tags after filtering in treatment: 3193478 INFO @ Tue, 16 Jun 2020 08:16:08: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:16:08: #1 finished! INFO @ Tue, 16 Jun 2020 08:16:08: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:16:08: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:16:08: #2 number of paired peaks: 417 WARNING @ Tue, 16 Jun 2020 08:16:08: Fewer paired peaks (417) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 417 pairs to build model! INFO @ Tue, 16 Jun 2020 08:16:08: start model_add_line... INFO @ Tue, 16 Jun 2020 08:16:08: start X-correlation... INFO @ Tue, 16 Jun 2020 08:16:08: end of X-cor INFO @ Tue, 16 Jun 2020 08:16:08: #2 finished! INFO @ Tue, 16 Jun 2020 08:16:08: #2 predicted fragment length is 31 bps INFO @ Tue, 16 Jun 2020 08:16:08: #2 alternative fragment length(s) may be 4,31,194,213,407,459,481,542 bps INFO @ Tue, 16 Jun 2020 08:16:08: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX146511/SRX146511.20_model.r WARNING @ Tue, 16 Jun 2020 08:16:08: #2 Since the d (31) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 08:16:08: #2 You may need to consider one of the other alternative d(s): 4,31,194,213,407,459,481,542 WARNING @ Tue, 16 Jun 2020 08:16:08: #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 08:16:08: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:16:08: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Tue, 16 Jun 2020 08:16:16: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 08:16:19: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX146511/SRX146511.20_peaks.xls INFO @ Tue, 16 Jun 2020 08:16:19: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX146511/SRX146511.20_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:16:19: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX146511/SRX146511.20_summits.bed INFO @ Tue, 16 Jun 2020 08:16:19: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (28 records, 4 fields): 1 millis CompletedMACS2peakCalling