Job ID = 6507994 SRX = SRX743644 Genome = ce11 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-26T13:37:02 prefetch.2.10.7: 1) Downloading 'SRR1630859'... 2020-06-26T13:37:02 prefetch.2.10.7: Downloading via HTTPS... 2020-06-26T13:38:54 prefetch.2.10.7: HTTPS download succeed 2020-06-26T13:38:54 prefetch.2.10.7: 'SRR1630859' is valid 2020-06-26T13:38:54 prefetch.2.10.7: 1) 'SRR1630859' was downloaded successfully Read 12110512 spots for SRR1630859/SRR1630859.sra Written 12110512 spots for SRR1630859/SRR1630859.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: 00:02:12 12110512 reads; of these: 12110512 (100.00%) were unpaired; of these: 5430144 (44.84%) aligned 0 times 5995875 (49.51%) aligned exactly 1 time 684493 (5.65%) aligned >1 times 55.16% overall alignment rate Time searching: 00:02:12 Overall time: 00:02:12 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] 787898 / 6680368 = 0.1179 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 @ Fri, 26 Jun 2020 22:44:14: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX743644/SRX743644.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX743644/SRX743644.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX743644/SRX743644.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX743644/SRX743644.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 @ Fri, 26 Jun 2020 22:44:14: #1 read tag files... INFO @ Fri, 26 Jun 2020 22:44:14: #1 read treatment tags... INFO @ Fri, 26 Jun 2020 22:44:20: 1000000 INFO @ Fri, 26 Jun 2020 22:44:27: 2000000 INFO @ Fri, 26 Jun 2020 22:44:33: 3000000 INFO @ Fri, 26 Jun 2020 22:44:40: 4000000 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 @ Fri, 26 Jun 2020 22:44:44: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX743644/SRX743644.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX743644/SRX743644.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX743644/SRX743644.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX743644/SRX743644.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 @ Fri, 26 Jun 2020 22:44:44: #1 read tag files... INFO @ Fri, 26 Jun 2020 22:44:44: #1 read treatment tags... INFO @ Fri, 26 Jun 2020 22:44:47: 5000000 INFO @ Fri, 26 Jun 2020 22:44:53: 1000000 INFO @ Fri, 26 Jun 2020 22:44:53: #1 tag size is determined as 52 bps INFO @ Fri, 26 Jun 2020 22:44:53: #1 tag size = 52 INFO @ Fri, 26 Jun 2020 22:44:53: #1 total tags in treatment: 5892470 INFO @ Fri, 26 Jun 2020 22:44:53: #1 user defined the maximum tags... INFO @ Fri, 26 Jun 2020 22:44:53: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 26 Jun 2020 22:44:54: #1 tags after filtering in treatment: 5892470 INFO @ Fri, 26 Jun 2020 22:44:54: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 26 Jun 2020 22:44:54: #1 finished! INFO @ Fri, 26 Jun 2020 22:44:54: #2 Build Peak Model... INFO @ Fri, 26 Jun 2020 22:44:54: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 26 Jun 2020 22:44:54: #2 number of paired peaks: 206 WARNING @ Fri, 26 Jun 2020 22:44:54: Fewer paired peaks (206) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 206 pairs to build model! INFO @ Fri, 26 Jun 2020 22:44:54: start model_add_line... INFO @ Fri, 26 Jun 2020 22:44:54: start X-correlation... INFO @ Fri, 26 Jun 2020 22:44:54: end of X-cor INFO @ Fri, 26 Jun 2020 22:44:54: #2 finished! INFO @ Fri, 26 Jun 2020 22:44:54: #2 predicted fragment length is 58 bps INFO @ Fri, 26 Jun 2020 22:44:54: #2 alternative fragment length(s) may be 3,58,206,402,488,515,548,562,591 bps INFO @ Fri, 26 Jun 2020 22:44:54: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX743644/SRX743644.05_model.r WARNING @ Fri, 26 Jun 2020 22:44:54: #2 Since the d (58) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 26 Jun 2020 22:44:54: #2 You may need to consider one of the other alternative d(s): 3,58,206,402,488,515,548,562,591 WARNING @ Fri, 26 Jun 2020 22:44:54: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Fri, 26 Jun 2020 22:44:54: #3 Call peaks... INFO @ Fri, 26 Jun 2020 22:44:54: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 26 Jun 2020 22:45:01: 2000000 INFO @ Fri, 26 Jun 2020 22:45:08: #3 Call peaks for each chromosome... INFO @ Fri, 26 Jun 2020 22:45:09: 3000000 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 @ Fri, 26 Jun 2020 22:45:14: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX743644/SRX743644.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX743644/SRX743644.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX743644/SRX743644.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX743644/SRX743644.