Job ID = 6366733 SRX = SRX2228886 Genome = ce11 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-15T23:31:50 prefetch.2.10.7: 1) Downloading 'SRR4380342'... 2020-06-15T23:31:50 prefetch.2.10.7: Downloading via HTTPS... 2020-06-15T23:32:43 prefetch.2.10.7: HTTPS download succeed 2020-06-15T23:32:44 prefetch.2.10.7: 'SRR4380342' is valid 2020-06-15T23:32:44 prefetch.2.10.7: 1) 'SRR4380342' was downloaded successfully 2020-06-15T23:32:44 prefetch.2.10.7: 'SRR4380342' has 0 unresolved dependencies Read 6284733 spots for SRR4380342/SRR4380342.sra Written 6284733 spots for SRR4380342/SRR4380342.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: 00:00:51 6284733 reads; of these: 6284733 (100.00%) were unpaired; of these: 3634018 (57.82%) aligned 0 times 2201653 (35.03%) aligned exactly 1 time 449062 (7.15%) aligned >1 times 42.18% overall alignment rate Time searching: 00:00:52 Overall time: 00:00:52 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] 652429 / 2650715 = 0.2461 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 08:35:01: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX2228886/SRX2228886.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX2228886/SRX2228886.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX2228886/SRX2228886.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX2228886/SRX2228886.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 08:35:01: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:35:01: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:35:06: 1000000 INFO @ Tue, 16 Jun 2020 08:35:11: #1 tag size is determined as 51 bps INFO @ Tue, 16 Jun 2020 08:35:11: #1 tag size = 51 INFO @ Tue, 16 Jun 2020 08:35:11: #1 total tags in treatment: 1998286 INFO @ Tue, 16 Jun 2020 08:35:11: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:35:11: #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 08:35:11: #1 tags after filtering in treatment: 1998286 INFO @ Tue, 16 Jun 2020 08:35:11: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:35:11: #1 finished! INFO @ Tue, 16 Jun 2020 08:35:11: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:35:11: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:35:11: #2 number of paired peaks: 510 WARNING @ Tue, 16 Jun 2020 08:35:11: Fewer paired peaks (510) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 510 pairs to build model! INFO @ Tue, 16 Jun 2020 08:35:11: start model_add_line... INFO @ Tue, 16 Jun 2020 08:35:11: start X-correlation... INFO @ Tue, 16 Jun 2020 08:35:11: end of X-cor INFO @ Tue, 16 Jun 2020 08:35:11: #2 finished! INFO @ Tue, 16 Jun 2020 08:35:11: #2 predicted fragment length is 53 bps INFO @ Tue, 16 Jun 2020 08:35:11: #2 alternative fragment length(s) may be 53 bps INFO @ Tue, 16 Jun 2020 08:35:11: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX2228886/SRX2228886.05_model.r WARNING @ Tue, 16 Jun 2020 08:35:12: #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 08:35:12: #2 You may need to consider one of the other alternative d(s): 53 WARNING @ Tue, 16 Jun 2020 08:35:12: #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 08:35:12: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:35:12: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 08:35:16: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 08:35:18: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX2228886/SRX2228886.05_peaks.xls INFO @ Tue, 16 Jun 2020 08:35:18: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX2228886/SRX2228886.05_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:35:18: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX2228886/SRX2228886.05_summits.bed INFO @ Tue, 16 Jun 2020 08:35:18: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (343 records, 4 fields): 1 millis CompletedMACS2peakCalling 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 08:35:31: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX2228886/SRX2228886.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX2228886/SRX2228886.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX2228886/SRX2228886.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX2228886/SRX2228886.