Job ID = 6367531 SRX = SRX331287 Genome = ce11 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-15T23:36:29 prefetch.2.10.7: 1) Downloading 'SRR947523'... 2020-06-15T23:36:29 prefetch.2.10.7: Downloading via HTTPS... 2020-06-15T23:37:12 prefetch.2.10.7: HTTPS download succeed 2020-06-15T23:37:12 prefetch.2.10.7: 'SRR947523' is valid 2020-06-15T23:37:12 prefetch.2.10.7: 1) 'SRR947523' was downloaded successfully Read 5427344 spots for SRR947523/SRR947523.sra Written 5427344 spots for SRR947523/SRR947523.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: 00:00:52 5427344 reads; of these: 5427344 (100.00%) were unpaired; of these: 93242 (1.72%) aligned 0 times 4504025 (82.99%) aligned exactly 1 time 830077 (15.29%) aligned >1 times 98.28% overall alignment rate Time searching: 00:00:52 Overall time: 00:00:52 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] 1058004 / 5334102 = 0.1983 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 08:40:07: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX331287/SRX331287.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX331287/SRX331287.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX331287/SRX331287.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX331287/SRX331287.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 08:40:07: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:40:07: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:40:11: 1000000 INFO @ Tue, 16 Jun 2020 08:40:16: 2000000 INFO @ Tue, 16 Jun 2020 08:40:20: 3000000 INFO @ Tue, 16 Jun 2020 08:40:24: 4000000 INFO @ Tue, 16 Jun 2020 08:40:25: #1 tag size is determined as 32 bps INFO @ Tue, 16 Jun 2020 08:40:25: #1 tag size = 32 INFO @ Tue, 16 Jun 2020 08:40:25: #1 total tags in treatment: 4276098 INFO @ Tue, 16 Jun 2020 08:40:25: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:40:25: #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 08:40:25: #1 tags after filtering in treatment: 4276098 INFO @ Tue, 16 Jun 2020 08:40:25: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:40:25: #1 finished! INFO @ Tue, 16 Jun 2020 08:40:25: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:40:25: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:40:26: #2 number of paired peaks: 266 WARNING @ Tue, 16 Jun 2020 08:40:26: Fewer paired peaks (266) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 266 pairs to build model! INFO @ Tue, 16 Jun 2020 08:40:26: start model_add_line... INFO @ Tue, 16 Jun 2020 08:40:26: start X-correlation... INFO @ Tue, 16 Jun 2020 08:40:26: end of X-cor INFO @ Tue, 16 Jun 2020 08:40:26: #2 finished! INFO @ Tue, 16 Jun 2020 08:40:26: #2 predicted fragment length is 32 bps INFO @ Tue, 16 Jun 2020 08:40:26: #2 alternative fragment length(s) may be 4,32,79,113,130,164,265,506,528,561,579,598 bps INFO @ Tue, 16 Jun 2020 08:40:26: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX331287/SRX331287.05_model.r WARNING @ Tue, 16 Jun 2020 08:40:26: #2 Since the d (32) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 08:40:26: #2 You may need to consider one of the other alternative d(s): 4,32,79,113,130,164,265,506,528,561,579,598 WARNING @ Tue, 16 Jun 2020 08:40:26: #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 08:40:26: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:40:26: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 08:40:34: #3 Call peaks for each chromosome... 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 08:40:37: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX331287/SRX331287.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX331287/SRX331287.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX331287/SRX331287.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX331287/SRX331287.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 08:40:37: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:40:37: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:40:38: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX331287/SRX331287.05_peaks.xls INFO @ Tue, 16 Jun 2020 08:40:38: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX331287/SRX331287.05_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:40:38: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX331287/SRX331287.05_summits.bed INFO @ Tue, 16 Jun 2020 08:40:38: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (184 records, 4 fields): 1 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 08:40:41: 1000000 INFO @ Tue, 16 Jun 2020 08:40:46: 2000000 INFO @ Tue, 16 Jun 2020 08:40:50: 3000000 INFO @ Tue, 16 Jun 2020 08:40:54: 4000000 INFO @ Tue, 16 Jun 2020 08:40:55: #1 tag size is determined as 32 bps INFO @ Tue, 16 Jun 2020 08:40:55: #1 tag size = 32 INFO @ Tue, 16 Jun 2020 08:40:55: #1 total tags in treatment: 4276098 INFO @ Tue, 16 Jun 2020 08:40:55: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:40:55: #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 08:40:55: #1 tags after filtering in treatment: 4276098 INFO @ Tue, 16 Jun 2020 