Job ID = 6365970 SRX = SRX043981 Genome = ce11 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-15T22:23:44 prefetch.2.10.7: 1) Downloading 'SRR107556'... 2020-06-15T22:23:44 prefetch.2.10.7: Downloading via HTTPS... 2020-06-15T22:24:24 prefetch.2.10.7: HTTPS download succeed 2020-06-15T22:24:24 prefetch.2.10.7: 'SRR107556' is valid 2020-06-15T22:24:24 prefetch.2.10.7: 1) 'SRR107556' was downloaded successfully Read 4793412 spots for SRR107556/SRR107556.sra Written 4793412 spots for SRR107556/SRR107556.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: 00:00:50 4793412 reads; of these: 4793412 (100.00%) were unpaired; of these: 814867 (17.00%) aligned 0 times 3446532 (71.90%) aligned exactly 1 time 532013 (11.10%) aligned >1 times 83.00% overall alignment rate Time searching: 00:00:50 Overall time: 00:00:50 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] 254611 / 3978545 = 0.0640 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 07:27:02: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX043981/SRX043981.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX043981/SRX043981.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX043981/SRX043981.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX043981/SRX043981.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 07:27:02: #1 read tag files... INFO @ Tue, 16 Jun 2020 07:27:02: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 07:27:07: 1000000 INFO @ Tue, 16 Jun 2020 07:27:13: 2000000 INFO @ Tue, 16 Jun 2020 07:27:18: 3000000 INFO @ Tue, 16 Jun 2020 07:27:22: #1 tag size is determined as 34 bps INFO @ Tue, 16 Jun 2020 07:27:22: #1 tag size = 34 INFO @ Tue, 16 Jun 2020 07:27:22: #1 total tags in treatment: 3723934 INFO @ Tue, 16 Jun 2020 07:27:22: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 07:27:22: #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 07:27:22: #1 tags after filtering in treatment: 3723934 INFO @ Tue, 16 Jun 2020 07:27:22: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 07:27:22: #1 finished! INFO @ Tue, 16 Jun 2020 07:27:22: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 07:27:22: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 07:27:22: #2 number of paired peaks: 286 WARNING @ Tue, 16 Jun 2020 07:27:22: Fewer paired peaks (286) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 286 pairs to build model! INFO @ Tue, 16 Jun 2020 07:27:22: start model_add_line... INFO @ Tue, 16 Jun 2020 07:27:22: start X-correlation... INFO @ Tue, 16 Jun 2020 07:27:22: end of X-cor INFO @ Tue, 16 Jun 2020 07:27:22: #2 finished! INFO @ Tue, 16 Jun 2020 07:27:22: #2 predicted fragment length is 37 bps INFO @ Tue, 16 Jun 2020 07:27:22: #2 alternative fragment length(s) may be 3,37,85,583 bps INFO @ Tue, 16 Jun 2020 07:27:22: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX043981/SRX043981.05_model.r WARNING @ Tue, 16 Jun 2020 07:27:22: #2 Since the d (37) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 07:27:22: #2 You may need to consider one of the other alternative d(s): 3,37,85,583 WARNING @ Tue, 16 Jun 2020 07:27:22: #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 07:27:22: #3 Call peaks... INFO @ Tue, 16 Jun 2020 07:27:22: #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 07:27:30: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 07:27:32: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX043981/SRX043981.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX043981/SRX043981.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX043981/SRX043981.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX043981/SRX043981.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 07:27:32: #1 read tag files... INFO @ Tue, 16 Jun 2020 07:27:32: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 07:27:35: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX043981/SRX043981.05_peaks.xls INFO @ Tue, 16 Jun 2020 07:27:35: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX043981/SRX043981.05_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 07:27:35: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX043981/SRX043981.05_summits.bed INFO @ Tue, 16 Jun 2020 07:27:35: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (197 records, 4 fields): 1 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 07:27:38: 1000000 INFO @ Tue, 16 Jun 2020 07:27:44: 2000000 INFO @ Tue, 16 Jun 2020 07:27:51: 3000000 INFO @ Tue, 16 Jun 2020 07:27:55: #1 tag size is determined as 34 bps INFO @ Tue, 16 Jun 2020 07:27:55: #1 tag size = 34 INFO @ Tue, 16 Jun 2020 07:27:55: #1 total tags in treatment: 3723934 INFO @ Tue, 16 Jun 2020 07:27:55: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 07:27:55: #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 07:27:55: #1 tags after filtering in treatment: 3723934 INFO @ Tue, 16 Jun 2020 