Job ID = 6626469 SRX = SRX7262227 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: 00:01:29 6929800 reads; of these: 6929800 (100.00%) were unpaired; of these: 677781 (9.78%) aligned 0 times 5039614 (72.72%) aligned exactly 1 time 1212405 (17.50%) aligned >1 times 90.22% overall alignment rate Time searching: 00:01:29 Overall time: 00:01:29 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] 1376030 / 6252019 = 0.2201 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 07:07:23: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX7262227/SRX7262227.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX7262227/SRX7262227.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX7262227/SRX7262227.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX7262227/SRX7262227.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 07:07:23: #1 read tag files... INFO @ Tue, 14 Jul 2020 07:07:23: #1 read treatment tags... INFO @ Tue, 14 Jul 2020 07:07:28: 1000000 INFO @ Tue, 14 Jul 2020 07:07:34: 2000000 INFO @ Tue, 14 Jul 2020 07:07:39: 3000000 INFO @ Tue, 14 Jul 2020 07:07:45: 4000000 INFO @ Tue, 14 Jul 2020 07:07:50: #1 tag size is determined as 50 bps INFO @ Tue, 14 Jul 2020 07:07:50: #1 tag size = 50 INFO @ Tue, 14 Jul 2020 07:07:50: #1 total tags in treatment: 4875989 INFO @ Tue, 14 Jul 2020 07:07:50: #1 user defined the maximum tags... INFO @ Tue, 14 Jul 2020 07:07:50: #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 07:07:50: #1 tags after filtering in treatment: 4875989 INFO @ Tue, 14 Jul 2020 07:07:50: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 14 Jul 2020 07:07:50: #1 finished! INFO @ Tue, 14 Jul 2020 07:07:50: #2 Build Peak Model... INFO @ Tue, 14 Jul 2020 07:07:50: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 14 Jul 2020 07:07:50: #2 number of paired peaks: 471 WARNING @ Tue, 14 Jul 2020 07:07:50: Fewer paired peaks (471) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 471 pairs to build model! INFO @ Tue, 14 Jul 2020 07:07:50: start model_add_line... INFO @ Tue, 14 Jul 2020 07:07:50: start X-correlation... INFO @ Tue, 14 Jul 2020 07:07:50: end of X-cor INFO @ Tue, 14 Jul 2020 07:07:50: #2 finished! INFO @ Tue, 14 Jul 2020 07:07:50: #2 predicted fragment length is 47 bps INFO @ Tue, 14 Jul 2020 07:07:50: #2 alternative fragment length(s) may be 4,47,570 bps INFO @ Tue, 14 Jul 2020 07:07:50: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX7262227/SRX7262227.05_model.r WARNING @ Tue, 14 Jul 2020 07:07:50: #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 07:07:50: #2 You may need to consider one of the other alternative d(s): 4,47,570 WARNING @ Tue, 14 Jul 2020 07:07:50: #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 07:07:50: #3 Call peaks... INFO @ Tue, 14 Jul 2020 07:07:50: #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 07:07:53: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX7262227/SRX7262227.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX7262227/SRX7262227.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX7262227/SRX7262227.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX7262227/SRX7262227.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 07:07:53: #1 read tag files... INFO @ Tue, 14 Jul 2020 07:07:53: #1 read treatment tags... INFO @ Tue, 14 Jul 2020 07:07:59: 1000000 INFO @ Tue, 14 Jul 2020 07:08:00: #3 Call peaks for each chromosome... INFO @ Tue, 14 Jul 2020 07:08:05: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX7262227/SRX7262227.05_peaks.xls INFO @ Tue, 14 Jul 2020 07:08:05: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX7262227/SRX7262227.05_peaks.narrowPeak INFO @ Tue, 14 Jul 2020 07:08:05: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX7262227/SRX7262227.05_summits.bed INFO @ Tue, 14 Jul 2020 07:08:05: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (573 records, 4 fields): 14 millis CompletedMACS2peakCalling INFO @ Tue, 14 Jul 2020 07:08:06: 2000000 INFO @ Tue, 14 Jul 2020 07:08:13: 3000000 INFO @ Tue, 14 Jul 2020 07:08:19: 4000000 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 07:08:23: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX7262227/SRX7262227.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX7262227/SRX7262227.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX7262227/SRX7262227.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX7262227/SRX7262227.