Job ID = 6366820 SRX = SRX2350719 Genome = ce11 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-15T23:04:08 prefetch.2.10.7: 1) Downloading 'SRR5024028'... 2020-06-15T23:04:08 prefetch.2.10.7: Downloading via HTTPS... 2020-06-15T23:05:16 prefetch.2.10.7: HTTPS download succeed 2020-06-15T23:05:17 prefetch.2.10.7: 'SRR5024028' is valid 2020-06-15T23:05:17 prefetch.2.10.7: 1) 'SRR5024028' was downloaded successfully Read 10290698 spots for SRR5024028/SRR5024028.sra Written 10290698 spots for SRR5024028/SRR5024028.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: 00:02:26 10290698 reads; of these: 10290698 (100.00%) were unpaired; of these: 539195 (5.24%) aligned 0 times 7192353 (69.89%) aligned exactly 1 time 2559150 (24.87%) aligned >1 times 94.76% overall alignment rate Time searching: 00:02:26 Overall time: 00:02:26 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] 1305796 / 9751503 = 0.1339 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 08:10:56: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX2350719/SRX2350719.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX2350719/SRX2350719.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX2350719/SRX2350719.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX2350719/SRX2350719.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 08:10:56: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:10:56: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:11:04: 1000000 INFO @ Tue, 16 Jun 2020 08:11:11: 2000000 INFO @ Tue, 16 Jun 2020 08:11:19: 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 08:11:26: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX2350719/SRX2350719.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX2350719/SRX2350719.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX2350719/SRX2350719.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX2350719/SRX2350719.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 08:11:26: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:11:26: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:11:27: 4000000 INFO @ Tue, 16 Jun 2020 08:11:34: 1000000 INFO @ Tue, 16 Jun 2020 08:11:35: 5000000 INFO @ Tue, 16 Jun 2020 08:11:42: 2000000 INFO @ Tue, 16 Jun 2020 08:11:44: 6000000 INFO @ Tue, 16 Jun 2020 08:11:50: 3000000 INFO @ Tue, 16 Jun 2020 08:11:52: 7000000 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 08:11:56: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX2350719/SRX2350719.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX2350719/SRX2350719.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX2350719/SRX2350719.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX2350719/SRX2350719.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 08:11:56: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:11:56: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:11:58: 4000000 INFO @ Tue, 16 Jun 2020 08:12:01: 8000000 INFO @ Tue, 16 Jun 2020 08:12:04: 1000000 INFO @ Tue, 16 Jun 2020 08:12:05: #1 tag size is determined as 51 bps INFO @ Tue, 16 Jun 2020 08:12:05: #1 tag size = 51 INFO @ Tue, 16 Jun 2020 08:12:05: #1 total tags in treatment: 8445707 INFO @ Tue, 16 Jun 2020 08:12:05: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:12:05: #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 08:12:05: #1 tags after filtering in treatment: 8445707 INFO @ Tue, 16 Jun 2020 08:12:05: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:12:05: #1 finished! INFO @ Tue, 16 Jun 2020 08:12:05: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:12:05: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:12:05: #2 number of paired peaks: 656 WARNING @ Tue, 16 Jun 2020 08:12:05: Fewer paired peaks (656) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 656 pairs to build model! INFO @ Tue, 16 Jun 2020 08:12:05: start model_add_line... INFO @ Tue, 16 Jun 2020 08:12:05: start X-correlation... INFO @ Tue, 16 Jun 2020 08:12:05: end of X-cor INFO @ Tue, 16 Jun 2020 08:12:05: #2 finished! INFO @ Tue, 16 Jun 2020 08:12:05: #2 predicted fragment length is 49 bps INFO @ Tue, 16 Jun 2020 08:12:05: #2 alternative fragment length(s) may be 3,49 bps INFO @ Tue, 16 Jun 2020 08:12:05: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX2350719/SRX2350719.05_model.r WARNING @ Tue, 16 Jun 2020 08:12:05: #2 Since the d (49) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 08:12:05: #2 You may need to consider one of the other alternative d(s): 3,49 WARNING @ Tue, 16 Jun 2020 08:12:05: #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 08:12:05: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:12:05: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 08:12:06: 5000000 INFO @ Tue, 16 Jun 2020 08:12:11: 2000000 INFO @ Tue, 16 Jun 2020 08:12:13: 6000000 INFO @ Tue, 16 Jun 2020 08:12:19: 3000000 INFO @ Tue, 16 Jun 2020 08:12:21: 7000000 INFO @ Tue, 16 Jun 2020 08:12:24: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 08:12:26: 4000000 INFO @ Tue, 16 Jun 2020 08:12:28: 8000000 INFO @ Tue, 16 Jun 2020 08:12:32: #1 tag size is determined as 51 bps INFO @ Tue, 16 Jun 2020 08:12:32: #1 tag