Job ID = 6366830 SRX = SRX2350729 Genome = ce11 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-15T23:05:08 prefetch.2.10.7: 1) Downloading 'SRR5024038'... 2020-06-15T23:05:08 prefetch.2.10.7: Downloading via HTTPS... 2020-06-15T23:06:24 prefetch.2.10.7: HTTPS download succeed 2020-06-15T23:06:24 prefetch.2.10.7: 1) 'SRR5024038' was downloaded successfully Read 11863154 spots for SRR5024038/SRR5024038.sra Written 11863154 spots for SRR5024038/SRR5024038.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: 00:02:51 11863154 reads; of these: 11863154 (100.00%) were unpaired; of these: 256022 (2.16%) aligned 0 times 9254830 (78.01%) aligned exactly 1 time 2352302 (19.83%) aligned >1 times 97.84% overall alignment rate Time searching: 00:02:51 Overall time: 00:02:51 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] 1267785 / 11607132 = 0.1092 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 08:13:16: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX2350729/SRX2350729.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX2350729/SRX2350729.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX2350729/SRX2350729.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX2350729/SRX2350729.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 08:13:16: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:13:16: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:13:22: 1000000 INFO @ Tue, 16 Jun 2020 08:13:28: 2000000 INFO @ Tue, 16 Jun 2020 08:13:34: 3000000 INFO @ Tue, 16 Jun 2020 08:13:40: 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 08:13:46: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX2350729/SRX2350729.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX2350729/SRX2350729.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX2350729/SRX2350729.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX2350729/SRX2350729.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 08:13:46: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:13:46: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:13:47: 5000000 INFO @ Tue, 16 Jun 2020 08:13:52: 1000000 INFO @ Tue, 16 Jun 2020 08:13:53: 6000000 INFO @ Tue, 16 Jun 2020 08:13:58: 2000000 INFO @ Tue, 16 Jun 2020 08:13:59: 7000000 INFO @ Tue, 16 Jun 2020 08:14:04: 3000000 INFO @ Tue, 16 Jun 2020 08:14:05: 8000000 INFO @ Tue, 16 Jun 2020 08:14:10: 4000000 INFO @ Tue, 16 Jun 2020 08:14:11: 9000000 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 08:14:16: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX2350729/SRX2350729.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX2350729/SRX2350729.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX2350729/SRX2350729.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX2350729/SRX2350729.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 08:14:16: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:14:16: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:14:16: 5000000 INFO @ Tue, 16 Jun 2020 08:14:17: 10000000 INFO @ Tue, 16 Jun 2020 08:14:19: #1 tag size is determined as 51 bps INFO @ Tue, 16 Jun 2020 08:14:19: #1 tag size = 51 INFO @ Tue, 16 Jun 2020 08:14:19: #1 total tags in treatment: 10339347 INFO @ Tue, 16 Jun 2020 08:14:19: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:14:19: #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 08:14:19: #1 tags after filtering in treatment: 10339347 INFO @ Tue, 16 Jun 2020 08:14:19: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:14:19: #1 finished! INFO @ Tue, 16 Jun 2020 08:14:19: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:14:19: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:14:20: #2 number of paired peaks: 372 WARNING @ Tue, 16 Jun 2020 08:14:20: Fewer paired peaks (372) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 372 pairs to build model! INFO @ Tue, 16 Jun 2020 08:14:20: start model_add_line... INFO @ Tue, 16 Jun 2020 08:14:20: start X-correlation... INFO @ Tue, 16 Jun 2020 08:14:20: end of X-cor INFO @ Tue, 16 Jun 2020 08:14:20: #2 finished! INFO @ Tue, 16 Jun 2020 08:14:20: #2 predicted fragment length is 49 bps INFO @ Tue, 16 Jun 2020 08:14:20: #2 alternative fragment length(s) may be 2,49,567 bps INFO @ Tue, 16 Jun 2020 08:14:20: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX2350729/SRX2350729.05_model.r WARNING @ Tue, 16 Jun 2020 08:14:20: #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 08:14:20: #2 You may need to consider one of the other alternative d(s): 2,49,567 WARNING @ Tue, 16 Jun 2020 08:14:20: #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 08:14:20: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:14:20: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 08:14:21: 1000000 INFO @ Tue, 16 Jun 2020 08:14:22: 6000000 INFO @ Tue, 16 Jun 2020 08:14:26: 2000000 INFO @ Tue, 16 Jun 2020 08:14:28: 7000000 INFO @ Tue, 16 Jun 2020 08:14:31: 3000000 INFO @ Tue, 16 Jun 2020 08:14:34: 8000000 INFO @ Tue, 16 Jun 2020 08:14:37: 4000000 INFO @ Tue, 16 Jun 2020 08:14:40: 9000000 INFO @ Tue, 16 Jun 2020 08:14:42: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 08:14:42: 5000000 INFO @ Tue, 16 Jun 2020 08:14:46: 10000000 INFO @ Tue, 16 Jun 2020 08:14:47: 6000000 INFO @ Tue, 16 Jun 2020 