Job ID = 6367404 SRX = SRX331163 Genome = ce11 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-15T23:23:31 prefetch.2.10.7: 1) Downloading 'SRR947395'... 2020-06-15T23:23:31 prefetch.2.10.7: Downloading via HTTPS... 2020-06-15T23:23:58 prefetch.2.10.7: HTTPS download succeed 2020-06-15T23:23:59 prefetch.2.10.7: 'SRR947395' is valid 2020-06-15T23:23:59 prefetch.2.10.7: 1) 'SRR947395' was downloaded successfully Read 6892318 spots for SRR947395/SRR947395.sra Written 6892318 spots for SRR947395/SRR947395.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: 00:01:05 6892318 reads; of these: 6892318 (100.00%) were unpaired; of these: 27355 (0.40%) aligned 0 times 5676871 (82.37%) aligned exactly 1 time 1188092 (17.24%) aligned >1 times 99.60% overall alignment rate Time searching: 00:01:05 Overall time: 00:01:05 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] 427531 / 6864963 = 0.0623 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 08:27:11: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX331163/SRX331163.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX331163/SRX331163.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX331163/SRX331163.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX331163/SRX331163.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 08:27:11: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:27:11: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:27:17: 1000000 INFO @ Tue, 16 Jun 2020 08:27:22: 2000000 INFO @ Tue, 16 Jun 2020 08:27:27: 3000000 INFO @ Tue, 16 Jun 2020 08:27:33: 4000000 INFO @ Tue, 16 Jun 2020 08:27:38: 5000000 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 08:27:41: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX331163/SRX331163.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX331163/SRX331163.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX331163/SRX331163.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX331163/SRX331163.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 08:27:41: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:27:41: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:27:43: 6000000 INFO @ Tue, 16 Jun 2020 08:27:45: #1 tag size is determined as 32 bps INFO @ Tue, 16 Jun 2020 08:27:45: #1 tag size = 32 INFO @ Tue, 16 Jun 2020 08:27:45: #1 total tags in treatment: 6437432 INFO @ Tue, 16 Jun 2020 08:27:45: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:27:45: #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 08:27:45: #1 tags after filtering in treatment: 6437432 INFO @ Tue, 16 Jun 2020 08:27:45: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:27:45: #1 finished! INFO @ Tue, 16 Jun 2020 08:27:45: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:27:45: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:27:46: #2 number of paired peaks: 437 WARNING @ Tue, 16 Jun 2020 08:27:46: Fewer paired peaks (437) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 437 pairs to build model! INFO @ Tue, 16 Jun 2020 08:27:46: start model_add_line... INFO @ Tue, 16 Jun 2020 08:27:46: start X-correlation... INFO @ Tue, 16 Jun 2020 08:27:46: end of X-cor INFO @ Tue, 16 Jun 2020 08:27:46: #2 finished! INFO @ Tue, 16 Jun 2020 08:27:46: #2 predicted fragment length is 36 bps INFO @ Tue, 16 Jun 2020 08:27:46: #2 alternative fragment length(s) may be 3,36,530,584 bps INFO @ Tue, 16 Jun 2020 08:27:46: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX331163/SRX331163.05_model.r WARNING @ Tue, 16 Jun 2020 08:27:46: #2 Since the d (36) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 08:27:46: #2 You may need to consider one of the other alternative d(s): 3,36,530,584 WARNING @ Tue, 16 Jun 2020 08:27:46: #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 08:27:46: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:27:46: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 08:27:46: 1000000 INFO @ Tue, 16 Jun 2020 08:27:51: 2000000 INFO @ Tue, 16 Jun 2020 08:27:55: 3000000 INFO @ Tue, 16 Jun 2020 08:27:58: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 08:28:00: 4000000 INFO @ Tue, 16 Jun 2020 08:28:04: 5000000 INFO @ Tue, 16 Jun 2020 08:28:05: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX331163/SRX331163.05_peaks.xls INFO @ Tue, 16 Jun 2020 08:28:05: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX331163/SRX331163.05_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:28:05: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX331163/SRX331163.05_summits.bed INFO @ Tue, 16 Jun 2020 08:28:05: Done! pass1 - making usageList (7 chroms): 0 millis pass2 - checking and writing primary data (564 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 08:28:09: 6000000 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 08:28:11: #1 tag size is determined as 32 bps INFO @ Tue, 16 Jun 2020 08:28:11: #1 tag size = 32 INFO @ Tue, 16 Jun 2020 08:28:11: #1 total tags in treatment: 6437432 INFO @ Tue, 16 Jun 2020 08:28:11: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:28:11: #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 08:28:11: #1 tags after filtering in treatment: 6437432 INFO @ Tue, 16 Jun 2020 08:28:11: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:28:11: #1 finished! INFO @ Tue, 16 Jun 2020 08:28:11: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:28:11: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:28:11: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX331163/SRX331163.