Job ID = 6626366 SRX = SRX7262206 Genome = ce10 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... Read 3581888 spots for SRR10581829/SRR10581829.sra Written 3581888 spots for SRR10581829/SRR10581829.sra fastq に変換しました。 bowtie でマッピング中... Your job 6626399 ("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: 00:00:40 3581888 reads; of these: 3581888 (100.00%) were unpaired; of these: 1074889 (30.01%) aligned 0 times 1980959 (55.30%) aligned exactly 1 time 526040 (14.69%) aligned >1 times 69.99% overall alignment rate Time searching: 00:00:40 Overall time: 00:00:40 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] 371198 / 2506999 = 0.1481 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 06:58:24: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX7262206/SRX7262206.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX7262206/SRX7262206.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX7262206/SRX7262206.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX7262206/SRX7262206.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 06:58:24: #1 read tag files... INFO @ Tue, 14 Jul 2020 06:58:24: #1 read treatment tags... INFO @ Tue, 14 Jul 2020 06:58:29: 1000000 INFO @ Tue, 14 Jul 2020 06:58:34: 2000000 INFO @ Tue, 14 Jul 2020 06:58:35: #1 tag size is determined as 50 bps INFO @ Tue, 14 Jul 2020 06:58:35: #1 tag size = 50 INFO @ Tue, 14 Jul 2020 06:58:35: #1 total tags in treatment: 2135801 INFO @ Tue, 14 Jul 2020 06:58:35: #1 user defined the maximum tags... INFO @ Tue, 14 Jul 2020 06:58:35: #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 06:58:35: #1 tags after filtering in treatment: 2135801 INFO @ Tue, 14 Jul 2020 06:58:35: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 14 Jul 2020 06:58:35: #1 finished! INFO @ Tue, 14 Jul 2020 06:58:35: #2 Build Peak Model... INFO @ Tue, 14 Jul 2020 06:58:35: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 14 Jul 2020 06:58:35: #2 number of paired peaks: 852 WARNING @ Tue, 14 Jul 2020 06:58:35: Fewer paired peaks (852) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 852 pairs to build model! INFO @ Tue, 14 Jul 2020 06:58:35: start model_add_line... INFO @ Tue, 14 Jul 2020 06:58:35: start X-correlation... INFO @ Tue, 14 Jul 2020 06:58:35: end of X-cor INFO @ Tue, 14 Jul 2020 06:58:35: #2 finished! INFO @ Tue, 14 Jul 2020 06:58:35: #2 predicted fragment length is 51 bps INFO @ Tue, 14 Jul 2020 06:58:35: #2 alternative fragment length(s) may be 51 bps INFO @ Tue, 14 Jul 2020 06:58:35: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX7262206/SRX7262206.05_model.r WARNING @ Tue, 14 Jul 2020 06:58:35: #2 Since the d (51) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 14 Jul 2020 06:58:35: #2 You may need to consider one of the other alternative d(s): 51 WARNING @ Tue, 14 Jul 2020 06:58:35: #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 06:58:35: #3 Call peaks... INFO @ Tue, 14 Jul 2020 06:58:35: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 14 Jul 2020 06:58:40: #3 Call peaks for each chromosome... INFO @ Tue, 14 Jul 2020 06:58:42: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX7262206/SRX7262206.05_peaks.xls INFO @ Tue, 14 Jul 2020 06:58:42: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX7262206/SRX7262206.05_peaks.narrowPeak INFO @ Tue, 14 Jul 2020 06:58:42: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX7262206/SRX7262206.05_summits.bed INFO @ Tue, 14 Jul 2020 06:58:42: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (372 records, 4 fields): 14 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 06:58:54: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX7262206/SRX7262206.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX7262206/SRX7262206.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX7262206/SRX7262206.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX7262206/SRX7262206.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 06:58:54: #1 read tag files... INFO @ Tue, 14 Jul 2020 06:58:54: #1 read treatment tags... INFO @ Tue, 14 Jul 2020 06:58:59: 1000000 INFO @ Tue, 14 Jul 2020 06:59:04: 2000000 INFO @ Tue, 14 Jul 2020 06:59:05: #1 tag size is determined as 50 bps INFO @ Tue, 14 Jul 2020 06:59:05: #1 tag size = 50 INFO @ Tue, 14 Jul 2020 06:59:05: #1 total tags in treatment: 2135801 INFO @ Tue, 14 Jul 2020 06:59:05: #1 user defined the maximum tags... INFO @ Tue, 14 Jul 2020 06:59:05: #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 06:59:05: #1 tags after filtering in treatment: 2135801 INFO @ Tue, 14 Jul 2020 06:59:05: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 14 Jul 2020 06:59:05: #1 finished! INFO @ Tue, 14 Jul 2020 06:59:05: #2 Build Peak Model... INFO @ Tue, 14 Jul 2020 06:59:05: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 14 Jul 2020 06:59:05: #2 number of paired peaks: 852 WARNING @ Tue, 14 Jul 2020 06:59:05: Fewer paired peaks (852) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 852 pairs to build model! INFO @ Tue, 14 Jul 2020 06:59:05: start model_add_line... INFO @ Tue, 14 Jul 2020 06:59:05: start X-correlation... INFO @ Tue, 14 Jul 2020 06:59:05: end of X-cor INFO @ Tue, 14 Jul 2020 06:59:05: #2 finished! INFO @ Tue, 14 Jul 2020 06:59:05: #2 predicted fragment length is 51 bps INFO @ Tue, 14 Jul 2020 06:59:05: #2 alternative fragment length(s) may be 51 bps INFO @ Tue, 14 Jul 2020 06:59:05: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX7262206/SRX7262206.10_model.r WARNING @ Tue, 14 Jul 2020 06:59:05: #2 Since the d (51) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 14 Jul 2020 06:59:05: #2 You may need to consider one of the other alternative d(s): 51 WARNING @ Tue, 14 Jul 2020 06:59:05: #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 06:59:05: #3 Call peaks... INFO @ Tue, 14 Jul 2020 06:59:05: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 14 Jul 2020 06:59:10: #3 Call peaks for each chromosome... INFO @ Tue, 14 Jul 2020 06:59:12: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX7262206/SRX7262206.10_peaks.xls INFO @ Tue, 14 Jul 2020 06:59:12: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX7262206/SRX7262206.10_peaks.narrowPeak INFO @ Tue, 14 Jul 2020 06:59:12: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX7262206/SRX7262206.10_summits.bed INFO @ Tue, 14 Jul 2020 06:59:12: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (200 records, 4 fields): 27 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 06:59:24: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX7262206/SRX7262206.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX7262206/SRX7262206.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX7262206/SRX7262206.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX7262206/SRX7262206.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 06:59:24: #1 read tag files... INFO @ Tue, 14 Jul 2020 06:59:24: #1 read treatment tags... INFO @ Tue, 14 Jul 2020 06:59:29: 1000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 14 Jul 2020 06:59:35: 2000000 INFO @ Tue, 14 Jul 2020 06:59:36: #1 tag size is determined as 50 bps INFO @ Tue, 14 Jul 2020 06:59:36: #1 tag size = 50 INFO @ Tue, 14 Jul 2020 06:59:36: #1 total tags in treatment: 2135801 INFO @ Tue, 14 Jul 2020 06:59:36: #1 user defined the maximum tags... INFO @ Tue, 14 Jul 2020 06:59:36: #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 06:59:36: #1 tags after filtering in treatment: 2135801 INFO @ Tue, 14 Jul 2020 06:59:36: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 14 Jul 2020 06:59:36: #1 finished! INFO @ Tue, 14 Jul 2020 06:59:36: #2 Build Peak Model... INFO @ Tue, 14 Jul 2020 06:59:36: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 14 Jul 2020 06:59:36: #2 number of paired peaks: 852 WARNING @ Tue, 14 Jul 2020 06:59:36: Fewer paired peaks (852) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 852 pairs to build model! INFO @ Tue, 14 Jul 2020 06:59:36: start model_add_line... INFO @ Tue, 14 Jul 2020 06:59:36: start X-correlation... INFO @ Tue, 14 Jul 2020 06:59:36: end of X-cor INFO @ Tue, 14 Jul 2020 06:59:36: #2 finished! INFO @ Tue, 14 Jul 2020 06:59:36: #2 predicted fragment length is 51 bps INFO @ Tue, 14 Jul 2020 06:59:36: #2 alternative fragment length(s) may be 51 bps INFO @ Tue, 14 Jul 2020 06:59:36: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX7262206/SRX7262206.20_model.r WARNING @ Tue, 14 Jul 2020 06:59:36: #2 Since the d (51) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 14 Jul 2020 06:59:36: #2 You may need to consider one of the other alternative d(s): 51 WARNING @ Tue, 14 Jul 2020 06:59:36: #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 06:59:36: #3 Call peaks... INFO @ Tue, 14 Jul 2020 06:59:36: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Tue, 14 Jul 2020 06:59:41: #3 Call peaks for each chromosome... INFO @ Tue, 14 Jul 2020 06:59:43: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX7262206/SRX7262206.20_peaks.xls INFO @ Tue, 14 Jul 2020 06:59:43: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX7262206/SRX7262206.20_peaks.narrowPeak INFO @ Tue, 14 Jul 2020 06:59:43: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX7262206/SRX7262206.20_summits.bed INFO @ Tue, 14 Jul 2020 06:59:43: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (70 records, 4 fields): 14 millis CompletedMACS2peakCalling