08:14:48: #1 tag size is determined as 51 bps INFO @ Tue, 16 Jun 2020 08:14:48: #1 tag size = 51 INFO @ Tue, 16 Jun 2020 08:14:48: #1 total tags in treatment: 10339347 INFO @ Tue, 16 Jun 2020 08:14:48: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:14:48: #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 08:14:48: #1 tags after filtering in treatment: 10339347 INFO @ Tue, 16 Jun 2020 08:14:48: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:14:48: #1 finished! INFO @ Tue, 16 Jun 2020 08:14:48: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:14:48: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:14:49: #2 number of paired peaks: 372 WARNING @ Tue, 16 Jun 2020 08:14:49: Fewer paired peaks (372) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 372 pairs to build model! INFO @ Tue, 16 Jun 2020 08:14:49: start model_add_line... INFO @ Tue, 16 Jun 2020 08:14:49: start X-correlation... INFO @ Tue, 16 Jun 2020 08:14:49: end of X-cor INFO @ Tue, 16 Jun 2020 08:14:49: #2 finished! INFO @ Tue, 16 Jun 2020 08:14:49: #2 predicted fragment length is 49 bps INFO @ Tue, 16 Jun 2020 08:14:49: #2 alternative fragment length(s) may be 2,49,567 bps INFO @ Tue, 16 Jun 2020 08:14:49: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX2350729/SRX2350729.10_model.r WARNING @ Tue, 16 Jun 2020 08:14:49: #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 08:14:49: #2 You may need to consider one of the other alternative d(s): 2,49,567 WARNING @ Tue, 16 Jun 2020 08:14:49: #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 08:14:49: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:14:49: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 08:14:53: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX2350729/SRX2350729.05_peaks.xls INFO @ Tue, 16 Jun 2020 08:14:53: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX2350729/SRX2350729.05_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:14:53: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX2350729/SRX2350729.05_summits.bed INFO @ Tue, 16 Jun 2020 08:14:53: Done! INFO @ Tue, 16 Jun 2020 08:14:53: 7000000 pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (690 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 08:14:58: 8000000 INFO @ Tue, 16 Jun 2020 08:15:03: 9000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 16 Jun 2020 08:15:09: 10000000 INFO @ Tue, 16 Jun 2020 08:15:10: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 08:15:10: #1 tag size is determined as 51 bps INFO @ Tue, 16 Jun 2020 08:15:10: #1 tag size = 51 INFO @ Tue, 16 Jun 2020 08:15:10: #1 total tags in treatment: 10339347 INFO @ Tue, 16 Jun 2020 08:15:10: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:15:10: #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 08:15:11: #1 tags after filtering in treatment: 10339347 INFO @ Tue, 16 Jun 2020 08:15:11: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:15:11: #1 finished! INFO @ Tue, 16 Jun 2020 08:15:11: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:15:11: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:15:11: #2 number of paired peaks: 372 WARNING @ Tue, 16 Jun 2020 08:15:11: Fewer paired peaks (372) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 372 pairs to build model! INFO @ Tue, 16 Jun 2020 08:15:11: start model_add_line... INFO @ Tue, 16 Jun 2020 08:15:11: start X-correlation... INFO @ Tue, 16 Jun 2020 08:15:11: end of X-cor INFO @ Tue, 16 Jun 2020 08:15:11: #2 finished! INFO @ Tue, 16 Jun 2020 08:15:11: #2 predicted fragment length is 49 bps INFO @ Tue, 16 Jun 2020 08:15:11: #2 alternative fragment length(s) may be 2,49,567 bps INFO @ Tue, 16 Jun 2020 08:15:11: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX2350729/SRX2350729.20_model.r WARNING @ Tue, 16 Jun 2020 08:15:11: #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 08:15:11: #2 You may need to consider one of the other alternative d(s): 2,49,567 WARNING @ Tue, 16 Jun 2020 08:15:11: #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 08:15:11: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:15:11: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 08:15:20: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX2350729/SRX2350729.10_peaks.xls INFO @ Tue, 16 Jun 2020 08:15:20: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX2350729/SRX2350729.10_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:15:21: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX2350729/SRX2350729.10_summits.bed INFO @ Tue, 16 Jun 2020 08:15:21: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (426 records, 4 fields): 1 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 08:15:33: #3 Call peaks for each chromosome... BigWig に変換しました。 INFO @ Tue, 16 Jun 2020 08:15:44: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX2350729/SRX2350729.20_peaks.xls INFO @ Tue, 16 Jun 2020 08:15:44: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX2350729/SRX2350729.20_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:15:44: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX2350729/SRX2350729.20_summits.bed INFO @ Tue, 16 Jun 2020 08:15:44: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (166 records, 4 fields): 2 millis CompletedMACS2peakCalling