Job ID = 6367938 SRX = SRX4344417 Genome = ce11 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-16T00:12:35 prefetch.2.10.7: 1) Downloading 'SRR7474962'... 2020-06-16T00:12:35 prefetch.2.10.7: Downloading via HTTPS... 2020-06-16T00:13:47 prefetch.2.10.7: HTTPS download succeed 2020-06-16T00:13:48 prefetch.2.10.7: 'SRR7474962' is valid 2020-06-16T00:13:48 prefetch.2.10.7: 1) 'SRR7474962' was downloaded successfully 2020-06-16T00:13:48 prefetch.2.10.7: 'SRR7474962' has 0 unresolved dependencies Read 16448041 spots for SRR7474962/SRR7474962.sra Written 16448041 spots for SRR7474962/SRR7474962.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: 00:03:15 16448041 reads; of these: 16448041 (100.00%) were unpaired; of these: 2371688 (14.42%) aligned 0 times 11900886 (72.35%) aligned exactly 1 time 2175467 (13.23%) aligned >1 times 85.58% overall alignment rate Time searching: 00:03:15 Overall time: 00:03:15 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] 7534678 / 14076353 = 0.5353 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 09:21:07: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX4344417/SRX4344417.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX4344417/SRX4344417.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX4344417/SRX4344417.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX4344417/SRX4344417.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 09:21:07: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:21:07: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:21:13: 1000000 INFO @ Tue, 16 Jun 2020 09:21:19: 2000000 INFO @ Tue, 16 Jun 2020 09:21:25: 3000000 INFO @ Tue, 16 Jun 2020 09:21:31: 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 09:21:36: 5000000 INFO @ Tue, 16 Jun 2020 09:21:37: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX4344417/SRX4344417.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX4344417/SRX4344417.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX4344417/SRX4344417.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX4344417/SRX4344417.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 09:21:37: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:21:37: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:21:42: 6000000 INFO @ Tue, 16 Jun 2020 09:21:42: 1000000 INFO @ Tue, 16 Jun 2020 09:21:45: #1 tag size is determined as 50 bps INFO @ Tue, 16 Jun 2020 09:21:45: #1 tag size = 50 INFO @ Tue, 16 Jun 2020 09:21:45: #1 total tags in treatment: 6541675 INFO @ Tue, 16 Jun 2020 09:21:45: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:21:45: #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 09:21:45: #1 tags after filtering in treatment: 6541675 INFO @ Tue, 16 Jun 2020 09:21:45: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 09:21:45: #1 finished! INFO @ Tue, 16 Jun 2020 09:21:45: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:21:45: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:21:46: #2 number of paired peaks: 566 WARNING @ Tue, 16 Jun 2020 09:21:46: Fewer paired peaks (566) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 566 pairs to build model! INFO @ Tue, 16 Jun 2020 09:21:46: start model_add_line... INFO @ Tue, 16 Jun 2020 09:21:46: start X-correlation... INFO @ Tue, 16 Jun 2020 09:21:46: end of X-cor INFO @ Tue, 16 Jun 2020 09:21:46: #2 finished! INFO @ Tue, 16 Jun 2020 09:21:46: #2 predicted fragment length is 57 bps INFO @ Tue, 16 Jun 2020 09:21:46: #2 alternative fragment length(s) may be 4,57 bps INFO @ Tue, 16 Jun 2020 09:21:46: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX4344417/SRX4344417.05_model.r WARNING @ Tue, 16 Jun 2020 09:21:46: #2 Since the d (57) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 09:21:46: #2 You may need to consider one of the other alternative d(s): 4,57 WARNING @ Tue, 16 Jun 2020 09:21:46: #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 09:21:46: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:21:46: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 09:21:48: 2000000 INFO @ Tue, 16 Jun 2020 09:21:53: 3000000 INFO @ Tue, 16 Jun 2020 09:21:58: 4000000 INFO @ Tue, 16 Jun 2020 09:22:01: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 09:22:03: 5000000 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 09:22:07: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX4344417/SRX4344417.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX4344417/SRX4344417.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX4344417/SRX4344417.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX4344417/SRX4344417.