Job ID = 6367498 SRX = SRX331255 Genome = ce11 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-15T23:29:50 prefetch.2.10.7: 1) Downloading 'SRR947487'... 2020-06-15T23:29:50 prefetch.2.10.7: Downloading via HTTPS... 2020-06-15T23:30:40 prefetch.2.10.7: HTTPS download succeed 2020-06-15T23:30:40 prefetch.2.10.7: 'SRR947487' is valid 2020-06-15T23:30:40 prefetch.2.10.7: 1) 'SRR947487' was downloaded successfully Read 6912189 spots for SRR947487/SRR947487.sra Written 6912189 spots for SRR947487/SRR947487.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: 00:01:09 6912189 reads; of these: 6912189 (100.00%) were unpaired; of these: 36938 (0.53%) aligned 0 times 5787289 (83.73%) aligned exactly 1 time 1087962 (15.74%) aligned >1 times 99.47% overall alignment rate Time searching: 00:01:09 Overall time: 00:01:09 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] 562705 / 6875251 = 0.0818 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 08:33:58: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX331255/SRX331255.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX331255/SRX331255.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX331255/SRX331255.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX331255/SRX331255.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 08:33:58: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:33:58: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:34:03: 1000000 INFO @ Tue, 16 Jun 2020 08:34:07: 2000000 INFO @ Tue, 16 Jun 2020 08:34:12: 3000000 INFO @ Tue, 16 Jun 2020 08:34:16: 4000000 INFO @ Tue, 16 Jun 2020 08:34:21: 5000000 INFO @ Tue, 16 Jun 2020 08:34:25: 6000000 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 08:34:27: #1 tag size is determined as 32 bps INFO @ Tue, 16 Jun 2020 08:34:27: #1 tag size = 32 INFO @ Tue, 16 Jun 2020 08:34:27: #1 total tags in treatment: 6312546 INFO @ Tue, 16 Jun 2020 08:34:27: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:34:27: #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 08:34:27: #1 tags after filtering in treatment: 6312546 INFO @ Tue, 16 Jun 2020 08:34:27: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:34:27: #1 finished! INFO @ Tue, 16 Jun 2020 08:34:27: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:34:27: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:34:27: #2 number of paired peaks: 405 WARNING @ Tue, 16 Jun 2020 08:34:27: Fewer paired peaks (405) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 405 pairs to build model! INFO @ Tue, 16 Jun 2020 08:34:27: start model_add_line... INFO @ Tue, 16 Jun 2020 08:34:28: start X-correlation... INFO @ Tue, 16 Jun 2020 08:34:28: end of X-cor INFO @ Tue, 16 Jun 2020 08:34:28: #2 finished! INFO @ Tue, 16 Jun 2020 08:34:28: #2 predicted fragment length is 33 bps INFO @ Tue, 16 Jun 2020 08:34:28: #2 alternative fragment length(s) may be 3,33,80,497,514,561 bps INFO @ Tue, 16 Jun 2020 08:34:28: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX331255/SRX331255.05_model.r WARNING @ Tue, 16 Jun 2020 08:34:28: #2 Since the d (33) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 08:34:28: #2 You may need to consider one of the other alternative d(s): 3,33,80,497,514,561 WARNING @ Tue, 16 Jun 2020 08:34:28: #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 08:34:28: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:34:28: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 08:34:28: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX331255/SRX331255.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX331255/SRX331255.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX331255/SRX331255.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX331255/SRX331255.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 08:34:28: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:34:28: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:34:33: 1000000 INFO @ Tue, 16 Jun 2020 08:34:38: 2000000 INFO @ Tue, 16 Jun 2020 08:34:40: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 08:34:42: 3000000 INFO @ Tue, 16 Jun 2020 08:34:46: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX331255/SRX331255.05_peaks.xls INFO @ Tue, 16 Jun 2020 08:34:46: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX331255/SRX331255.05_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:34:46: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX331255/SRX331255.05_summits.bed INFO @ Tue, 16 Jun 2020 08:34:46: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (500 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 08:34:47: 4000000 INFO @ Tue, 16 Jun 2020 08:34:51: 5000000 INFO @ Tue, 16 Jun 2020 08:34:56: 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 08:34:57: #1 tag size is determined as 32 bps INFO @ Tue, 16 Jun 2020 08:34:57: #1 tag size = 32 INFO @ Tue, 16 Jun 2020 08:34:57: #1 total tags in treatment: 6312546 INFO @ Tue, 16 Jun 2020 08:34:57: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:34:57: #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 