size = 51 INFO @ Tue, 16 Jun 2020 08:12:32: #1 total tags in treatment: 8445707 INFO @ Tue, 16 Jun 2020 08:12:32: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:12:32: #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 08:12:32: #1 tags after filtering in treatment: 8445707 INFO @ Tue, 16 Jun 2020 08:12:32: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:12:32: #1 finished! INFO @ Tue, 16 Jun 2020 08:12:32: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:12:32: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:12:32: #2 number of paired peaks: 656 WARNING @ Tue, 16 Jun 2020 08:12:32: Fewer paired peaks (656) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 656 pairs to build model! INFO @ Tue, 16 Jun 2020 08:12:32: start model_add_line... INFO @ Tue, 16 Jun 2020 08:12:32: start X-correlation... INFO @ Tue, 16 Jun 2020 08:12:32: end of X-cor INFO @ Tue, 16 Jun 2020 08:12:32: #2 finished! INFO @ Tue, 16 Jun 2020 08:12:32: #2 predicted fragment length is 49 bps INFO @ Tue, 16 Jun 2020 08:12:32: #2 alternative fragment length(s) may be 3,49 bps INFO @ Tue, 16 Jun 2020 08:12:32: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX2350719/SRX2350719.10_model.r WARNING @ Tue, 16 Jun 2020 08:12:32: #2 Since the d (49) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 08:12:32: #2 You may need to consider one of the other alternative d(s): 3,49 WARNING @ Tue, 16 Jun 2020 08:12:32: #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 08:12:32: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:12:32: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 08:12:33: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX2350719/SRX2350719.05_peaks.xls INFO @ Tue, 16 Jun 2020 08:12:33: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX2350719/SRX2350719.05_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:12:33: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX2350719/SRX2350719.05_summits.bed INFO @ Tue, 16 Jun 2020 08:12:33: Done! INFO @ Tue, 16 Jun 2020 08:12:33: 5000000 pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (762 records, 4 fields): 2 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 16 Jun 2020 08:12:40: 6000000 INFO @ Tue, 16 Jun 2020 08:12:47: 7000000 INFO @ Tue, 16 Jun 2020 08:12:51: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 08:12:54: 8000000 BigWig に変換しました。 INFO @ Tue, 16 Jun 2020 08:12:57: #1 tag size is determined as 51 bps INFO @ Tue, 16 Jun 2020 08:12:57: #1 tag size = 51 INFO @ Tue, 16 Jun 2020 08:12:57: #1 total tags in treatment: 8445707 INFO @ Tue, 16 Jun 2020 08:12:57: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:12:57: #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 08:12:57: #1 tags after filtering in treatment: 8445707 INFO @ Tue, 16 Jun 2020 08:12:57: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:12:57: #1 finished! INFO @ Tue, 16 Jun 2020 08:12:57: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:12:57: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:12:57: #2 number of paired peaks: 656 WARNING @ Tue, 16 Jun 2020 08:12:57: Fewer paired peaks (656) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 656 pairs to build model! INFO @ Tue, 16 Jun 2020 08:12:57: start model_add_line... INFO @ Tue, 16 Jun 2020 08:12:57: start X-correlation... INFO @ Tue, 16 Jun 2020 08:12:57: end of X-cor INFO @ Tue, 16 Jun 2020 08:12:57: #2 finished! INFO @ Tue, 16 Jun 2020 08:12:57: #2 predicted fragment length is 49 bps INFO @ Tue, 16 Jun 2020 08:12:57: #2 alternative fragment length(s) may be 3,49 bps INFO @ Tue, 16 Jun 2020 08:12:57: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX2350719/SRX2350719.20_model.r WARNING @ Tue, 16 Jun 2020 08:12:57: #2 Since the d (49) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 08:12:57: #2 You may need to consider one of the other alternative d(s): 3,49 WARNING @ Tue, 16 Jun 2020 08:12:57: #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 08:12:57: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:12:57: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 08:12:59: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX2350719/SRX2350719.10_peaks.xls INFO @ Tue, 16 Jun 2020 08:12:59: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX2350719/SRX2350719.10_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:12:59: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX2350719/SRX2350719.10_summits.bed INFO @ Tue, 16 Jun 2020 08:12:59: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (480 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 08:13:16: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 08:13:25: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX2350719/SRX2350719.20_peaks.xls INFO @ Tue, 16 Jun 2020 08:13:25: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX2350719/SRX2350719.20_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:13:25: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX2350719/SRX2350719.20_summits.bed INFO @ Tue, 16 Jun 2020 08:13:25: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (202 records, 4 fields): 1 millis CompletedMACS2peakCalling