Job ID = 6367525 SRX = SRX331281 Genome = ce11 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-15T23:33:05 prefetch.2.10.7: 1) Downloading 'SRR947516'... 2020-06-15T23:33:05 prefetch.2.10.7: Downloading via HTTPS... 2020-06-15T23:33:51 prefetch.2.10.7: HTTPS download succeed 2020-06-15T23:33:51 prefetch.2.10.7: 'SRR947516' is valid 2020-06-15T23:33:51 prefetch.2.10.7: 1) 'SRR947516' was downloaded successfully Read 6605665 spots for SRR947516/SRR947516.sra Written 6605665 spots for SRR947516/SRR947516.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 6605665 reads; of these: 6605665 (100.00%) were unpaired; of these: 141219 (2.14%) aligned 0 times 5207938 (78.84%) aligned exactly 1 time 1256508 (19.02%) aligned >1 times 97.86% 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] 913709 / 6464446 = 0.1413 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 08:36:48: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX331281/SRX331281.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX331281/SRX331281.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX331281/SRX331281.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX331281/SRX331281.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 08:36:48: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:36:48: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:36:53: 1000000 INFO @ Tue, 16 Jun 2020 08:36:58: 2000000 INFO @ Tue, 16 Jun 2020 08:37:02: 3000000 INFO @ Tue, 16 Jun 2020 08:37:07: 4000000 INFO @ Tue, 16 Jun 2020 08:37:12: 5000000 INFO @ Tue, 16 Jun 2020 08:37:14: #1 tag size is determined as 32 bps INFO @ Tue, 16 Jun 2020 08:37:14: #1 tag size = 32 INFO @ Tue, 16 Jun 2020 08:37:14: #1 total tags in treatment: 5550737 INFO @ Tue, 16 Jun 2020 08:37:14: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:37:14: #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 08:37:14: #1 tags after filtering in treatment: 5550737 INFO @ Tue, 16 Jun 2020 08:37:14: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:37:14: #1 finished! INFO @ Tue, 16 Jun 2020 08:37:14: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:37:14: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:37:15: #2 number of paired peaks: 405 WARNING @ Tue, 16 Jun 2020 08:37:15: 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 08:37:15: start model_add_line... INFO @ Tue, 16 Jun 2020 08:37:15: start X-correlation... INFO @ Tue, 16 Jun 2020 08:37:15: end of X-cor INFO @ Tue, 16 Jun 2020 08:37:15: #2 finished! INFO @ Tue, 16 Jun 2020 08:37:15: #2 predicted fragment length is 28 bps INFO @ Tue, 16 Jun 2020 08:37:15: #2 alternative fragment length(s) may be 3,28,103,440,527,566,588 bps INFO @ Tue, 16 Jun 2020 08:37:15: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX331281/SRX331281.05_model.r WARNING @ Tue, 16 Jun 2020 08:37:15: #2 Since the d (28) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 08:37:15: #2 You may need to consider one of the other alternative d(s): 3,28,103,440,527,566,588 WARNING @ Tue, 16 Jun 2020 08:37:15: #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 08:37:15: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:37:15: #3 Pre-compute pvalue-qvalue table... 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 08:37:18: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX331281/SRX331281.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX331281/SRX331281.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX331281/SRX331281.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX331281/SRX331281.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 08:37:18: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:37:18: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:37:23: 1000000 INFO @ Tue, 16 Jun 2020 08:37:26: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 08:37:28: 2000000 INFO @ Tue, 16 Jun 2020 08:37:31: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX331281/SRX331281.05_peaks.xls INFO @ Tue, 16 Jun 2020 08:37:31: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX331281/SRX331281.05_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:37:31: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX331281/SRX331281.05_summits.bed INFO @ Tue, 16 Jun 2020 08:37:31: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (506 records, 4 fields): 1 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 08:37:32: 3000000 INFO @ Tue, 16 Jun 2020 08:37:37: 4000000 INFO @ Tue, 16 Jun 2020 08:37:42: 5000000 INFO @ Tue, 16 Jun 2020 08:37:44: #1 tag size is determined as 32 bps INFO @ Tue, 16 Jun 2020 08:37:44: #1 tag size = 32 INFO @ Tue, 16 Jun 2020 08:37:44: #1 total tags in treatment: 5550737 INFO @ Tue, 16 Jun 2020 08:37:44: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:37:44: #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 08:37:44: #1 tags after filtering