07:27:55: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 07:27:55: #1 finished! INFO @ Tue, 16 Jun 2020 07:27:55: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 07:27:55: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 07:27:55: #2 number of paired peaks: 286 WARNING @ Tue, 16 Jun 2020 07:27:55: Fewer paired peaks (286) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 286 pairs to build model! INFO @ Tue, 16 Jun 2020 07:27:55: start model_add_line... INFO @ Tue, 16 Jun 2020 07:27:55: start X-correlation... INFO @ Tue, 16 Jun 2020 07:27:55: end of X-cor INFO @ Tue, 16 Jun 2020 07:27:55: #2 finished! INFO @ Tue, 16 Jun 2020 07:27:55: #2 predicted fragment length is 37 bps INFO @ Tue, 16 Jun 2020 07:27:55: #2 alternative fragment length(s) may be 3,37,85,583 bps INFO @ Tue, 16 Jun 2020 07:27:55: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX043981/SRX043981.10_model.r WARNING @ Tue, 16 Jun 2020 07:27:55: #2 Since the d (37) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 07:27:55: #2 You may need to consider one of the other alternative d(s): 3,37,85,583 WARNING @ Tue, 16 Jun 2020 07:27:55: #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 07:27:55: #3 Call peaks... INFO @ Tue, 16 Jun 2020 07:27:55: #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 07:28:02: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX043981/SRX043981.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX043981/SRX043981.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX043981/SRX043981.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX043981/SRX043981.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 07:28:02: #1 read tag files... INFO @ Tue, 16 Jun 2020 07:28:02: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 07:28:04: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 07:28:08: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX043981/SRX043981.10_peaks.xls INFO @ Tue, 16 Jun 2020 07:28:08: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX043981/SRX043981.10_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 07:28:08: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX043981/SRX043981.10_summits.bed INFO @ Tue, 16 Jun 2020 07:28:08: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (74 records, 4 fields): 0 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 07:28:08: 1000000 INFO @ Tue, 16 Jun 2020 07:28:15: 2000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 16 Jun 2020 07:28:21: 3000000 INFO @ Tue, 16 Jun 2020 07:28:26: #1 tag size is determined as 34 bps INFO @ Tue, 16 Jun 2020 07:28:26: #1 tag size = 34 INFO @ Tue, 16 Jun 2020 07:28:26: #1 total tags in treatment: 3723934 INFO @ Tue, 16 Jun 2020 07:28:26: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 07:28:26: #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 07:28:26: #1 tags after filtering in treatment: 3723934 INFO @ Tue, 16 Jun 2020 07:28:26: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 07:28:26: #1 finished! INFO @ Tue, 16 Jun 2020 07:28:26: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 07:28:26: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 07:28:26: #2 number of paired peaks: 286 WARNING @ Tue, 16 Jun 2020 07:28:26: Fewer paired peaks (286) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 286 pairs to build model! INFO @ Tue, 16 Jun 2020 07:28:26: start model_add_line... INFO @ Tue, 16 Jun 2020 07:28:26: start X-correlation... INFO @ Tue, 16 Jun 2020 07:28:26: end of X-cor INFO @ Tue, 16 Jun 2020 07:28:26: #2 finished! INFO @ Tue, 16 Jun 2020 07:28:26: #2 predicted fragment length is 37 bps INFO @ Tue, 16 Jun 2020 07:28:26: #2 alternative fragment length(s) may be 3,37,85,583 bps INFO @ Tue, 16 Jun 2020 07:28:26: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX043981/SRX043981.20_model.r WARNING @ Tue, 16 Jun 2020 07:28:26: #2 Since the d (37) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 07:28:26: #2 You may need to consider one of the other alternative d(s): 3,37,85,583 WARNING @ Tue, 16 Jun 2020 07:28:26: #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 07:28:26: #3 Call peaks... INFO @ Tue, 16 Jun 2020 07:28:26: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Tue, 16 Jun 2020 07:28:34: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 07:28:38: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX043981/SRX043981.20_peaks.xls INFO @ Tue, 16 Jun 2020 07:28:38: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX043981/SRX043981.20_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 07:28:38: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX043981/SRX043981.20_summits.bed INFO @ Tue, 16 Jun 2020 07:28:38: Done! pass1 - making usageList (5 chroms): 0 millis pass2 - checking and writing primary data (7 records, 4 fields): 1 millis CompletedMACS2peakCalling