Job ID = 6626446 SRX = SRX7262194 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: 00:02:10 9435488 reads; of these: 9435488 (100.00%) were unpaired; of these: 222256 (2.36%) aligned 0 times 7105696 (75.31%) aligned exactly 1 time 2107536 (22.34%) aligned >1 times 97.64% overall alignment rate Time searching: 00:02:10 Overall time: 00:02:10 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] 982120 / 9213232 = 0.1066 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 07:06:34: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX7262194/SRX7262194.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX7262194/SRX7262194.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX7262194/SRX7262194.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX7262194/SRX7262194.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 07:06:34: #1 read tag files... INFO @ Tue, 14 Jul 2020 07:06:34: #1 read treatment tags... INFO @ Tue, 14 Jul 2020 07:06:39: 1000000 INFO @ Tue, 14 Jul 2020 07:06:44: 2000000 INFO @ Tue, 14 Jul 2020 07:06:49: 3000000 INFO @ Tue, 14 Jul 2020 07:06:54: 4000000 INFO @ Tue, 14 Jul 2020 07:06:59: 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 07:07:04: 6000000 INFO @ Tue, 14 Jul 2020 07:07:04: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX7262194/SRX7262194.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX7262194/SRX7262194.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX7262194/SRX7262194.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX7262194/SRX7262194.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 07:07:04: #1 read tag files... INFO @ Tue, 14 Jul 2020 07:07:04: #1 read treatment tags... INFO @ Tue, 14 Jul 2020 07:07:09: 7000000 INFO @ Tue, 14 Jul 2020 07:07:10: 1000000 INFO @ Tue, 14 Jul 2020 07:07:14: 8000000 INFO @ Tue, 14 Jul 2020 07:07:15: #1 tag size is determined as 50 bps INFO @ Tue, 14 Jul 2020 07:07:15: #1 tag size = 50 INFO @ Tue, 14 Jul 2020 07:07:15: #1 total tags in treatment: 8231112 INFO @ Tue, 14 Jul 2020 07:07:15: #1 user defined the maximum tags... INFO @ Tue, 14 Jul 2020 07:07:15: #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 07:07:15: #1 tags after filtering in treatment: 8231112 INFO @ Tue, 14 Jul 2020 07:07:15: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 14 Jul 2020 07:07:15: #1 finished! INFO @ Tue, 14 Jul 2020 07:07:15: #2 Build Peak Model... INFO @ Tue, 14 Jul 2020 07:07:15: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 14 Jul 2020 07:07:16: 2000000 INFO @ Tue, 14 Jul 2020 07:07:16: #2 number of paired peaks: 465 WARNING @ Tue, 14 Jul 2020 07:07:16: Fewer paired peaks (465) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 465 pairs to build model! INFO @ Tue, 14 Jul 2020 07:07:16: start model_add_line... INFO @ Tue, 14 Jul 2020 07:07:16: start X-correlation... INFO @ Tue, 14 Jul 2020 07:07:16: end of X-cor INFO @ Tue, 14 Jul 2020 07:07:16: #2 finished! INFO @ Tue, 14 Jul 2020 07:07:16: #2 predicted fragment length is 47 bps INFO @ Tue, 14 Jul 2020 07:07:16: #2 alternative fragment length(s) may be 2,47,578 bps INFO @ Tue, 14 Jul 2020 07:07:16: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX7262194/SRX7262194.05_model.r WARNING @ Tue, 14 Jul 2020 07:07:16: #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 07:07:16: #2 You may need to consider one of the other alternative d(s): 2,47,578 WARNING @ Tue, 14 Jul 2020 07:07:16: #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 07:07:16: #3 Call peaks... INFO @ Tue, 14 Jul 2020 07:07:16: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 14 Jul 2020 07:07:21: 3000000 INFO @ Tue, 14 Jul 2020 07:07:27: 4000000 INFO @ Tue, 14 Jul 2020 07:07:32: #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, 14 Jul 2020 07:07:32: 5000000 INFO @ Tue, 14 Jul 2020 07:07:34: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX7262194/SRX7262194.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX7262194/SRX7262194.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX7262194/SRX7262194.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX7262194/SRX7262194.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 07:07:34: #1 read tag files... INFO @ Tue, 14 Jul 2020 07:07:34: #1 read treatment tags... INFO @ Tue, 14 Jul 2020 07:07:38: 6000000 INFO @ Tue, 14 Jul 2020 07:07:39: 1000000 INFO @ Tue, 14 Jul 2020 07:07:40: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX7262194/SRX7262194.05_peaks.xls INFO @ Tue, 14 Jul 2020 07:07:40: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX7262194/SRX7262194.05_peaks.narrowPeak INFO @ Tue, 14 Jul 2020 07:07:40: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX7262194/SRX7262194.05_summits.bed INFO @ Tue, 14 Jul 2020 07:07:40: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (656 records, 4 fields): 21 millis CompletedMACS2peakCalling INFO @ Tue, 14 Jul 2020 07:07:44: 7000000 INFO @ Tue, 14 Jul 2020 07:07:44: 2000000 INFO @ Tue, 14 Jul 2020 