Job ID = 6366840 SRX = SRX2350739 Genome = ce11 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-15T23:00:08 prefetch.2.10.7: 1) Downloading 'SRR5024048'... 2020-06-15T23:00:08 prefetch.2.10.7: Downloading via HTTPS... 2020-06-15T23:01:07 prefetch.2.10.7: HTTPS download succeed 2020-06-15T23:01:08 prefetch.2.10.7: 'SRR5024048' is valid 2020-06-15T23:01:08 prefetch.2.10.7: 1) 'SRR5024048' was downloaded successfully Read 8201532 spots for SRR5024048/SRR5024048.sra Written 8201532 spots for SRR5024048/SRR5024048.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: 00:00:01 Multiseed full-index search: 00:01:58 8201532 reads; of these: 8201532 (100.00%) were unpaired; of these: 133300 (1.63%) aligned 0 times 7082435 (86.36%) aligned exactly 1 time 985797 (12.02%) aligned >1 times 98.37% overall alignment rate Time searching: 00:01:59 Overall time: 00:01:59 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] 726350 / 8068232 = 0.0900 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 08:06:00: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX2350739/SRX2350739.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX2350739/SRX2350739.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX2350739/SRX2350739.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX2350739/SRX2350739.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 08:06:00: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:06:00: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:06:07: 1000000 INFO @ Tue, 16 Jun 2020 08:06:13: 2000000 INFO @ Tue, 16 Jun 2020 08:06:19: 3000000 INFO @ Tue, 16 Jun 2020 08:06:26: 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 08:06:30: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX2350739/SRX2350739.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX2350739/SRX2350739.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX2350739/SRX2350739.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX2350739/SRX2350739.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 08:06:30: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:06:30: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:06:32: 5000000 INFO @ Tue, 16 Jun 2020 08:06:37: 1000000 INFO @ Tue, 16 Jun 2020 08:06:39: 6000000 INFO @ Tue, 16 Jun 2020 08:06:44: 2000000 INFO @ Tue, 16 Jun 2020 08:06:46: 7000000 INFO @ Tue, 16 Jun 2020 08:06:48: #1 tag size is determined as 51 bps INFO @ Tue, 16 Jun 2020 08:06:48: #1 tag size = 51 INFO @ Tue, 16 Jun 2020 08:06:48: #1 total tags in treatment: 7341882 INFO @ Tue, 16 Jun 2020 08:06:48: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:06:48: #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 08:06:48: #1 tags after filtering in treatment: 7341882 INFO @ Tue, 16 Jun 2020 08:06:48: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:06:48: #1 finished! INFO @ Tue, 16 Jun 2020 08:06:48: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:06:48: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:06:49: #2 number of paired peaks: 155 WARNING @ Tue, 16 Jun 2020 08:06:49: Fewer paired peaks (155) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 155 pairs to build model! INFO @ Tue, 16 Jun 2020 08:06:49: start model_add_line... INFO @ Tue, 16 Jun 2020 08:06:49: start X-correlation... INFO @ Tue, 16 Jun 2020 08:06:49: end of X-cor INFO @ Tue, 16 Jun 2020 08:06:49: #2 finished! INFO @ Tue, 16 Jun 2020 08:06:49: #2 predicted fragment length is 51 bps INFO @ Tue, 16 Jun 2020 08:06:49: #2 alternative fragment length(s) may be 4,51,178,203,224,400,418,486 bps INFO @ Tue, 16 Jun 2020 08:06:49: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX2350739/SRX2350739.05_model.r WARNING @ Tue, 16 Jun 2020 08:06:49: #2 Since the d (51) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 08:06:49: #2 You may need to consider one of the other alternative d(s): 4,51,178,203,224,400,418,486 WARNING @ Tue, 16 Jun 2020 08:06:49: #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 08:06:49: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:06:49: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 08:06:50: 3000000 INFO @ Tue, 16 Jun 2020 08:06:57: 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 08:07:00: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX2350739/SRX2350739.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX2350739/SRX2350739.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX2350739/SRX2350739.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX2350739/SRX2350739.