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 @ Fri, 26 Jun 2020 22:45:14: #1 read tag files... INFO @ Fri, 26 Jun 2020 22:45:14: #1 read treatment tags... INFO @ Fri, 26 Jun 2020 22:45:15: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX743644/SRX743644.05_peaks.xls INFO @ Fri, 26 Jun 2020 22:45:15: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX743644/SRX743644.05_peaks.narrowPeak INFO @ Fri, 26 Jun 2020 22:45:15: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX743644/SRX743644.05_summits.bed INFO @ Fri, 26 Jun 2020 22:45:15: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (289 records, 4 fields): 1 millis CompletedMACS2peakCalling INFO @ Fri, 26 Jun 2020 22:45:17: 4000000 INFO @ Fri, 26 Jun 2020 22:45:22: 1000000 INFO @ Fri, 26 Jun 2020 22:45:26: 5000000 INFO @ Fri, 26 Jun 2020 22:45:30: 2000000 INFO @ Fri, 26 Jun 2020 22:45:33: #1 tag size is determined as 52 bps INFO @ Fri, 26 Jun 2020 22:45:33: #1 tag size = 52 INFO @ Fri, 26 Jun 2020 22:45:33: #1 total tags in treatment: 5892470 INFO @ Fri, 26 Jun 2020 22:45:33: #1 user defined the maximum tags... INFO @ Fri, 26 Jun 2020 22:45:33: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 26 Jun 2020 22:45:33: #1 tags after filtering in treatment: 5892470 INFO @ Fri, 26 Jun 2020 22:45:33: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 26 Jun 2020 22:45:33: #1 finished! INFO @ Fri, 26 Jun 2020 22:45:33: #2 Build Peak Model... INFO @ Fri, 26 Jun 2020 22:45:33: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 26 Jun 2020 22:45:34: #2 number of paired peaks: 206 WARNING @ Fri, 26 Jun 2020 22:45:34: Fewer paired peaks (206) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 206 pairs to build model! INFO @ Fri, 26 Jun 2020 22:45:34: start model_add_line... INFO @ Fri, 26 Jun 2020 22:45:34: start X-correlation... INFO @ Fri, 26 Jun 2020 22:45:34: end of X-cor INFO @ Fri, 26 Jun 2020 22:45:34: #2 finished! INFO @ Fri, 26 Jun 2020 22:45:34: #2 predicted fragment length is 58 bps INFO @ Fri, 26 Jun 2020 22:45:34: #2 alternative fragment length(s) may be 3,58,206,402,488,515,548,562,591 bps INFO @ Fri, 26 Jun 2020 22:45:34: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX743644/SRX743644.10_model.r WARNING @ Fri, 26 Jun 2020 22:45:34: #2 Since the d (58) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 26 Jun 2020 22:45:34: #2 You may need to consider one of the other alternative d(s): 3,58,206,402,488,515,548,562,591 WARNING @ Fri, 26 Jun 2020 22:45:34: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Fri, 26 Jun 2020 22:45:34: #3 Call peaks... INFO @ Fri, 26 Jun 2020 22:45:34: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 26 Jun 2020 22:45:37: 3000000 INFO @ Fri, 26 Jun 2020 22:45:44: 4000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Fri, 26 Jun 2020 22:45:48: #3 Call peaks for each chromosome... INFO @ Fri, 26 Jun 2020 22:45:51: 5000000 INFO @ Fri, 26 Jun 2020 22:45:56: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX743644/SRX743644.10_peaks.xls INFO @ Fri, 26 Jun 2020 22:45:56: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX743644/SRX743644.10_peaks.narrowPeak INFO @ Fri, 26 Jun 2020 22:45:56: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX743644/SRX743644.10_summits.bed INFO @ Fri, 26 Jun 2020 22:45:56: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (108 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Fri, 26 Jun 2020 22:45:57: #1 tag size is determined as 52 bps INFO @ Fri, 26 Jun 2020 22:45:57: #1 tag size = 52 INFO @ Fri, 26 Jun 2020 22:45:57: #1 total tags in treatment: 5892470 INFO @ Fri, 26 Jun 2020 22:45:57: #1 user defined the maximum tags... INFO @ Fri, 26 Jun 2020 22:45:57: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 26 Jun 2020 22:45:57: #1 tags after filtering in treatment: 5892470 INFO @ Fri, 26 Jun 2020 22:45:57: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 26 Jun 2020 22:45:57: #1 finished! INFO @ Fri, 26 Jun 2020 22:45:57: #2 Build Peak Model... INFO @ Fri, 26 Jun 2020 22:45:57: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 26 Jun 2020 22:45:57: #2 number of paired peaks: 206 WARNING @ Fri, 26 Jun 2020 22:45:57: Fewer paired peaks (206) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 206 pairs to build model! INFO @ Fri, 26 Jun 2020 22:45:57: start model_add_line... INFO @ Fri, 26 Jun 2020 22:45:58: start X-correlation... INFO @ Fri, 26 Jun 2020 22:45:58: end of X-cor INFO @ Fri, 26 Jun 2020 22:45:58: #2 finished! INFO @ Fri, 26 Jun 2020 22:45:58: #2 predicted fragment length is 58 bps INFO @ Fri, 26 Jun 2020 22:45:58: #2 alternative fragment length(s) may be 3,58,206,402,488,515,548,562,591 bps INFO @ Fri, 26 Jun 2020 22:45:58: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX743644/SRX743644.20_model.r WARNING @ Fri, 26 Jun 2020 22:45:58: #2 Since the d (58) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 26 Jun 2020 22:45:58: #2 You may need to consider one of the other alternative d(s): 3,58,206,402,488,515,548,562,591 WARNING @ Fri, 26 Jun 2020 22:45:58: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Fri, 26 Jun 2020 22:45:58: #3 Call peaks... INFO @ Fri, 26 Jun 2020 22:45:58: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Fri, 26 Jun 2020 22:46:12: #3 Call peaks for each chromosome... INFO @ Fri, 26 Jun 2020 22:46:20: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX743644/SRX743644.20_peaks.xls INFO @ Fri, 26 Jun 2020 22:46:20: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX743644/SRX743644.20_peaks.narrowPeak INFO @ Fri, 26 Jun 2020 22:46:20: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX743644/SRX743644.20_summits.bed INFO @ Fri, 26 Jun 2020 22:46:20: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (28 records, 4 fields): 1 millis CompletedMACS2peakCalling