Job ID = 6368555 SRX = SRX5020782 Genome = ce11 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-16T00:14:20 prefetch.2.10.7: 1) Downloading 'SRR8201405'... 2020-06-16T00:14:20 prefetch.2.10.7: Downloading via HTTPS... 2020-06-16T00:15:23 prefetch.2.10.7: HTTPS download succeed 2020-06-16T00:15:24 prefetch.2.10.7: 'SRR8201405' is valid 2020-06-16T00:15:24 prefetch.2.10.7: 1) 'SRR8201405' was downloaded successfully Read 6376353 spots for SRR8201405/SRR8201405.sra Written 6376353 spots for SRR8201405/SRR8201405.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: 00:01:17 6376353 reads; of these: 6376353 (100.00%) were unpaired; of these: 987725 (15.49%) aligned 0 times 4447452 (69.75%) aligned exactly 1 time 941176 (14.76%) aligned >1 times 84.51% overall alignment rate Time searching: 00:01:17 Overall time: 00:01:17 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] 516540 / 5388628 = 0.0959 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 09:18:51: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX5020782/SRX5020782.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX5020782/SRX5020782.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX5020782/SRX5020782.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX5020782/SRX5020782.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 09:18:51: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:18:51: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:18:57: 1000000 INFO @ Tue, 16 Jun 2020 09:19:03: 2000000 INFO @ Tue, 16 Jun 2020 09:19:09: 3000000 INFO @ Tue, 16 Jun 2020 09:19:15: 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 09:19:20: #1 tag size is determined as 51 bps INFO @ Tue, 16 Jun 2020 09:19:20: #1 tag size = 51 INFO @ Tue, 16 Jun 2020 09:19:20: #1 total tags in treatment: 4872088 INFO @ Tue, 16 Jun 2020 09:19:20: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:19:20: #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 09:19:20: #1 tags after filtering in treatment: 4872088 INFO @ Tue, 16 Jun 2020 09:19:20: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 09:19:20: #1 finished! INFO @ Tue, 16 Jun 2020 09:19:20: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:19:20: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:19:21: #2 number of paired peaks: 528 WARNING @ Tue, 16 Jun 2020 09:19:21: Fewer paired peaks (528) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 528 pairs to build model! INFO @ Tue, 16 Jun 2020 09:19:21: start model_add_line... INFO @ Tue, 16 Jun 2020 09:19:21: start X-correlation... INFO @ Tue, 16 Jun 2020 09:19:21: end of X-cor INFO @ Tue, 16 Jun 2020 09:19:21: #2 finished! INFO @ Tue, 16 Jun 2020 09:19:21: #2 predicted fragment length is 58 bps INFO @ Tue, 16 Jun 2020 09:19:21: #2 alternative fragment length(s) may be 58,123 bps INFO @ Tue, 16 Jun 2020 09:19:21: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX5020782/SRX5020782.05_model.r WARNING @ Tue, 16 Jun 2020 09:19:21: #2 Since the d (58) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 09:19:21: #2 You may need to consider one of the other alternative d(s): 58,123 WARNING @ Tue, 16 Jun 2020 09:19:21: #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 09:19:21: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:19:21: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 09:19:21: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX5020782/SRX5020782.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX5020782/SRX5020782.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX5020782/SRX5020782.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX5020782/SRX5020782.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 09:19:21: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:19:21: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:19:27: 1000000 INFO @ Tue, 16 Jun 2020 09:19:31: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 09:19:33: 2000000 INFO @ Tue, 16 Jun 2020 09:19:36: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX5020782/SRX5020782.05_peaks.xls INFO @ Tue, 16 Jun 2020 09:19:36: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX5020782/SRX5020782.05_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:19:36: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX5020782/SRX5020782.05_summits.bed INFO @ Tue, 16 Jun 2020 09:19:36: Done! pass1 - making usageList (7 chroms): 0 millis pass2 - checking and writing primary data (795 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 09:19:39: 3000000 INFO @ Tue, 16 Jun 2020 09:19:45: 4000000 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 09:19:50: #1 tag size is determined as 51 bps INFO @ Tue, 16 Jun 2020 09:19:50: #1 tag size = 51 INFO @ Tue, 16 Jun 2020 09:19:50: #1 total tags in treatment: 4872088 INFO @ Tue, 16 Jun 2020 09:19:50: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:19:50: #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 