Job ID = 6366862 SRX = SRX235170 Genome = ce11 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-15T23:04:38 prefetch.2.10.7: 1) Downloading 'SRR708618'... 2020-06-15T23:04:38 prefetch.2.10.7: Downloading via HTTPS... 2020-06-15T23:05:06 prefetch.2.10.7: HTTPS download succeed 2020-06-15T23:05:07 prefetch.2.10.7: 'SRR708618' is valid 2020-06-15T23:05:07 prefetch.2.10.7: 1) 'SRR708618' was downloaded successfully Read 7590148 spots for SRR708618/SRR708618.sra Written 7590148 spots for SRR708618/SRR708618.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: 00:01:10 7590148 reads; of these: 7590148 (100.00%) were unpaired; of these: 863188 (11.37%) aligned 0 times 5653251 (74.48%) aligned exactly 1 time 1073709 (14.15%) aligned >1 times 88.63% overall alignment rate Time searching: 00:01:10 Overall time: 00:01:10 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] 410752 / 6726960 = 0.0611 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 08:08:24: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX235170/SRX235170.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX235170/SRX235170.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX235170/SRX235170.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX235170/SRX235170.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 08:08:24: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:08:24: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:08:29: 1000000 INFO @ Tue, 16 Jun 2020 08:08:33: 2000000 INFO @ Tue, 16 Jun 2020 08:08:38: 3000000 INFO @ Tue, 16 Jun 2020 08:08:42: 4000000 INFO @ Tue, 16 Jun 2020 08:08:47: 5000000 INFO @ Tue, 16 Jun 2020 08:08:51: 6000000 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 08:08:53: #1 tag size is determined as 32 bps INFO @ Tue, 16 Jun 2020 08:08:53: #1 tag size = 32 INFO @ Tue, 16 Jun 2020 08:08:53: #1 total tags in treatment: 6316208 INFO @ Tue, 16 Jun 2020 08:08:53: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:08:53: #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 08:08:53: #1 tags after filtering in treatment: 6316208 INFO @ Tue, 16 Jun 2020 08:08:53: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:08:53: #1 finished! INFO @ Tue, 16 Jun 2020 08:08:53: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:08:53: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:08:53: #2 number of paired peaks: 385 WARNING @ Tue, 16 Jun 2020 08:08:53: Fewer paired peaks (385) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 385 pairs to build model! INFO @ Tue, 16 Jun 2020 08:08:53: start model_add_line... INFO @ Tue, 16 Jun 2020 08:08:53: start X-correlation... INFO @ Tue, 16 Jun 2020 08:08:53: end of X-cor INFO @ Tue, 16 Jun 2020 08:08:53: #2 finished! INFO @ Tue, 16 Jun 2020 08:08:53: #2 predicted fragment length is 31 bps INFO @ Tue, 16 Jun 2020 08:08:53: #2 alternative fragment length(s) may be 2,31,505 bps INFO @ Tue, 16 Jun 2020 08:08:53: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX235170/SRX235170.05_model.r WARNING @ Tue, 16 Jun 2020 08:08:53: #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 08:08:53: #2 You may need to consider one of the other alternative d(s): 2,31,505 WARNING @ Tue, 16 Jun 2020 08:08:53: #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 08:08:53: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:08:53: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 08:08:54: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX235170/SRX235170.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX235170/SRX235170.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX235170/SRX235170.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX235170/SRX235170.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 08:08:54: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:08:54: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:08:59: 1000000 INFO @ Tue, 16 Jun 2020 08:09:03: 2000000 INFO @ Tue, 16 Jun 2020 08:09:07: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 08:09:08: 3000000 INFO @ Tue, 16 Jun 2020 08:09:12: 4000000 INFO @ Tue, 16 Jun 2020 08:09:13: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX235170/SRX235170.05_peaks.xls INFO @ Tue, 16 Jun 2020 08:09:13: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX235170/SRX235170.05_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:09:13: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX235170/SRX235170.05_summits.bed INFO @ Tue, 16 Jun 2020 08:09:13: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (462 records, 4 fields): 1 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 08:09:17: 5000000 INFO @ Tue, 16 Jun 2020 08:09:21: 6000000 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 08:09:22: #1 tag size is determined as 32 bps INFO @ Tue, 16 Jun 2020 08:09:22: #1 tag size = 32 INFO @ Tue, 16 Jun 2020 08:09:22: #1 total tags in treatment: 6316208 INFO @ Tue, 16 Jun 2020 08:09:22: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:09:22: #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 08:09:23: #1 tags after filtering in treatment: 6316208 INFO @ Tue, 16 Jun 2020 08:09:23: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:09:23: #1 finished! INFO @ Tue, 16 Jun 2020 08:09:23: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:09:23: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:09:23: #2 number of paired peaks: 385 WARNING @ Tue, 16 Jun 2020 08:09:23: Fewer paired peaks (385) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 385 pairs to build model! INFO @ Tue, 16 Jun 2020 08:09:23: start model_add_line... INFO @ Tue, 16 Jun 2020 08:09:23: start X-correlation... INFO @ Tue, 16 Jun 2020 08:09:23: end of X-cor INFO @ Tue, 16 Jun 2020 08:09:23: #2 finished! INFO @ Tue, 16 Jun 2020 08:09:23: #2 predicted fragment length is 31 bps INFO @ Tue, 16 Jun 2020 08:09:23: #2 alternative fragment length(s) may be 2,31,505 bps INFO @ Tue, 16 Jun 2020 08:09:23: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX235170/SRX235170.10_model.r WARNING @ Tue, 16 Jun 2020 08:09:23: #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 08:09:23: #2 You may need to consider one of the other alternative d(s): 2,31,505 WARNING @ Tue, 16 Jun 2020 08:09:23: #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 08:09:23: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:09:23: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 08:09:24: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX235170/SRX235170.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX235170/SRX235170.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX235170/SRX235170.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX235170/SRX235170.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 08:09:24: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:09:24: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:09:29: 1000000 INFO @ Tue, 16 Jun 2020 08:09:34: 2000000 INFO @ Tue, 16 Jun 2020 08:09:37: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 08:09:39: 3000000 INFO @ Tue, 16 Jun 2020 08:09:43: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX235170/SRX235170.10_peaks.xls INFO @ Tue, 16 Jun 2020 08:09:43: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX235170/SRX235170.10_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:09:43: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX235170/SRX235170.10_summits.bed INFO @ Tue, 16 Jun 2020 08:09:43: Done! INFO @ Tue, 16 Jun 2020 08:09:43: 4000000 pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (220 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 08:09:48: 5000000 INFO @ Tue, 16 Jun 2020 08:09:52: 6000000 INFO @ Tue, 16 Jun 2020 08:09:54: #1 tag size is determined as 32 bps INFO @ Tue, 16 Jun 2020 08:09:54: #1 tag size = 32 INFO @ Tue, 16 Jun 2020 08:09:54: #1 total tags in treatment: 6316208 INFO @ Tue, 16 Jun 2020 08:09:54: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:09:54: #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 08:09:54: #1 tags after filtering in treatment: 6316208 INFO @ Tue, 16 Jun 2020 08:09:54: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:09:54: #1 finished! INFO @ Tue, 16 Jun 2020 08:09:54: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:09:54: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:09:54: #2 number of paired peaks: 385 WARNING @ Tue, 16 Jun 2020 08:09:54: Fewer paired peaks (385) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 385 pairs to build model! INFO @ Tue, 16 Jun 2020 08:09:54: start model_add_line... INFO @ Tue, 16 Jun 2020 08:09:55: start X-correlation... INFO @ Tue, 16 Jun 2020 08:09:55: end of X-cor INFO @ Tue, 16 Jun 2020 08:09:55: #2 finished! INFO @ Tue, 16 Jun 2020 08:09:55: #2 predicted fragment length is 31 bps INFO @ Tue, 16 Jun 2020 08:09:55: #2 alternative fragment length(s) may be 2,31,505 bps INFO @ Tue, 16 Jun 2020 08:09:55: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX235170/SRX235170.20_model.r WARNING @ Tue, 16 Jun 2020 08:09:55: #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 08:09:55: #2 You may need to consider one of the other alternative d(s): 2,31,505 WARNING @ Tue, 16 Jun 2020 08:09:55: #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 08:09:55: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:09:55: #3 Pre-compute pvalue-qvalue table... BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 16 Jun 2020 08:10:08: #3 Call peaks for each chromosome... BigWig に変換しました。 INFO @ Tue, 16 Jun 2020 08:10:15: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX235170/SRX235170.20_peaks.xls INFO @ Tue, 16 Jun 2020 08:10:15: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX235170/SRX235170.20_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:10:15: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX235170/SRX235170.20_summits.bed INFO @ Tue, 16 Jun 2020 08:10:15: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (53 records, 4 fields): 2 millis CompletedMACS2peakCalling