Job ID = 6368602 SRX = SRX5020827 Genome = ce11 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-16T00:20:21 prefetch.2.10.7: 1) Downloading 'SRR8201450'... 2020-06-16T00:20:21 prefetch.2.10.7: Downloading via HTTPS... 2020-06-16T00:22:44 prefetch.2.10.7: HTTPS download succeed 2020-06-16T00:22:45 prefetch.2.10.7: 'SRR8201450' is valid 2020-06-16T00:22:45 prefetch.2.10.7: 1) 'SRR8201450' was downloaded successfully Read 12808518 spots for SRR8201450/SRR8201450.sra Written 12808518 spots for SRR8201450/SRR8201450.sra fastq に変換しました。 bowtie でマッピング中... Time loading reference: 00:00:01 Time loading forward index: 00:00:00 Time loading mirror index: 00:00:00 Multiseed full-index search: 00:03:06 12808518 reads; of these: 12808518 (100.00%) were unpaired; of these: 106816 (0.83%) aligned 0 times 10514688 (82.09%) aligned exactly 1 time 2187014 (17.07%) aligned >1 times 99.17% overall alignment rate Time searching: 00:03:07 Overall time: 00:03:07 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_sort_core] merging from 8 files... [bam_rmdupse_core] 941881 / 12701702 = 0.0742 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 09:30:09: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX5020827/SRX5020827.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX5020827/SRX5020827.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX5020827/SRX5020827.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX5020827/SRX5020827.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 09:30:09: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:30:09: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:30:14: 1000000 INFO @ Tue, 16 Jun 2020 09:30:20: 2000000 INFO @ Tue, 16 Jun 2020 09:30:25: 3000000 INFO @ Tue, 16 Jun 2020 09:30:31: 4000000 INFO @ Tue, 16 Jun 2020 09:30:36: 5000000 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 09:30:39: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX5020827/SRX5020827.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX5020827/SRX5020827.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX5020827/SRX5020827.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX5020827/SRX5020827.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 09:30:39: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:30:39: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:30:42: 6000000 INFO @ Tue, 16 Jun 2020 09:30:45: 1000000 INFO @ Tue, 16 Jun 2020 09:30:48: 7000000 INFO @ Tue, 16 Jun 2020 09:30:51: 2000000 INFO @ Tue, 16 Jun 2020 09:30:54: 8000000 INFO @ Tue, 16 Jun 2020 09:30:57: 3000000 INFO @ Tue, 16 Jun 2020 09:31:00: 9000000 INFO @ Tue, 16 Jun 2020 09:31:03: 4000000 INFO @ Tue, 16 Jun 2020 09:31:06: 10000000 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 09:31:09: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX5020827/SRX5020827.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX5020827/SRX5020827.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX5020827/SRX5020827.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX5020827/SRX5020827.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 09:31:09: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:31:09: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:31:09: 5000000 INFO @ Tue, 16 Jun 2020 09:31:12: 11000000 INFO @ Tue, 16 Jun 2020 09:31:15: 1000000 INFO @ Tue, 16 Jun 2020 09:31:15: 6000000 INFO @ Tue, 16 Jun 2020 09:31:17: #1 tag size is determined as 51 bps INFO @ Tue, 16 Jun 2020 09:31:17: #1 tag size = 51 INFO @ Tue, 16 Jun 2020 09:31:17: #1 total tags in treatment: 11759821 INFO @ Tue, 16 Jun 2020 09:31:17: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:31:17: #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 09:31:17: #1 tags after filtering in treatment: 11759821 INFO @ Tue, 16 Jun 2020 09:31:17: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 09:31:17: #1 finished! INFO @ Tue, 16 Jun 2020 09:31:17: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:31:17: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:31:18: #2 number of paired peaks: 306 WARNING @ Tue, 16 Jun 2020 09:31:18: Fewer paired peaks (306) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 306 pairs to build model! INFO @ Tue, 16 Jun 2020 09:31:18: start model_add_line... INFO @ Tue, 16 Jun 2020 09:31:18: start X-correlation... INFO @ Tue, 16 Jun 2020 09:31:18: end of X-cor INFO @ Tue, 16 Jun 2020 09:31:18: #2 finished! INFO @ Tue, 16 Jun 2020 09:31:18: #2 predicted fragment length is 49 bps INFO @ Tue, 16 Jun 2020 09:31:18: #2 alternative fragment length(s) may be 2,49,510,534 bps INFO @ Tue, 16 Jun 2020 09:31:18: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX5020827/SRX5020827.05_model.r WARNING @ Tue, 16 Jun 2020 09:31:18: #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 09:31:18: #2 You may need to consider one of the other alternative d(s): 2,49,510,534 WARNING @ Tue, 16 Jun 2020 09:31:18: #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 09:31:18: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:31:18: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 09:31:21: 2000000 INFO @ Tue, 16 Jun 2020 09:31:21: 7000000 INFO @ Tue, 16 Jun 2020 09:31:26: 3000000 INFO @ Tue, 16 Jun 2020 09:31:27: 8000000 INFO @ Tue, 16 Jun 2020 09:31:32: 4000000 INFO @ Tue, 16 Jun 2020 09:31:33: 9000000 INFO @ Tue, 16 Jun 2020 09:31:38: 5000000 INFO @ Tue, 16 Jun 2020 09:31:39: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 09:31:39: 