Job ID = 6626420 SRX = SRX7262243 Genome = ce10 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... Read 10477384 spots for SRR10581866/SRR10581866.sra Written 10477384 spots for SRR10581866/SRR10581866.sra fastq に変換しました。 bowtie でマッピング中... Your job 6626559 ("srTce11") has been submitted Time loading reference: 00:00:00 Time loading forward index: 00:00:00 Time loading mirror index: 00:00:00 Multiseed full-index search: 00:02:15 10477384 reads; of these: 10477384 (100.00%) were unpaired; of these: 1582686 (15.11%) aligned 0 times 7406403 (70.69%) aligned exactly 1 time 1488295 (14.20%) aligned >1 times 84.89% overall alignment rate Time searching: 00:02:15 Overall time: 00:02:15 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] 794423 / 8894698 = 0.0893 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 07:06:14: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX7262243/SRX7262243.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX7262243/SRX7262243.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX7262243/SRX7262243.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX7262243/SRX7262243.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 07:06:14: #1 read tag files... INFO @ Tue, 14 Jul 2020 07:06:14: #1 read treatment tags... INFO @ Tue, 14 Jul 2020 07:06:20: 1000000 INFO @ Tue, 14 Jul 2020 07:06:26: 2000000 INFO @ Tue, 14 Jul 2020 07:06:32: 3000000 INFO @ Tue, 14 Jul 2020 07:06:38: 4000000 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 07:06:44: 5000000 INFO @ Tue, 14 Jul 2020 07:06:45: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX7262243/SRX7262243.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX7262243/SRX7262243.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX7262243/SRX7262243.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX7262243/SRX7262243.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 07:06:45: #1 read tag files... INFO @ Tue, 14 Jul 2020 07:06:45: #1 read treatment tags... INFO @ Tue, 14 Jul 2020 07:06:50: 6000000 INFO @ Tue, 14 Jul 2020 07:06:53: 1000000 INFO @ Tue, 14 Jul 2020 07:06:57: 7000000 INFO @ Tue, 14 Jul 2020 07:07:01: 2000000 INFO @ Tue, 14 Jul 2020 07:07:04: 8000000 INFO @ Tue, 14 Jul 2020 07:07:04: #1 tag size is determined as 50 bps INFO @ Tue, 14 Jul 2020 07:07:04: #1 tag size = 50 INFO @ Tue, 14 Jul 2020 07:07:04: #1 total tags in treatment: 8100275 INFO @ Tue, 14 Jul 2020 07:07:04: #1 user defined the maximum tags... INFO @ Tue, 14 Jul 2020 07:07:04: #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 07:07:05: #1 tags after filtering in treatment: 8100275 INFO @ Tue, 14 Jul 2020 07:07:05: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 14 Jul 2020 07:07:05: #1 finished! INFO @ Tue, 14 Jul 2020 07:07:05: #2 Build Peak Model... INFO @ Tue, 14 Jul 2020 07:07:05: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 14 Jul 2020 07:07:05: #2 number of paired peaks: 335 WARNING @ Tue, 14 Jul 2020 07:07:05: Fewer paired peaks (335) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 335 pairs to build model! INFO @ Tue, 14 Jul 2020 07:07:05: start model_add_line... INFO @ Tue, 14 Jul 2020 07:07:05: start X-correlation... INFO @ Tue, 14 Jul 2020 07:07:05: end of X-cor INFO @ Tue, 14 Jul 2020 07:07:05: #2 finished! INFO @ Tue, 14 Jul 2020 07:07:05: #2 predicted fragment length is 47 bps INFO @ Tue, 14 Jul 2020 07:07:05: #2 alternative fragment length(s) may be 4,47,486,581 bps INFO @ Tue, 14 Jul 2020 07:07:05: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX7262243/SRX7262243.05_model.r WARNING @ Tue, 14 Jul 2020 07:07:05: #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 07:07:05: #2 You may need to consider one of the other alternative d(s): 4,47,486,581 WARNING @ Tue, 14 Jul 2020 07:07:05: #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 07:07:05: #3 Call peaks... INFO @ Tue, 14 Jul 2020 07:07:05: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 14 Jul 2020 07:07:08: 3000000 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 07:07:14: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX7262243/SRX7262243.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX7262243/SRX7262243.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX7262243/SRX7262243.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX7262243/SRX7262243.