Job ID = 6366997 SRX = SRX257696 Genome = ce11 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-15T23:17:01 prefetch.2.10.7: 1) Downloading 'SRR800713'... 2020-06-15T23:17:01 prefetch.2.10.7: Downloading via HTTPS... 2020-06-15T23:18:10 prefetch.2.10.7: HTTPS download succeed 2020-06-15T23:18:10 prefetch.2.10.7: 'SRR800713' is valid 2020-06-15T23:18:10 prefetch.2.10.7: 1) 'SRR800713' was downloaded successfully Read 13338445 spots for SRR800713/SRR800713.sra Written 13338445 spots for SRR800713/SRR800713.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: 00:02:34 13338445 reads; of these: 13338445 (100.00%) were unpaired; of these: 88323 (0.66%) aligned 0 times 10992850 (82.41%) aligned exactly 1 time 2257272 (16.92%) aligned >1 times 99.34% overall alignment rate Time searching: 00:02:34 Overall time: 00:02:34 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] 2113894 / 13250122 = 0.1595 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 08:24:53: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX257696/SRX257696.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX257696/SRX257696.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX257696/SRX257696.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX257696/SRX257696.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 08:24:53: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:24:53: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:24:59: 1000000 INFO @ Tue, 16 Jun 2020 08:25:05: 2000000 INFO @ Tue, 16 Jun 2020 08:25:10: 3000000 INFO @ Tue, 16 Jun 2020 08:25:16: 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 08:25:22: 5000000 INFO @ Tue, 16 Jun 2020 08:25:23: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX257696/SRX257696.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX257696/SRX257696.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX257696/SRX257696.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX257696/SRX257696.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 08:25:23: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:25:23: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:25:28: 6000000 INFO @ Tue, 16 Jun 2020 08:25:30: 1000000 INFO @ Tue, 16 Jun 2020 08:25:34: 7000000 INFO @ Tue, 16 Jun 2020 08:25:36: 2000000 INFO @ Tue, 16 Jun 2020 08:25:40: 8000000 INFO @ Tue, 16 Jun 2020 08:25:42: 3000000 INFO @ Tue, 16 Jun 2020 08:25:46: 9000000 INFO @ Tue, 16 Jun 2020 08:25:48: 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 08:25:52: 10000000 INFO @ Tue, 16 Jun 2020 08:25:53: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX257696/SRX257696.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX257696/SRX257696.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX257696/SRX257696.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX257696/SRX257696.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 08:25:53: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:25:53: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:25:54: 5000000 INFO @ Tue, 16 Jun 2020 08:25:58: 11000000 INFO @ Tue, 16 Jun 2020 08:25:59: #1 tag size is determined as 42 bps INFO @ Tue, 16 Jun 2020 08:25:59: #1 tag size = 42 INFO @ Tue, 16 Jun 2020 08:25:59: #1 total tags in treatment: 11136228 INFO @ Tue, 16 Jun 2020 08:25:59: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:25:59: #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 08:25:59: #1 tags after filtering in treatment: 11136228 INFO @ Tue, 16 Jun 2020 08:25:59: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:25:59: #1 finished! INFO @ Tue, 16 Jun 2020 08:25:59: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:25:59: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:26:00: 1000000 INFO @ Tue, 16 Jun 2020 08:26:00: 6000000 INFO @ Tue, 16 Jun 2020 08:26:00: #2 number of paired peaks: 381 WARNING @ Tue, 16 Jun 2020 08:26:00: Fewer paired peaks (381) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 381 pairs to build model! INFO @ Tue, 16 Jun 2020 08:26:00: start model_add_line... INFO @ Tue, 16 Jun 2020 08:26:00: start X-correlation... INFO @ Tue, 16 Jun 2020 08:26:00: end of X-cor INFO @ Tue, 16 Jun 2020 08:26:00: #2 finished! INFO @ Tue, 16 Jun 2020 08:26:00: #2 predicted fragment length is 41 bps INFO @ Tue, 16 Jun 2020 08:26:00: #2 alternative fragment length(s) may be 2,41 bps INFO @ Tue, 16 Jun 2020 08:26:00: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX257696/SRX257696.05_model.r WARNING @ Tue, 16 Jun 2020 08:26:00: #2 Since the d (41) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 08:26:00: #2 You may need to consider one of the other alternative d(s): 2,41 WARNING @ Tue, 16 Jun 2020 08:26:00: #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 08:26:00: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:26:00: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 08:26:06: 2000000 INFO @ Tue, 16 Jun 2020 08:26:06: 7000000 INFO @ Tue, 16 Jun 2020 08:26:12: 3000000 INFO @ Tue, 16 Jun 2020 08:26:12: 8000000 INFO @ Tue, 16 Jun 2020 08:26:18: 4000000 INFO @ Tue, 16 Jun 2020 08:26:18: 9000000 INFO @ Tue, 16 Jun 2020 08:26:23: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 08:26:24: 5000000 INFO @ Tue, 16 Jun 2020 08:26:24: 10000000 INFO @ Tue, 16 Jun 2020 08:26:30: 11000000 INFO @ Tue, 16 Jun 2020 08:26:30: 6000000 INFO @ Tue, 16 Jun 2020 08:26:31: #1 tag size is determined as 42 bps INFO @ Tue, 16 Jun 2020 08:26:31: #1 tag size = 42 INFO @ Tue, 16 Jun 2020 08:26:31: #1 total tags in treatment: 11136228 INFO @ Tue, 16 Jun 2020 08:26:31: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:26:31: #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 08:26:31: #1 tags after filtering in treatment: 11136228 INFO @ Tue, 16 Jun 2020 08:26:31: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:26:31: #1 finished! INFO @ Tue, 16 Jun 2020 08:26:31: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:26:31: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:26:32: #2 number of paired peaks: 381 WARNING @ Tue, 16 Jun 2020 08:26:32: Fewer paired peaks (381) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 381 pairs to build model! INFO @ Tue, 16 Jun 2020 08:26:32: start model_add_line... INFO @ Tue, 16 Jun 2020 08:26:32: start X-correlation... INFO @ Tue, 16 Jun 2020 08:26:32: end of X-cor INFO @ Tue, 16 Jun 2020 08:26:32: #2 finished! INFO @ Tue, 16 Jun 2020 08:26:32: #2 predicted fragment length is 41 bps INFO @ Tue, 16 Jun 2020 08:26:32: #2 alternative fragment length(s) may be 2,41 bps INFO @ Tue, 16 Jun 2020 08:26:32: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX257696/SRX257696.10_model.r WARNING @ Tue, 16 Jun 2020 08:26:32: #2 Since the d (41) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 08:26:32: #2 You may need to consider one of the other alternative d(s): 2,41 WARNING @ Tue, 16 Jun 2020 08:26:32: #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 08:26:32: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:26:32: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 08:26:35: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX257696/SRX257696.05_peaks.xls INFO @ Tue, 16 Jun 2020 08:26:35: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX257696/SRX257696.05_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:26:35: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX257696/SRX257696.05_summits.bed INFO @ Tue, 16 Jun 2020 08:26:35: Done! pass1 - making usageList (7 chroms): 0 millis pass2 - checking and writing primary data (938 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 08:26:36: 7000000 INFO @ Tue, 16 Jun 2020 08:26:42: 8000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 16 Jun 2020 08:26:47: 9000000 INFO @ Tue, 16 Jun 2020 08:26:53: 10000000 INFO @ Tue, 16 Jun 2020 08:26:55: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 08:26:59: 11000000 INFO @ Tue, 16 Jun 2020 08:26:59: #1 tag size is determined as 42 bps INFO @ Tue, 16 Jun 2020 08:26:59: #1 tag size = 42 INFO @ Tue, 16 Jun 2020 08:26:59: #1 total tags in treatment: 11136228 INFO @ Tue, 16 Jun 2020 08:26:59: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:26:59: #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 08:27:00: #1 tags after filtering in treatment: 11136228 INFO @ Tue, 16 Jun 2020 08:27:00: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:27:00: #1 finished! INFO @ Tue, 16 Jun 2020 08:27:00: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:27:00: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:27:00: #2 number of paired peaks: 381 WARNING @ Tue, 16 Jun 2020 08:27:00: Fewer paired peaks (381) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 381 pairs to build model! INFO @ Tue, 16 Jun 2020 08:27:00: start model_add_line... INFO @ Tue, 16 Jun 2020 08:27:00: start X-correlation... INFO @ Tue, 16 Jun 2020 08:27:00: end of X-cor INFO @ Tue, 16 Jun 2020 08:27:00: #2 finished! INFO @ Tue, 16 Jun 2020 08:27:00: #2 predicted fragment length is 41 bps INFO @ Tue, 16 Jun 2020 08:27:00: #2 alternative fragment length(s) may be 2,41 bps INFO @ Tue, 16 Jun 2020 08:27:00: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX257696/SRX257696.20_model.r WARNING @ Tue, 16 Jun 2020 08:27:00: #2 Since the d (41) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 08:27:00: #2 You may need to consider one of the other alternative d(s): 2,41 WARNING @ Tue, 16 Jun 2020 08:27:00: #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 08:27:00: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:27:00: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 08:27:06: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX257696/SRX257696.10_peaks.xls INFO @ Tue, 16 Jun 2020 08:27:06: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX257696/SRX257696.10_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:27:06: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX257696/SRX257696.10_summits.bed INFO @ Tue, 16 Jun 2020 08:27:06: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (363 records, 4 fields): 1 millis CompletedMACS2peakCalling BigWig に変換しました。 INFO @ Tue, 16 Jun 2020 08:27:25: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 08:27:36: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX257696/SRX257696.20_peaks.xls INFO @ Tue, 16 Jun 2020 08:27:36: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX257696/SRX257696.20_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:27:36: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX257696/SRX257696.20_summits.bed INFO @ Tue, 16 Jun 2020 08:27:36: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (130 records, 4 fields): 1 millis CompletedMACS2peakCalling