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 08:35:31: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:35:31: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:35:36: 1000000 INFO @ Tue, 16 Jun 2020 08:35:41: #1 tag size is determined as 51 bps INFO @ Tue, 16 Jun 2020 08:35:41: #1 tag size = 51 INFO @ Tue, 16 Jun 2020 08:35:41: #1 total tags in treatment: 1998286 INFO @ Tue, 16 Jun 2020 08:35:41: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:35:41: #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 08:35:41: #1 tags after filtering in treatment: 1998286 INFO @ Tue, 16 Jun 2020 08:35:41: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:35:41: #1 finished! INFO @ Tue, 16 Jun 2020 08:35:41: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:35:41: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:35:41: #2 number of paired peaks: 510 WARNING @ Tue, 16 Jun 2020 08:35:41: Fewer paired peaks (510) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 510 pairs to build model! INFO @ Tue, 16 Jun 2020 08:35:41: start model_add_line... INFO @ Tue, 16 Jun 2020 08:35:41: start X-correlation... INFO @ Tue, 16 Jun 2020 08:35:41: end of X-cor INFO @ Tue, 16 Jun 2020 08:35:41: #2 finished! INFO @ Tue, 16 Jun 2020 08:35:41: #2 predicted fragment length is 53 bps INFO @ Tue, 16 Jun 2020 08:35:41: #2 alternative fragment length(s) may be 53 bps INFO @ Tue, 16 Jun 2020 08:35:41: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX2228886/SRX2228886.10_model.r WARNING @ Tue, 16 Jun 2020 08:35:41: #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 08:35:41: #2 You may need to consider one of the other alternative d(s): 53 WARNING @ Tue, 16 Jun 2020 08:35:41: #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 08:35:41: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:35:41: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 08:35:46: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 08:35:48: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX2228886/SRX2228886.10_peaks.xls INFO @ Tue, 16 Jun 2020 08:35:48: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX2228886/SRX2228886.10_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:35:48: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX2228886/SRX2228886.10_summits.bed INFO @ Tue, 16 Jun 2020 08:35:48: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (211 records, 4 fields): 1 millis CompletedMACS2peakCalling 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 08:36:01: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX2228886/SRX2228886.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX2228886/SRX2228886.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX2228886/SRX2228886.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX2228886/SRX2228886.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 08:36:01: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:36:01: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:36:06: 1000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 16 Jun 2020 08:36:11: #1 tag size is determined as 51 bps INFO @ Tue, 16 Jun 2020 08:36:11: #1 tag size = 51 INFO @ Tue, 16 Jun 2020 08:36:11: #1 total tags in treatment: 1998286 INFO @ Tue, 16 Jun 2020 08:36:11: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:36:11: #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 08:36:11: #1 tags after filtering in treatment: 1998286 INFO @ Tue, 16 Jun 2020 08:36:11: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:36:11: #1 finished! INFO @ Tue, 16 Jun 2020 08:36:11: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:36:11: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:36:12: #2 number of paired peaks: 510 WARNING @ Tue, 16 Jun 2020 08:36:12: Fewer paired peaks (510) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 510 pairs to build model! INFO @ Tue, 16 Jun 2020 08:36:12: start model_add_line... INFO @ Tue, 16 Jun 2020 08:36:12: start X-correlation... INFO @ Tue, 16 Jun 2020 08:36:12: end of X-cor INFO @ Tue, 16 Jun 2020 08:36:12: #2 finished! INFO @ Tue, 16 Jun 2020 08:36:12: #2 predicted fragment length is 53 bps INFO @ Tue, 16 Jun 2020 08:36:12: #2 alternative fragment length(s) may be 53 bps INFO @ Tue, 16 Jun 2020 08:36:12: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX2228886/SRX2228886.20_model.r WARNING @ Tue, 16 Jun 2020 08:36:12: #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 08:36:12: #2 You may need to consider one of the other alternative d(s): 53 WARNING @ Tue, 16 Jun 2020 08:36:12: #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 08:36:12: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:36:12: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Tue, 16 Jun 2020 08:36:16: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 08:36:18: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX2228886/SRX2228886.20_peaks.xls INFO @ Tue, 16 Jun 2020 08:36:18: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX2228886/SRX2228886.20_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:36:18: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX2228886/SRX2228886.20_summits.bed INFO @ Tue, 16 Jun 2020 08:36:18: Done! pass1 - making usageList (6 chroms): 2 millis pass2 - checking and writing primary data (92 records, 4 fields): 1 millis CompletedMACS2peakCalling