09:19:50: #1 tags after filtering in treatment: 4872088 INFO @ Tue, 16 Jun 2020 09:19:50: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 09:19:50: #1 finished! INFO @ Tue, 16 Jun 2020 09:19:50: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:19:50: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:19:50: #2 number of paired peaks: 528 WARNING @ Tue, 16 Jun 2020 09:19:50: Fewer paired peaks (528) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 528 pairs to build model! INFO @ Tue, 16 Jun 2020 09:19:50: start model_add_line... INFO @ Tue, 16 Jun 2020 09:19:50: start X-correlation... INFO @ Tue, 16 Jun 2020 09:19:50: end of X-cor INFO @ Tue, 16 Jun 2020 09:19:50: #2 finished! INFO @ Tue, 16 Jun 2020 09:19:50: #2 predicted fragment length is 58 bps INFO @ Tue, 16 Jun 2020 09:19:50: #2 alternative fragment length(s) may be 58,123 bps INFO @ Tue, 16 Jun 2020 09:19:50: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX5020782/SRX5020782.10_model.r WARNING @ Tue, 16 Jun 2020 09:19:50: #2 Since the d (58) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 09:19:50: #2 You may need to consider one of the other alternative d(s): 58,123 WARNING @ Tue, 16 Jun 2020 09:19:50: #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 09:19:50: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:19:50: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 09:19:51: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX5020782/SRX5020782.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX5020782/SRX5020782.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX5020782/SRX5020782.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX5020782/SRX5020782.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 09:19:51: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:19:51: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:19:57: 1000000 INFO @ Tue, 16 Jun 2020 09:20:00: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 09:20:03: 2000000 INFO @ Tue, 16 Jun 2020 09:20:06: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX5020782/SRX5020782.10_peaks.xls INFO @ Tue, 16 Jun 2020 09:20:06: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX5020782/SRX5020782.10_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:20:06: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX5020782/SRX5020782.10_summits.bed INFO @ Tue, 16 Jun 2020 09:20:06: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (434 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 09:20:09: 3000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 16 Jun 2020 09:20:15: 4000000 INFO @ Tue, 16 Jun 2020 09:20:20: #1 tag size is determined as 51 bps INFO @ Tue, 16 Jun 2020 09:20:20: #1 tag size = 51 INFO @ Tue, 16 Jun 2020 09:20:20: #1 total tags in treatment: 4872088 INFO @ Tue, 16 Jun 2020 09:20:20: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:20:20: #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 09:20:20: #1 tags after filtering in treatment: 4872088 INFO @ Tue, 16 Jun 2020 09:20:20: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 09:20:20: #1 finished! INFO @ Tue, 16 Jun 2020 09:20:20: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:20:20: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:20:20: #2 number of paired peaks: 528 WARNING @ Tue, 16 Jun 2020 09:20:20: Fewer paired peaks (528) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 528 pairs to build model! INFO @ Tue, 16 Jun 2020 09:20:20: start model_add_line... INFO @ Tue, 16 Jun 2020 09:20:20: start X-correlation... INFO @ Tue, 16 Jun 2020 09:20:20: end of X-cor INFO @ Tue, 16 Jun 2020 09:20:20: #2 finished! INFO @ Tue, 16 Jun 2020 09:20:20: #2 predicted fragment length is 58 bps INFO @ Tue, 16 Jun 2020 09:20:20: #2 alternative fragment length(s) may be 58,123 bps INFO @ Tue, 16 Jun 2020 09:20:20: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX5020782/SRX5020782.20_model.r WARNING @ Tue, 16 Jun 2020 09:20:20: #2 Since the d (58) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 09:20:20: #2 You may need to consider one of the other alternative d(s): 58,123 WARNING @ Tue, 16 Jun 2020 09:20:20: #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 09:20:20: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:20:20: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Tue, 16 Jun 2020 09:20:30: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 09:20:35: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX5020782/SRX5020782.20_peaks.xls INFO @ Tue, 16 Jun 2020 09:20:35: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX5020782/SRX5020782.20_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:20:35: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX5020782/SRX5020782.20_summits.bed INFO @ Tue, 16 Jun 2020 09:20:35: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (176 records, 4 fields): 2 millis CompletedMACS2peakCalling