Job ID = 6626511 SRX = SRX7262239 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: 00:01:07 4289752 reads; of these: 4289752 (100.00%) were unpaired; of these: 339309 (7.91%) aligned 0 times 3110058 (72.50%) aligned exactly 1 time 840385 (19.59%) aligned >1 times 92.09% overall alignment rate Time searching: 00:01:07 Overall time: 00:01:07 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] 980711 / 3950443 = 0.2483 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 07:17:26: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX7262239/SRX7262239.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX7262239/SRX7262239.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX7262239/SRX7262239.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX7262239/SRX7262239.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 07:17:26: #1 read tag files... INFO @ Tue, 14 Jul 2020 07:17:26: #1 read treatment tags... INFO @ Tue, 14 Jul 2020 07:17:34: 1000000 INFO @ Tue, 14 Jul 2020 07:17:43: 2000000 INFO @ Tue, 14 Jul 2020 07:17:49: #1 tag size is determined as 50 bps INFO @ Tue, 14 Jul 2020 07:17:49: #1 tag size = 50 INFO @ Tue, 14 Jul 2020 07:17:49: #1 total tags in treatment: 2969732 INFO @ Tue, 14 Jul 2020 07:17:49: #1 user defined the maximum tags... INFO @ Tue, 14 Jul 2020 07:17:49: #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 07:17:49: #1 tags after filtering in treatment: 2969732 INFO @ Tue, 14 Jul 2020 07:17:49: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 14 Jul 2020 07:17:49: #1 finished! INFO @ Tue, 14 Jul 2020 07:17:49: #2 Build Peak Model... INFO @ Tue, 14 Jul 2020 07:17:49: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 14 Jul 2020 07:17:50: #2 number of paired peaks: 552 WARNING @ Tue, 14 Jul 2020 07:17:50: Fewer paired peaks (552) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 552 pairs to build model! INFO @ Tue, 14 Jul 2020 07:17:50: start model_add_line... INFO @ Tue, 14 Jul 2020 07:17:50: start X-correlation... INFO @ Tue, 14 Jul 2020 07:17:50: end of X-cor INFO @ Tue, 14 Jul 2020 07:17:50: #2 finished! INFO @ Tue, 14 Jul 2020 07:17:50: #2 predicted fragment length is 48 bps INFO @ Tue, 14 Jul 2020 07:17:50: #2 alternative fragment length(s) may be 4,48,575 bps INFO @ Tue, 14 Jul 2020 07:17:50: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX7262239/SRX7262239.05_model.r WARNING @ Tue, 14 Jul 2020 07:17:50: #2 Since the d (48) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 14 Jul 2020 07:17:50: #2 You may need to consider one of the other alternative d(s): 4,48,575 WARNING @ Tue, 14 Jul 2020 07:17:50: #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 07:17:50: #3 Call peaks... INFO @ Tue, 14 Jul 2020 07:17:50: #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, 14 Jul 2020 07:17:56: #3 Call peaks for each chromosome... INFO @ Tue, 14 Jul 2020 07:17:56: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX7262239/SRX7262239.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX7262239/SRX7262239.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX7262239/SRX7262239.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX7262239/SRX7262239.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 07:17:56: #1 read tag files... INFO @ Tue, 14 Jul 2020 07:17:56: #1 read treatment tags... INFO @ Tue, 14 Jul 2020 07:17:59: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX7262239/SRX7262239.05_peaks.xls INFO @ Tue, 14 Jul 2020 07:17:59: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX7262239/SRX7262239.05_peaks.narrowPeak INFO @ Tue, 14 Jul 2020 07:17:59: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX7262239/SRX7262239.05_summits.bed INFO @ Tue, 14 Jul 2020 07:17:59: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (523 records, 4 fields): 14 millis CompletedMACS2peakCalling INFO @ Tue, 14 Jul 2020 07:18:04: 1000000 INFO @ Tue, 14 Jul 2020 07:18:11: 2000000 INFO @ Tue, 14 Jul 2020 07:18:18: #1 tag size is determined as 50 bps INFO @ Tue, 14 Jul 2020 07:18:18: #1 tag size = 50 INFO @ Tue, 14 Jul 2020 07:18:18: #1 total tags in treatment: 2969732 INFO @ Tue, 14 Jul 2020 07:18:18: #1 user defined the maximum tags... INFO @ Tue, 14 Jul 2020 07:18:18: #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 07:18:18: #1 tags after filtering in treatment: 2969732 INFO @ Tue, 14 Jul 2020 07:18:18: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 14 Jul 2020 07:18:18: #1 finished! INFO @ Tue, 14 Jul 2020 07:18:18: #2 Build Peak Model... INFO @ Tue, 14 Jul 2020 07:18:18: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 14 Jul 2020 