08:34:57: #1 tags after filtering in treatment: 6312546 INFO @ Tue, 16 Jun 2020 08:34:57: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:34:57: #1 finished! INFO @ Tue, 16 Jun 2020 08:34:57: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:34:57: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:34:58: #2 number of paired peaks: 405 WARNING @ Tue, 16 Jun 2020 08:34:58: Fewer paired peaks (405) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 405 pairs to build model! INFO @ Tue, 16 Jun 2020 08:34:58: start model_add_line... INFO @ Tue, 16 Jun 2020 08:34:58: start X-correlation... INFO @ Tue, 16 Jun 2020 08:34:58: end of X-cor INFO @ Tue, 16 Jun 2020 08:34:58: #2 finished! INFO @ Tue, 16 Jun 2020 08:34:58: #2 predicted fragment length is 33 bps INFO @ Tue, 16 Jun 2020 08:34:58: #2 alternative fragment length(s) may be 3,33,80,497,514,561 bps INFO @ Tue, 16 Jun 2020 08:34:58: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX331255/SRX331255.10_model.r WARNING @ Tue, 16 Jun 2020 08:34:58: #2 Since the d (33) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 08:34:58: #2 You may need to consider one of the other alternative d(s): 3,33,80,497,514,561 WARNING @ Tue, 16 Jun 2020 08:34:58: #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 08:34:58: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:34:58: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 08:34:58: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX331255/SRX331255.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX331255/SRX331255.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX331255/SRX331255.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX331255/SRX331255.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 08:34:58: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:34:58: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:35:03: 1000000 INFO @ Tue, 16 Jun 2020 08:35:07: 2000000 INFO @ Tue, 16 Jun 2020 08:35:10: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 08:35:12: 3000000 INFO @ Tue, 16 Jun 2020 08:35:16: 4000000 INFO @ Tue, 16 Jun 2020 08:35:16: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX331255/SRX331255.10_peaks.xls INFO @ Tue, 16 Jun 2020 08:35:16: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX331255/SRX331255.10_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:35:16: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX331255/SRX331255.10_summits.bed INFO @ Tue, 16 Jun 2020 08:35:16: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (237 records, 4 fields): 1 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 08:35:21: 5000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 16 Jun 2020 08:35:25: 6000000 INFO @ Tue, 16 Jun 2020 08:35:26: #1 tag size is determined as 32 bps INFO @ Tue, 16 Jun 2020 08:35:26: #1 tag size = 32 INFO @ Tue, 16 Jun 2020 08:35:26: #1 total tags in treatment: 6312546 INFO @ Tue, 16 Jun 2020 08:35:26: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:35:26: #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 08:35:27: #1 tags after filtering in treatment: 6312546 INFO @ Tue, 16 Jun 2020 08:35:27: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:35:27: #1 finished! INFO @ Tue, 16 Jun 2020 08:35:27: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:35:27: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:35:27: #2 number of paired peaks: 405 WARNING @ Tue, 16 Jun 2020 08:35:27: Fewer paired peaks (405) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 405 pairs to build model! INFO @ Tue, 16 Jun 2020 08:35:27: start model_add_line... INFO @ Tue, 16 Jun 2020 08:35:27: start X-correlation... INFO @ Tue, 16 Jun 2020 08:35:27: end of X-cor INFO @ Tue, 16 Jun 2020 08:35:27: #2 finished! INFO @ Tue, 16 Jun 2020 08:35:27: #2 predicted fragment length is 33 bps INFO @ Tue, 16 Jun 2020 08:35:27: #2 alternative fragment length(s) may be 3,33,80,497,514,561 bps INFO @ Tue, 16 Jun 2020 08:35:27: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX331255/SRX331255.20_model.r WARNING @ Tue, 16 Jun 2020 08:35:27: #2 Since the d (33) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 08:35:27: #2 You may need to consider one of the other alternative d(s): 3,33,80,497,514,561 WARNING @ Tue, 16 Jun 2020 08:35:27: #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 08:35:27: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:35:27: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Tue, 16 Jun 2020 08:35:39: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 08:35:45: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX331255/SRX331255.20_peaks.xls INFO @ Tue, 16 Jun 2020 08:35:45: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX331255/SRX331255.20_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:35:45: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX331255/SRX331255.20_summits.bed INFO @ Tue, 16 Jun 2020 08:35:45: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (60 records, 4 fields): 1 millis CompletedMACS2peakCalling