Job ID = 6626408 SRX = SRX7262238 Genome = ce10 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... Read 3029738 spots for SRR10581861/SRR10581861.sra Written 3029738 spots for SRR10581861/SRR10581861.sra fastq に変換しました。 bowtie でマッピング中... Your job 6626476 ("srTce11") has been submitted Time loading reference: 00:00:00 Time loading forward index: 00:00:01 Time loading mirror index: 00:00:00 Multiseed full-index search: 00:00:44 3029738 reads; of these: 3029738 (100.00%) were unpaired; of these: 147942 (4.88%) aligned 0 times 2389040 (78.85%) aligned exactly 1 time 492756 (16.26%) aligned >1 times 95.12% overall alignment rate Time searching: 00:00:45 Overall time: 00:00:45 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] 105032 / 2881796 = 0.0364 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 07:00:25: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX7262238/SRX7262238.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX7262238/SRX7262238.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX7262238/SRX7262238.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX7262238/SRX7262238.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 07:00:25: #1 read tag files... INFO @ Tue, 14 Jul 2020 07:00:25: #1 read treatment tags... INFO @ Tue, 14 Jul 2020 07:00:31: 1000000 INFO @ Tue, 14 Jul 2020 07:00:36: 2000000 INFO @ Tue, 14 Jul 2020 07:00:40: #1 tag size is determined as 50 bps INFO @ Tue, 14 Jul 2020 07:00:40: #1 tag size = 50 INFO @ Tue, 14 Jul 2020 07:00:40: #1 total tags in treatment: 2776764 INFO @ Tue, 14 Jul 2020 07:00:40: #1 user defined the maximum tags... INFO @ Tue, 14 Jul 2020 07:00:40: #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 07:00:40: #1 tags after filtering in treatment: 2776764 INFO @ Tue, 14 Jul 2020 07:00:40: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 14 Jul 2020 07:00:40: #1 finished! INFO @ Tue, 14 Jul 2020 07:00:40: #2 Build Peak Model... INFO @ Tue, 14 Jul 2020 07:00:40: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 14 Jul 2020 07:00:40: #2 number of paired peaks: 362 WARNING @ Tue, 14 Jul 2020 07:00:40: Fewer paired peaks (362) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 362 pairs to build model! INFO @ Tue, 14 Jul 2020 07:00:40: start model_add_line... INFO @ Tue, 14 Jul 2020 07:00:40: start X-correlation... INFO @ Tue, 14 Jul 2020 07:00:40: end of X-cor INFO @ Tue, 14 Jul 2020 07:00:40: #2 finished! INFO @ Tue, 14 Jul 2020 07:00:40: #2 predicted fragment length is 48 bps INFO @ Tue, 14 Jul 2020 07:00:40: #2 alternative fragment length(s) may be 48,500,589 bps INFO @ Tue, 14 Jul 2020 07:00:40: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX7262238/SRX7262238.05_model.r WARNING @ Tue, 14 Jul 2020 07:00:40: #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 07:00:40: #2 You may need to consider one of the other alternative d(s): 48,500,589 WARNING @ Tue, 14 Jul 2020 07:00:40: #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 07:00:40: #3 Call peaks... INFO @ Tue, 14 Jul 2020 07:00:40: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 14 Jul 2020 07:00:46: #3 Call peaks for each chromosome... INFO @ Tue, 14 Jul 2020 07:00:49: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX7262238/SRX7262238.05_peaks.xls INFO @ Tue, 14 Jul 2020 07:00:49: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX7262238/SRX7262238.05_peaks.narrowPeak INFO @ Tue, 14 Jul 2020 07:00:49: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX7262238/SRX7262238.05_summits.bed INFO @ Tue, 14 Jul 2020 07:00:49: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (351 records, 4 fields): 7 millis CompletedMACS2peakCalling 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 07:00:55: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX7262238/SRX7262238.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX7262238/SRX7262238.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX7262238/SRX7262238.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX7262238/SRX7262238.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 07:00:55: #1 read tag files... INFO @ Tue, 14 Jul 2020 07:00:55: #1 read treatment tags... INFO @ Tue, 14 Jul 2020 07:01:00: 1000000 INFO @ Tue, 14 Jul 2020 07:01:05: 2000000 INFO @ Tue, 14 Jul 2020 07:01:09: #1 tag size is determined as 50 bps INFO @ Tue, 14 Jul 2020 07:01:09: #1 tag size = 50 INFO @ Tue, 14 Jul 2020 07:01:09: #1 total tags in treatment: 2776764 INFO @ Tue, 14 Jul 2020 07:01:09: #1 user defined the maximum tags... INFO @ Tue, 14 Jul 2020 07:01:09: #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 07:01:09: #1 tags after filtering in treatment: 2776764 INFO @ Tue, 14 Jul 2020 07:01:09: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 14 Jul 