07:07:49: 3000000 INFO @ Tue, 14 Jul 2020 07:07:50: 8000000 INFO @ Tue, 14 Jul 2020 07:07:51: #1 tag size is determined as 50 bps INFO @ Tue, 14 Jul 2020 07:07:51: #1 tag size = 50 INFO @ Tue, 14 Jul 2020 07:07:51: #1 total tags in treatment: 8231112 INFO @ Tue, 14 Jul 2020 07:07:51: #1 user defined the maximum tags... INFO @ Tue, 14 Jul 2020 07:07:51: #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 07:07:51: #1 tags after filtering in treatment: 8231112 INFO @ Tue, 14 Jul 2020 07:07:51: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 14 Jul 2020 07:07:51: #1 finished! INFO @ Tue, 14 Jul 2020 07:07:51: #2 Build Peak Model... INFO @ Tue, 14 Jul 2020 07:07:51: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 14 Jul 2020 07:07:52: #2 number of paired peaks: 465 WARNING @ Tue, 14 Jul 2020 07:07:52: Fewer paired peaks (465) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 465 pairs to build model! INFO @ Tue, 14 Jul 2020 07:07:52: start model_add_line... INFO @ Tue, 14 Jul 2020 07:07:52: start X-correlation... INFO @ Tue, 14 Jul 2020 07:07:52: end of X-cor INFO @ Tue, 14 Jul 2020 07:07:52: #2 finished! INFO @ Tue, 14 Jul 2020 07:07:52: #2 predicted fragment length is 47 bps INFO @ Tue, 14 Jul 2020 07:07:52: #2 alternative fragment length(s) may be 2,47,578 bps INFO @ Tue, 14 Jul 2020 07:07:52: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX7262194/SRX7262194.10_model.r WARNING @ Tue, 14 Jul 2020 07:07:52: #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 07:07:52: #2 You may need to consider one of the other alternative d(s): 2,47,578 WARNING @ Tue, 14 Jul 2020 07:07:52: #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 07:07:52: #3 Call peaks... INFO @ Tue, 14 Jul 2020 07:07:52: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 14 Jul 2020 07:07:54: 4000000 INFO @ Tue, 14 Jul 2020 07:07:59: 5000000 INFO @ Tue, 14 Jul 2020 07:08:04: 6000000 INFO @ Tue, 14 Jul 2020 07:08:07: #3 Call peaks for each chromosome... BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 14 Jul 2020 07:08:09: 7000000 INFO @ Tue, 14 Jul 2020 07:08:14: 8000000 INFO @ Tue, 14 Jul 2020 07:08:15: #1 tag size is determined as 50 bps INFO @ Tue, 14 Jul 2020 07:08:15: #1 tag size = 50 INFO @ Tue, 14 Jul 2020 07:08:15: #1 total tags in treatment: 8231112 INFO @ Tue, 14 Jul 2020 07:08:15: #1 user defined the maximum tags... INFO @ Tue, 14 Jul 2020 07:08:15: #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 07:08:15: #1 tags after filtering in treatment: 8231112 INFO @ Tue, 14 Jul 2020 07:08:15: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 14 Jul 2020 07:08:15: #1 finished! INFO @ Tue, 14 Jul 2020 07:08:15: #2 Build Peak Model... INFO @ Tue, 14 Jul 2020 07:08:15: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 14 Jul 2020 07:08:15: #2 number of paired peaks: 465 WARNING @ Tue, 14 Jul 2020 07:08:15: Fewer paired peaks (465) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 465 pairs to build model! INFO @ Tue, 14 Jul 2020 07:08:15: start model_add_line... INFO @ Tue, 14 Jul 2020 07:08:15: start X-correlation... INFO @ Tue, 14 Jul 2020 07:08:15: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX7262194/SRX7262194.10_peaks.xls INFO @ Tue, 14 Jul 2020 07:08:15: end of X-cor INFO @ Tue, 14 Jul 2020 07:08:15: #2 finished! INFO @ Tue, 14 Jul 2020 07:08:15: #2 predicted fragment length is 47 bps INFO @ Tue, 14 Jul 2020 07:08:15: #2 alternative fragment length(s) may be 2,47,578 bps INFO @ Tue, 14 Jul 2020 07:08:15: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX7262194/SRX7262194.20_model.r INFO @ Tue, 14 Jul 2020 07:08:15: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX7262194/SRX7262194.10_peaks.narrowPeak WARNING @ Tue, 14 Jul 2020 07:08:15: #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 07:08:15: #2 You may need to consider one of the other alternative d(s): 2,47,578 WARNING @ Tue, 14 Jul 2020 07:08:15: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 14 Jul 2020 07:08:15: #3 Call peaks... INFO @ Tue, 14 Jul 2020 07:08:15: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 14 Jul 2020 07:08:16: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX7262194/SRX7262194.10_summits.bed INFO @ Tue, 14 Jul 2020 07:08:16: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (422 records, 4 fields): 16 millis CompletedMACS2peakCalling BigWig に変換しました。 INFO @ Tue, 14 Jul 2020 07:08:32: #3 Call peaks for each chromosome... INFO @ Tue, 14 Jul 2020 07:08:40: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX7262194/SRX7262194.20_peaks.xls INFO @ Tue, 14 Jul 2020 07:08:40: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX7262194/SRX7262194.20_peaks.narrowPeak INFO @ Tue, 14 Jul 2020 07:08:40: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX7262194/SRX7262194.20_summits.bed INFO @ Tue, 14 Jul 2020 07:08:40: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (170 records, 4 fields): 12 millis CompletedMACS2peakCalling