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 08:07:00: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:07:00: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:07:04: 5000000 INFO @ Tue, 16 Jun 2020 08:07:04: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 08:07:08: 1000000 INFO @ Tue, 16 Jun 2020 08:07:11: 6000000 INFO @ Tue, 16 Jun 2020 08:07:12: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX2350739/SRX2350739.05_peaks.xls INFO @ Tue, 16 Jun 2020 08:07:12: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX2350739/SRX2350739.05_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:07:12: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX2350739/SRX2350739.05_summits.bed INFO @ Tue, 16 Jun 2020 08:07:12: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (292 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 08:07:16: 2000000 INFO @ Tue, 16 Jun 2020 08:07:18: 7000000 INFO @ Tue, 16 Jun 2020 08:07:21: #1 tag size is determined as 51 bps INFO @ Tue, 16 Jun 2020 08:07:21: #1 tag size = 51 INFO @ Tue, 16 Jun 2020 08:07:21: #1 total tags in treatment: 7341882 INFO @ Tue, 16 Jun 2020 08:07:21: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:07:21: #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 08:07:21: #1 tags after filtering in treatment: 7341882 INFO @ Tue, 16 Jun 2020 08:07:21: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:07:21: #1 finished! INFO @ Tue, 16 Jun 2020 08:07:21: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:07:21: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:07:21: #2 number of paired peaks: 155 WARNING @ Tue, 16 Jun 2020 08:07:21: Fewer paired peaks (155) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 155 pairs to build model! INFO @ Tue, 16 Jun 2020 08:07:21: start model_add_line... INFO @ Tue, 16 Jun 2020 08:07:21: start X-correlation... INFO @ Tue, 16 Jun 2020 08:07:21: end of X-cor INFO @ Tue, 16 Jun 2020 08:07:21: #2 finished! INFO @ Tue, 16 Jun 2020 08:07:21: #2 predicted fragment length is 51 bps INFO @ Tue, 16 Jun 2020 08:07:21: #2 alternative fragment length(s) may be 4,51,178,203,224,400,418,486 bps INFO @ Tue, 16 Jun 2020 08:07:21: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX2350739/SRX2350739.10_model.r WARNING @ Tue, 16 Jun 2020 08:07:21: #2 Since the d (51) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 08:07:21: #2 You may need to consider one of the other alternative d(s): 4,51,178,203,224,400,418,486 WARNING @ Tue, 16 Jun 2020 08:07:21: #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 08:07:21: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:07:21: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 08:07:24: 3000000 INFO @ Tue, 16 Jun 2020 08:07:32: 4000000 INFO @ Tue, 16 Jun 2020 08:07:37: #3 Call peaks for each chromosome... BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 16 Jun 2020 08:07:39: 5000000 INFO @ Tue, 16 Jun 2020 08:07:45: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX2350739/SRX2350739.10_peaks.xls INFO @ Tue, 16 Jun 2020 08:07:45: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX2350739/SRX2350739.10_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:07:45: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX2350739/SRX2350739.10_summits.bed INFO @ Tue, 16 Jun 2020 08:07:45: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (163 records, 4 fields): 1 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 08:07:47: 6000000 INFO @ Tue, 16 Jun 2020 08:07:54: 7000000 BigWig に変換しました。 INFO @ Tue, 16 Jun 2020 08:07:57: #1 tag size is determined as 51 bps INFO @ Tue, 16 Jun 2020 08:07:57: #1 tag size = 51 INFO @ Tue, 16 Jun 2020 08:07:57: #1 total tags in treatment: 7341882 INFO @ Tue, 16 Jun 2020 08:07:57: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:07:57: #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 08:07:57: #1 tags after filtering in treatment: 7341882 INFO @ Tue, 16 Jun 2020 08:07:57: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:07:57: #1 finished! INFO @ Tue, 16 Jun 2020 08:07:57: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:07:57: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:07:57: #2 number of paired peaks: 155 WARNING @ Tue, 16 Jun 2020 08:07:57: Fewer paired peaks (155) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 155 pairs to build model! INFO @ Tue, 16 Jun 2020 08:07:57: start model_add_line... INFO @ Tue, 16 Jun 2020 08:07:57: start X-correlation... INFO @ Tue, 16 Jun 2020 08:07:57: end of X-cor INFO @ Tue, 16 Jun 2020 08:07:57: #2 finished! INFO @ Tue, 16 Jun 2020 08:07:57: #2 predicted fragment length is 51 bps INFO @ Tue, 16 Jun 2020 08:07:57: #2 alternative fragment length(s) may be 4,51,178,203,224,400,418,486 bps INFO @ Tue, 16 Jun 2020 08:07:57: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX2350739/SRX2350739.20_model.r WARNING @ Tue, 16 Jun 2020 08:07:57: #2 Since the d (51) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 08:07:57: #2 You may need to consider one of the other alternative d(s): 4,51,178,203,224,400,418,486 WARNING @ Tue, 16 Jun 2020 08:07:57: #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 08:07:57: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:07:57: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 08:08:13: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 08:08:21: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX2350739/SRX2350739.20_peaks.xls INFO @ Tue, 16 Jun 2020 08:08:21: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX2350739/SRX2350739.20_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:08:21: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX2350739/SRX2350739.20_summits.bed INFO @ Tue, 16 Jun 2020 08:08:21: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (52 records, 4 fields): 1 millis CompletedMACS2peakCalling