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 07:08:23: #1 read tag files... INFO @ Tue, 14 Jul 2020 07:08:23: #1 read treatment tags... INFO @ Tue, 14 Jul 2020 07:08:25: #1 tag size is determined as 50 bps INFO @ Tue, 14 Jul 2020 07:08:25: #1 tag size = 50 INFO @ Tue, 14 Jul 2020 07:08:25: #1 total tags in treatment: 4875989 INFO @ Tue, 14 Jul 2020 07:08:25: #1 user defined the maximum tags... INFO @ Tue, 14 Jul 2020 07:08:25: #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 07:08:25: #1 tags after filtering in treatment: 4875989 INFO @ Tue, 14 Jul 2020 07:08:25: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 14 Jul 2020 07:08:25: #1 finished! INFO @ Tue, 14 Jul 2020 07:08:25: #2 Build Peak Model... INFO @ Tue, 14 Jul 2020 07:08:25: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 14 Jul 2020 07:08:25: #2 number of paired peaks: 471 WARNING @ Tue, 14 Jul 2020 07:08:25: Fewer paired peaks (471) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 471 pairs to build model! INFO @ Tue, 14 Jul 2020 07:08:25: start model_add_line... INFO @ Tue, 14 Jul 2020 07:08:26: start X-correlation... INFO @ Tue, 14 Jul 2020 07:08:26: end of X-cor INFO @ Tue, 14 Jul 2020 07:08:26: #2 finished! INFO @ Tue, 14 Jul 2020 07:08:26: #2 predicted fragment length is 47 bps INFO @ Tue, 14 Jul 2020 07:08:26: #2 alternative fragment length(s) may be 4,47,570 bps INFO @ Tue, 14 Jul 2020 07:08:26: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX7262227/SRX7262227.10_model.r WARNING @ Tue, 14 Jul 2020 07:08:26: #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 07:08:26: #2 You may need to consider one of the other alternative d(s): 4,47,570 WARNING @ Tue, 14 Jul 2020 07:08:26: #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 07:08:26: #3 Call peaks... INFO @ Tue, 14 Jul 2020 07:08:26: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 14 Jul 2020 07:08:30: 1000000 INFO @ Tue, 14 Jul 2020 07:08:36: #3 Call peaks for each chromosome... INFO @ Tue, 14 Jul 2020 07:08:36: 2000000 INFO @ Tue, 14 Jul 2020 07:08:41: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX7262227/SRX7262227.10_peaks.xls INFO @ Tue, 14 Jul 2020 07:08:41: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX7262227/SRX7262227.10_peaks.narrowPeak INFO @ Tue, 14 Jul 2020 07:08:41: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX7262227/SRX7262227.10_summits.bed INFO @ Tue, 14 Jul 2020 07:08:41: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (353 records, 4 fields): 24 millis CompletedMACS2peakCalling INFO @ Tue, 14 Jul 2020 07:08:43: 3000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 14 Jul 2020 07:08:50: 4000000 INFO @ Tue, 14 Jul 2020 07:08:55: #1 tag size is determined as 50 bps INFO @ Tue, 14 Jul 2020 07:08:55: #1 tag size = 50 INFO @ Tue, 14 Jul 2020 07:08:55: #1 total tags in treatment: 4875989 INFO @ Tue, 14 Jul 2020 07:08:55: #1 user defined the maximum tags... INFO @ Tue, 14 Jul 2020 07:08:55: #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 07:08:55: #1 tags after filtering in treatment: 4875989 INFO @ Tue, 14 Jul 2020 07:08:55: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 14 Jul 2020 07:08:55: #1 finished! INFO @ Tue, 14 Jul 2020 07:08:55: #2 Build Peak Model... INFO @ Tue, 14 Jul 2020 07:08:55: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 14 Jul 2020 07:08:56: #2 number of paired peaks: 471 WARNING @ Tue, 14 Jul 2020 07:08:56: Fewer paired peaks (471) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 471 pairs to build model! INFO @ Tue, 14 Jul 2020 07:08:56: start model_add_line... INFO @ Tue, 14 Jul 2020 07:08:56: start X-correlation... INFO @ Tue, 14 Jul 2020 07:08:56: end of X-cor INFO @ Tue, 14 Jul 2020 07:08:56: #2 finished! INFO @ Tue, 14 Jul 2020 07:08:56: #2 predicted fragment length is 47 bps INFO @ Tue, 14 Jul 2020 07:08:56: #2 alternative fragment length(s) may be 4,47,570 bps INFO @ Tue, 14 Jul 2020 07:08:56: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX7262227/SRX7262227.20_model.r WARNING @ Tue, 14 Jul 2020 07:08:56: #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 07:08:56: #2 You may need to consider one of the other alternative d(s): 4,47,570 WARNING @ Tue, 14 Jul 2020 07:08:56: #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 07:08:56: #3 Call peaks... INFO @ Tue, 14 Jul 2020 07:08:56: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Tue, 14 Jul 2020 07:09:06: #3 Call peaks for each chromosome... INFO @ Tue, 14 Jul 2020 07:09:11: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX7262227/SRX7262227.20_peaks.xls INFO @ Tue, 14 Jul 2020 07:09:11: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX7262227/SRX7262227.20_peaks.narrowPeak INFO @ Tue, 14 Jul 2020 07:09:11: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX7262227/SRX7262227.20_summits.bed INFO @ Tue, 14 Jul 2020 07:09:11: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (145 records, 4 fields): 64 millis CompletedMACS2peakCalling