2020 07:01:09: #1 finished! INFO @ Tue, 14 Jul 2020 07:01:09: #2 Build Peak Model... INFO @ Tue, 14 Jul 2020 07:01:09: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 14 Jul 2020 07:01:09: #2 number of paired peaks: 362 WARNING @ Tue, 14 Jul 2020 07:01:09: Fewer paired peaks (362) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 362 pairs to build model! INFO @ Tue, 14 Jul 2020 07:01:09: start model_add_line... INFO @ Tue, 14 Jul 2020 07:01:09: start X-correlation... INFO @ Tue, 14 Jul 2020 07:01:09: end of X-cor INFO @ Tue, 14 Jul 2020 07:01:09: #2 finished! INFO @ Tue, 14 Jul 2020 07:01:09: #2 predicted fragment length is 48 bps INFO @ Tue, 14 Jul 2020 07:01:09: #2 alternative fragment length(s) may be 48,500,589 bps INFO @ Tue, 14 Jul 2020 07:01:09: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX7262238/SRX7262238.10_model.r WARNING @ Tue, 14 Jul 2020 07:01:09: #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 07:01:09: #2 You may need to consider one of the other alternative d(s): 48,500,589 WARNING @ Tue, 14 Jul 2020 07:01:09: #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 07:01:09: #3 Call peaks... INFO @ Tue, 14 Jul 2020 07:01:09: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 14 Jul 2020 07:01:15: #3 Call peaks for each chromosome... INFO @ Tue, 14 Jul 2020 07:01:18: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX7262238/SRX7262238.10_peaks.xls INFO @ Tue, 14 Jul 2020 07:01:18: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX7262238/SRX7262238.10_peaks.narrowPeak INFO @ Tue, 14 Jul 2020 07:01:18: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX7262238/SRX7262238.10_summits.bed INFO @ Tue, 14 Jul 2020 07:01:18: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (190 records, 4 fields): 11 millis CompletedMACS2peakCalling 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 07:01:25: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX7262238/SRX7262238.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX7262238/SRX7262238.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX7262238/SRX7262238.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX7262238/SRX7262238.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 07:01:25: #1 read tag files... INFO @ Tue, 14 Jul 2020 07:01:25: #1 read treatment tags... INFO @ Tue, 14 Jul 2020 07:01:31: 1000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 14 Jul 2020 07:01:36: 2000000 INFO @ Tue, 14 Jul 2020 07:01:41: #1 tag size is determined as 50 bps INFO @ Tue, 14 Jul 2020 07:01:41: #1 tag size = 50 INFO @ Tue, 14 Jul 2020 07:01:41: #1 total tags in treatment: 2776764 INFO @ Tue, 14 Jul 2020 07:01:41: #1 user defined the maximum tags... INFO @ Tue, 14 Jul 2020 07:01:41: #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 07:01:41: #1 tags after filtering in treatment: 2776764 INFO @ Tue, 14 Jul 2020 07:01:41: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 14 Jul 2020 07:01:41: #1 finished! INFO @ Tue, 14 Jul 2020 07:01:41: #2 Build Peak Model... INFO @ Tue, 14 Jul 2020 07:01:41: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 14 Jul 2020 07:01:41: #2 number of paired peaks: 362 WARNING @ Tue, 14 Jul 2020 07:01:41: Fewer paired peaks (362) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 362 pairs to build model! INFO @ Tue, 14 Jul 2020 07:01:41: start model_add_line... INFO @ Tue, 14 Jul 2020 07:01:41: start X-correlation... INFO @ Tue, 14 Jul 2020 07:01:41: end of X-cor INFO @ Tue, 14 Jul 2020 07:01:41: #2 finished! INFO @ Tue, 14 Jul 2020 07:01:41: #2 predicted fragment length is 48 bps INFO @ Tue, 14 Jul 2020 07:01:41: #2 alternative fragment length(s) may be 48,500,589 bps INFO @ Tue, 14 Jul 2020 07:01:41: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX7262238/SRX7262238.20_model.r WARNING @ Tue, 14 Jul 2020 07:01:41: #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 07:01:41: #2 You may need to consider one of the other alternative d(s): 48,500,589 WARNING @ Tue, 14 Jul 2020 07:01:41: #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 07:01:41: #3 Call peaks... INFO @ Tue, 14 Jul 2020 07:01:41: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Tue, 14 Jul 2020 07:01:47: #3 Call peaks for each chromosome... INFO @ Tue, 14 Jul 2020 07:01:50: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX7262238/SRX7262238.20_peaks.xls INFO @ Tue, 14 Jul 2020 07:01:50: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX7262238/SRX7262238.20_peaks.narrowPeak INFO @ Tue, 14 Jul 2020 07:01:50: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX7262238/SRX7262238.20_summits.bed INFO @ Tue, 14 Jul 2020 07:01:50: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (62 records, 4 fields): 15 millis CompletedMACS2peakCalling