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 07:07:14: #1 read tag files... INFO @ Tue, 14 Jul 2020 07:07:14: #1 read treatment tags... INFO @ Tue, 14 Jul 2020 07:07:15: 4000000 INFO @ Tue, 14 Jul 2020 07:07:21: 1000000 INFO @ Tue, 14 Jul 2020 07:07:21: #3 Call peaks for each chromosome... INFO @ Tue, 14 Jul 2020 07:07:23: 5000000 INFO @ Tue, 14 Jul 2020 07:07:28: 2000000 INFO @ Tue, 14 Jul 2020 07:07:29: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX7262243/SRX7262243.05_peaks.xls INFO @ Tue, 14 Jul 2020 07:07:29: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX7262243/SRX7262243.05_peaks.narrowPeak INFO @ Tue, 14 Jul 2020 07:07:29: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX7262243/SRX7262243.05_summits.bed INFO @ Tue, 14 Jul 2020 07:07:29: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (559 records, 4 fields): 21 millis CompletedMACS2peakCalling INFO @ Tue, 14 Jul 2020 07:07:30: 6000000 INFO @ Tue, 14 Jul 2020 07:07:35: 3000000 INFO @ Tue, 14 Jul 2020 07:07:38: 7000000 INFO @ Tue, 14 Jul 2020 07:07:42: 4000000 INFO @ Tue, 14 Jul 2020 07:07:45: 8000000 INFO @ Tue, 14 Jul 2020 07:07:45: #1 tag size is determined as 50 bps INFO @ Tue, 14 Jul 2020 07:07:45: #1 tag size = 50 INFO @ Tue, 14 Jul 2020 07:07:45: #1 total tags in treatment: 8100275 INFO @ Tue, 14 Jul 2020 07:07:45: #1 user defined the maximum tags... INFO @ Tue, 14 Jul 2020 07:07:45: #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 07:07:46: #1 tags after filtering in treatment: 8100275 INFO @ Tue, 14 Jul 2020 07:07:46: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 14 Jul 2020 07:07:46: #1 finished! INFO @ Tue, 14 Jul 2020 07:07:46: #2 Build Peak Model... INFO @ Tue, 14 Jul 2020 07:07:46: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 14 Jul 2020 07:07:46: #2 number of paired peaks: 335 WARNING @ Tue, 14 Jul 2020 07:07:46: Fewer paired peaks (335) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 335 pairs to build model! INFO @ Tue, 14 Jul 2020 07:07:46: start model_add_line... INFO @ Tue, 14 Jul 2020 07:07:46: start X-correlation... INFO @ Tue, 14 Jul 2020 07:07:46: end of X-cor INFO @ Tue, 14 Jul 2020 07:07:46: #2 finished! INFO @ Tue, 14 Jul 2020 07:07:46: #2 predicted fragment length is 47 bps INFO @ Tue, 14 Jul 2020 07:07:46: #2 alternative fragment length(s) may be 4,47,486,581 bps INFO @ Tue, 14 Jul 2020 07:07:46: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX7262243/SRX7262243.10_model.r WARNING @ Tue, 14 Jul 2020 07:07:46: #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 07:07:46: #2 You may need to consider one of the other alternative d(s): 4,47,486,581 WARNING @ Tue, 14 Jul 2020 07:07:46: #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 07:07:46: #3 Call peaks... INFO @ Tue, 14 Jul 2020 07:07:46: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 14 Jul 2020 07:07:49: 5000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 14 Jul 2020 07:07:56: 6000000 INFO @ Tue, 14 Jul 2020 07:08:02: #3 Call peaks for each chromosome... INFO @ Tue, 14 Jul 2020 07:08:06: 7000000 BigWig に変換しました。 INFO @ Tue, 14 Jul 2020 07:08:10: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX7262243/SRX7262243.10_peaks.xls INFO @ Tue, 14 Jul 2020 07:08:10: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX7262243/SRX7262243.10_peaks.narrowPeak INFO @ Tue, 14 Jul 2020 07:08:10: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX7262243/SRX7262243.10_summits.bed INFO @ Tue, 14 Jul 2020 07:08:10: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (339 records, 4 fields): 12 millis CompletedMACS2peakCalling 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: 8100275 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: 8100275 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: 335 WARNING @ Tue, 14 Jul 2020 07:08:15: Fewer paired peaks (335) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 335 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: 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 4,47,486,581 bps INFO @ Tue, 14 Jul 2020 07:08:15: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX7262243/SRX7262243.20_model.r 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): 4,47,486,581 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 07:08:32: #3 Call peaks for each chromosome... INFO @ Tue, 14 Jul 2020 07:08:39: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX7262243/SRX7262243.20_peaks.xls INFO @ Tue, 14 Jul 2020 07:08:39: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX7262243/SRX7262243.20_peaks.narrowPeak INFO @ Tue, 14 Jul 2020 07:08:40: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX7262243/SRX7262243.20_summits.bed INFO @ Tue, 14 Jul 2020 07:08:40: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (144 records, 4 fields): 22 millis CompletedMACS2peakCalling