Job ID = 6626426 SRX = SRX7262192 Genome = ce11 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 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: 00:02:30 10020192 reads; of these: 10020192 (100.00%) were unpaired; of these: 286213 (2.86%) aligned 0 times 7967862 (79.52%) aligned exactly 1 time 1766117 (17.63%) aligned >1 times 97.14% overall alignment rate Time searching: 00:02:30 Overall time: 00:02:30 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] 839995 / 9733979 = 0.0863 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, 14 Jul 2020 07:05:30: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX7262192/SRX7262192.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX7262192/SRX7262192.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX7262192/SRX7262192.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX7262192/SRX7262192.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, 14 Jul 2020 07:05:30: #1 read tag files... INFO @ Tue, 14 Jul 2020 07:05:30: #1 read treatment tags... INFO @ Tue, 14 Jul 2020 07:05:35: 1000000 INFO @ Tue, 14 Jul 2020 07:05:40: 2000000 INFO @ Tue, 14 Jul 2020 07:05:45: 3000000 INFO @ Tue, 14 Jul 2020 07:05:50: 4000000 INFO @ Tue, 14 Jul 2020 07:05:55: 5000000 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, 14 Jul 2020 07:06:00: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX7262192/SRX7262192.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX7262192/SRX7262192.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX7262192/SRX7262192.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX7262192/SRX7262192.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, 14 Jul 2020 07:06:00: #1 read tag files... INFO @ Tue, 14 Jul 2020 07:06:00: #1 read treatment tags... INFO @ Tue, 14 Jul 2020 07:06:00: 6000000 INFO @ Tue, 14 Jul 2020 07:06:05: 1000000 INFO @ Tue, 14 Jul 2020 07:06:06: 7000000 INFO @ Tue, 14 Jul 2020 07:06:11: 2000000 INFO @ Tue, 14 Jul 2020 07:06:11: 8000000 INFO @ Tue, 14 Jul 2020 07:06:16: #1 tag size is determined as 50 bps INFO @ Tue, 14 Jul 2020 07:06:16: #1 tag size = 50 INFO @ Tue, 14 Jul 2020 07:06:16: #1 total tags in treatment: 8893984 INFO @ Tue, 14 Jul 2020 07:06:16: #1 user defined the maximum tags... INFO @ Tue, 14 Jul 2020 07:06:16: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 14 Jul 2020 07:06:16: #1 tags after filtering in treatment: 8893984 INFO @ Tue, 14 Jul 2020 07:06:16: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 14 Jul 2020 07:06:16: #1 finished! INFO @ Tue, 14 Jul 2020 07:06:16: #2 Build Peak Model... INFO @ Tue, 14 Jul 2020 07:06:16: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 14 Jul 2020 07:06:16: 3000000 INFO @ Tue, 14 Jul 2020 07:06:17: #2 number of paired peaks: 309 WARNING @ Tue, 14 Jul 2020 07:06:17: Fewer paired peaks (309) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 309 pairs to build model! INFO @ Tue, 14 Jul 2020 07:06:17: start model_add_line... INFO @ Tue, 14 Jul 2020 07:06:17: start X-correlation... INFO @ Tue, 14 Jul 2020 07:06:17: end of X-cor INFO @ Tue, 14 Jul 2020 07:06:17: #2 finished! INFO @ Tue, 14 Jul 2020 07:06:17: #2 predicted fragment length is 47 bps INFO @ Tue, 14 Jul 2020 07:06:17: #2 alternative fragment length(s) may be 3,47 bps INFO @ Tue, 14 Jul 2020 07:06:17: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX7262192/SRX7262192.05_model.r WARNING @ Tue, 14 Jul 2020 07:06:17: #2 Since the d (47) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 14 Jul 2020 07:06:17: #2 You may need to consider one of the other alternative d(s): 3,47 WARNING @ Tue, 14 Jul 2020 07:06:17: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 14 Jul 2020 07:06:17: #3 Call peaks... INFO @ Tue, 14 Jul 2020 07:06:17: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 14 Jul 2020 07:06:22: 4000000 INFO @ Tue, 14 Jul 2020 07:06:27: 5000000 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, 14 Jul 2020 07:06:30: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX7262192/SRX7262192.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX7262192/SRX7262192.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX7262192/SRX7262192.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX7262192/SRX7262192.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, 14 Jul 2020 07:06:30: #1 read tag files... INFO @ Tue, 14 Jul 2020 07:06:30: #1 read treatment tags... INFO @ Tue, 14 Jul 2020 07:06:32: 6000000 INFO @ Tue, 14 Jul 2020 07:06:34: #3 Call peaks for each chromosome... INFO @ Tue, 14 Jul 2020 07:06:35: 1000000 INFO @ Tue, 14 Jul 2020 07:06:38: 7000000 INFO @ Tue, 14 Jul 2020 07:06:41: 2000000 INFO @ Tue, 14 Jul 2020 07:06:42: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX7262192/SRX7262192.05_peaks.xls INFO @ Tue, 14 Jul 2020 07:06:43: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX7262192/SRX7262192.05_peaks.narrowPeak INFO @ Tue, 14 Jul 2020 07:06:43: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX7262192/SRX7262192.05_summits.bed INFO @ Tue, 14 Jul 2020 07:06:43: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (643 