Job ID = 6365953 SRX = SRX043965 Genome = ce11 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-15T22:19:14 prefetch.2.10.7: 1) Downloading 'SRR107538'... 2020-06-15T22:19:14 prefetch.2.10.7: Downloading via HTTPS... 2020-06-15T22:19:50 prefetch.2.10.7: HTTPS download succeed 2020-06-15T22:19:50 prefetch.2.10.7: 'SRR107538' is valid 2020-06-15T22:19:50 prefetch.2.10.7: 1) 'SRR107538' was downloaded successfully Read 3926903 spots for SRR107538/SRR107538.sra Written 3926903 spots for SRR107538/SRR107538.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: 00:00:39 3926903 reads; of these: 3926903 (100.00%) were unpaired; of these: 1327710 (33.81%) aligned 0 times 2238560 (57.01%) aligned exactly 1 time 360633 (9.18%) aligned >1 times 66.19% overall alignment rate Time searching: 00:00:39 Overall time: 00:00:39 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] 171099 / 2599193 = 0.0658 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 07:21:59: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX043965/SRX043965.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX043965/SRX043965.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX043965/SRX043965.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX043965/SRX043965.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 07:21:59: #1 read tag files... INFO @ Tue, 16 Jun 2020 07:21:59: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 07:22:05: 1000000 INFO @ Tue, 16 Jun 2020 07:22:11: 2000000 INFO @ Tue, 16 Jun 2020 07:22:14: #1 tag size is determined as 34 bps INFO @ Tue, 16 Jun 2020 07:22:14: #1 tag size = 34 INFO @ Tue, 16 Jun 2020 07:22:14: #1 total tags in treatment: 2428094 INFO @ Tue, 16 Jun 2020 07:22:14: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 07:22:14: #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 07:22:14: #1 tags after filtering in treatment: 2428094 INFO @ Tue, 16 Jun 2020 07:22:14: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 07:22:14: #1 finished! INFO @ Tue, 16 Jun 2020 07:22:14: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 07:22:14: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 07:22:14: #2 number of paired peaks: 295 WARNING @ Tue, 16 Jun 2020 07:22:14: Fewer paired peaks (295) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 295 pairs to build model! INFO @ Tue, 16 Jun 2020 07:22:14: start model_add_line... INFO @ Tue, 16 Jun 2020 07:22:14: start X-correlation... INFO @ Tue, 16 Jun 2020 07:22:14: end of X-cor INFO @ Tue, 16 Jun 2020 07:22:14: #2 finished! INFO @ Tue, 16 Jun 2020 07:22:14: #2 predicted fragment length is 37 bps INFO @ Tue, 16 Jun 2020 07:22:14: #2 alternative fragment length(s) may be 4,37,520,538,563,597 bps INFO @ Tue, 16 Jun 2020 07:22:14: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX043965/SRX043965.05_model.r WARNING @ Tue, 16 Jun 2020 07:22:14: #2 Since the d (37) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 07:22:14: #2 You may need to consider one of the other alternative d(s): 4,37,520,538,563,597 WARNING @ Tue, 16 Jun 2020 07:22:14: #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 07:22:14: #3 Call peaks... INFO @ Tue, 16 Jun 2020 07:22:14: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 07:22:20: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 07:22:23: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX043965/SRX043965.05_peaks.xls INFO @ Tue, 16 Jun 2020 07:22:23: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX043965/SRX043965.05_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 07:22:23: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX043965/SRX043965.05_summits.bed INFO @ Tue, 16 Jun 2020 07:22:23: Done! pass1 - making usageList (7 chroms): 0 millis pass2 - checking and writing primary data (233 records, 4 fields): 2 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 07:22:29: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX043965/SRX043965.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX043965/SRX043965.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX043965/SRX043965.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX043965/SRX043965.