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 09:22:07: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:22:07: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:22:09: 6000000 INFO @ Tue, 16 Jun 2020 09:22:09: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX4344417/SRX4344417.05_peaks.xls INFO @ Tue, 16 Jun 2020 09:22:09: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX4344417/SRX4344417.05_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:22:09: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX4344417/SRX4344417.05_summits.bed INFO @ Tue, 16 Jun 2020 09:22:09: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (1077 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 09:22:12: #1 tag size is determined as 50 bps INFO @ Tue, 16 Jun 2020 09:22:12: #1 tag size = 50 INFO @ Tue, 16 Jun 2020 09:22:12: #1 total tags in treatment: 6541675 INFO @ Tue, 16 Jun 2020 09:22:12: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:22:12: #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 09:22:12: #1 tags after filtering in treatment: 6541675 INFO @ Tue, 16 Jun 2020 09:22:12: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 09:22:12: #1 finished! INFO @ Tue, 16 Jun 2020 09:22:12: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:22:12: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:22:12: #2 number of paired peaks: 566 WARNING @ Tue, 16 Jun 2020 09:22:12: Fewer paired peaks (566) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 566 pairs to build model! INFO @ Tue, 16 Jun 2020 09:22:12: start model_add_line... INFO @ Tue, 16 Jun 2020 09:22:12: start X-correlation... INFO @ Tue, 16 Jun 2020 09:22:12: end of X-cor INFO @ Tue, 16 Jun 2020 09:22:12: #2 finished! INFO @ Tue, 16 Jun 2020 09:22:12: #2 predicted fragment length is 57 bps INFO @ Tue, 16 Jun 2020 09:22:12: #2 alternative fragment length(s) may be 4,57 bps INFO @ Tue, 16 Jun 2020 09:22:12: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX4344417/SRX4344417.10_model.r WARNING @ Tue, 16 Jun 2020 09:22:12: #2 Since the d (57) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 09:22:12: #2 You may need to consider one of the other alternative d(s): 4,57 WARNING @ Tue, 16 Jun 2020 09:22:12: #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 09:22:12: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:22:12: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 09:22:12: 1000000 INFO @ Tue, 16 Jun 2020 09:22:18: 2000000 INFO @ Tue, 16 Jun 2020 09:22:23: 3000000 INFO @ Tue, 16 Jun 2020 09:22:28: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 09:22:28: 4000000 INFO @ Tue, 16 Jun 2020 09:22:33: 5000000 INFO @ Tue, 16 Jun 2020 09:22:36: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX4344417/SRX4344417.10_peaks.xls INFO @ Tue, 16 Jun 2020 09:22:36: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX4344417/SRX4344417.10_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:22:36: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX4344417/SRX4344417.10_summits.bed INFO @ Tue, 16 Jun 2020 09:22:36: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (608 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 09:22:39: 6000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 16 Jun 2020 09:22:41: #1 tag size is determined as 50 bps INFO @ Tue, 16 Jun 2020 09:22:41: #1 tag size = 50 INFO @ Tue, 16 Jun 2020 09:22:41: #1 total tags in treatment: 6541675 INFO @ Tue, 16 Jun 2020 09:22:41: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:22:41: #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 09:22:41: #1 tags after filtering in treatment: 6541675 INFO @ Tue, 16 Jun 2020 09:22:41: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 09:22:41: #1 finished! INFO @ Tue, 16 Jun 2020 09:22:41: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:22:41: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:22:42: #2 number of paired peaks: 566 WARNING @ Tue, 16 Jun 2020 09:22:42: Fewer paired peaks (566) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 566 pairs to build model! INFO @ Tue, 16 Jun 2020 09:22:42: start model_add_line... INFO @ Tue, 16 Jun 2020 09:22:42: start X-correlation... INFO @ Tue, 16 Jun 2020 09:22:42: end of X-cor INFO @ Tue, 16 Jun 2020 09:22:42: #2 finished! INFO @ Tue, 16 Jun 2020 09:22:42: #2 predicted fragment length is 57 bps INFO @ Tue, 16 Jun 2020 09:22:42: #2 alternative fragment length(s) may be 4,57 bps INFO @ Tue, 16 Jun 2020 09:22:42: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX4344417/SRX4344417.20_model.r WARNING @ Tue, 16 Jun 2020 09:22:42: #2 Since the d (57) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 09:22:42: #2 You may need to consider one of the other alternative d(s): 4,57 WARNING @ Tue, 16 Jun 2020 09:22:42: #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 09:22:42: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:22:42: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Tue, 16 Jun 2020 09:22:58: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 09:23:05: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX4344417/SRX4344417.20_peaks.xls INFO @ Tue, 16 Jun 2020 09:23:05: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX4344417/SRX4344417.20_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:23:05: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX4344417/SRX4344417.20_summits.bed INFO @ Tue, 16 Jun 2020 09:23:05: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (242 records, 4 fields): 1 millis CompletedMACS2peakCalling