08:40:55: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:40:55: #1 finished! INFO @ Tue, 16 Jun 2020 08:40:55: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:40:55: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:40:56: #2 number of paired peaks: 266 WARNING @ Tue, 16 Jun 2020 08:40:56: Fewer paired peaks (266) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 266 pairs to build model! INFO @ Tue, 16 Jun 2020 08:40:56: start model_add_line... INFO @ Tue, 16 Jun 2020 08:40:56: start X-correlation... INFO @ Tue, 16 Jun 2020 08:40:56: end of X-cor INFO @ Tue, 16 Jun 2020 08:40:56: #2 finished! INFO @ Tue, 16 Jun 2020 08:40:56: #2 predicted fragment length is 32 bps INFO @ Tue, 16 Jun 2020 08:40:56: #2 alternative fragment length(s) may be 4,32,79,113,130,164,265,506,528,561,579,598 bps INFO @ Tue, 16 Jun 2020 08:40:56: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX331287/SRX331287.10_model.r WARNING @ Tue, 16 Jun 2020 08:40:56: #2 Since the d (32) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 08:40:56: #2 You may need to consider one of the other alternative d(s): 4,32,79,113,130,164,265,506,528,561,579,598 WARNING @ Tue, 16 Jun 2020 08:40:56: #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 08:40:56: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:40:56: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 08:41:04: #3 Call peaks for each chromosome... 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 08:41:07: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX331287/SRX331287.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX331287/SRX331287.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX331287/SRX331287.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX331287/SRX331287.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 08:41:07: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:41:07: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:41:08: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX331287/SRX331287.10_peaks.xls INFO @ Tue, 16 Jun 2020 08:41:08: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX331287/SRX331287.10_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:41:08: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX331287/SRX331287.10_summits.bed INFO @ Tue, 16 Jun 2020 08:41:08: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (50 records, 4 fields): 1 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 08:41:12: 1000000 INFO @ Tue, 16 Jun 2020 08:41:17: 2000000 INFO @ Tue, 16 Jun 2020 08:41:22: 3000000 INFO @ Tue, 16 Jun 2020 08:41:27: 4000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 16 Jun 2020 08:41:29: #1 tag size is determined as 32 bps INFO @ Tue, 16 Jun 2020 08:41:29: #1 tag size = 32 INFO @ Tue, 16 Jun 2020 08:41:29: #1 total tags in treatment: 4276098 INFO @ Tue, 16 Jun 2020 08:41:29: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:41:29: #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 08:41:29: #1 tags after filtering in treatment: 4276098 INFO @ Tue, 16 Jun 2020 08:41:29: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:41:29: #1 finished! INFO @ Tue, 16 Jun 2020 08:41:29: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:41:29: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:41:29: #2 number of paired peaks: 266 WARNING @ Tue, 16 Jun 2020 08:41:29: Fewer paired peaks (266) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 266 pairs to build model! INFO @ Tue, 16 Jun 2020 08:41:29: start model_add_line... INFO @ Tue, 16 Jun 2020 08:41:29: start X-correlation... INFO @ Tue, 16 Jun 2020 08:41:29: end of X-cor INFO @ Tue, 16 Jun 2020 08:41:29: #2 finished! INFO @ Tue, 16 Jun 2020 08:41:29: #2 predicted fragment length is 32 bps INFO @ Tue, 16 Jun 2020 08:41:29: #2 alternative fragment length(s) may be 4,32,79,113,130,164,265,506,528,561,579,598 bps INFO @ Tue, 16 Jun 2020 08:41:29: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX331287/SRX331287.20_model.r WARNING @ Tue, 16 Jun 2020 08:41:29: #2 Since the d (32) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 08:41:29: #2 You may need to consider one of the other alternative d(s): 4,32,79,113,130,164,265,506,528,561,579,598 WARNING @ Tue, 16 Jun 2020 08:41:29: #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 08:41:29: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:41:29: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 08:41:37: #3 Call peaks for each chromosome... BigWig に変換しました。 INFO @ Tue, 16 Jun 2020 08:41:42: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX331287/SRX331287.20_peaks.xls INFO @ Tue, 16 Jun 2020 08:41:42: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX331287/SRX331287.20_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:41:42: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX331287/SRX331287.20_summits.bed INFO @ Tue, 16 Jun 2020 08:41:42: Done! pass1 - making usageList (5 chroms): 1 millis pass2 - checking and writing primary data (6 records, 4 fields): 1 millis CompletedMACS2peakCalling