Job ID = 14157995 SRX = SRX7879262 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: 00:04:01 32553506 reads; of these: 32553506 (100.00%) were unpaired; of these: 24758154 (76.05%) aligned 0 times 6526692 (20.05%) aligned exactly 1 time 1268660 (3.90%) aligned >1 times 23.95% overall alignment rate Time searching: 00:04:01 Overall time: 00:04:01 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] 2853772 / 7795352 = 0.3661 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/3.8.3/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Wed, 08 Dec 2021 13:52:25: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX7879262/SRX7879262.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX7879262/SRX7879262.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX7879262/SRX7879262.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX7879262/SRX7879262.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 @ Wed, 08 Dec 2021 13:52:25: #1 read tag files... INFO @ Wed, 08 Dec 2021 13:52:25: #1 read treatment tags... INFO @ Wed, 08 Dec 2021 13:52:31: 1000000 INFO @ Wed, 08 Dec 2021 13:52:36: 2000000 INFO @ Wed, 08 Dec 2021 13:52:41: 3000000 INFO @ Wed, 08 Dec 2021 13:52:46: 4000000 INFO @ Wed, 08 Dec 2021 13:52:51: #1 tag size is determined as 50 bps INFO @ Wed, 08 Dec 2021 13:52:51: #1 tag size = 50 INFO @ Wed, 08 Dec 2021 13:52:51: #1 total tags in treatment: 4941580 INFO @ Wed, 08 Dec 2021 13:52:51: #1 user defined the maximum tags... INFO @ Wed, 08 Dec 2021 13:52:51: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Wed, 08 Dec 2021 13:52:52: #1 tags after filtering in treatment: 4941580 INFO @ Wed, 08 Dec 2021 13:52:52: #1 Redundant rate of treatment: 0.00 INFO @ Wed, 08 Dec 2021 13:52:52: #1 finished! INFO @ Wed, 08 Dec 2021 13:52:52: #2 Build Peak Model... INFO @ Wed, 08 Dec 2021 13:52:52: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 08 Dec 2021 13:52:52: #2 number of paired peaks: 496 WARNING @ Wed, 08 Dec 2021 13:52:52: Fewer paired peaks (496) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 496 pairs to build model! INFO @ Wed, 08 Dec 2021 13:52:52: start model_add_line... INFO @ Wed, 08 Dec 2021 13:52:52: start X-correlation... INFO @ Wed, 08 Dec 2021 13:52:52: end of X-cor INFO @ Wed, 08 Dec 2021 13:52:52: #2 finished! INFO @ Wed, 08 Dec 2021 13:52:52: #2 predicted fragment length is 48 bps INFO @ Wed, 08 Dec 2021 13:52:52: #2 alternative fragment length(s) may be 4,48,468,570,587 bps INFO @ Wed, 08 Dec 2021 13:52:52: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX7879262/SRX7879262.05_model.r WARNING @ Wed, 08 Dec 2021 13:52:52: #2 Since the d (48) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Wed, 08 Dec 2021 13:52:52: #2 You may need to consider one of the other alternative d(s): 4,48,468,570,587 WARNING @ Wed, 08 Dec 2021 13:52:52: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Wed, 08 Dec 2021 13:52:52: #3 Call peaks... INFO @ Wed, 08 Dec 2021 13:52:52: #3 Pre-compute pvalue-qvalue table... WARNING: Skipping mount /opt/pkg/singularity/3.8.3/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Wed, 08 Dec 2021 13:52:55: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX7879262/SRX7879262.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX7879262/SRX7879262.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX7879262/SRX7879262.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX7879262/SRX7879262.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 @ Wed, 08 Dec 2021 13:52:55: #1 read tag files... INFO @ Wed, 08 Dec 2021 13:52:55: #1 read treatment tags... INFO @ Wed, 08 Dec 2021 13:53:00: 1000000 INFO @ Wed, 08 Dec 2021 13:53:02: #3 Call peaks for each chromosome... INFO @ Wed, 08 Dec 2021 13:53:05: 2000000 INFO @ Wed, 08 Dec 2021 13:53:07: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX7879262/SRX7879262.05_peaks.xls INFO @ Wed, 08 Dec 2021 13:53:07: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX7879262/SRX7879262.05_peaks.narrowPeak INFO @ Wed, 08 Dec 2021 13:53:07: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX7879262/SRX7879262.05_summits.bed INFO @ Wed, 08 Dec 2021 13:53:07: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (630 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Wed, 08 Dec 2021 13:53:10: 3000000 INFO @ Wed, 08 Dec 2021 13:53:18: 4000000 BedGraph に変換中... WARNING: Skipping mount /opt/pkg/singularity/3.8.3/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Wed, 08 Dec 2021 13:53:25: #1 tag size is determined as 50 bps INFO @ Wed, 08 Dec 2021 13:53:25: #1 tag size = 50 INFO @ Wed, 08 Dec 2021 13:53:25: #1 total tags in treatment: 4941580 INFO @ Wed, 08 Dec 2021 13:53:25: #1 user defined the maximum tags... INFO @ Wed, 08 Dec 2021 13:53:25: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Wed, 08 Dec 2021 13:53:25: #1 tags after filtering in treatment: 4941580 INFO @ Wed, 08 Dec 2021 13:53:25: #1 Redundant rate of treatment: 0.00 INFO @ Wed, 08 Dec 2021 13:53:25: #1 finished! INFO @ Wed, 08 Dec 