07:18:18: #2 number of paired peaks: 552 WARNING @ Tue, 14 Jul 2020 07:18:18: Fewer paired peaks (552) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 552 pairs to build model! INFO @ Tue, 14 Jul 2020 07:18:18: start model_add_line... INFO @ Tue, 14 Jul 2020 07:18:18: start X-correlation... INFO @ Tue, 14 Jul 2020 07:18:18: end of X-cor INFO @ Tue, 14 Jul 2020 07:18:18: #2 finished! INFO @ Tue, 14 Jul 2020 07:18:18: #2 predicted fragment length is 48 bps INFO @ Tue, 14 Jul 2020 07:18:18: #2 alternative fragment length(s) may be 4,48,575 bps INFO @ Tue, 14 Jul 2020 07:18:18: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX7262239/SRX7262239.10_model.r WARNING @ Tue, 14 Jul 2020 07:18:18: #2 Since the d (48) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 14 Jul 2020 07:18:18: #2 You may need to consider one of the other alternative d(s): 4,48,575 WARNING @ Tue, 14 Jul 2020 07:18:18: #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 07:18:18: #3 Call peaks... INFO @ Tue, 14 Jul 2020 07:18:18: #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, 14 Jul 2020 07:18:25: #3 Call peaks for each chromosome... INFO @ Tue, 14 Jul 2020 07:18:26: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX7262239/SRX7262239.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX7262239/SRX7262239.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX7262239/SRX7262239.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX7262239/SRX7262239.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 07:18:26: #1 read tag files... INFO @ Tue, 14 Jul 2020 07:18:26: #1 read treatment tags... INFO @ Tue, 14 Jul 2020 07:18:28: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX7262239/SRX7262239.10_peaks.xls INFO @ Tue, 14 Jul 2020 07:18:28: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX7262239/SRX7262239.10_peaks.narrowPeak INFO @ Tue, 14 Jul 2020 07:18:28: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX7262239/SRX7262239.10_summits.bed INFO @ Tue, 14 Jul 2020 07:18:28: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (316 records, 4 fields): 18 millis CompletedMACS2peakCalling INFO @ Tue, 14 Jul 2020 07:18:34: 1000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 14 Jul 2020 07:18:41: 2000000 BigWig に変換しました。 INFO @ Tue, 14 Jul 2020 07:18:47: #1 tag size is determined as 50 bps INFO @ Tue, 14 Jul 2020 07:18:47: #1 tag size = 50 INFO @ Tue, 14 Jul 2020 07:18:47: #1 total tags in treatment: 2969732 INFO @ Tue, 14 Jul 2020 07:18:47: #1 user defined the maximum tags... INFO @ Tue, 14 Jul 2020 07:18:47: #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 07:18:47: #1 tags after filtering in treatment: 2969732 INFO @ Tue, 14 Jul 2020 07:18:47: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 14 Jul 2020 07:18:47: #1 finished! INFO @ Tue, 14 Jul 2020 07:18:47: #2 Build Peak Model... INFO @ Tue, 14 Jul 2020 07:18:47: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 14 Jul 2020 07:18:47: #2 number of paired peaks: 552 WARNING @ Tue, 14 Jul 2020 07:18:47: Fewer paired peaks (552) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 552 pairs to build model! INFO @ Tue, 14 Jul 2020 07:18:47: start model_add_line... INFO @ Tue, 14 Jul 2020 07:18:47: start X-correlation... INFO @ Tue, 14 Jul 2020 07:18:47: end of X-cor INFO @ Tue, 14 Jul 2020 07:18:47: #2 finished! INFO @ Tue, 14 Jul 2020 07:18:47: #2 predicted fragment length is 48 bps INFO @ Tue, 14 Jul 2020 07:18:47: #2 alternative fragment length(s) may be 4,48,575 bps INFO @ Tue, 14 Jul 2020 07:18:47: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX7262239/SRX7262239.20_model.r WARNING @ Tue, 14 Jul 2020 07:18:47: #2 Since the d (48) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 14 Jul 2020 07:18:47: #2 You may need to consider one of the other alternative d(s): 4,48,575 WARNING @ Tue, 14 Jul 2020 07:18:47: #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 07:18:47: #3 Call peaks... INFO @ Tue, 14 Jul 2020 07:18:47: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 14 Jul 2020 07:18:53: #3 Call peaks for each chromosome... INFO @ Tue, 14 Jul 2020 07:18:57: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX7262239/SRX7262239.20_peaks.xls INFO @ Tue, 14 Jul 2020 07:18:57: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX7262239/SRX7262239.20_peaks.narrowPeak INFO @ Tue, 14 Jul 2020 07:18:57: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX7262239/SRX7262239.20_summits.bed INFO @ Tue, 14 Jul 2020 07:18:57: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (123 records, 4 fields): 17 millis CompletedMACS2peakCalling