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Tue, 14 Jul 2020 07:06:43: 8000000 INFO @ Tue, 14 Jul 2020 07:06:46: 3000000 INFO @ Tue, 14 Jul 2020 07:06:48: #1 tag size is determined as 50 bps INFO @ Tue, 14 Jul 2020 07:06:48: #1 tag size = 50 INFO @ Tue, 14 Jul 2020 07:06:48: #1 total tags in treatment: 8893984 INFO @ Tue, 14 Jul 2020 07:06:48: #1 user defined the maximum tags... INFO @ Tue, 14 Jul 2020 07:06:48: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 14 Jul 2020 07:06:48: #1 tags after filtering in treatment: 8893984 INFO @ Tue, 14 Jul 2020 07:06:48: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 14 Jul 2020 07:06:48: #1 finished! INFO @ Tue, 14 Jul 2020 07:06:48: #2 Build Peak Model... INFO @ Tue, 14 Jul 2020 07:06:48: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 14 Jul 2020 07:06:49: #2 number of paired peaks: 309 WARNING @ Tue, 14 Jul 2020 07:06:49: Fewer paired peaks (309) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 309 pairs to build model! INFO @ Tue, 14 Jul 2020 07:06:49: start model_add_line... INFO @ Tue, 14 Jul 2020 07:06:49: start X-correlation... INFO @ Tue, 14 Jul 2020 07:06:49: end of X-cor INFO @ Tue, 14 Jul 2020 07:06:49: #2 finished! INFO @ Tue, 14 Jul 2020 07:06:49: #2 predicted fragment length is 47 bps INFO @ Tue, 14 Jul 2020 07:06:49: #2 alternative fragment length(s) may be 3,47 bps INFO @ Tue, 14 Jul 2020 07:06:49: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX7262192/SRX7262192.10_model.r WARNING @ Tue, 14 Jul 2020 07:06:49: #2 Since the d (47) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 14 Jul 2020 07:06:49: #2 You may need to consider one of the other alternative d(s): 3,47 WARNING @ Tue, 14 Jul 2020 07:06:49: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 14 Jul 2020 07:06:49: #3 Call peaks... INFO @ Tue, 14 Jul 2020 07:06:49: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 14 Jul 2020 07:06:52: 4000000 INFO @ Tue, 14 Jul 2020 07:06:57: 5000000 INFO @ Tue, 14 Jul 2020 07:07:02: 6000000 INFO @ Tue, 14 Jul 2020 07:07:07: #3 Call peaks for each chromosome... INFO @ Tue, 14 Jul 2020 07:07:08: 7000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 14 Jul 2020 07:07:13: 8000000 INFO @ Tue, 14 Jul 2020 07:07:15: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX7262192/SRX7262192.10_peaks.xls INFO @ Tue, 14 Jul 2020 07:07:15: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX7262192/SRX7262192.10_peaks.narrowPeak INFO @ Tue, 14 Jul 2020 07:07:15: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX7262192/SRX7262192.10_summits.bed INFO @ Tue, 14 Jul 2020 07:07:15: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (397 records, 4 fields): 14 millis CompletedMACS2peakCalling INFO @ Tue, 14 Jul 2020 07:07:18: #1 tag size is determined as 50 bps INFO @ Tue, 14 Jul 2020 07:07:18: #1 tag size = 50 INFO @ Tue, 14 Jul 2020 07:07:18: #1 total tags in treatment: 8893984 INFO @ Tue, 14 Jul 2020 07:07:18: #1 user defined the maximum tags... INFO @ Tue, 14 Jul 2020 07:07:18: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 14 Jul 2020 07:07:18: #1 tags after filtering in treatment: 8893984 INFO @ Tue, 14 Jul 2020 07:07:18: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 14 Jul 2020 07:07:18: #1 finished! INFO @ Tue, 14 Jul 2020 07:07:18: #2 Build Peak Model... INFO @ Tue, 14 Jul 2020 07:07:18: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 14 Jul 2020 07:07:18: #2 number of paired peaks: 309 WARNING @ Tue, 14 Jul 2020 07:07:18: Fewer paired peaks (309) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 309 pairs to build model! INFO @ Tue, 14 Jul 2020 07:07:18: start model_add_line... INFO @ Tue, 14 Jul 2020 07:07:18: start X-correlation... INFO @ Tue, 14 Jul 2020 07:07:18: end of X-cor INFO @ Tue, 14 Jul 2020 07:07:18: #2 finished! INFO @ Tue, 14 Jul 2020 07:07:18: #2 predicted fragment length is 47 bps INFO @ Tue, 14 Jul 2020 07:07:18: #2 alternative fragment length(s) may be 3,47 bps INFO @ Tue, 14 Jul 2020 07:07:18: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX7262192/SRX7262192.20_model.r WARNING @ Tue, 14 Jul 2020 07:07:18: #2 Since the d (47) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 14 Jul 2020 07:07:18: #2 You may need to consider one of the other alternative d(s): 3,47 WARNING @ Tue, 14 Jul 2020 07:07:18: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 14 Jul 2020 07:07:18: #3 Call peaks... INFO @ Tue, 14 Jul 2020 07:07:18: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Tue, 14 Jul 2020 07:07:36: #3 Call peaks for each chromosome... INFO @ Tue, 14 Jul 2020 07:07:44: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX7262192/SRX7262192.20_peaks.xls INFO @ Tue, 14 Jul 2020 07:07:44: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX7262192/SRX7262192.20_peaks.narrowPeak INFO @ Tue, 14 Jul 2020 07:07:44: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX7262192/SRX7262192.20_summits.bed INFO @ Tue, 14 Jul 2020 07:07:44: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (166 records, 4 fields): 17 millis CompletedMACS2peakCalling