10000000 INFO @ Tue, 16 Jun 2020 09:31:44: 6000000 INFO @ Tue, 16 Jun 2020 09:31:45: 11000000 INFO @ Tue, 16 Jun 2020 09:31:50: #1 tag size is determined as 51 bps INFO @ Tue, 16 Jun 2020 09:31:50: #1 tag size = 51 INFO @ Tue, 16 Jun 2020 09:31:50: #1 total tags in treatment: 11759821 INFO @ Tue, 16 Jun 2020 09:31:50: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:31:50: #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 09:31:50: 7000000 INFO @ Tue, 16 Jun 2020 09:31:50: #1 tags after filtering in treatment: 11759821 INFO @ Tue, 16 Jun 2020 09:31:50: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 09:31:50: #1 finished! INFO @ Tue, 16 Jun 2020 09:31:50: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:31:50: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:31:50: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX5020827/SRX5020827.05_peaks.xls INFO @ Tue, 16 Jun 2020 09:31:50: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX5020827/SRX5020827.05_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:31:50: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX5020827/SRX5020827.05_summits.bed INFO @ Tue, 16 Jun 2020 09:31:50: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (629 records, 4 fields): 1 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 09:31:51: #2 number of paired peaks: 306 WARNING @ Tue, 16 Jun 2020 09:31:51: Fewer paired peaks (306) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 306 pairs to build model! INFO @ Tue, 16 Jun 2020 09:31:51: start model_add_line... INFO @ Tue, 16 Jun 2020 09:31:51: start X-correlation... INFO @ Tue, 16 Jun 2020 09:31:51: end of X-cor INFO @ Tue, 16 Jun 2020 09:31:51: #2 finished! INFO @ Tue, 16 Jun 2020 09:31:51: #2 predicted fragment length is 49 bps INFO @ Tue, 16 Jun 2020 09:31:51: #2 alternative fragment length(s) may be 2,49,510,534 bps INFO @ Tue, 16 Jun 2020 09:31:51: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX5020827/SRX5020827.10_model.r WARNING @ Tue, 16 Jun 2020 09:31:51: #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 09:31:51: #2 You may need to consider one of the other alternative d(s): 2,49,510,534 WARNING @ Tue, 16 Jun 2020 09:31:51: #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 09:31:51: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:31:51: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 09:31:55: 8000000 INFO @ Tue, 16 Jun 2020 09:32:01: 9000000 INFO @ Tue, 16 Jun 2020 09:32:07: 10000000 INFO @ Tue, 16 Jun 2020 09:32:12: 11000000 INFO @ Tue, 16 Jun 2020 09:32:12: #3 Call peaks for each chromosome... BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 16 Jun 2020 09:32:16: #1 tag size is determined as 51 bps INFO @ Tue, 16 Jun 2020 09:32:16: #1 tag size = 51 INFO @ Tue, 16 Jun 2020 09:32:16: #1 total tags in treatment: 11759821 INFO @ Tue, 16 Jun 2020 09:32:16: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:32:16: #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 09:32:17: #1 tags after filtering in treatment: 11759821 INFO @ Tue, 16 Jun 2020 09:32:17: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 09:32:17: #1 finished! INFO @ Tue, 16 Jun 2020 09:32:17: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:32:17: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:32:17: #2 number of paired peaks: 306 WARNING @ Tue, 16 Jun 2020 09:32:17: Fewer paired peaks (306) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 306 pairs to build model! INFO @ Tue, 16 Jun 2020 09:32:17: start model_add_line... INFO @ Tue, 16 Jun 2020 09:32:17: start X-correlation... INFO @ Tue, 16 Jun 2020 09:32:17: end of X-cor INFO @ Tue, 16 Jun 2020 09:32:17: #2 finished! INFO @ Tue, 16 Jun 2020 09:32:17: #2 predicted fragment length is 49 bps INFO @ Tue, 16 Jun 2020 09:32:17: #2 alternative fragment length(s) may be 2,49,510,534 bps INFO @ Tue, 16 Jun 2020 09:32:17: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX5020827/SRX5020827.20_model.r WARNING @ Tue, 16 Jun 2020 09:32:17: #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 09:32:17: #2 You may need to consider one of the other alternative d(s): 2,49,510,534 WARNING @ Tue, 16 Jun 2020 09:32:17: #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 09:32:17: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:32:17: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 09:32:23: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX5020827/SRX5020827.10_peaks.xls INFO @ Tue, 16 Jun 2020 09:32:23: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX5020827/SRX5020827.10_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:32:23: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX5020827/SRX5020827.10_summits.bed INFO @ Tue, 16 Jun 2020 09:32:23: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (412 records, 4 fields): 1 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 09:32:38: #3 Call peaks for each chromosome... BigWig に変換しました。 INFO @ Tue, 16 Jun 2020 09:32:49: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX5020827/SRX5020827.20_peaks.xls INFO @ Tue, 16 Jun 2020 09:32:49: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX5020827/SRX5020827.20_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:32:49: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX5020827/SRX5020827.20_summits.bed INFO @ Tue, 16 Jun 2020 09:32:49: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (177 records, 4 fields): 1 millis CompletedMACS2peakCalling