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 07:22:29: #1 read tag files... INFO @ Tue, 16 Jun 2020 07:22:29: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 07:22:36: 1000000 INFO @ Tue, 16 Jun 2020 07:22:43: 2000000 INFO @ Tue, 16 Jun 2020 07:22:46: #1 tag size is determined as 34 bps INFO @ Tue, 16 Jun 2020 07:22:46: #1 tag size = 34 INFO @ Tue, 16 Jun 2020 07:22:46: #1 total tags in treatment: 2428094 INFO @ Tue, 16 Jun 2020 07:22:46: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 07:22:46: #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 07:22:46: #1 tags after filtering in treatment: 2428094 INFO @ Tue, 16 Jun 2020 07:22:46: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 07:22:46: #1 finished! INFO @ Tue, 16 Jun 2020 07:22:46: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 07:22:46: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 07:22:46: #2 number of paired peaks: 295 WARNING @ Tue, 16 Jun 2020 07:22:46: Fewer paired peaks (295) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 295 pairs to build model! INFO @ Tue, 16 Jun 2020 07:22:46: start model_add_line... INFO @ Tue, 16 Jun 2020 07:22:46: start X-correlation... INFO @ Tue, 16 Jun 2020 07:22:46: end of X-cor INFO @ Tue, 16 Jun 2020 07:22:46: #2 finished! INFO @ Tue, 16 Jun 2020 07:22:46: #2 predicted fragment length is 37 bps INFO @ Tue, 16 Jun 2020 07:22:46: #2 alternative fragment length(s) may be 4,37,520,538,563,597 bps INFO @ Tue, 16 Jun 2020 07:22:46: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX043965/SRX043965.10_model.r WARNING @ Tue, 16 Jun 2020 07:22:46: #2 Since the d (37) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 07:22:46: #2 You may need to consider one of the other alternative d(s): 4,37,520,538,563,597 WARNING @ Tue, 16 Jun 2020 07:22:46: #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 07:22:46: #3 Call peaks... INFO @ Tue, 16 Jun 2020 07:22:46: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 07:22:52: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 07:22:55: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX043965/SRX043965.10_peaks.xls INFO @ Tue, 16 Jun 2020 07:22:55: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX043965/SRX043965.10_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 07:22:55: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX043965/SRX043965.10_summits.bed INFO @ Tue, 16 Jun 2020 07:22:55: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (93 records, 4 fields): 2 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 07:22:59: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX043965/SRX043965.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX043965/SRX043965.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX043965/SRX043965.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX043965/SRX043965.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 07:22:59: #1 read tag files... INFO @ Tue, 16 Jun 2020 07:22:59: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 07:23:06: 1000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 16 Jun 2020 07:23:13: 2000000 INFO @ Tue, 16 Jun 2020 07:23:16: #1 tag size is determined as 34 bps INFO @ Tue, 16 Jun 2020 07:23:16: #1 tag size = 34 INFO @ Tue, 16 Jun 2020 07:23:16: #1 total tags in treatment: 2428094 INFO @ Tue, 16 Jun 2020 07:23:16: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 07:23:16: #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 07:23:16: #1 tags after filtering in treatment: 2428094 INFO @ Tue, 16 Jun 2020 07:23:16: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 07:23:16: #1 finished! INFO @ Tue, 16 Jun 2020 07:23:16: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 07:23:16: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 07:23:16: #2 number of paired peaks: 295 WARNING @ Tue, 16 Jun 2020 07:23:16: Fewer paired peaks (295) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 295 pairs to build model! INFO @ Tue, 16 Jun 2020 07:23:16: start model_add_line... INFO @ Tue, 16 Jun 2020 07:23:16: start X-correlation... INFO @ Tue, 16 Jun 2020 07:23:16: end of X-cor INFO @ Tue, 16 Jun 2020 07:23:16: #2 finished! INFO @ Tue, 16 Jun 2020 07:23:16: #2 predicted fragment length is 37 bps INFO @ Tue, 16 Jun 2020 07:23:16: #2 alternative fragment length(s) may be 4,37,520,538,563,597 bps INFO @ Tue, 16 Jun 2020 07:23:16: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX043965/SRX043965.20_model.r WARNING @ Tue, 16 Jun 2020 07:23:16: #2 Since the d (37) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 07:23:16: #2 You may need to consider one of the other alternative d(s): 4,37,520,538,563,597 WARNING @ Tue, 16 Jun 2020 07:23:16: #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 07:23:16: #3 Call peaks... INFO @ Tue, 16 Jun 2020 07:23:16: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Tue, 16 Jun 2020 07:23:22: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 07:23:25: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX043965/SRX043965.20_peaks.xls INFO @ Tue, 16 Jun 2020 07:23:25: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX043965/SRX043965.20_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 07:23:25: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX043965/SRX043965.20_summits.bed INFO @ Tue, 16 Jun 2020 07:23:25: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (14 records, 4 fields): 1 millis CompletedMACS2peakCalling