in treatment: 5550737 INFO @ Tue, 16 Jun 2020 08:37:44: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:37:44: #1 finished! INFO @ Tue, 16 Jun 2020 08:37:44: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:37:44: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:37:45: #2 number of paired peaks: 405 WARNING @ Tue, 16 Jun 2020 08:37:45: 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 08:37:45: start model_add_line... INFO @ Tue, 16 Jun 2020 08:37:45: start X-correlation... INFO @ Tue, 16 Jun 2020 08:37:45: end of X-cor INFO @ Tue, 16 Jun 2020 08:37:45: #2 finished! INFO @ Tue, 16 Jun 2020 08:37:45: #2 predicted fragment length is 28 bps INFO @ Tue, 16 Jun 2020 08:37:45: #2 alternative fragment length(s) may be 3,28,103,440,527,566,588 bps INFO @ Tue, 16 Jun 2020 08:37:45: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX331281/SRX331281.10_model.r WARNING @ Tue, 16 Jun 2020 08:37:45: #2 Since the d (28) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 08:37:45: #2 You may need to consider one of the other alternative d(s): 3,28,103,440,527,566,588 WARNING @ Tue, 16 Jun 2020 08:37:45: #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 08:37:45: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:37:45: #3 Pre-compute pvalue-qvalue table... 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 08:37:48: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX331281/SRX331281.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX331281/SRX331281.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX331281/SRX331281.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX331281/SRX331281.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 08:37:48: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:37:48: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:37:53: 1000000 INFO @ Tue, 16 Jun 2020 08:37:56: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 08:37:58: 2000000 INFO @ Tue, 16 Jun 2020 08:38:01: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX331281/SRX331281.10_peaks.xls INFO @ Tue, 16 Jun 2020 08:38:01: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX331281/SRX331281.10_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:38:01: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX331281/SRX331281.10_summits.bed INFO @ Tue, 16 Jun 2020 08:38:01: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (220 records, 4 fields): 1 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 08:38:02: 3000000 INFO @ Tue, 16 Jun 2020 08:38:07: 4000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 16 Jun 2020 08:38:12: 5000000 INFO @ Tue, 16 Jun 2020 08:38:15: #1 tag size is determined as 32 bps INFO @ Tue, 16 Jun 2020 08:38:15: #1 tag size = 32 INFO @ Tue, 16 Jun 2020 08:38:15: #1 total tags in treatment: 5550737 INFO @ Tue, 16 Jun 2020 08:38:15: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:38:15: #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 08:38:15: #1 tags after filtering in treatment: 5550737 INFO @ Tue, 16 Jun 2020 08:38:15: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:38:15: #1 finished! INFO @ Tue, 16 Jun 2020 08:38:15: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:38:15: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:38:15: #2 number of paired peaks: 405 WARNING @ Tue, 16 Jun 2020 08:38:15: 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 08:38:15: start model_add_line... INFO @ Tue, 16 Jun 2020 08:38:15: start X-correlation... INFO @ Tue, 16 Jun 2020 08:38:15: end of X-cor INFO @ Tue, 16 Jun 2020 08:38:15: #2 finished! INFO @ Tue, 16 Jun 2020 08:38:15: #2 predicted fragment length is 28 bps INFO @ Tue, 16 Jun 2020 08:38:15: #2 alternative fragment length(s) may be 3,28,103,440,527,566,588 bps INFO @ Tue, 16 Jun 2020 08:38:15: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX331281/SRX331281.20_model.r WARNING @ Tue, 16 Jun 2020 08:38:15: #2 Since the d (28) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 08:38:15: #2 You may need to consider one of the other alternative d(s): 3,28,103,440,527,566,588 WARNING @ Tue, 16 Jun 2020 08:38:15: #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 08:38:15: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:38:15: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Tue, 16 Jun 2020 08:38:26: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 08:38:32: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX331281/SRX331281.20_peaks.xls INFO @ Tue, 16 Jun 2020 08:38:32: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX331281/SRX331281.20_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:38:32: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX331281/SRX331281.20_summits.bed INFO @ Tue, 16 Jun 2020 08:38:32: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (54 records, 4 fields): 1 millis CompletedMACS2peakCalling