2021 13:53:25: #2 Build Peak Model... INFO @ Wed, 08 Dec 2021 13:53:25: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 08 Dec 2021 13:53:26: #2 number of paired peaks: 496 WARNING @ Wed, 08 Dec 2021 13:53:26: Fewer paired peaks (496) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 496 pairs to build model! INFO @ Wed, 08 Dec 2021 13:53:26: start model_add_line... INFO @ Wed, 08 Dec 2021 13:53:26: start X-correlation... INFO @ Wed, 08 Dec 2021 13:53:26: end of X-cor INFO @ Wed, 08 Dec 2021 13:53:26: #2 finished! INFO @ Wed, 08 Dec 2021 13:53:26: #2 predicted fragment length is 48 bps INFO @ Wed, 08 Dec 2021 13:53:26: #2 alternative fragment length(s) may be 4,48,468,570,587 bps INFO @ Wed, 08 Dec 2021 13:53:26: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX7879262/SRX7879262.10_model.r WARNING @ Wed, 08 Dec 2021 13:53:26: #2 Since the d (48) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Wed, 08 Dec 2021 13:53:26: #2 You may need to consider one of the other alternative d(s): 4,48,468,570,587 WARNING @ Wed, 08 Dec 2021 13:53:26: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Wed, 08 Dec 2021 13:53:26: #3 Call peaks... INFO @ Wed, 08 Dec 2021 13:53:26: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 08 Dec 2021 13:53:29: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX7879262/SRX7879262.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX7879262/SRX7879262.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX7879262/SRX7879262.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX7879262/SRX7879262.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 @ Wed, 08 Dec 2021 13:53:29: #1 read tag files... INFO @ Wed, 08 Dec 2021 13:53:29: #1 read treatment tags... INFO @ Wed, 08 Dec 2021 13:53:37: 1000000 INFO @ Wed, 08 Dec 2021 13:53:40: #3 Call peaks for each chromosome... INFO @ Wed, 08 Dec 2021 13:53:46: 2000000 INFO @ Wed, 08 Dec 2021 13:53:47: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX7879262/SRX7879262.10_peaks.xls INFO @ Wed, 08 Dec 2021 13:53:47: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX7879262/SRX7879262.10_peaks.narrowPeak INFO @ Wed, 08 Dec 2021 13:53:47: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX7879262/SRX7879262.10_summits.bed INFO @ Wed, 08 Dec 2021 13:53:47: Done! pass1 - making usageList (6 chroms): 20 millis pass2 - checking and writing primary data (381 records, 4 fields): 13 millis CompletedMACS2peakCalling INFO @ Wed, 08 Dec 2021 13:53:53: 3000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Wed, 08 Dec 2021 13:54:02: 4000000 INFO @ Wed, 08 Dec 2021 13:54:10: #1 tag size is determined as 50 bps INFO @ Wed, 08 Dec 2021 13:54:10: #1 tag size = 50 INFO @ Wed, 08 Dec 2021 13:54:10: #1 total tags in treatment: 4941580 INFO @ Wed, 08 Dec 2021 13:54:10: #1 user defined the maximum tags... INFO @ Wed, 08 Dec 2021 13:54:10: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Wed, 08 Dec 2021 13:54:10: #1 tags after filtering in treatment: 4941580 INFO @ Wed, 08 Dec 2021 13:54:10: #1 Redundant rate of treatment: 0.00 INFO @ Wed, 08 Dec 2021 13:54:10: #1 finished! INFO @ Wed, 08 Dec 2021 13:54:10: #2 Build Peak Model... INFO @ Wed, 08 Dec 2021 13:54:10: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 08 Dec 2021 13:54:10: #2 number of paired peaks: 496 WARNING @ Wed, 08 Dec 2021 13:54:10: Fewer paired peaks (496) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 496 pairs to build model! INFO @ Wed, 08 Dec 2021 13:54:10: start model_add_line... INFO @ Wed, 08 Dec 2021 13:54:11: start X-correlation... INFO @ Wed, 08 Dec 2021 13:54:11: end of X-cor INFO @ Wed, 08 Dec 2021 13:54:11: #2 finished! INFO @ Wed, 08 Dec 2021 13:54:11: #2 predicted fragment length is 48 bps INFO @ Wed, 08 Dec 2021 13:54:11: #2 alternative fragment length(s) may be 4,48,468,570,587 bps INFO @ Wed, 08 Dec 2021 13:54:11: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX7879262/SRX7879262.20_model.r WARNING @ Wed, 08 Dec 2021 13:54:11: #2 Since the d (48) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Wed, 08 Dec 2021 13:54:11: #2 You may need to consider one of the other alternative d(s): 4,48,468,570,587 WARNING @ Wed, 08 Dec 2021 13:54:11: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Wed, 08 Dec 2021 13:54:11: #3 Call peaks... INFO @ Wed, 08 Dec 2021 13:54:11: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Wed, 08 Dec 2021 13:54:24: #3 Call peaks for each chromosome... INFO @ Wed, 08 Dec 2021 13:54:30: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX7879262/SRX7879262.20_peaks.xls INFO @ Wed, 08 Dec 2021 13:54:30: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX7879262/SRX7879262.20_peaks.narrowPeak INFO @ Wed, 08 Dec 2021 13:54:30: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX7879262/SRX7879262.20_summits.bed INFO @ Wed, 08 Dec 2021 13:54:30: Done! pass1 - making usageList (6 chroms): 32 millis pass2 - checking and writing primary data (149 records, 4 fields): 34 millis CompletedMACS2peakCalling