Job ID = 6367035 SRX = SRX2761380 Genome = ce11 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-15T23:16:31 prefetch.2.10.7: 1) Downloading 'SRR5476954'... 2020-06-15T23:16:31 prefetch.2.10.7: Downloading via HTTPS... 2020-06-15T23:17:47 prefetch.2.10.7: HTTPS download succeed 2020-06-15T23:17:48 prefetch.2.10.7: 'SRR5476954' is valid 2020-06-15T23:17:48 prefetch.2.10.7: 1) 'SRR5476954' was downloaded successfully Read 8854069 spots for SRR5476954/SRR5476954.sra Written 8854069 spots for SRR5476954/SRR5476954.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: 00:02:08 8854069 reads; of these: 8854069 (100.00%) were unpaired; of these: 537553 (6.07%) aligned 0 times 6308398 (71.25%) aligned exactly 1 time 2008118 (22.68%) aligned >1 times 93.93% overall alignment rate Time searching: 00:02:08 Overall time: 00:02:08 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] 1507539 / 8316516 = 0.1813 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 08:22:56: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX2761380/SRX2761380.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX2761380/SRX2761380.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX2761380/SRX2761380.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX2761380/SRX2761380.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 08:22:56: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:22:56: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:23:04: 1000000 INFO @ Tue, 16 Jun 2020 08:23:12: 2000000 INFO @ Tue, 16 Jun 2020 08:23:20: 3000000 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 08:23:26: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX2761380/SRX2761380.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX2761380/SRX2761380.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX2761380/SRX2761380.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX2761380/SRX2761380.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 08:23:26: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:23:26: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:23:28: 4000000 INFO @ Tue, 16 Jun 2020 08:23:35: 1000000 INFO @ Tue, 16 Jun 2020 08:23:37: 5000000 INFO @ Tue, 16 Jun 2020 08:23:43: 2000000 INFO @ Tue, 16 Jun 2020 08:23:45: 6000000 INFO @ Tue, 16 Jun 2020 08:23:51: 3000000 INFO @ Tue, 16 Jun 2020 08:23:52: #1 tag size is determined as 51 bps INFO @ Tue, 16 Jun 2020 08:23:52: #1 tag size = 51 INFO @ Tue, 16 Jun 2020 08:23:52: #1 total tags in treatment: 6808977 INFO @ Tue, 16 Jun 2020 08:23:52: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:23:52: #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 08:23:52: #1 tags after filtering in treatment: 6808977 INFO @ Tue, 16 Jun 2020 08:23:52: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:23:52: #1 finished! INFO @ Tue, 16 Jun 2020 08:23:52: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:23:52: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:23:52: #2 number of paired peaks: 631 WARNING @ Tue, 16 Jun 2020 08:23:52: Fewer paired peaks (631) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 631 pairs to build model! INFO @ Tue, 16 Jun 2020 08:23:52: start model_add_line... INFO @ Tue, 16 Jun 2020 08:23:52: start X-correlation... INFO @ Tue, 16 Jun 2020 08:23:52: end of X-cor INFO @ Tue, 16 Jun 2020 08:23:52: #2 finished! INFO @ Tue, 16 Jun 2020 08:23:52: #2 predicted fragment length is 53 bps INFO @ Tue, 16 Jun 2020 08:23:52: #2 alternative fragment length(s) may be 4,53 bps INFO @ Tue, 16 Jun 2020 08:23:52: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX2761380/SRX2761380.05_model.r WARNING @ Tue, 16 Jun 2020 08:23:52: #2 Since the d (53) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 08:23:52: #2 You may need to consider one of the other alternative d(s): 4,53 WARNING @ Tue, 16 Jun 2020 08:23:52: #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 08:23:52: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:23:52: #3 Pre-compute pvalue-qvalue table... 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 08:23:56: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX2761380/SRX2761380.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX2761380/SRX2761380.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX2761380/SRX2761380.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX2761380/SRX2761380.