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX331163/SRX331163.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX331163/SRX331163.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX331163/SRX331163.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 08:28:11: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:28:11: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:28:11: #2 number of paired peaks: 437 WARNING @ Tue, 16 Jun 2020 08:28:11: Fewer paired peaks (437) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 437 pairs to build model! INFO @ Tue, 16 Jun 2020 08:28:11: start model_add_line... INFO @ Tue, 16 Jun 2020 08:28:11: start X-correlation... INFO @ Tue, 16 Jun 2020 08:28:11: end of X-cor INFO @ Tue, 16 Jun 2020 08:28:11: #2 finished! INFO @ Tue, 16 Jun 2020 08:28:11: #2 predicted fragment length is 36 bps INFO @ Tue, 16 Jun 2020 08:28:11: #2 alternative fragment length(s) may be 3,36,530,584 bps INFO @ Tue, 16 Jun 2020 08:28:11: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX331163/SRX331163.10_model.r WARNING @ Tue, 16 Jun 2020 08:28:11: #2 Since the d (36) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 08:28:11: #2 You may need to consider one of the other alternative d(s): 3,36,530,584 WARNING @ Tue, 16 Jun 2020 08:28:11: #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 08:28:11: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:28:11: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 08:28:16: 1000000 INFO @ Tue, 16 Jun 2020 08:28:20: 2000000 INFO @ Tue, 16 Jun 2020 08:28:24: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 08:28:25: 3000000 INFO @ Tue, 16 Jun 2020 08:28:29: 4000000 INFO @ Tue, 16 Jun 2020 08:28:30: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX331163/SRX331163.10_peaks.xls INFO @ Tue, 16 Jun 2020 08:28:30: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX331163/SRX331163.10_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:28:30: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX331163/SRX331163.10_summits.bed INFO @ Tue, 16 Jun 2020 08:28:30: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (258 records, 4 fields): 1 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 08:28:33: 5000000 INFO @ Tue, 16 Jun 2020 08:28:38: 6000000 INFO @ Tue, 16 Jun 2020 08:28:40: #1 tag size is determined as 32 bps INFO @ Tue, 16 Jun 2020 08:28:40: #1 tag size = 32 INFO @ Tue, 16 Jun 2020 08:28:40: #1 total tags in treatment: 6437432 INFO @ Tue, 16 Jun 2020 08:28:40: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:28:40: #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 08:28:40: #1 tags after filtering in treatment: 6437432 INFO @ Tue, 16 Jun 2020 08:28:40: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:28:40: #1 finished! INFO @ Tue, 16 Jun 2020 08:28:40: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:28:40: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:28:40: #2 number of paired peaks: 437 WARNING @ Tue, 16 Jun 2020 08:28:40: Fewer paired peaks (437) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 437 pairs to build model! INFO @ Tue, 16 Jun 2020 08:28:40: start model_add_line... INFO @ Tue, 16 Jun 2020 08:28:40: start X-correlation... INFO @ Tue, 16 Jun 2020 08:28:40: end of X-cor INFO @ Tue, 16 Jun 2020 08:28:40: #2 finished! INFO @ Tue, 16 Jun 2020 08:28:40: #2 predicted fragment length is 36 bps INFO @ Tue, 16 Jun 2020 08:28:40: #2 alternative fragment length(s) may be 3,36,530,584 bps INFO @ Tue, 16 Jun 2020 08:28:40: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX331163/SRX331163.20_model.r WARNING @ Tue, 16 Jun 2020 08:28:41: #2 Since the d (36) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 08:28:41: #2 You may need to consider one of the other alternative d(s): 3,36,530,584 WARNING @ Tue, 16 Jun 2020 08:28:41: #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 08:28:41: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:28:41: #3 Pre-compute pvalue-qvalue table... BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 16 Jun 2020 08:28:53: #3 Call peaks for each chromosome... BigWig に変換しました。 INFO @ Tue, 16 Jun 2020 08:28:59: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX331163/SRX331163.20_peaks.xls INFO @ Tue, 16 Jun 2020 08:28:59: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX331163/SRX331163.20_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:28:59: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX331163/SRX331163.20_summits.bed INFO @ Tue, 16 Jun 2020 08:28:59: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (82 records, 4 fields): 1 millis CompletedMACS2peakCalling