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 08:23:56: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:23:56: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:23:59: 4000000 INFO @ Tue, 16 Jun 2020 08:24:05: 1000000 INFO @ Tue, 16 Jun 2020 08:24:07: 5000000 INFO @ Tue, 16 Jun 2020 08:24:08: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 08:24:12: 2000000 INFO @ Tue, 16 Jun 2020 08:24:15: 6000000 INFO @ Tue, 16 Jun 2020 08:24:16: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX2761380/SRX2761380.05_peaks.xls INFO @ Tue, 16 Jun 2020 08:24:16: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX2761380/SRX2761380.05_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:24:16: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX2761380/SRX2761380.05_summits.bed INFO @ Tue, 16 Jun 2020 08:24:16: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (798 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 08:24:20: 3000000 INFO @ Tue, 16 Jun 2020 08:24:21: #1 tag size is determined as 51 bps INFO @ Tue, 16 Jun 2020 08:24:21: #1 tag size = 51 INFO @ Tue, 16 Jun 2020 08:24:21: #1 total tags in treatment: 6808977 INFO @ Tue, 16 Jun 2020 08:24:21: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:24:21: #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 08:24:21: #1 tags after filtering in treatment: 6808977 INFO @ Tue, 16 Jun 2020 08:24:21: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:24:21: #1 finished! INFO @ Tue, 16 Jun 2020 08:24:21: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:24:21: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:24:21: #2 number of paired peaks: 631 WARNING @ Tue, 16 Jun 2020 08:24:21: Fewer paired peaks (631) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 631 pairs to build model! INFO @ Tue, 16 Jun 2020 08:24:21: start model_add_line... INFO @ Tue, 16 Jun 2020 08:24:21: start X-correlation... INFO @ Tue, 16 Jun 2020 08:24:21: end of X-cor INFO @ Tue, 16 Jun 2020 08:24:21: #2 finished! INFO @ Tue, 16 Jun 2020 08:24:21: #2 predicted fragment length is 53 bps INFO @ Tue, 16 Jun 2020 08:24:21: #2 alternative fragment length(s) may be 4,53 bps INFO @ Tue, 16 Jun 2020 08:24:21: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX2761380/SRX2761380.10_model.r WARNING @ Tue, 16 Jun 2020 08:24:21: #2 Since the d (53) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 08:24:21: #2 You may need to consider one of the other alternative d(s): 4,53 WARNING @ Tue, 16 Jun 2020 08:24:21: #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 08:24:21: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:24:21: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 08:24:28: 4000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 16 Jun 2020 08:24:35: 5000000 INFO @ Tue, 16 Jun 2020 08:24:37: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 08:24:42: 6000000 INFO @ Tue, 16 Jun 2020 08:24:46: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX2761380/SRX2761380.10_peaks.xls INFO @ Tue, 16 Jun 2020 08:24:46: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX2761380/SRX2761380.10_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:24:46: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX2761380/SRX2761380.10_summits.bed INFO @ Tue, 16 Jun 2020 08:24:46: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (448 records, 4 fields): 1 millis CompletedMACS2peakCalling BigWig に変換しました。 INFO @ Tue, 16 Jun 2020 08:24:48: #1 tag size is determined as 51 bps INFO @ Tue, 16 Jun 2020 08:24:48: #1 tag size = 51 INFO @ Tue, 16 Jun 2020 08:24:48: #1 total tags in treatment: 6808977 INFO @ Tue, 16 Jun 2020 08:24:48: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:24:48: #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 08:24:48: #1 tags after filtering in treatment: 6808977 INFO @ Tue, 16 Jun 2020 08:24:48: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:24:48: #1 finished! INFO @ Tue, 16 Jun 2020 08:24:48: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:24:48: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:24:49: #2 number of paired peaks: 631 WARNING @ Tue, 16 Jun 2020 08:24:49: Fewer paired peaks (631) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 631 pairs to build model! INFO @ Tue, 16 Jun 2020 08:24:49: start model_add_line... INFO @ Tue, 16 Jun 2020 08:24:49: start X-correlation... INFO @ Tue, 16 Jun 2020 08:24:49: end of X-cor INFO @ Tue, 16 Jun 2020 08:24:49: #2 finished! INFO @ Tue, 16 Jun 2020 08:24:49: #2 predicted fragment length is 53 bps INFO @ Tue, 16 Jun 2020 08:24:49: #2 alternative fragment length(s) may be 4,53 bps INFO @ Tue, 16 Jun 2020 08:24:49: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX2761380/SRX2761380.20_model.r WARNING @ Tue, 16 Jun 2020 08:24:49: #2 Since the d (53) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 08:24:49: #2 You may need to consider one of the other alternative d(s): 4,53 WARNING @ Tue, 16 Jun 2020 08:24:49: #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 08:24:49: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:24:49: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 08:25:04: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 08:25:12: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX2761380/SRX2761380.20_peaks.xls INFO @ Tue, 16 Jun 2020 08:25:12: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX2761380/SRX2761380.20_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:25:12: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX2761380/SRX2761380.20_summits.bed INFO @ Tue, 16 Jun 2020 08:25:12: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (189 records, 4 fields): 1 millis CompletedMACS2peakCalling